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Sample GSM2198256 Query DataSets for GSM2198256
Status Public on Jun 15, 2016
Title Cd47_1.5h_CaptureC_merge
Sample type SRA
 
Source name Cd47_1.5h
Organism Mus musculus
Characteristics cell line: G1E ER4
treatment: estradiol 13h
transgene: stably expressing YFP-MD
nocodazole: 1.5h release
promoter anchor: Cd47 promoter
raw file ids merged: 825_979_973
Treatment protocol Except where indicated in the text as uninduced, we induced cells to mature with 100nM estradiol to activate GATA1-ER. During estradiol induction, we simultaneously treated cells with nocodazole (200ng/ml) for 7h-13h, washed once, and replated into fresh medium lacking nocodazole for varying times (40min-360min), ensuring all samples are exposed to estradiol for the same duration of 13h. We fixed cells with 1% formaldehyde, stained with DAPI, and sorted on a BD FACSAria based on YFP-MD and DAPI signal.
Growth protocol G1E erythroblasts were previously derived through deletion of GATA1 in mouse embryonic stem cells, followed by in vitro differentiation (Weiss, Yu, and Orkin 1997). We cultured a sub-line of G1E cells, G1E-ER4, in which GATA1-ER was retrovirally transduced (referred to in main text as “G1E GATA1-ER"), as previously described (Weiss, Yu, and Orkin 1997). We retrovirally transduced G1E-ER4 cells with the YFP-MD construct (Kadauke et al. 2012) and sorted for a pool of YFP-positive cells.
Extracted molecule genomic DNA
Extraction protocol After cell fixation with 1% formaldehyde for 10min and cell sorting as described above, Capture-C was performed with a double-capture procedure (Davies et al. 2016). Chromatin was digested using DpnII. We used biotin labelled DNA oligos to pull down the target restriction fragments.
Capture-C libraries were sequenced on Nextseq500 with 2x75 bp paired end sequencing.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description Cd47 promoter anchor
825_979_973_Cd47
Data processing Library strategy: Capture-C
The raw reads were processed using published scripts (https://github.com/telenius/captureC/releases).
Custom scripts in R to normalize data by the total number of reads representing fragments ligated to the anchor region in the library.
For each time point and anchor, used custom scripts in R to combine reads representing fragments ligated to the anchor region in the library into one .bedgraph file merged across restriction digestion and/or capture replicates.
Genome_build: mm9
Supplementary_files_format_and_content: .bedgraph files containing coverage of reads (read counts of ligation products to given anchor region, per thousand total reads that represent ligation products to given anchor region).
 
Submission date Jun 13, 2016
Last update date May 15, 2019
Contact name Ross Hardison
E-mail(s) rch8@psu.edu
Organization name Pennsylvania State University
Street address 303 Wartik Lab
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
 
Platform ID GPL19057
Series (2)
GSE83290 A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition [CaptureC]
GSE83293 A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition
Relations
BioSample SAMN05235294
SRA SRX1850298

Supplementary file Size Download File type/resource
GSM2198256_Cd47_1.5h_merge.bedgraph.gz 214.3 Kb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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