|
Status |
Public on Oct 03, 2023 |
Title |
cR_H9_EOS_d10_rep_2, Z10A-1 |
Sample type |
SRA |
|
|
Source name |
chemically reset cR-H9-EOS
|
Organism |
Homo sapiens |
Characteristics |
cell line: chemically reset cR-H9-EOS cell type: chemically reset hPSC during formative transition biological replicate: 2 day of_formative_transition: 10 culture condition: N2B27 and 2uM XAV939
|
Extracted molecule |
genomic DNA |
Extraction protocol |
To isolate nuclei, 50.000 cells were resuspended in 50ul cold lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal C-630), the mixture was pipetted up and down 16 times and immediately centrifuged at 500g for 10min at +4C. The pellet was used for tagmentation reaction, which was performed with 2.5ul TDE1 in 50ul total volume (FC-121-1031, Nextera DNA Library Prep Kit, Illumina). The samples were then further amplified (Nextera kit FC-121-1030) and barcoded with the corresponding indices (FC-121-1011). The final libraries were then cleaned up with 1.2x vol AMPure XP beads.
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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|
Description |
cR_H9_EOS_d10_R1.mLb.clN.bigWig cR_H9_EOS_d10_R2.mLb.clN.bigWig cR_H9_EOS_d10_R1.mLb.clN_peaks.xls cR_H9_EOS_d10_R2.mLb.clN_peaks.xls
|
Data processing |
nf-core/atacseq v1.1.0 pipeline used to process the data FastQC v0.11.8 used for quality control TrimGalore v0.5.0 used for trimming low quality bases + adapter sequences BWA BWA v0.7.17-r1188 used for read mapping Samtools v1.9 used for sorting bam files BEDTools v2.27.1 used for converting sorted bam files into bedgraph files MACS2 v2.1.2 used for calling peaks Assembly: hg38 Supplementary files format and content: bigWig, XLS files with MACS2 peaks
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|
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Submission date |
Nov 21, 2022 |
Last update date |
Oct 03, 2023 |
Contact name |
Laura Biggins |
E-mail(s) |
laura.biggins@babraham.ac.uk
|
Organization name |
The Babraham Institute
|
Department |
Bioinformatics
|
Street address |
Babraham Research Campus
|
City |
Cambridge |
ZIP/Postal code |
CB22 3AT |
Country |
United Kingdom |
|
|
Platform ID |
GPL24676 |
Series (2) |
GSE218509 |
Epigenetic dynamics during capacitation of naïve human pluripotent stem cells [ATAC-seq] |
GSE218512 |
Epigenetic dynamics during capacitation of naïve human pluripotent stem cells |
|
Relations |
BioSample |
SAMN31824132 |
SRA |
SRX18337676 |