<figure><img src="image_1.png" /></figure>

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# Samples collection and assays-by-sequence provided to the scientific community

Hervé Acloque

► To cite this version:

Hervé Acloque. Samples collection and assays-by-sequence provided to the scientific community. Final conference of the GENE-SWitCH project, EAAP; INRAE; INRAE-T, Nov 2023, Brussels, Belgium. hal-04498288

HAL Id: hal-04498288

https://hal.inrae.fr/hal-04498288

Submitted on 11 Mar 2024

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<figure><img src="image_1.png" /></figure>

GENE-SWitCH...

The regulatory GENomE of SWine and CHicken:
functional annotation during development

**Samples collection and assays-by-sequence
provided to the scientific community**

Hervé Acloque - INRAE

November 6, 2023

GENE-SWitCH Final Conference

<figure><img src="image_2.png" /></figure>

This project has received funding from the European Union's Horizon 2020

Research and Innovation Programme under the grant agreement n° 817998

@GeneSwitch - www.gene-switch.eu
<figure><img src="image_2.png" /></figure>

GENE-SWitCH...

The regulatory GENomE of SWine and CHicken:
functional annotation during development

**Samples collection and assays-by-sequence
provided to the scientific community**

Hervé Acloque - INRAE

November 6, 2023

GENE-SWitCH Final Conference

<figure><img src="image_3.png" /></figure>

This project has received funding from the European Union's Horizon 2020

Research and Innovation Programme under the grant agreement n° 817998

@GeneSwitch - www.gene-switch.eu
# The regulatory GENomE of SWine and CHicken: functional annotation during development

<figure><img src="image_3.png" /></figure>

Genome and
epigenome from
chicken and pig

<figure><img src="image_4.png" /></figure>

<figure><img src="image_5.png" /></figure>

GENE-SWITCH

Functional
Annotation

## Key features to build organisms

<figure><img src="image_6.png" /></figure>

## Key features to build phenotypes

<figure><img src="image_7.png" /></figure>
# The regulatory GENomE of SWine and CHicken: functional annotation during development

<figure><img src="image_4.png" /></figure>

Genome and
epigenome from
chicken and pig

<figure><img src="image_5.png" /></figure>

<figure><img src="image_6.png" /></figure>

GENE-SWITCH

Functional
Annotation

## Key features to build organisms

<figure><img src="image_7.png" /></figure>

## Key features to build phenotypes

<figure><img src="image_8.png" /></figure>
A dynamic of regulatory elements exist in the skeletal
muscle during pig fetal and adult development

<figure><img src="image_8.png" /><figcaption>A</figcaption></figure>

ATAC-seq data

<figure><img src="image_9.png" /></figure>

RNA-seq data
A dynamic of regulatory elements exist in the skeletal
muscle during pig fetal and adult development

A

<figure><img src="image_9.png" /><figcaption>ATAC-seq data</figcaption></figure>

<figure><img src="image_10.png" /><figcaption>RNA-seq data</figcaption></figure>
# Functional annotation of 7 tissues during development

<figure><img src="image_10.png" /></figure>

### 3 developmental stages:
Early organogenesis

<figure><img src="image_11.png" /></figure>

<figure><img src="image_12.png" /></figure>

<figure><img src="image_13.png" /></figure>

Late organogenesis

<figure><img src="image_14.png" /></figure>

<figure><img src="image_15.png" /></figure>

<figure><img src="image_16.png" /></figure>

Newborns

<figure><img src="image_17.png" /></figure>

<figure><img src="image_18.png" /></figure>

<figure><img src="image_19.png" /></figure>

<figure><img src="image_20.png" /></figure>

### 7 Tissues: liver, skeletal muscle, small intestine, cerebellum, dorsal epidermis, lung and kidney

<figure><img src="image_21.png" /></figure>

Endoderm

<figure><img src="image_22.png" /></figure>

Mesoderm

<figure><img src="image_23.png" /></figure>

Ectoderm
# Functional annotation of 7 tissues during development

<figure><img src="image_11.png" /></figure>

### 3 developmental stages:
Early organogenesis

<figure><img src="image_12.png" /></figure>

<figure><img src="image_13.png" /></figure>

<figure><img src="image_14.png" /></figure>

Late organogenesis

<figure><img src="image_15.png" /></figure>

<figure><img src="image_16.png" /></figure>

<figure><img src="image_17.png" /></figure>

Newborns

<figure><img src="image_18.png" /></figure>

<figure><img src="image_19.png" /></figure>

<figure><img src="image_20.png" /></figure>

<figure><img src="image_21.png" /></figure>

### 7 Tissues: liver, skeletal muscle, small intestine, cerebellum, dorsal epidermis, lung and kidney

<figure><img src="image_22.png" /></figure>

Endoderm

<figure><img src="image_23.png" /></figure>

Mesoderm

<figure><img src="image_24.png" /></figure>

Ectoderm
# Sampling and biobanking of tissues

INRAO

<figure><img src="image_24.png" /></figure>

<figure><img src="image_25.png" /></figure>

<figure><img src="image_26.png" /></figure>

<figure><img src="image_27.png" /></figure>

<figure><img src="image_28.png" /></figure>

ROSLIN

<figure><img src="image_29.png" /></figure>

<figure><img src="image_30.png" /></figure>

<table><thead><tr><th></th><th>Fetus 30D</th><th>Fetus 70D</th><th>Piglet</th><th>Embryo 8D</th><th>Embryo 15D</th><th>Chick</th></tr><tr><th></th><th colspan="3">Large White</th><th colspan="3">Advanced Intercross Line (AIL)</th></tr></thead><tbody><tr><th></th><td>2 pools of males and 2 pools of females</td><td>2 males and 2 females</td><td>2 males and 2 females</td><td>2 pools of males and 2 pools of females</td><td>2 males and 2 females</td><td>2 males and 2 females</td></tr></tbody></table>

