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