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Sample GSM3868676 Query DataSets for GSM3868676
Status Public on Aug 08, 2019
Title repA input 0h
Sample type SRA
 
Source name mouse embryonic stem cells stably expressing a cRAF-ErT2 expression cassette
Organism Mus musculus
Characteristics cell type: mouse embryonic stem cells stably expressing a cRAF-ErT2 expression cassette
treatment: 0h 4OHT
antibody: input
strain: E14tg2a
background strain: 129SV
Stage: embryonic
Treatment protocol Cells were left untreated (0h), or treated with 250nM 4OHT for 2h, 4h or 8h
Growth protocol mESCs were grown in serum containing medium, supplemented with 1x LIF (made in house) and 2uM Chir99021. 24hrs prior to treatment, media was changed to serum containing media supplemented with 1x LIF and 250nM PD173074.
Extracted molecule genomic DNA
Extraction protocol Cells we fixed in 1% formaldehyde at RT for 10 minutes and subsequently 2mM disuccinimidyl glutarate , nuclei extracted and chromatin sonicated using a bioruptor (10 cycles, 30s on 30s off). Cleared chromatin was incubated with anti-ESRRB (R&D, PP-H6705-00), or anti SOX2 antibody (R&D, AF2018). Input DNA serves as negative control for antibody enrichment.
Libraries were prepared using the NEB Next Ultra 2 kit.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description A_I_0h
Data processing reads were mapped uning bowtie2
duplicate reads were removed
reads were quality filtered
reads were counted using bedtools coverage
peaks were called using MACS2 (narrow)
Genome_build: mm10
Supplementary_files_format_and_content: MACS PEAK BED
 
Submission date Jun 10, 2019
Last update date Feb 27, 2020
Contact name Josh M Brickman
E-mail(s) joshua.brickman@sund.ku.dk
Organization name Copenhagen University
Department reNEW
Lab Brickman
Street address 3B Blegdamsvej
City Copenhagen
ZIP/Postal code 2200
Country Denmark
 
Platform ID GPL19057
Series (2)
GSE132444 Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation
GSE132483 Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation [ESRRB_SOX2]
Relations
BioSample SAMN12008680
SRA SRX6032055

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not applicable for this record

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