Biobanking of 6 additional tissues: **gonads, cerebral cortex, large intestine, heart, stomach, spleen**

Metadata on individuals, tissues and pool of tissues are available on the FAANG Data Portal and the BioSamples database.

All the protocols for tissue sampling and DNA/RNA extraction are also publicly available on the FAANG Data Portal and the BioSamples database.
# Sampling and biobanking of tissues

INRAO

<figure><img src="image_25.png" /></figure>

<figure><img src="image_26.png" /></figure>

<figure><img src="image_27.png" /></figure>

<figure><img src="image_28.png" /></figure>

<figure><img src="image_29.png" /></figure>

ROSLIN

<figure><img src="image_30.png" /></figure>

<figure><img src="image_31.png" /></figure>

<table><thead><tr><th></th><th>Fetus 30D</th><th>Fetus 70D</th><th>Piglet</th><th>Embryo 8D</th><th>Embryo 15D</th><th>Chick</th></tr><tr><th></th><th colspan="2">Large White</th><th colspan="3">Advanced Intercross Line (AIL)</th></tr></thead><tbody><tr><th></th><td>2 pools of males and 2 pools of females</td><td>2 males and 2 females</td><td>2 males and 2 females</td><td>2 pools of males and 2 pools of females</td><td>2 males and 2 females</td><td>2 males and 2 females</td></tr></tbody></table>

Biobanking of 6 additional tissues: **gonads, cerebral cortex, large intestine, heart, stomach, spleen**

Metadata on individuals, tissues and pool of tissues are available on the FAANG Data Portal and the BioSamples database.

All the protocols for tissue sampling and DNA/RNA extraction are also publicly available on the FAANG Data Portal and the BioSamples database.
Sampling and biobanking of tissues

SSC_INRAE_GS_WP1_FT_30dpf_1

SAMEA7628703

Updated on: 22-10-2020 08:53

birth date 2019-11-21 (YYYY-MM-DD) birth location Nouzilly birth location latitude 47.32432 (decimal degree)

birth location longitude 0.46596 (decimal degree) birth weight 1.89 (grams) breed Large white

father id FR22XPX201805117 health status normal insemination date 2019-10-22 (YYYY-MM-DD)

material organism mother id FR17MAG201711684 mother parity 5.0 mother weight 252.0 (kilograms)

organism Sus scrofa pregnancy length 30.0 (day) project FAANG

sample description Pig_large_white_fetus_30dpf sample name SSC_INRAE_GS_WP1_FT_30dpf_1

secondary project GENE-SWitCH sex Male

submission description Samples used for GENE-SWitCH WorkPackage 1. It includes fetus of 30d, 70d and one day old pi glets.

submission title INRAE-FAANG-ACLOQUE-Pig-200915 derived from (reverse) SAMEA7628751

derived from (reverse) SAMEA7628787 derived from (reverse) SAMEA7628823

derived from (reverse) SAMEA7628859 derived from (reverse) SAMEA7628895

derived from (reverse) SAMEA7628931 derived from (reverse) SAMEA7628967

derived from (reverse) SAMEA7629059 derived from (reverse) SAMEA7629095

derived from (reverse) SAMEA7629131 derived from (reverse) SAMEA7629167
Sampling and biobanking of tissues

SSC_INRAE_GS_WP1_FT_30dpf_1

SAMEA7628703

Updated on: 22-10-2020 08:53

birth date 2019-11-21 (YYYY-MM-DD) birth location Nouzilly birth location latitude 47.32432 (decimal degree)

birth location longitude 0.46596 (decimal degree) birth weight 1.89 (grams) breed Large white

father id FR22XPX201805117 health status normal insemination date 2019-10-22 (YYYY-MM-DD)

material organism mother id FR17MAG201711684 mother parity 5.0 mother weight 252.0 (kilograms)

organism Sus scrofa pregnancy length 30.0 (day) project FAANG

sample description Pig_large_white_fetus_30dpf sample name SSC_INRAE_GS_WP1_FT_30dpf_1

secondary project GENE-SWitCH sex Male

submission description Samples used for GENE-SWitCH WorkPackage 1. It includes fetus of 30d, 70d and one day old pi glets.

