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| Status |
Public on Oct 03, 2023 |
| Title |
HNES1_d10_rep_1, C10A-2 |
| Sample type |
SRA |
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| Source name |
embryo-derived HNES1
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| Organism |
Homo sapiens |
| Characteristics |
cell line: embryo-derived HNES1
cell type: embryo-derived naive hPSC during formative transition
biological replicate: 1
day of_formative_transition: 10
culture condition: N2B27 and 2uM XAV939
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| 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 |
HNES1_d10_R1.mLb.clN.bigWig
HNES1_d10_R2.mLb.clN.bigWig
HNES1_d10_R1.mLb.clN_peaks.xls
HNES1_d10_R2.mLb.clN_peaks.xls
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| 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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| Submission date |
Nov 21, 2022 |
| Last update date |
Oct 03, 2023 |
| Contact name |
Laura Biggins |
| E-mail(s) |
laura.biggins@babraham.ac.uk
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| Organization name |
The Babraham Institute
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| Department |
Bioinformatics
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| Street address |
Babraham Research Campus
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| City |
Cambridge |
| ZIP/Postal code |
CB22 3AT |
| Country |
United Kingdom |
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| 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 |
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| Relations |
| BioSample |
SAMN31824137 |
| SRA |
SRX18337671 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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