Transcriptome profiling of derived-hepatocyte progenitors from human iPSCs with nanoCAGE - part2 - sequencing data (FASTQ files)

This repository contains raw sequencing data (FASTQ files) produced from Illumina MiSeq run IDs "181114_M00528_0390_000000000-C7P58" (aka "NC_LIMMS3") and "190218_M00528_0406_000000000-CB4HR" (aka "NC_LIMMS4") . Sequencing libraries were prepared following the latest version of the nanoCAGE protocol (Poulain et al., Methods Mol Biol. 2017;1543:57-109. doi: 10.1007/978-1-4939-6716-2_4). They respectively contain a mix of 13 ("NC_LIMMS3") and 24 ("NC_LIMMS4") samples tagged by specific barcode sequences at the 5'-ends (see tables below).  The tagmentation step included in the protocol was performed using an equimolar mix of 12 Nextera XT N-series index primers (N701 to N712), therefore "NNNNNNNN" was indicated as index sequence on the Illumina Sample Sheet for the demultiplexing (see tables below). Libraries were sequenced paired-end on Illumina MiSeq system with the MiSeq Reagent Kit v3 (150 cycles: 58 cycles used for READ1, 8 cycles used for the Index, and 84 cycles used for READ2). Genomic alignments (BED files) of paired-end reads on human genome assemblies hg19 and hg38 using the MOIRAI pipeline (Hasegawa et al. BMC Bioinformatics 2014 May 16;15:144. doi: 10.1186/1471-2105-15-144) were deposited at Zenodo under the following Digital Object Identifier: 10.5281/zenodo.2572394.

"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