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Sample GSM2197829 Query DataSets for GSM2197829
Status Public on Jun 15, 2016
Title 642_3h_Pol2_Rep2
Sample type SRA
Source name 642_3h_Pol2
Organism Mus musculus
Characteristics cell line: G1E ER4
treatment: estradiol 13h
transgene: stably expressing YFP-MD
nocodazole: 3h release
antibody: anti-Pol II N-20 (Santa Cruz, cat# sc899)
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 All samples, including input, were processed for library construction for Illumina sequencing using Illumina’s TruSeq ChIP Sample Preparation Kit (Illumina cat# IP-202- 1012). In brief, DNA fragments were repaired to generate blunt ends, purified using Agencourt AMPure XP Beads (Beckman Coulter cat# A63881), and a single “A” nucleotide was added to each end. Double-stranded Illumina adaptors were ligated to the fragments. Ligation products were purified using Agencourt AMPure XP Beads, and subject to size selection using SPRIselect Beads (Beckman Coulter cat# B23318)in which both a left side size selection was performed at 0.9x volume, and a right side size selection was performed at 0.6x volume according to manufacturer’s specifications. Library fragments were then amplified for 16 cycles of PCR and products were purified using Agencourt AMPure XP Beads. Constructed libraries were run on the Agilent Bioananlyzer 2100 (Agilent Technologies) using either the DNA 7500 kit (cat# 5067-1504) or the High Sensitivity DNA kit (cat# 5067-4626) as appropriate to determine the average size and confirm the absence of unligated adaptors. The mean library size is approximately 330 bp. The ChIP-seq libraries were quantitated by qPCR using the Kapa SYBR FAST Universal kit (Kapa Biosystems) according to the Illumina’s Sequencing Library qPCR Quantification Guide. Libraries were multiplexed and sequenced on the Illumina HiSeq 2000 using Illumina’s kits and reagents as appropriate. We sequenced 3 biological replicates for the 0min, 60min, 90min, 180min, and 360min time points; two biological replicates for 240min time point; and one replicate for 40min time point.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description Rep2
3h_pool.bigWig (pooled file across Rep1, Rep2, Rep3)
Data processing Basecalls using bcl2fastq-1.8.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome mm9 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle and peaks called using MACS with parameters --format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Filter blacklist regions from peaks, and convert the *peaks.xls file from MACs to broadpeak format (see UCSC Genome Browser for format specs)
R scripts for further steps that generate additional processed tabular files in are available at the following repository:
Genome_build: mm9
Supplementary_files_format_and_content: .bigwig files containing read coverage (not normalized to total library size).
Supplementary_files_format_and_content: Pooled .bigWig files across biological replicates are linked as supplementary files on the Series record.
Supplementary_files_format_and_content: contains two tables that include Pol II RPKM's at the 5' 2.5kb region of active genes and intergenic enhancers, as well as results of principal components analysis and other analyses as described in the accompanying publication. Information on the columns are described in the README_SupplementalTablesDescription.xls file. R scripts that generate the two tables are available at the following repository:
Submission date Jun 13, 2016
Last update date May 15, 2019
Contact name Ross Hardison
Organization name Pennsylvania State University
Street address 303 Wartik Lab
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
Platform ID GPL13112
Series (2)
GSE83263 A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition [Pol2ChIP]
GSE83293 A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition
BioSample SAMN05233865
SRA SRX1838937

Supplementary file Size Download File type/resource
GSM2197829_642.bigWig 4.4 Gb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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