cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10927004
title: A constitutive interferon-high immunophenotype defines response to immunotherapy in colorectal cancer.

description: Laser capture microdissection (LCM) RNA-seq, NanoString CosMx spatial transcriptomics and in-vitro cell line (HCT116) ±CD8 co-culture RNA-seq data supporting the paper: "A constitutive interferon-high immunophenotype defines response to immunotherapy in colorectal cancer". 

 

This dataset is accessible under request because it includes sensitive data.

Users wishing to access the dataset will need to sign a Data Sharing Agreement document that will be provided at the time of the request submission.

Please write your request at human-biology@crick.ac.uk.

For unrestriced access to in-vitro cell line RNA-seq data only, see https://doi.org/10.5281/zenodo.14246643

 

The provided data includes: 



LCM RNA-seq:



CRC_LCM-salmon-counts.tsv (tab-delimited text file includes raw salmon counts for each sample) 

CRC_LCM-normalised-counts.txt (tab-delimited text file includes DESeq2 vst-normalised values for each sample)

CRC_LCM-metadata.txt (tab-delimited text file of associated metadata)



NanoString CosMx data:



SeuratObject_Base.RDS (Seurat R object containing the aggregated single cell raw count matrix for all four samples. Cells below the minimum transcripts, genes and negative probes/transcripts ratio are included in the Seurat object as well. The recommended Seurat version to work with this object is >=5.0.0.)

CosMx_S0_processed_metadata_plus_cell_anno.rds (data frame containing metadata for all cells from samples CR48 and UH20 (Slide1) remained after initial filtering steps and clustering. Results from the unsupervised cell clustering can be found in column 'final_anno'. The 'geometry' column contains single cell polygon shapes defined using the R package sf. Use st_as_sf() function on the data frame to convert it into a sf data frame.) 

CosMx_S1_processed_metadata_plus_cell_anno.rds (data frame containing metadata for all cells from samples CR21 and CR36 (Slide2) remained after initial filtering steps and clustering. Results from the unsupervised cell clustering can be found in column 'final_anno'. The 'geometry' column contains single cell polygon shapes defined using the R package sf. Use st_as_sf() function on the data frame to convert it into a sf data frame)

CosMx raw csv flat files for each sample:- raw count expression matrix ('_exprMat_file_')- single cell centroid coordinates + metadata table ('_metadata_file_')- cell polygon coordinates file ('-polygons_')- transcript coordinates + metadata file ('_tx_file_')- fov coordinates file ('_fov_position_file_')



In-vitro cell line co-culture RNA-seq:



salmon.merged.gene_counts.tsv(tab-delimited text file, includes raw gene counts for each sample)

HCT116_EpiT_EpiOnly_dds_object_NCG7.rds (DESeq2 R object containing raw counts for NCG7 genes with >=10 counts in >=1 sample).
DOI: 10.5281/zenodo.10927005
title: A constitutive interferon-high immunophenotype defines response to immunotherapy in colorectal cancer.

description: Laser capture microdissection (LCM) RNA-seq, NanoString CosMx spatial transcriptomics and in-vitro cell line (HCT116) ±CD8 co-culture RNA-seq data supporting the paper: "A constitutive interferon-high immunophenotype defines response to immunotherapy in colorectal cancer". 

 

This dataset is accessible under request because it includes sensitive data.

Users wishing to access the dataset will need to sign a Data Sharing Agreement document that will be provided at the time of the request submission.

Please write your request at human-biology@crick.ac.uk.

For unrestriced access to in-vitro cell line RNA-seq data only, see https://doi.org/10.5281/zenodo.14246643

 

The provided data includes: 



LCM RNA-seq:



CRC_LCM-salmon-counts.tsv (tab-delimited text file includes raw salmon counts for each sample) 

CRC_LCM-normalised-counts.txt (tab-delimited text file includes DESeq2 vst-normalised values for each sample)

CRC_LCM-metadata.txt (tab-delimited text file of associated metadata)



NanoString CosMx data:



SeuratObject_Base.RDS (Seurat R object containing the aggregated single cell raw count matrix for all four samples. Cells below the minimum transcripts, genes and negative probes/transcripts ratio are included in the Seurat object as well. The recommended Seurat version to work with this object is >=5.0.0.)

