|
Status |
Public on Jun 15, 2016 |
Title |
Myc_1.5h_CaptureC_merge |
Sample type |
SRA |
|
|
Source name |
Myc_1.5h
|
Organism |
Mus musculus |
Characteristics |
cell line: G1E ER4 treatment: estradiol 13h transgene: stably expressing YFP-MD nocodazole: 1.5h release promoter anchor: Myc 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.
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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.
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
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|
Description |
Myc promoter anchor 825_979_973_Myc
|
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).
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|
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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 |
SAMN05234817 |
SRA |
SRX1850288 |