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| Status |
Public on Apr 18, 2023 |
| Title |
NanogKO:Esrrb:Nanog (44JN), Esrrb ChIP, rep2, S4 |
| 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
chip antibody: Esrrb R&D, #PP-H6705-00
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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 |
Chromatin was crosslinked for 10 min in 1% FA (single fixation), or with a subsequent 45 min fixation with 2 mM Di(N-succinimidyl) glutarate (double fixation) and stopped in glycine.
NEBNext Ultra II DNA library kit
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Raw reads where processed with bcl2fastq (v 2.19.1)
Raw sequence reads were aligned to the mm10 reference genome (with Bowtie2)
quality filtered with samtools (v 1.4.1) flags (-b -F4 -q13)
Normalised bigwigs for visualisation was generated with bamCoverage (anaconda2 v 4.4.0) using binsize 5 and RPKM.
Peaks were called using macs2 (anaconda2 v 2.2.0) against condition and replicate specific input samples specifying q ≤ 0.01)
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
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| 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) |
| GSE207562 |
A Bipartate function of ESRRB integrates signaling over time to balance self-renewal and differentiation [ChIP-Seq] |
| GSE207565 |
A Bipartate function of ESRRB integrates signaling over time to balance self-renewal and differentiation |
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| Relations |
| BioSample |
SAMN29533034 |
| SRA |
SRX16038362 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6297275_sort_Es_B_44JN.bam_nodup.bam_filtF4q13.bam.bw |
202.1 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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