CosMx_S0_processed_metadata_plus_cell_anno.rds (data frame containing metadata for all cells from samples CR48 and UH20 (Slide1) remained after initial filtering steps and clustering. Results from the unsupervised cell clustering can be found in column 'final_anno'. The 'geometry' column contains single cell polygon shapes defined using the R package sf. Use st_as_sf() function on the data frame to convert it into a sf data frame.) 

CosMx_S1_processed_metadata_plus_cell_anno.rds (data frame containing metadata for all cells from samples CR21 and CR36 (Slide2) remained after initial filtering steps and clustering. Results from the unsupervised cell clustering can be found in column 'final_anno'. The 'geometry' column contains single cell polygon shapes defined using the R package sf. Use st_as_sf() function on the data frame to convert it into a sf data frame)

CosMx raw csv flat files for each sample:- raw count expression matrix ('_exprMat_file_')- single cell centroid coordinates + metadata table ('_metadata_file_')- cell polygon coordinates file ('-polygons_')- transcript coordinates + metadata file ('_tx_file_')- fov coordinates file ('_fov_position_file_')



In-vitro cell line co-culture RNA-seq:



salmon.merged.gene_counts.tsv(tab-delimited text file, includes raw gene counts for each sample)

HCT116_EpiT_EpiOnly_dds_object_NCG7.rds (DESeq2 R object containing raw counts for NCG7 genes with >=10 counts in >=1 sample).
DOI: 10.6084/m9.figshare.c.3613421_d5.v1
title: Additional file 1: Table S1. of Microsatellite markers from tea green leafhopper Empoasca (Matsumurasca) onukii: a powerful tool for studying genetic structure in tea plantations

description: Characteristics of 21 microsatellite markers in E. (M.) onukii. (XLS 27Â kb)
DOI: 10.6084/m9.figshare.c.3613421_d4.v1
title: Additional file 2: Table S2. of Microsatellite markers from tea green leafhopper Empoasca (Matsumurasca) onukii: a powerful tool for studying genetic structure in tea plantations

description: Number of alleles and heterozygosity in each E. (M.) onukii. population. (XLS 29Â kb)
DOI: 10.6084/m9.figshare.c.3613421_d2.v1
title: Additional file 3: Table S3. of Microsatellite markers from tea green leafhopper Empoasca (Matsumurasca) onukii: a powerful tool for studying genetic structure in tea plantations

description: Allelic frequencies of 21 microsatellite markers from Genepop for five populations. (XLS 56Â kb)
DOI: 10.6084/m9.figshare.c.3613421_d1.v1
title: Additional file 5: Table S4. of Microsatellite markers from tea green leafhopper Empoasca (Matsumurasca) onukii: a powerful tool for studying genetic structure in tea plantations

description: AMOVA result of five E. (M.) onukii populations among two groups. (XLS 20Â kb)
DOI: 10.6084/m9.figshare.c.3613253_d16.v1
title: Additional file 7: Table S3. of Genome-wide identification of long noncoding RNA genes and their potential association with fecundity and virulence in rice brown planthopper, Nilaparvata lugens

description: Specifically expressed lncRNAs in the fat body of TN1 strain of N. lugens. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3613253_d15.v1
title: Additional file 10: Table S6. of Genome-wide identification of long noncoding RNA genes and their potential association with fecundity and virulence in rice brown planthopper, Nilaparvata lugens

description: Specifically expressed lncRNAs in the 5th instar nymph of HFP population (XLSX 16Â kb)
DOI: 10.15468/dl.7dhctv
title: Occurrence Download