submission title INRAE-FAANG-ACLOQUE-Pig-200915 derived from (reverse) SAMEA7628751

derived from (reverse) SAMEA7628787 derived from (reverse) SAMEA7628823

derived from (reverse) SAMEA7628859 derived from (reverse) SAMEA7628895

derived from (reverse) SAMEA7628931 derived from (reverse) SAMEA7628967

derived from (reverse) SAMEA7629059 derived from (reverse) SAMEA7629095

derived from (reverse) SAMEA7629131 derived from (reverse) SAMEA7629167
# A set of complementary molecular assays to unravel regulatory developmental switches

<figure><img src="image_31.png" /></figure>
# A set of complementary molecular assays to unravel regulatory developmental switches

<figure><img src="image_32.png" /></figure>
<table><thead><tr><th>Assay</th><th>Aim</th><th>Accesion</th><th>Libraries</th></tr></thead><tbody><tr><td rowspan="2">ATAC-seq</td><td>Chromatin accessibility</td><td>PRJEB44468</td><td>84</td></tr><tr><td></td><td>PRJEB45945</td><td>84</td></tr><tr><td rowspan="5">ChIP-seq</td><td>H3K27Ac</td><td></td><td></td></tr><tr><td>H3K4me1</td><td>Chromatin conformation</td><td></td></tr><tr><td>H3K4me3</td><td>Map regulatory elements (promoters, enhancers and repressors)</td><td></td></tr><tr><td>H3K27me3</td><td>Structural annotations</td><td>On-going</td></tr><tr><td>CTCF</td><td></td><td></td></tr><tr><td rowspan="5">RNA-seq</td><td>totRNA-seq (polyA+)</td><td></td><td>PRJEB41970</td><td>84</td></tr><tr><td></td><td>TSS and TTS identification</td><td>PRJEB42025</td><td>84</td></tr><tr><td>smallRNA-seq</td><td>Transcripts structures and categories</td><td>PRJEB42001</td><td>84</td></tr><tr><td></td><td>Transcripts numbers</td><td>PRJEB42041</td><td>84</td></tr><tr><td>Iso-seq</td><td></td><td>PRJEB50963</td><td>21</td></tr><tr><td rowspan="4">DNA methylation</td><td></td><td></td><td>PRJEB48060</td><td>21</td></tr><tr><td>RRBS</td><td>Functional Elements</td><td>PRJEB41822</td><td>63</td></tr><tr><td></td><td>Active and inactive promoters</td><td>PRJEB41829</td><td>63</td></tr><tr><td>WGBS</td><td>Active and inactive chromatin</td><td>PRJEB42772</td><td>21</td></tr><tr><td></td><td></td><td>PRJEB42775</td><td>21</td></tr><tr><td rowspan="2">Promoter Capture Hi-C (liver and muscle only)</td><td></td><td>Interaction maps</td><td>PRJEB44486</td><td>12</td></tr><tr><td></td><td>Enhancer-promoter interactions</td><td>PRJEB53986</td><td>12</td></tr></tbody></table>
<table><thead><tr><th>Assay</th><th>Aim</th><th>Accesion</th><th>Libraries</th></tr></thead><tbody><tr><td rowspan="2">ATAC-seq</td><td>Chromatin accessibility</td><td>PRJEB44468</td><td>84</td></tr><tr><td></td><td>PRJEB45945</td><td>84</td></tr><tr><td rowspan="5">ChIP-seq</td><td>H3K27Ac</td><td></td><td></td></tr><tr><td>H3K4me1</td><td>Chromatin conformation</td><td></td></tr><tr><td>H3K4me3</td><td>Map regulatory elements (promoters, enhancers and repressors)</td><td>On-going</td></tr><tr><td>H3K27me3</td><td>Structural annotations</td><td></td></tr><tr><td>CTCF</td><td></td><td></td></tr><tr><td rowspan="5">RNA-seq</td><td>totRNA-seq (polyA+)</td><td></td><td>PRJEB41970</td><td>84</td></tr><tr><td></td><td>TSS and TTS identification</td><td>PRJEB42025</td><td>84</td></tr><tr><td>smallRNA-seq</td><td>Transcripts structures and categories</td><td>PRJEB42001</td><td>84</td></tr><tr><td></td><td>Transcripts numbers</td><td>PRJEB42041</td><td>84</td></tr><tr><td>Iso-seq</td><td></td><td>PRJEB50963</td><td>21</td></tr><tr><td rowspan="4">DNA methylation</td><td></td><td></td><td>PRJEB48060</td><td>21</td></tr><tr><td>RRBS</td><td>Functional Elements</td><td>PRJEB41822</td><td>63</td></tr><tr><td></td><td>Active and inactive promoters</td><td>PRJEB41829</td><td>63</td></tr><tr><td>WGBS</td><td>Active and inactive chromatin</td><td>PRJEB42772</td><td>21</td></tr><tr><td></td><td></td><td>PRJEB42775</td><td>21</td></tr><tr><td rowspan="2">Promoter Capture Hi-C (liver and muscle only)</td><td></td><td>Interaction maps</td><td>PRJEB44486</td><td>12</td></tr><tr><td></td><td>Enhancer-promoter interactions</td><td>PRJEB53986</td><td>12</td></tr></tbody></table>
Pipelines used for the different assays

