DOI: 10.5281/zenodo.2572393
title: Transcriptome profiling of derived-hepatocyte progenitors from human iPSCs with nanoCAGE - part2 - genomic alignments (hg19 + hg38)

description: This repository contains genomic alignments (BED files) of paired-end nanoCAGE sequencing data (CAGEscan data) collected from Illumina MiSeq run IDs "181114_M00528_0390_000000000-C7P58" (aka "NC_LIMMS3") and "190218_M00528_0406_000000000-CB4HR" (aka "NC_LIMMS4") FASTQ files were processed with the MOIRAI pipeline OP-WORKFLOW-CAGEscan-short-reads-v2.1 (Hasegawa et al. BMC Bioinformatics 2014 May 16;15:144. doi: 10.1186/1471-2105-15-144.). Filtered pairs of reads were aligned on the human genome assemblies hg19 and hg38. See tables below for a detailed description of the samples contained in each nanoCAGE library, including barcodes and index sequences used for the demultiplexing of sequencing reads. Corresponding raw sequencing data files (FASTQ files) were deposited at Zenodo under the following Digital Object Identifier: 10.5281/zenodo.2572390.


"181114_M00528_0390_000000000-C7P58" ("NC_LIMMS3"):


sample_name    group    barcode_sequence    index_sequence
LIMMS43_04_PETRI_S4D7_rep1    iPSC_CLONE_TODAI    ACAGAT    NNNNNNNN
LIMMS44_24_PETRI_S4D7_rep2    iPSC_CLONE_TODAI    ATCGTG    NNNNNNNN
LIMMS45_31_PETRI_S4D7_rep3    iPSC_CLONE_TODAI    CACGAT    NNNNNNNN
LIMMS46_36_PETRI_S4D14_rep1    iPSC_CLONE_TODAI    CACTGA    NNNNNNNN
LIMMS47_46_PETRI_S4D14_rep2    iPSC_CLONE_TODAI    CTGACG    NNNNNNNN
LIMMS48_63_PETRI_S4D14_rep3    iPSC_CLONE_TODAI    GAGTGA    NNNNNNNN
LIMMS49_79_PETRI_CELLARTIS_rep1    iPSC_CLONE_TODAI    GTATAC    NNNNNNNN
LIMMS50_92_PETRI_CELLARTIS_rep2    iPSC_CLONE_TODAI    TCGAGC    NNNNNNNN
LIMMS51_09_PETRI_CELLARTIS_rep3    iPSC_CLONE_TODAI    ACATGA    NNNNNNNN
LIMMS52_21_PETRI_TODAI_rep1    iPSC_CLONE_CELLARTIS    ATCATA    NNNNNNNN
LIMMS53_33_PETRI_TODAI_rep2    iPSC_CLONE_CELLARTIS    CACGTG    NNNNNNNN
LIMMS54_45_PETRI_TODAI_rep3    iPSC_CLONE_CELLARTIS    CGATGA    NNNNNNNN
LIMMS55_57_iPSC_rep1    CONTROL_iPSC    GAGATA    NNNNNNNN


"190218_M00528_0406_000000000-CB4HR" ("NC_LIMMS4"):


sample_name    group    barcode_sequence    index_sequence
LIMMS56_04_iPSC_rep4    CONTROL_iPSC    ACAGAT    NNNNNNNN
LIMMS57_24_LSECS_1_11    LSECS_PETRI_MONO    ATCGTG    NNNNNNNN
LIMMS58_31_LSECS_2_11    LSECS_PETRI_MONO    CACGAT    NNNNNNNN
LIMMS59_36_LSECS_3_11    LSECS_PETRI_MONO    CACTGA    NNNNNNNN
LIMMS60_46_LSECS_1-06    LSECS_PETRI_MONO    CTGACG    NNNNNNNN
LIMMS61_63_B3_MONO_11_D3    BC_MONO_D3    GAGTGA    NNNNNNNN
LIMMS62_79_B9_CO_10_D14    BC_CO_D14    GTATAC    NNNNNNNN
LIMMS63_92_B13_CO_11_D3    BC_CO_D3    TCGAGC    NNNNNNNN
LIMMS64_09_P2_10_D14    PETRI_MONO    ACATGA    NNNNNNNN
LIMMS65_21_P3_10_D14    PETRI_MONO    ATCATA    NNNNNNNN
LIMMS66_33_P3_11_D14    PETRI_MONO    CACGTG    NNNNNNNN
LIMMS67_45_B1_MONO_10_D14    BC_MONO_D14    CGATGA    NNNNNNNN
LIMMS68_57_B2_MONO_10_D14    BC_MONO_D14    GAGATA    NNNNNNNN
LIMMS69_69_B1_MONO_11_D14    BC_MONO_D14    GCTCTC    NNNNNNNN
LIMMS70_81_B2_MONO_11_D14    BC_MONO_D14    GTATGA    NNNNNNNN
LIMMS71_93_B6_CO_10_D14    BC_CO_D14    TCGATA    NNNNNNNN
LIMMS72_11_B7_CO_10_D14    BC_CO_D14    AGTAGC    NNNNNNNN
LIMMS73_23_B8_CO_10_D14    BC_CO_D14    ATCGCA    NNNNNNNN
LIMMS74_35_B9_CO_11_D3    BC_CO_D3    CACTCT    NNNNNNNN
LIMMS75_47_B11_CO_11_D14    BC_CO_D14    CTGAGC    NNNNNNNN
LIMMS76_59_B12_CO_11_D14    BC_CO_D14    GAGCGT    NNNNNNNN
LIMMS77_71_B14_CO_11_D14    BC_CO_D14    GCTGCA    NNNNNNNN
LIMMS78_83_B15_CO_11_D14    BC_CO_D14    TATAGC    NNNNNNNN
LIMMS79_95_iPSC_rep1_4    CONTROL_iPSC    TCGCGT    NNNNNNNN