description: A dataset containing 488 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Physiculus japonicus Hilgendorf, 1879",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 488 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036169-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28032005
title: <b>Development and Validation of a Clinical Prediction Model for Reintubation Within 48 Hours Based on Pre-Extubation Osmolarity Stratification in ICU</b>

description: <b>Development and Validation of a Clinical Prediction Model for Reintubation Within 48 Hours Based on Pre-Extubation Osmolarity Stratification in ICU</b>
DOI: 10.6084/m9.figshare.28032005.v2
title: <b>Development and Validation of a Clinical Prediction Model for Reintubation Within 48 Hours Based on Pre-Extubation Osmolarity Stratification in ICU</b>

description: <b>Development and Validation of a Clinical Prediction Model for Reintubation Within 48 Hours Based on Pre-Extubation Osmolarity Stratification in ICU</b>
DOI: 10.6084/m9.figshare.c.3613151_d1.v1
title: Additional file 6: Table S3. of Genome-wide analysis of excretory/secretory proteins in Echinococcus multilocularis: insights into functional characteristics of the tapeworm secretome

description: The KEGG pathways found in E. multilocularis predicted ES proteins by KAAS. (XLS 24 kb)
DOI: 10.6084/m9.figshare.c.3613130_d2.v1
title: Additional file 1: of Refractive shift of silicone oil tamponade in pseudophakic eye

description: Original data of this study. (XLS 74 kb)
DOI: 10.6084/m9.figshare.c.3613037_d13.v1
title: Additional file 5: Table S5. of Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.)

description: The genetic position of all the recombination hotspots in the genetic map. (XLSX 34Â kb)
DOI: 10.6084/m9.figshare.c.3613037_d12.v1
title: Additional file 12: Table S10. of Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.)

description: The KOG annotation result all the candidate genes of the stable QTLs of cotton boll weight. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3613037_d11.v1
title: Additional file 11: Table S9. of Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.)

description: The number of the candidate genes and the genes ID in each pathway in the KEGG annotation (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3613037_d10.v1
title: Additional file 13: Table S11. of Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.)

description: The number of the candidate genes in each function categories of the KOG annotation. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3613037_d9.v1
title: Additional file 1: Table S1. of Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.)

description: Distribution of the SNP markersâ   type on the genetic map. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3613037_d8.v1
title: Additional file 2: Table S2. of Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.)

description: The markers and their genetic distance in the genetic map. (XLSX 149Â kb)
DOI: 10.6084/m9.figshare.c.3613037_d7.v1
title: Additional file 6: Table S6. of Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.)

description: All the QTLs identified including the ones that can be detected only in one environment. (XLSX 29Â kb)
DOI: 10.6084/m9.figshare.c.3613037_d6.v1
title: Additional file 10: Table S8. of Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.)

description: The KEGG annotation result of all the candidate genes of the stable QTLs of cotton boll weight. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3613037_d5.v1
title: Additional file 3: Table S3. of Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.)

description: The X2_value and P_value of all the markers in the genetic map. (XLSX 233Â kb)
DOI: 10.15468/dl.f3athy
title: Occurrence Download

description: A dataset containing 77 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Indonesia",
 "Geometry POLYGON((79.43475 -11.52082,139.56525 -11.52082,139.56525 12.52082,79.43475 12.52082,79.43475 -11.52082))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Willughbeia coriacea Wall."
 ]
}

 The dataset includes 77 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036170-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3612986_d14.v1
title: Additional file 9: Table S8. of Differential transcriptomic responses to Fusarium graminearum infection in two barley quantitative trait loci associated with Fusarium head blight resistance

description: List of 139 genes with higher expression levels in the 2Hb8 R NIL in both mock and fungal treatments compared to M69 at 48 hai. (XLSX 24Â kb)
DOI: 10.6084/m9.figshare.c.3612977_d12.v1
title: Additional file 1: Table S1. of Genome-wide identification and expression profiling of serine proteases and homologs in the diamondback moth, Plutella xylostella (L.)

