Transcriptome profiling of derived-hepatocyte progenitors from human iPSCs with nanoCAGE - part1 - genomic alignments (hg19 + hg38)
- 1. RIKEN Center for Life Science Technologies, Yokohama
- 2. LIMMS, Institute of Industrial Science, University of Tokyo
Description
This repository contains genomic alignments (BED files) of paired-end nanoCAGE sequencing data (CAGEscan data) collected from Illumina MiSeq run IDs "170630_M00528_0292_000000000-B9JY8" (aka "NC_LIMMS") and "180221_M00528_0334_000000000-B6PJM" (aka "NC_LIMMS2"). FASTQ files were processed with the MOIRAI pipeline OP-WORKFLOW-CAGEscan-short-reads-v2.1 (Hasegawa et al. BMC Bioinformatics 2014 May 16;15:144. doi: 10.1186/1471-2105-15-144.). Filtered pairs of reads were aligned on the human genome assemblies hg19 and hg38. See tables below for a detailed description of the samples contained in each nanoCAGE library, including barcodes and index sequences used for the demultiplexing of sequencing reads. Corresponding raw sequencing data files (FASTQ files) were deposited at Zenodo under the following Digital Object Identifier: 10.5281/zenodo.1014009.
"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
Files
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Additional details
Related works
- Is derived from
- Dataset: 10.5281/zenodo.1014009 (DOI)
- Is referenced by
- Journal article: 10.1016/j.bej.2018.11.001 (DOI)
- Journal article: 10.1002/bit.26970 (DOI)
- Journal article: 10.1016/j.procbio.2019.09.034 (DOI)
References
- Lereau-Bernier M, et al. Profiling of derived-hepatocyte progenitors from induced pluripotent stem cells using nanoCAGE promoter analysis. Biochem Eng J. 2019 Feb;142:7–17.
- Danoy M, et al. Optimized protocol for the hepatic differentiation of induced pluripotent stem cells in a fluidic microenvironment. Biotechnol Bioeng. 2019 Jul;116:1762-1776.
- Jellali R, Poulain S, Lereau-Bernier M, et al. Integration of metabolomic and transcriptomic profiling to compare two protocols of differentiation of human induced pluripotent stem cells into hepatocytes. Process Biochem, 2020 Jan;88:138-147.