Transcriptome profiling of derived-hepatocyte progenitors from human iPSCs with nanoCAGE - part 1 - sequencing data (FASTQ files)
| Main Authors: | Stéphane Poulain, Éric Leclerc, Charles Plessy |
|---|---|
| Format: | info dataset |
| Terbitan: |
, 2017
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/1014009 |
Daftar Isi:
- 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