<table><thead><tr><th>Assay</th><th>Pipelines</th></tr></thead><tbody><tr><td>ATAC-seq</td><td>nf-core ATACseq :<br>https://nf-co.re/atacseq</td></tr><tr><td>ChIP-seq</td><td>nf-core ChIPseq : https://nf-co.re/chipseq</td></tr><tr><td rowspan="3">RNA-seq</td><td>totRNAseq</td><td>dedicated pipeline TAGADA (Kurylo et al. 2023) :<br>https://github.com/FAANG/analysis-TAGADA</td></tr><tr><td>smallRNAseq</td><td>nf-core smRNAseq :<br>https://nf-co.re/smrnaseq</td></tr><tr><td>Iso-seq</td><td>Dedicated pipeline (Guizard et al. 2023):<br>https://github.com/FAANG/analysis-isoseq<br>nf-core/isoseq</td></tr><tr><td rowspan="2">DNA<br>methylation</td><td>RRBS</td><td>Dedicated pipeline adapted from nf-core/methylseq<br>https://github.com/FAANG/GSM-pipeline</td></tr><tr><td>WGBS</td><td></td></tr><tr><td>Promoter Capture Hi-C</td><td>under development</td></tr></tbody></table>
Pipelines used for the different assays

<table><thead><tr><th>Assay</th><th></th><th>Pipelines</th></tr></thead><tbody><tr><td>ATAC-seq</td><td></td><td>nf-core ATACseq :<br>https://nf-co.re/atacseq</td></tr><tr><td>ChIP-seq</td><td></td><td>nf-core ChIPseq : https://nf-co.re/chipseq</td></tr><tr><td rowspan="3">RNA-seq</td><td>totRNAseq</td><td>dedicated pipeline TAGADA (Kurylo et al. 2023) :<br>https://github.com/FAANG/analysis-TAGADA</td></tr><tr><td>smallRNAseq</td><td>nf-core smRNAseq :<br>https://nf-co.re/smrnaseq</td></tr><tr><td>Iso-seq</td><td>Dedicated pipeline (Guizard et al. 2023):<br>https://github.com/FAANG/analysis-isoseq<br>nf-core/isoseq</td></tr><tr><td rowspan="2">DNA<br>methylation</td><td>RRBS</td><td>Dedicated pipeline adapted from nf-core/methylseq<br>https://github.com/FAANG/GSM-pipeline</td></tr><tr><td>WGBS</td><td></td></tr><tr><td>Promoter Capture Hi-C</td><td></td><td>under development</td></tr></tbody></table>
# Achievements: ATAC-seq

<table><thead><tr><th>Assay</th><th>Aim</th><th>Accesion</th><th>Libraries</th></tr></thead><tbody><tr><td rowspan="2">ATAC-seq</td><td rowspan="2">Chromatin accessibility</td><td>PRJEB44468</td><td>84</td></tr><tr><td>PRJEB45945</td><td>84</td></tr></tbody></table>

<table><thead><tr><th></th><th>Raw reads<br>150PE (median<br>by assay)</th><th>Uniquely<br>mapped PE<br>reads (median<br>by assay)</th><th>% MT<br>reads<br>(mean by<br>assay)</th><th>Number of<br>peaks<br>(median per<br>tissue)</th></tr></thead><tbody><tr><td>Pig</td><td>84,710,247</td><td>57,104,004</td><td>2,33%</td><td>68,490</td></tr><tr><td>Chicken</td><td>92,284,762</td><td>59,681,384</td><td>4,88%</td><td>80,306</td></tr></tbody></table>

## Protocol:

https://data.faang.org/api/fire_api/experiments/DIAGENODE_SOP_GENESWITCH_ATAC-SEQ_20201118.pdf

## Commercial kit (DIAGENODE):

**ATAC-seq package for tissue (C01080006)**
# Achievements: ATAC-seq

<table><thead><tr><th>Assay</th><th>Aim</th><th>Accesion</th><th>Libraries</th></tr></thead><tbody><tr><td rowspan="2">ATAC-seq</td><td rowspan="2">Chromatin accessibility</td><td>PRJEB44468</td><td>84</td></tr><tr><td>PRJEB45945</td><td>84</td></tr></tbody></table>

<table><thead><tr><th></th><th>Raw reads<br>150PE (median<br>by assay)</th><th>Uniquely<br>mapped PE<br>reads (median<br>by assay)</th><th>% MT<br>reads<br>(mean by<br>assay)</th><th>Number of<br>peaks<br>(median per<br>tissue)</th></tr></thead><tbody><tr><td>Pig</td><td>84,710,247</td><td>57,104,004</td><td>2,33%</td><td>68,490</td></tr><tr><td>Chicken</td><td>92,284,762</td><td>59,681,384</td><td>4,88%</td><td>80,306</td></tr></tbody></table>

## Protocol:

https://data.faang.org/api/fire_api/experiments/DIAGENODE_SOP_GENESWITCH_ATAC-SEQ_20201118.pdf