description: Description of serine protease (SP) and serine protease homolog (SPH) genes in P. xylostella. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.c.3612986_d12.v1
title: Additional file 14: Table S13. of Differential transcriptomic responses to Fusarium graminearum infection in two barley quantitative trait loci associated with Fusarium head blight resistance

description: List of 34 up-regulated genes in both R NILs when compared to respective susceptible recurrent parents at 48 hai. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3612977_d10.v1
title: Additional file 10: Table S3. of Genome-wide identification and expression profiling of serine proteases and homologs in the diamondback moth, Plutella xylostella (L.)

description: RPKM values of the PxSP and PxSPH genes at different developmental stages obtained from the RNA-seq data. (XLSX 33 kb)
DOI: 10.6084/m9.figshare.c.3612986_d11.v1
title: Additional file 5: Table S4. of Differential transcriptomic responses to Fusarium graminearum infection in two barley quantitative trait loci associated with Fusarium head blight resistance

description: Lists of DEGs identified in pairwise comparisons in TableÂ 1. (XLSX 734Â kb)
DOI: 10.6084/m9.figshare.c.3612986_d10.v1
title: Additional file 18: Table S17. of Differential transcriptomic responses to Fusarium graminearum infection in two barley quantitative trait loci associated with Fusarium head blight resistance

description: Lists of differentially expressed lncRNAs identified in all pairwise comparisons. (XLSX 131Â kb)
DOI: 10.6084/m9.figshare.c.3612986_d9.v1
title: Additional file 2: Table S1. of Differential transcriptomic responses to Fusarium graminearum infection in two barley quantitative trait loci associated with Fusarium head blight resistance

description: Pearson correlation coefficients between DON and ergosterol concentrations. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3612977_d9.v1
title: Additional file 2: Table S2. of Genome-wide identification and expression profiling of serine proteases and homologs in the diamondback moth, Plutella xylostella (L.)

description: The predicted amino acid sequences of 221 SPs/SPHs. (XLSX 55 kb)
DOI: 10.6084/m9.figshare.c.3612986_d6.v1
title: Additional file 10: Table S9. of Differential transcriptomic responses to Fusarium graminearum infection in two barley quantitative trait loci associated with Fusarium head blight resistance

description: List of 201 genes with higher expression levels in comparison 2Hb8 R/M69_M48 and lower expression in comparison 2Hb8 R/M69_F96. (XLSX 29Â kb)
DOI: 10.6084/m9.figshare.c.3612986_d3.v1
title: Additional file 12: Table S11. of Differential transcriptomic responses to Fusarium graminearum infection in two barley quantitative trait loci associated with Fusarium head blight resistance

description: List of 19 candidate genes for the 2Hb8 QTL. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3612986_d2.v1
title: Additional file 6: Table S5. of Differential transcriptomic responses to Fusarium graminearum infection in two barley quantitative trait loci associated with Fusarium head blight resistance

description: Primer sequences and results of qPCR validation of RNA-Seq experiments. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3612986_d1.v1
title: Additional file 4: Table S3. of Differential transcriptomic responses to Fusarium graminearum infection in two barley quantitative trait loci associated with Fusarium head blight resistance

description: Detailed information of RNA-Seq samples. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3612977_d3.v1
title: Additional file 13: Table S4. of Genome-wide identification and expression profiling of serine proteases and homologs in the diamondback moth, Plutella xylostella (L.)

description: RPKM values of the PxSP and PxSPH genes at different developmental tissues obtained from the RNA-seq data. (XLSX 23 kb)
DOI: 10.15468/dl.csr37h
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Physiculus maximowiczi (Herzenstein, 1896)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 40 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036171-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3612638_d14.v1
title: Additional file 2: of The similar and different evolutionary trends of MATE family occurred between rice and Arabidopsis thaliana

description: Coding sequence data of the MATE gene family. (TXT 154 kb)
DOI: 10.6084/m9.figshare.c.3612695_d1.v1
title: Additional file 4: File S3. of Mendelian inheritance of trimodal CpG methylation sites suggests distal cis-acting genetic effects

description: Table of eQTL SNPs for trimodal sites with known SNP associations. (TXT 53Â kb)
DOI: 10.6084/m9.figshare.c.3612638_d10.v1
title: Additional file 1: of The similar and different evolutionary trends of MATE family occurred between rice and Arabidopsis thaliana

description: Protein sequence data of the MATE gene family. (TXT 52 kb)
DOI: 10.15468/dl.rjbghr
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Macrogalidia musschenbroekii (Schlegel, 1877)",
 "Country is Indonesia"
 ]
}

