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

<p>This repository contains raw sequencing data (FASTQ files) produced from Illumina MiSeq run IDs &quot;181114_M00528_0390_000000000-C7P58&quot; (aka &quot;NC_LIMMS3&quot;) and &quot;190218_M00528_0406_000000000-CB4HR&quot; (aka &quot;NC_LIMMS4&quot;) . Sequencing libraries&nbsp;were&nbsp;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&nbsp;respectively contain&nbsp;a mix of 13 (&quot;NC_LIMMS3&quot;) and 24 (&quot;NC_LIMMS4&quot;) samples&nbsp;tagged by specific barcode sequences at the 5&#39;-ends (see&nbsp;tables below).&nbsp; 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 &quot;NNNNNNNN&quot; was indicated as index sequence on the Illumina Sample Sheet for the demultiplexing (see tables below). Libraries were&nbsp;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&nbsp;2014 May 16;15:144. doi: 10.1186/1471-2105-15-144) were deposited at&nbsp;Zenodo under the following Digital Object Identifier: 10.5281/zenodo.2572394.</p> <p><em><strong>&quot;181114_M00528_0390_000000000-C7P58&quot; (&quot;NC_LIMMS3&quot;):</strong></em></p> <p><strong>sample_name&nbsp;&nbsp; &nbsp;group&nbsp;&nbsp; &nbsp;barcode_sequence &nbsp;&nbsp; index_sequence</strong><br> LIMMS43_04_PETRI_S4D7_rep1&nbsp;&nbsp; &nbsp;iPSC_CLONE_TODAI&nbsp;&nbsp; &nbsp;ACAGAT&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS44_24_PETRI_S4D7_rep2&nbsp;&nbsp; &nbsp;iPSC_CLONE_TODAI&nbsp;&nbsp; &nbsp;ATCGTG&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS45_31_PETRI_S4D7_rep3&nbsp;&nbsp; &nbsp;iPSC_CLONE_TODAI&nbsp;&nbsp; &nbsp;CACGAT&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS46_36_PETRI_S4D14_rep1&nbsp;&nbsp; &nbsp;iPSC_CLONE_TODAI&nbsp;&nbsp; &nbsp;CACTGA&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS47_46_PETRI_S4D14_rep2&nbsp;&nbsp; &nbsp;iPSC_CLONE_TODAI&nbsp;&nbsp; &nbsp;CTGACG&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS48_63_PETRI_S4D14_rep3&nbsp;&nbsp; &nbsp;iPSC_CLONE_TODAI&nbsp;&nbsp; &nbsp;GAGTGA&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS49_79_PETRI_CELLARTIS_rep1&nbsp;&nbsp; &nbsp;iPSC_CLONE_TODAI&nbsp;&nbsp; &nbsp;GTATAC&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS50_92_PETRI_CELLARTIS_rep2&nbsp;&nbsp; &nbsp;iPSC_CLONE_TODAI&nbsp;&nbsp; &nbsp;TCGAGC&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS51_09_PETRI_CELLARTIS_rep3&nbsp;&nbsp; &nbsp;iPSC_CLONE_TODAI&nbsp;&nbsp; &nbsp;ACATGA&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS52_21_PETRI_TODAI_rep1&nbsp;&nbsp; &nbsp;iPSC_CLONE_CELLARTIS&nbsp;&nbsp; &nbsp;ATCATA&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS53_33_PETRI_TODAI_rep2&nbsp;&nbsp; &nbsp;iPSC_CLONE_CELLARTIS&nbsp;&nbsp; &nbsp;CACGTG&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS54_45_PETRI_TODAI_rep3&nbsp;&nbsp; &nbsp;iPSC_CLONE_CELLARTIS&nbsp;&nbsp; &nbsp;CGATGA&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS55_57_iPSC_rep1&nbsp;&nbsp; &nbsp;CONTROL_iPSC&nbsp;&nbsp; &nbsp;GAGATA&nbsp;&nbsp; &nbsp;NNNNNNNN</p> <p><em><strong>&quot;190218_M00528_0406_000000000-CB4HR&quot; (&quot;NC_LIMMS4&quot;):</strong></em></p> <p><strong>sample_name&nbsp;&nbsp; &nbsp;group&nbsp;&nbsp; &nbsp;barcode_sequence &nbsp;&nbsp; index_sequence</strong><br> LIMMS56_04_iPSC_rep4&nbsp;&nbsp; &nbsp;CONTROL_iPSC&nbsp;&nbsp; &nbsp;ACAGAT&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS57_24_LSECS_1_11&nbsp;&nbsp; &nbsp;LSECS_PETRI_MONO&nbsp;&nbsp; &nbsp;ATCGTG&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS58_31_LSECS_2_11&nbsp;&nbsp; &nbsp;LSECS_PETRI_MONO&nbsp;&nbsp; &nbsp;CACGAT&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS59_36_LSECS_3_11&nbsp;&nbsp; &nbsp;LSECS_PETRI_MONO&nbsp;&nbsp; &nbsp;CACTGA&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS60_46_LSECS_1-06&nbsp;&nbsp; &nbsp;LSECS_PETRI_MONO&nbsp;&nbsp; &nbsp;CTGACG&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS61_63_B3_MONO_11_D3&nbsp;&nbsp; &nbsp;BC_MONO_D3&nbsp;&nbsp; &nbsp;GAGTGA&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS62_79_B9_CO_10_D14&nbsp;&nbsp; &nbsp;BC_CO_D14&nbsp;&nbsp; &nbsp;GTATAC&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS63_92_B13_CO_11_D3&nbsp;&nbsp; &nbsp;BC_CO_D3&nbsp;&nbsp; &nbsp;TCGAGC&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS64_09_P2_10_D14&nbsp;&nbsp; &nbsp;PETRI_MONO&nbsp;&nbsp; &nbsp;ACATGA&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS65_21_P3_10_D14&nbsp;&nbsp; &nbsp;PETRI_MONO&nbsp;&nbsp; &nbsp;ATCATA&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS66_33_P3_11_D14&nbsp;&nbsp; &nbsp;PETRI_MONO&nbsp;&nbsp; &nbsp;CACGTG&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS67_45_B1_MONO_10_D14&nbsp;&nbsp; &nbsp;BC_MONO_D14&nbsp;&nbsp; &nbsp;CGATGA&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS68_57_B2_MONO_10_D14&nbsp;&nbsp; &nbsp;BC_MONO_D14&nbsp;&nbsp; &nbsp;GAGATA&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS69_69_B1_MONO_11_D14&nbsp;&nbsp; &nbsp;BC_MONO_D14&nbsp;&nbsp; &nbsp;GCTCTC&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS70_81_B2_MONO_11_D14&nbsp;&nbsp; &nbsp;BC_MONO_D14&nbsp;&nbsp; &nbsp;GTATGA&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS71_93_B6_CO_10_D14&nbsp;&nbsp; &nbsp;BC_CO_D14&nbsp;&nbsp; &nbsp;TCGATA&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS72_11_B7_CO_10_D14&nbsp;&nbsp; &nbsp;BC_CO_D14&nbsp;&nbsp; &nbsp;AGTAGC&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS73_23_B8_CO_10_D14&nbsp;&nbsp; &nbsp;BC_CO_D14&nbsp;&nbsp; &nbsp;ATCGCA&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS74_35_B9_CO_11_D3&nbsp;&nbsp; &nbsp;BC_CO_D3&nbsp;&nbsp; &nbsp;CACTCT&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS75_47_B11_CO_11_D14&nbsp;&nbsp; &nbsp;BC_CO_D14&nbsp;&nbsp; &nbsp;CTGAGC&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS76_59_B12_CO_11_D14&nbsp;&nbsp; &nbsp;BC_CO_D14&nbsp;&nbsp; &nbsp;GAGCGT&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS77_71_B14_CO_11_D14&nbsp;&nbsp; &nbsp;BC_CO_D14&nbsp;&nbsp; &nbsp;GCTGCA&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS78_83_B15_CO_11_D14&nbsp;&nbsp; &nbsp;BC_CO_D14&nbsp;&nbsp; &nbsp;TATAGC&nbsp;&nbsp; &nbsp;NNNNNNNN<br> LIMMS79_95_iPSC_rep1_4&nbsp;&nbsp; &nbsp;CONTROL_iPSC&nbsp;&nbsp; &nbsp;TCGCGT&nbsp;&nbsp; &nbsp;NNNNNNNN</p>