## Commercial kit (DIAGENODE):

**ATAC-seq package for tissue (C01080006)**
# Achievements: ATAC-seq

## Quality control: reads distribution at TSS for pig and chicken libraries

<figure><img src="image_32.png" /></figure>

### deeptools: Read Distribution Profile after Annotation

<figure><img src="image_33.png" /></figure>

<figure><img src="image_34.png" /></figure>

### deeptools: Read Distribution Profile after Annotation

<figure><img src="image_35.png" /></figure>
# Achievements: ATAC-seq

Quality control: reads distribution at TSS for pig and chicken libraries

<figure><img src="image_33.png" /></figure>

<figure><img src="image_34.png" /></figure>

<figure><img src="image_35.png" /></figure>

<figure><img src="image_36.png" /></figure>
# Achievements: ATAC-seq

<figure><img src="image_36.png" /></figure>

Small intestine marker: NKX2.3

<figure><img src="image_37.png" /></figure>
# Achievements: ATAC-seq

<figure><img src="image_37.png" /></figure>

Small intestine marker: NKX2.3

<figure><img src="image_38.png" /></figure>
Achievements: ATAC-seq

<figure><img src="image_38.png" /></figure>

<figure><img src="image_39.png" /></figure>

HNF4A

<figure><img src="image_40.png" /></figure>
Achievements: ATAC-seq

<figure><img src="image_39.png" /></figure>

<figure><img src="image_40.png" /></figure>

HNF4A

<figure><img src="image_41.png" /></figure>
# Achievements: RNA-seq

INRAO

<figure><img src="image_41.png" /></figure>

Inserm

<figure><img src="image_42.png" /></figure>

PROSLIN

EMBL-EBI

RESULTS

<figure><img src="image_43.png" /></figure>

<table><thead><tr><th>Assays</th><th>Species</th><th>Date of released</th><th>Accession number</th><th>Number of libraries</th></tr></thead><tbody><tr><td rowspan="2">totRNAseq (polyA+)</td><td>Pig</td><td>2020-12</td><td>PRJEB41970</td><td>84</td></tr><tr><td>Chicken</td><td>2020-12</td><td>PRJEB42025</td><td>84</td></tr><tr><td rowspan="2">smallRNA-seq</td><td>Pig</td><td>2020-12</td><td>PRJEB42001</td><td>84</td></tr><tr><td>Chicken</td><td>2020-12</td><td>PRJEB42041</td><td>84</td></tr></tbody></table>

<table><thead><tr><th></th><th>Raw reads (median)</th><th>Uniquely mapped PE reads (median)</th></tr></thead><tbody><tr><td>Pig dataset (totRNAseq)</td><td>150,082,484</td><td>143,342,894</td></tr><tr><td>Pig dataset (smallRNAseq)</td><td>67,614,012</td><td>16,898,621</td></tr><tr><td>Chicken dataset (totRNAseq)</td><td>112,414,695</td><td>105,321,362</td></tr><tr><td>Chicken dataset (smallRNAseq)</td><td>66,104,048</td><td>20,486,160</td></tr></tbody></table>
# Achievements: RNA-seq

INRAO

<figure><img src="image_42.png" /></figure>

Inserm

<figure><img src="image_43.png" /></figure>

<figure><img src="image_44.png" /></figure>

PROSLIN

EMBL-EBI

<figure><img src="image_45.png" /></figure>

RESULTS

<table><thead><tr><th>Assays</th><th>Species</th><th>Date of released</th><th>Accession number</th><th>Number of libraries</th></tr></thead><tbody><tr><td rowspan="2">totRNAseq (polyA+)</td><td>Pig</td><td>2020-12</td><td>PRJEB41970</td><td>84</td></tr><tr><td>Chicken</td><td>2020-12</td><td>PRJEB42025</td><td>84</td></tr><tr><td rowspan="2">smallRNA-seq</td><td>Pig</td><td>2020-12</td><td>PRJEB42001</td><td>84</td></tr><tr><td>Chicken</td><td>2020-12</td><td>PRJEB42041</td><td>84</td></tr></tbody></table>

<table><thead><tr><th></th><th>Raw reads (median)</th><th>Uniquely mapped PE reads (median)</th></tr></thead><tbody><tr><td>Pig dataset (totRNAseq)</td><td>150,082,484</td><td>143,342,894</td></tr><tr><td>Pig dataset (smallRNAseq)</td><td>67,614,012</td><td>16,898,621</td></tr><tr><td>Chicken dataset (totRNAseq)</td><td>112,414,695</td><td>105,321,362</td></tr><tr><td>Chicken dataset (smallRNAseq)</td><td>66,104,048</td><td>20,486,160</td></tr></tbody></table>
Achievements: mRNA-seq

