|
| Status |
Public on Oct 03, 2023 |
| Title |
cR_H9_EOS_d20X_rep_2, Z23X-2 |
| 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 after formative transition
biological replicate: 2
day of_formative_transition: 23
culture condition: N2B27 + 2uM XAV939 + 3ng/ml Activin A + 10ng/ml FGF2 (XAF)
|
| 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.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
cR_H9_EOS_d20X_R1.mLb.clN.bigWig
cR_H9_EOS_d20X_R2.mLb.clN.bigWig
cR_H9_EOS_d20X_R1.mLb.clN_peaks.xls
cR_H9_EOS_d20X_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
|
| |
|
| 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 |
SAMN31824123 |
| SRA |
SRX18337685 |
