Transcriptome profiling of derived-hepatocyte progenitors from human iPSCs with nanoCAGE - part2 - genomic alignments (hg19 + hg38)
Authors/Creators
- 1. RIKEN Center for Integrative Medical Sciences (IMS), Yokohama
- 2. LIMMS, Institute of Industrial Science, University of Tokyo
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
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Related works
- Is supplement to
- 10.5281/zenodo.2572390 (DOI)