Hierarchical clustering

<figure><img src="image_44.png" /></figure>

stage

<figure><img src="image_45.png" /></figure>

stage1

stage2

stage3

tissue

<figure><img src="image_46.png" /></figure>

cerebellum

ileum

kidney

liver

lung

muscle

skin

sex

<figure><img src="image_47.png" /></figure>

female

male

3 stages cluster
together

2 stages cluster
together

1 stage clusters
together
# Achievements: mRNA-seq

## Hierarchical clustering

<figure><img src="image_46.png" /></figure>

stage

<figure><img src="image_47.png" /></figure>

stage1

stage2

stage3

tissue

<figure><img src="image_48.png" /></figure>

cerebellum

ileum

kidney

liver

lung

muscle

skin

sex

<figure><img src="image_49.png" /></figure>

female

male

3 stages cluster
together

2 stages cluster
together

1 stage clusters
together
Achievements: smallRNA-seq

<figure><img src="image_48.png" /></figure>

<figure><img src="image_49.png" /></figure>

<figure><img src="image_50.png" /></figure>

<figure><img src="image_51.png" /></figure>
Achievements: smallRNA-seq

<figure><img src="image_50.png" /></figure>

<figure><img src="image_51.png" /></figure>

<figure><img src="image_52.png" /></figure>

<figure><img src="image_53.png" /></figure>
# Achievements: smallRNA-seq

## Hierarchical clustering

<figure><img src="image_52.png" /></figure>
# Achievements: smallRNA-seq

## Hierarchical clustering

<figure><img src="image_54.png" /></figure>

3 stages cluster
together

2 stages cluster
together

1 stage clusters
together
# Achievements: Iso-seq

<figure><img src="image_53.png" /></figure>

<table><thead><tr><th>Assays</th><th>Species</th><th>Date of released</th><th>Accession number</th><th>Number of libraries</th></tr></thead><tbody><tr><td rowspan="2">Iso-seq</td><td>Pig</td><td>2022-03</td><td>PRJEB50963</td><td>21</td></tr><tr><td>Chicken</td><td>2022-03</td><td>PRJEB48060</td><td>21</td></tr></tbody></table>

<table><thead><tr><th>Species</th><th>Mapped reads (median)</th><th>Total Genes (median per tissue)</th><th>Total Transcripts (median per tissue)</th></tr></thead><tbody><tr><td>Pig</td><td>3,080,464</td><td>19,578</td><td>85,311</td></tr><tr><td>Chicken (GRCg7w)</td><td>2,416,260</td><td>12,224</td><td>68,802</td></tr></tbody></table>

## Protocol:

https://data.faang.org/api/fire_api/experiments/ROSLIN_SOP_GENESWITCH WP1 Iso-seq 20210809.pdf
# Achievements: Iso-seq

<figure><img src="image_55.png" /></figure>

<table><thead><tr><th>Assays</th><th>Species</th><th>Date of released</th><th>Accession number</th><th>Number of libraries</th></tr></thead><tbody><tr><td rowspan="2">Iso-seq</td><td>Pig</td><td>2022-03</td><td>PRJEB50963</td><td>21</td></tr><tr><td>Chicken</td><td>2022-03</td><td>PRJEB48060</td><td>21</td></tr></tbody></table>

<table><thead><tr><th>Species</th><th>Mapped reads (median)</th><th>Total Genes (median per tissue)</th><th>Total Transcripts (median per tissue)</th></tr></thead><tbody><tr><td>Pig</td><td>3,080,464</td><td>19,578</td><td>85,311</td></tr><tr><td>Chicken (GRCg7w)</td><td>2,416,260</td><td>12,224</td><td>68,802</td></tr></tbody></table>

Protocol:

https://data.faang.org/api/fire_api/experiments/ROSLIN_SOP_GENESWITCH WP1 Iso-seq 20210809.pdf
# Achievements: Iso-seq

<figure><img src="image_54.png" /></figure>

HROSLIN

EMBL-EBI

<figure><img src="image_55.png" /></figure>

<figure><img src="image_56.png" /></figure>

<figure><img src="image_57.png" /></figure>

<figure><img src="image_58.png" /></figure>
# Achievements: Iso-seq

<figure><img src="image_56.png" /></figure>

HROSLIN

EMBL-EBI

<figure><img src="image_57.png" /></figure>

<figure><img src="image_58.png" /></figure>

<figure><img src="image_59.png" /></figure>

<figure><img src="image_60.png" /></figure>
<figure><img src="image_59.png" /></figure>

<figure><img src="image_60.png" /></figure>

WAGENINGEN
UNIVERSITY & RESEARCH

# Achievements: DNA methylation

<table><thead><tr><th>Assays</th><th>Species</th><th>Date of released</th><th>Accession number</th><th>Number of libraries</th></tr></thead><tbody><tr><td rowspan="2">RRBS</td><td>Pig</td><td>2020-12</td><td>PRJEB41822</td><td>63</td></tr><tr><td>Chicken</td><td>2020-12</td><td>PRJEB41829</td><td>63</td></tr><tr><td rowspan="2">WGBS</td><td>Pig</td><td>2021-01</td><td>PRJEB42772</td><td>21</td></tr><tr><td>Chicken</td><td>2021-01</td><td>PRJEB42775</td><td>21</td></tr></tbody></table>

<table><thead><tr><th></th><th>Raw reads (RRBS,mean) or coverage (WGBS)</th><th>Uniquely mapped reads (mean)</th></tr></thead><tbody><tr><td>Pig dataset (RRBS)</td><td>59,265,612</td><td>41,485,928</td></tr><tr><td>Pig dataset (WGBS)</td><td>36X</td><td></td></tr><tr><td>Chicken dataset (RRBS)</td><td>54,671,484</td><td>37,176,609</td></tr><tr><td>Chicken dataset (WGBS)</td><td>31X</td><td></td></tr></tbody></table>
<figure><img src="image_61.png" /></figure>

