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| Status |
Public on Apr 18, 2023 |
| Title |
NanogKO:Esrrb (44J) rep1 S2 |
| Sample type |
SRA |
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| Source name |
N{delta}:cE:iN
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| Organism |
Mus musculus |
| Characteristics |
cell line: N{delta}:cE:iN
cell type: ESC
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| Treatment protocol |
no treatment
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| Growth protocol |
SL (Serum:Lif) medium: GMEM (Sigma) supplemented with 10% fetal bovine serum (FBS) (Gibco), 100 μM 2-mercaptoethanol (Sigma), 1× MEM non-essential amino acids, 2 mM l-glutamine, 1 mM sodium pyruvate (all from Gibco), 1,000 U ml−1 leukaemia inhibitory factor (LIF) (made in house)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were flow sorted using AriaIII (BD Biosciences, BD Diva Software) cell sorter, for PECAM+PDGFRA- cells.
Nuclei preparation and transposase treatment was carried out as described in (Stewart-Morgan et al. 2019)
NEBNext Ultra II DNA library kit
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Raw reads where processed with bcl2fastq (v 2.19.1)
Cutadapt trimming (v 2.2.0)
Raw sequence reads were aligned to the mm10 reference genome (with Bowtie2)
quality filtered with samtools (v 1.4.1) flags (-b -f3 -F4 -F8 -q7)
Normalised bigwigs for visualisation was generated with bamCoverage (v 4.4.0) using binsize 5 and RPKM.
Peaks were called using macs2 (v 2.2.0) -f BAMPE, -q 0.001
Consensus peaks pr condition was defined as peaks present in all 3 biological replicates, and these were combined to generate a counttable for downstream analysis (reads within defined peaks were counted using bedtools, v 2.26.0, coverage).
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak bed (except for Input sample)
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| Submission date |
Jul 06, 2022 |
| Last update date |
Apr 19, 2023 |
| Contact name |
Josh M Brickman |
| E-mail(s) |
joshua.brickman@sund.ku.dk
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| Organization name |
Copenhagen University
|
| Department |
reNEW
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| Lab |
Brickman
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| Street address |
3B Blegdamsvej
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| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE207563 |
A Bipartate function of ESRRB integrates signaling over time to balance self-renewal and differentiation [ATAC-Seq] |
| GSE207565 |
A Bipartate function of ESRRB integrates signaling over time to balance self-renewal and differentiation |
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| Relations |
| BioSample |
SAMN29532941 |
| SRA |
SRX16038353 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6297287_S2.bw |
536.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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