Transcriptome profiling of derived-hepatocyte progenitors from human iPSCs with nanoCAGE - part 1 - sequencing data (FASTQ files)

<p>This repository contains raw sequencing data (FASTQ files) produced from Illumina MiSeq run IDs "170630_M00528_0292_000000000-B9JY8" (aka "NC_LIMMS") and "180221_M00528_0334_000000000-B6PJM" (aka "NC_LIMMS2") . 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 24 ("NC_LIMMS") and 18 ("NC_LIMMS2") samples&nbsp;tagged by specific barcode sequences at the 5'-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 "NNNNNNNN" 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.1017276.</p> <p>&nbsp;</p> <p><em><strong>"170630_M00528_0292_000000000-B9JY8" ("NC_LIMMS") :</strong></em></p> <p><strong>ID&nbsp;&nbsp; Sample_name&nbsp;&nbsp; Barcode_number&nbsp;&nbsp; Barcode_sequence &nbsp; Index_sequence</strong></p> <p>1&nbsp;&nbsp; iPSC_control_rep1&nbsp;&nbsp; 4&nbsp;&nbsp; ACAGAT&nbsp;&nbsp; NNNNNNNN</p> <p>2&nbsp;&nbsp; iPSC_control_rep2&nbsp;&nbsp; 24&nbsp;&nbsp; ATCGTG&nbsp;&nbsp; NNNNNNNN</p> <p>3&nbsp;&nbsp; iPSC_control_rep3&nbsp;&nbsp; 31&nbsp;&nbsp; CACGAT&nbsp;&nbsp; NNNNNNNN</p> <p>4&nbsp;&nbsp; S3P1_OK_rep1&nbsp;&nbsp; 36&nbsp;&nbsp; CACTGA&nbsp;&nbsp; NNNNNNNN</p> <p>5&nbsp;&nbsp; S3P1_OK_rep2&nbsp;&nbsp; 46&nbsp;&nbsp; CTGACG&nbsp;&nbsp; NNNNNNNN</p> <p>6&nbsp;&nbsp; S3P1_OK_rep3&nbsp;&nbsp; 63&nbsp;&nbsp; GAGTGA&nbsp;&nbsp; NNNNNNNN</p> <p>7&nbsp;&nbsp; S4P1_OK_rep1&nbsp;&nbsp; 79&nbsp;&nbsp; GTATAC&nbsp;&nbsp; NNNNNNNN</p> <p>8&nbsp;&nbsp; S4P1_OK_rep2&nbsp;&nbsp; 92&nbsp;&nbsp; TCGAGC&nbsp;&nbsp; NNNNNNNN</p> <p>9&nbsp;&nbsp; S4P1_OK_rep3&nbsp;&nbsp; 9&nbsp;&nbsp; ACATGA&nbsp;&nbsp; NNNNNNNN</p> <p>10&nbsp;&nbsp; S4P2_OK_rep1&nbsp;&nbsp; 21&nbsp;&nbsp; ATCATA&nbsp;&nbsp; NNNNNNNN</p> <p>11&nbsp;&nbsp; S4P2_OK_rep2&nbsp;&nbsp; 33&nbsp;&nbsp; CACGTG&nbsp;&nbsp; NNNNNNNN</p> <p>12&nbsp;&nbsp; S4P2_OK_rep3&nbsp;&nbsp; 45&nbsp;&nbsp; CGATGA&nbsp;&nbsp; NNNNNNNN</p> <p>13&nbsp;&nbsp; S1P1_rep1&nbsp;&nbsp; 57&nbsp;&nbsp; GAGATA&nbsp;&nbsp; NNNNNNNN</p> <p>14&nbsp;&nbsp; S1P1_rep2&nbsp;&nbsp; 69&nbsp;&nbsp; GCTCTC&nbsp;&nbsp; NNNNNNNN</p> <p>15&nbsp;&nbsp; S1P1_rep3&nbsp;&nbsp; 81&nbsp;&nbsp; GTATGA&nbsp;&nbsp; NNNNNNNN</p> <p>16&nbsp;&nbsp; S3P1_FAILED_rep1&nbsp;&nbsp; 93&nbsp;&nbsp; TCGATA&nbsp;&nbsp; NNNNNNNN</p> <p>17&nbsp;&nbsp; S3P1_FAILED_rep2&nbsp;&nbsp; 11&nbsp;&nbsp; AGTAGC&nbsp;&nbsp; NNNNNNNN</p> <p>18&nbsp;&nbsp; S3P1_FAILED_rep3&nbsp;&nbsp; 