<figure><img src="image_62.png" /></figure>

WAGENINGEN
UNIVERSITY & RESEARCH

# Achievements: DNA methylation

<table><thead><tr><th>Assays</th><th>Species</th><th>Date of released</th><th>Accession number</th><th>Number of libraries</th></tr></thead><tbody><tr><td rowspan="2">RRBS</td><td>Pig</td><td>2020-12</td><td>PRJEB41822</td><td>63</td></tr><tr><td>Chicken</td><td>2020-12</td><td>PRJEB41829</td><td>63</td></tr><tr><td rowspan="2">WGBS</td><td>Pig</td><td>2021-01</td><td>PRJEB42772</td><td>21</td></tr><tr><td>Chicken</td><td>2021-01</td><td>PRJEB42775</td><td>21</td></tr></tbody></table>

<table><thead><tr><th></th><th>Raw reads (RRBS,mean) or coverage (WGBS)</th><th>Uniquely mapped reads (mean)</th></tr></thead><tbody><tr><td>Pig dataset (RRBS)</td><td>59,265,612</td><td>41,485,928</td></tr><tr><td>Pig dataset (WGBS)</td><td>36X</td><td></td></tr><tr><td>Chicken dataset (RRBS)</td><td>54,671,484</td><td>37,176,609</td></tr><tr><td>Chicken dataset (WGBS)</td><td>31X</td><td></td></tr></tbody></table>
Achievements: DNA methylation
Methylation levels at promoters

<figure><img src="image_61.png" /></figure>

<figure><img src="image_62.png" /></figure>

<figure><img src="image_63.png" /></figure>

<figure><img src="image_64.png" /></figure>
# Achievements: DNA methylation
## Methylation levels at promoters

<figure><img src="image_63.png" /></figure>

<figure><img src="image_64.png" /></figure>

<figure><img src="image_65.png" /></figure>

<figure><img src="image_66.png" /></figure>
On-going ChIP-seq

INRAO

<figure><img src="image_65.png" /></figure>

<figure><img src="image_66.png" /></figure>

WAGENINGEN

UNIVERSITY & RESEARCH

* Protocols have been optimized for pig and chicken (ChIPmentation)

* Pig and chicken libraries have been produced and sequenced

* QC and dataset validation are on-going
On-going ChIP-seq

INRAO

<figure><img src="image_67.png" /></figure>

<figure><img src="image_68.png" /></figure>

WAGENINGEN
UNIVERSITY & RESEARCH

* Protocols have been optimized for pig and chicken (ChIPmentation)

* Pig and chicken libraries have been produced and sequenced

* QC and dataset validation are on-going
Achievements: ChIP-seq (on-going)

<table><thead><tr><th></th><th>H3K4<br>me3</th><th>H3K27<br>Ac</th><th>H3K27<br>me3</th><th>H3K4<br>me1</th><th>H3K4<br>me3</th><th>H3K27<br>Ac</th><th>H3K27<br>me3</th><th>H3K4<br>me1</th></tr></thead><tbody><tr><th>Liver</th><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>Kidney</th><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>Muscle</th><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr></tbody></table>

<figure><img src="image_67.png" /></figure>

4 replicates

<figure><img src="image_68.png" /></figure>

2 replicates

<figure><img src="image_69.png" /></figure>

3 replicates

<figure><img src="image_70.png" /></figure>

1 replicate

<figure><img src="image_71.png" /></figure>

0 replicate
Achievements: ChIP-seq (on-going)

<table><thead><tr><th></th><th>H3K4<br>me3</th><th>H3K27<br>Ac</th><th>H3K27<br>me3</th><th>H3K4<br>me1</th><th>H3K4<br>me3</th><th>H3K27<br>Ac</th><th>H3K27<br>me3</th><th>H3K4<br>me1</th></tr></thead><tbody><tr><th>Liver</th><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>Kidney</th><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>Muscle</th><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr></tbody></table>

<figure><img src="image_69.png" /></figure>

4 replicates

<figure><img src="image_70.png" /></figure>

2 replicates

<figure><img src="image_71.png" /></figure>

3 replicates

<figure><img src="image_72.png" /></figure>

1 replicate

<figure><img src="image_73.png" /></figure>

0 replicate
Achievements: ChIP-seq (on-going)

<figure><img src="image_72.png" /></figure>

HoxC complex
Achievements: ChIP-seq (on-going)

<figure><img src="image_74.png" /></figure>

HoxC complex
# Achievement: Promoter Capture Hi-C

<figure><img src="image_73.png" /></figure>

<table><thead><tr><th>Assays</th><th>Species</th><th>Date of released</th><th>Accession number</th><th>Number of libraries</th></tr></thead><tbody><tr><td rowspan="2">Capture Hi-C</td><td>Pig</td><td>2021-04</td><td>PRJEB44486</td><td>12</td></tr><tr><td>Chicken</td><td>2022-06</td><td>PRJEB53986</td><td>12</td></tr></tbody></table>

