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Sample GSM2948938 Query DataSets for GSM2948938
Status Public on Jan 28, 2018
Title BRD4-IPS-Mull_M_Y-rCr33.01
Sample type SRA
 
Source name Cell Line
Organism Mus musculus
Characteristics strain background: C57BL/6
cell line: Mull_M_Y-rCr33.01
cell type: iPSCs from mature Muller cell MakeRetina rCr33.01
chip antibody: BRD4 (Bethyl,A301-985A)
Extracted molecule genomic DNA
Extraction protocol After removal of IRMEFs, iPS cells were collected after washing with PBS. Then cells were subjected to crosslinking in 1% formaldehyde (Thermo scientific, 28906) for 10 minutes at room temperature, followed by the addition of glycine at the final concentration of 0.125 M to quench the reaction. After centrifuge, cells were washed with cold PBS, counted and pelleted as 10 million cells for each nuclei preparation.
The nuclei were isolated and prepared for shearing using TruChIP chromatin shearing kit (Covaris, 520127) according to manufacturer’s protocol. After shearing, ChIP was performed using the iDeal ChIP-seq kit (Diagenode, C01010051). The antibodies used were: anti-H3K4me3 (Diagenode, C15410003-50), anti-H3K4me2 (Abcam, ab7766), anti-H3K4me1 (Abcam, ab8895), anti-H3K9/14ac (Diagenode, C15410200), anti-H3K27ac (Abcam, ab4729), anti-H3K36me3 (Active Motif, 61101), anti-H3K27me3 (Active Motif, 39155), and anti-CTCF (Active Motif, 61311). After de-crosslinking, DNA was extracted using MinElute PCR-purification kit (Qiagen, 28006) or Agencourt AMPure XP beads (Beckman Coulter, A63881) and subjected to library preparation using NEBNext ChIP-Seq Library Prep Master Mix Set for illumina (NEB, E6240L). The ChIP experiments and library preparation for antibodies including anti-RNA polymerase II (Abcam, ab5095), anti-Brd4 (Bethyl Laboratories, A301-985A) and anti-H3K9me3 (Active Motif, 39161), were performed by Active Motif.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Basecalls performed using CASAVA
BWA (version 0.5.9-r26-dev, default parameter) to align the ChIP-Seq reads to mouse genome mm9(MGSCv37 from Sanger), Picard(version 1.65(1160)) then have been used for marking duplicated reads. Then only non-duplicated reads with have been kept by samtools (parameter “-q 1 -F 1024” version 0.1.18 (r982:295)). We followed the ENCODE criterion to quality control (QC) the data that non-duplicated version of SPP (version 1.11) have been used to draw cross-correlation and calculated relative strand correlation value (RSC) under support of R (version 2.14.0) with packages caTools(version 1.17) and bitops(version 1.0-6) and estimated the fragment size.
We required > 10M unique mapped reads for point-source factor (H3K4me2/3, H3K9/14Ac, H3K27Ac, CTCF, RNAPolII, BRD4) and RSC > 1. We required 20M unique mapped reads for broad markers (H3K9me3, H3K27me3, H3K36me3). We required 10M unique mapped reads for INPUTs and RSC < 1. We noticed H3K4me1 is point-source factor in some stages while broad in other stages so we QC H3K4me1 as broad markers. Then upon manually inspection, the cross-correlation plot generated by SPP, the best fragment size estimated (the smallest fragment size estimated by SPP in all our cases) were used to extend each reads and generate bigwig file to view on IGV (version 2.3.40).
All profiles were manually inspected for clear peaks and good signal to noise separation. We followed ENCODE guideline for quality control.
We extended reads and generate the final bigwig track normalized to 30M reads for visualization.
Genome_build: mm9(MGSCv37)
Supplementary_files_format_and_content: bigwig
 
Submission date Jan 26, 2018
Last update date Jan 29, 2018
Contact name Beisi Xu
E-mail(s) beisi.xu@stjude.org
Organization name St Jude Children's Research Hosipital
Department Center for Applied Bioinformatics
Street address 262 Danny Thomas Pl
City Memphis
State/province Tennessee
ZIP/Postal code 38105
Country USA
 
Platform ID GPL13112
Series (2)
GSE87064 The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis
GSE109712 Retinal Cell Type Epigenetic Memory Predicts Reprogramming Efficiency and Retinogenesis in 3D Organoid Cultures [ChIP-seq_Mm]
Relations
BioSample SAMN08405669
SRA SRX3602864

Supplementary file Size Download File type/resource
GSM2948938_BRD4-IPS-Mull_M_Y-rCr33.01.bw 143.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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