 The dataset includes 18 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036172-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3612557_d8.v1
title: Additional file 3: Table S1. of cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs

description: Comparison of BGISEQ-500 to Agilent. (XLSX 135Â kb)
DOI: 10.6084/m9.figshare.c.3612581_d6.v1
title: Additional file 6: of Genome-wide profiling of chicken dendritic cell response to infectious bursal disease

description: Primary GO categorisation, KEGG and BIOCARTA pathway analyses (Target gene were predicted by miRDB and miTarget based on differentially expressed mRNAs in IBDV-stimulated chicken DCs). (XLSX 132 kb)
DOI: 10.6084/m9.figshare.c.3612581_d5.v1
title: Additional file 4: of Genome-wide profiling of chicken dendritic cell response to infectious bursal disease

description: Primary GO categorisation, KEGG and BIOCARTA pathway analyses based on differentially expressed mRNAs in IBDV-stimulated chicken DCs. (XLS 111 kb)
DOI: 10.6084/m9.figshare.c.3612581_d3.v1
title: Additional file 9: of Genome-wide profiling of chicken dendritic cell response to infectious bursal disease

description: Primary GO categorisation, KEGG and BIOCARTA pathway analyses (Target gene (cis, trans and co-expression) of lncRNAs were predicted based on differentially expressed mRNAs in IBDV-stimulated chicken DCs). (XLSX 335 kb)
DOI: 10.6084/m9.figshare.c.3612581_d4.v1
title: Additional file 8: of Genome-wide profiling of chicken dendritic cell response to infectious bursal disease

description: The cis, trans and co-expressed target gene of different expressed lncRNAs. (The cis target genes were selected by mapping the genomic location of lncRNA and those proteins encoding mRNA. The trans target were extracted from the 3′ UTR sequence of different expressed lncRNA and mRNA, which then predicted by RNAplex with the free energy of RNAplex
DOI: 10.6084/m9.figshare.c.3612581_d2.v1
title: Additional file 7: of Genome-wide profiling of chicken dendritic cell response to infectious bursal disease

description: Selected data of significant alterated lncRNAs stimulated by IBDV (the results of the significantly up- or down-regulated genes were subject to P-valueâ
DOI: 10.6084/m9.figshare.c.3612557_d3.v1
title: Additional file 1: Table S3. of cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs

description: miRNA read count of the BGISEQ-500. (XLSX 250Â kb)
DOI: 10.6084/m9.figshare.c.3612545_d5.v1
title: Additional file 2: of Spatial analysis of gender variation in the prevalence of hypertension among the middle-aged and elderly population in Zhejiang Province, China

description: Data for SCM analysis. data for SCM analysis.txt. It is the dataset supporting the conclusions of SCM analysis, which were run in the free software WinBUGS version 1.4.3 with the GEOBUGS version 1.2 add on. (TXT 880 bytes)
DOI: 10.6084/m9.figshare.c.3612557_d2.v1
title: Additional file 4: Table S2. of cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs

description: List of novel miRNA candidates. (XLSX 6531Â kb)
DOI: 10.6084/m9.figshare.c.3612545_d1.v1
title: Additional file 1: of Spatial analysis of gender variation in the prevalence of hypertension among the middle-aged and elderly population in Zhejiang Province, China

description: Data for logistic analysis. data.dta. It is the dataset supporting the conclusions of logistic analysis, which were performed in Stata (version 11, Stata Corp, College Station, USA). (DTA 145 kb)