* Protocols have been optimized for pig and chicken (Arima HiC + Agilent SureSelect)

https://data.faang.org/api/fire_api/experiments/INRAE_SOP_GENESWITCH WP1 PROMOTER CAPTURE HI-C 20210325.pdf

* ~15,000 promoters being captured for each species
# Achievement: Promoter Capture Hi-C

<figure><img src="image_75.png" /></figure>

<table><thead><tr><th>Assays</th><th>Species</th><th>Date of released</th><th>Accession number</th><th>Number of libraries</th></tr></thead><tbody><tr><td rowspan="2">Capture Hi-C</td><td>Pig</td><td>2021-04</td><td>PRJEB44486</td><td>12</td></tr><tr><td>Chicken</td><td>2022-06</td><td>PRJEB53986</td><td>12</td></tr></tbody></table>

* Protocols have been optimized for pig and chicken (Arima HiC + Agilent SureSelect)

https://data.faang.org/api/fire_api/experiments/INRAE_SOP_GENESWITCH_WP1_PROMOTER_CAPTURE_HI-C_20210325.pdf

* ~15,000 promoters being captured for each species
<figure><img src="image_74.png" /><figcaption>Achievement: Promoter Capture Hi-C</figcaption></figure>

<figure><img src="image_75.png" /></figure>
<figure><img src="image_76.png" /><figcaption>Achievement: Promoter Capture Hi-C</figcaption></figure>

<figure><img src="image_77.png" /></figure>
• FAIR principles applied to GENE-SWitCH

All metadata regarding samples, experiments and analysis are publicly available on the FAANG Data Portal. It includes protocols, sample descriptors, experimental parameters and analysis parameters.

All raw sequences have been deposited in the
European Nucleotide Archive (ENA), pipelines are
publicly available either on github or nf-core.

All the information and material related to GENE-SWitCH are easily Findable, Accessible, Interoperable and Reusable from the FAANG Data Portal.
• FAIR principles applied to GENE-SWitCH

All metadata regarding samples, experiments and analysis are publicly available on the FAANG Data Portal. It includes protocols, sample descriptors, experimental parameters and analysis parameters.

All raw sequences have been deposited in the
European Nucleotide Archive (ENA), pipelines are
publicly available either on github or nf-core.

All the information and material related to GENE-SWitCH are easily Findable, Accessible, Interoperable and Reusable from the FAANG Data Portal.
• Accessible through the FAANG data portal

https://data.faang.org/projects/GENE-SWitCH

<figure><img src="image_76.png" /></figure>
• Accessible through the FAANG data portal

https://data.faang.org/projects/GENE-SWitCH

<figure><img src="image_78.png" /></figure>
Acknowledgments

<figure><img src="image_77.png" /></figure>

ROSLIN

Megan Davey, Jonathan Smith, Jacqueline Smith, Kasia Miedzinska, Sebastien Guizard, Mick Watson

INRAO

Mayrone Mongellaz, Sylvain Foissac, Cyril Kurilo, Cervin Guyomard, Marine Beinat, Jérôme Lluch, Tabatha Bulach, Jules Sabban, Hervé Acloque, Elisabetta Giuffra

<figure><img src="image_78.png" /></figure>

Celine Sabatel, Wassim Lakhal, Laurence Servais

<figure><img src="image_79.png" /></figure>

Inserm

Sarah Djebali

<figure><img src="image_80.png" /></figure>

WAGENINGEN
UNIVERSITY & RESEARCH

Jani de Vos, Ole Madsen, Martijn Derks

EMBL-EBI

<figure><img src="image_81.png" /></figure>

Alexey Sokolov, Peter Harrison

<figure><img src="image_82.png" /></figure>

This project has received funding from the European Union's Horizon 2020
Research and Innovation Programme under the grant agreement n° 817998
@GeneSwitch - www.gene-switch.eu
Acknowledgments

<figure><img src="image_79.png" /></figure>

ROSLIN

Megan Davey, Jonathan Smith, Jacqueline Smith, Kasia Miedzinska, Sebastien Guizard, Mick Watson

INRAO

Mayrone Mongellaz, Sylvain Foissac, Cyril Kurilo, Cervin Guyomard, Marine Beinat, Jérôme Lluch, Tabatha Bulach, Jules Sabban, Hervé Acloque, Elisabetta Giuffra

<figure><img src="image_80.png" /></figure>

Celine Sabatel, Wassim Lakhal, Laurence Servais

<figure><img src="image_81.png" /></figure>

Inserm

Sarah Djebali

<figure><img src="image_82.png" /></figure>

WAGENINGEN
UNIVERSITY & RESEARCH

Jani de Vos, Ole Madsen, Martijn Derks

EMBL-EBI

<figure><img src="image_83.png" /></figure>

Alexey Sokolov, Peter Harrison

<figure><img src="image_84.png" /></figure>

This project has received funding from the European Union's Horizon 2020
Research and Innovation Programme under the grant agreement n° 817998
@GeneSwitch - www.gene-switch.eu
Thank you for your attention

<figure><img src="image_83.png" /></figure>
Thank you for your attention

<figure><img src="image_85.png" /></figure>

GENE-SWITCH

<figure><img src="image_86.png" /></figure>