DOI: 10.5281/zenodo.1014009
title: Transcriptome profiling of derived-hepatocyte progenitors from human iPSCs with nanoCAGE - part 1 - sequencing data (FASTQ files)

description: 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 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 24 ("NC_LIMMS") and 18 ("NC_LIMMS2") 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.1017276.

 

"170630_M00528_0292_000000000-B9JY8" ("NC_LIMMS") :

ID   Sample_name   Barcode_number   Barcode_sequence   Index_sequence

1   iPSC_control_rep1   4   ACAGAT   NNNNNNNN

2   iPSC_control_rep2   24   ATCGTG   NNNNNNNN

3   iPSC_control_rep3   31   CACGAT   NNNNNNNN

4   S3P1_OK_rep1   36   CACTGA   NNNNNNNN

5   S3P1_OK_rep2   46   CTGACG   NNNNNNNN

6   S3P1_OK_rep3   63   GAGTGA   NNNNNNNN

7   S4P1_OK_rep1   79   GTATAC   NNNNNNNN

8   S4P1_OK_rep2   92   TCGAGC   NNNNNNNN

9   S4P1_OK_rep3   9   ACATGA   NNNNNNNN

10   S4P2_OK_rep1   21   ATCATA   NNNNNNNN

11   S4P2_OK_rep2   33   CACGTG   NNNNNNNN

12   S4P2_OK_rep3   45   CGATGA   NNNNNNNN

13   S1P1_rep1   57   GAGATA   NNNNNNNN

14   S1P1_rep2   69   GCTCTC   NNNNNNNN

15   S1P1_rep3   81   GTATGA   NNNNNNNN

16   S3P1_FAILED_rep1   93   TCGATA   NNNNNNNN

17   S3P1_FAILED_rep2   11   AGTAGC   NNNNNNNN

18   S3P1_FAILED_rep3   23   ATCGCA   NNNNNNNN

19   S4P1_FAILED_rep1   35   CACTCT   NNNNNNNN

20   S4P1_FAILED_rep2   47   CTGAGC   NNNNNNNN

21   S4P1_FAILED_rep3   59   GAGCGT   NNNNNNNN

22   S4P2_FAILED_rep1   71   GCTGCA   NNNNNNNN

23   S4P2_FAILED_rep2   83   TATAGC   NNNNNNNN

24   S4P2_FAILED_rep3   95   TCGCGT   NNNNNNNN

 

"180221_M00528_0334_000000000-B6PJM" ("NC_LIMMS2"):

ID   Sample_name   Barcode_number   Barcode_sequence   Index_sequence

25   PETRI_rep1   04   ACAGAT   NNNNNNNN

26   PETRI_rep2   24   ATCGTG   NNNNNNNN

27   PETRI_rep3   31   CACGAT   NNNNNNNN

28   BIOCHIP_E_rep1   6   CACTGA   NNNNNNNN

29   BIOCHIP_M_rep1   46   CTGACG   NNNNNNNN

30   BIOCHIP_S_rep1   63   GAGTGA   NNNNNNNN

31   BIOCHIP_E_rep2   79   GTATAC   NNNNNNNN

32   BIOCHIP_M_rep2   92   TCGAGC   NNNNNNNN

33   BIOCHIP_S_rep2   09   ACATGA   NNNNNNNN

34   BIOCHIP_E_rep3   21   ATCATA   NNNNNNNN

35   BIOCHIP_M_rep3   33   CACGTG   NNNNNNNN

36   BIOCHIP_S_rep3   45   CGATGA   NNNNNNNN

37   HEPATOCYTES_rep1   57   GAGATA   NNNNNNNN

38   HEPATOCYTES_rep2   69   GCTCTC   NNNNNNNN

39   iPSC_control_rep1-2   81   GTATGA   NNNNNNNN

40   BIOCHIP_E_rep2-2   93   TCGATA   NNNNNNNN

41   BIOCHIP_M_rep1-2    11   AGTAGC   NNNNNNNN

42   BIOCHIP_S_rep2-2   23   ATCGCA   NNNNNNNN