23&nbsp;&nbsp; ATCGCA&nbsp;&nbsp; NNNNNNNN</p> <p>19&nbsp;&nbsp; S4P1_FAILED_rep1&nbsp;&nbsp; 35&nbsp;&nbsp; CACTCT&nbsp;&nbsp; NNNNNNNN</p> <p>20&nbsp;&nbsp; S4P1_FAILED_rep2&nbsp;&nbsp; 47&nbsp;&nbsp; CTGAGC&nbsp;&nbsp; NNNNNNNN</p> <p>21&nbsp;&nbsp; S4P1_FAILED_rep3&nbsp;&nbsp; 59&nbsp;&nbsp; GAGCGT&nbsp;&nbsp; NNNNNNNN</p> <p>22&nbsp;&nbsp; S4P2_FAILED_rep1&nbsp;&nbsp; 71&nbsp;&nbsp; GCTGCA&nbsp;&nbsp; NNNNNNNN</p> <p>23&nbsp;&nbsp; S4P2_FAILED_rep2&nbsp;&nbsp; 83&nbsp;&nbsp; TATAGC&nbsp;&nbsp; NNNNNNNN</p> <p>24&nbsp;&nbsp; S4P2_FAILED_rep3&nbsp;&nbsp; 95&nbsp;&nbsp; TCGCGT&nbsp;&nbsp; NNNNNNNN</p> <p>&nbsp;</p> <p><em><strong>"180221_M00528_0334_000000000-B6PJM" ("NC_LIMMS2"):</strong></em></p> <p><strong>ID&nbsp;&nbsp; Sample_name&nbsp;&nbsp; Barcode_number&nbsp;&nbsp; Barcode_sequence &nbsp; Index_sequence</strong></p> <p>25&nbsp;&nbsp; PETRI_rep1&nbsp;&nbsp; 04&nbsp;&nbsp; ACAGAT&nbsp;&nbsp; NNNNNNNN</p> <p>26&nbsp;&nbsp; PETRI_rep2&nbsp;&nbsp; 24&nbsp;&nbsp; ATCGTG&nbsp;&nbsp; NNNNNNNN</p> <p>27&nbsp;&nbsp; PETRI_rep3&nbsp;&nbsp; 31&nbsp;&nbsp; CACGAT&nbsp;&nbsp; NNNNNNNN</p> <p>28&nbsp;&nbsp; BIOCHIP_E_rep1&nbsp;&nbsp; 6&nbsp;&nbsp; CACTGA&nbsp;&nbsp; NNNNNNNN</p> <p>29&nbsp;&nbsp; BIOCHIP_M_rep1&nbsp;&nbsp; 46&nbsp;&nbsp; CTGACG&nbsp;&nbsp; NNNNNNNN</p> <p>30&nbsp;&nbsp; BIOCHIP_S_rep1&nbsp;&nbsp; 63&nbsp;&nbsp; GAGTGA&nbsp;&nbsp; NNNNNNNN</p> <p>31&nbsp;&nbsp; BIOCHIP_E_rep2&nbsp;&nbsp; 79&nbsp;&nbsp; GTATAC&nbsp;&nbsp; NNNNNNNN</p> <p>32&nbsp;&nbsp; BIOCHIP_M_rep2&nbsp;&nbsp; 92&nbsp;&nbsp; TCGAGC&nbsp;&nbsp; NNNNNNNN</p> <p>33&nbsp;&nbsp; BIOCHIP_S_rep2&nbsp;&nbsp; 09&nbsp;&nbsp; ACATGA&nbsp;&nbsp; NNNNNNNN</p> <p>34&nbsp;&nbsp; BIOCHIP_E_rep3&nbsp;&nbsp; 21&nbsp;&nbsp; ATCATA&nbsp;&nbsp; NNNNNNNN</p> <p>35&nbsp;&nbsp; BIOCHIP_M_rep3&nbsp;&nbsp; 33&nbsp;&nbsp; CACGTG&nbsp;&nbsp; NNNNNNNN</p> <p>36&nbsp;&nbsp; BIOCHIP_S_rep3&nbsp;&nbsp; 45&nbsp;&nbsp; CGATGA&nbsp;&nbsp; NNNNNNNN</p> <p>37&nbsp;&nbsp; HEPATOCYTES_rep1&nbsp;&nbsp; 57&nbsp;&nbsp; GAGATA&nbsp;&nbsp; NNNNNNNN</p> <p>38&nbsp;&nbsp; HEPATOCYTES_rep2&nbsp;&nbsp; 69&nbsp;&nbsp; GCTCTC&nbsp;&nbsp; NNNNNNNN</p> <p>39&nbsp;&nbsp; iPSC_control_rep1-2&nbsp;&nbsp; 81&nbsp;&nbsp; GTATGA&nbsp;&nbsp; NNNNNNNN</p> <p>40&nbsp;&nbsp; BIOCHIP_E_rep2-2&nbsp;&nbsp; 93&nbsp;&nbsp; TCGATA&nbsp;&nbsp; NNNNNNNN</p> <p>41&nbsp;&nbsp; BIOCHIP_M_rep1-2&nbsp;&nbsp;&nbsp; 11&nbsp;&nbsp; AGTAGC&nbsp;&nbsp; NNNNNNNN</p> <p>42&nbsp;&nbsp; BIOCHIP_S_rep2-2&nbsp;&nbsp; 23&nbsp;&nbsp; ATCGCA&nbsp;&nbsp; NNNNNNNN</p>