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 |
| ctrlnum |
1014009 |
|---|---|
| fullrecord |
<?xml version="1.0"?>
<dc schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd"><creator>Stéphane Poulain</creator><creator>Éric Leclerc</creator><creator>Charles Plessy</creator><date>2017-10-17</date><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
</description><identifier>https://zenodo.org/record/1014009</identifier><identifier>10.5281/zenodo.1014009</identifier><identifier>oai:zenodo.org:1014009</identifier><relation>doi:10.1016/j.bej.2018.11.001</relation><relation>doi:10.5281/zenodo.1017276</relation><relation>doi:10.5281/zenodo.1014008</relation><rights>info:eu-repo/semantics/closedAccess</rights><subject>nanoCAGE</subject><subject>hiPSCs</subject><subject>hepatocytes</subject><subject>differentiation</subject><subject>protocol</subject><subject>biochip</subject><subject>cell culture</subject><subject>transcriptome</subject><title>Transcriptome profiling of derived-hepatocyte progenitors from human iPSCs with nanoCAGE - part 1 - sequencing data (FASTQ files)</title><type>Other:info:eu-repo/semantics/other</type><type>Other:dataset</type><recordID>1014009</recordID></dc>
|
| format |
Other:info:eu-repo/semantics/other Other Other:dataset |
| author |
Stéphane Poulain Éric Leclerc Charles Plessy |
| title |
Transcriptome profiling of derived-hepatocyte progenitors from human iPSCs with nanoCAGE - part 1 - sequencing data (FASTQ files) |
| publishDate |
2017 |
| topic |
nanoCAGE hiPSCs hepatocytes differentiation protocol biochip cell culture transcriptome |
| url |
https://zenodo.org/record/1014009 |
| contents |
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
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1739495417386631168 |
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17.60897 |