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Sample GSM4078561 Query DataSets for GSM4078561
Status Public on Nov 16, 2020
Title BT12 cells, IPAc, Solv_F, ChIP-seq
Sample type SRA
 
Source name Atypical Teratoid/Rhabdoid Tumor
Organism Homo sapiens
Characteristics cell line: BT12
treatment: Solvent
timepoint: 18hours
replicate: 3
chip antibody: H3K27ac (Active Motif 39135)
Treatment protocol BT12 cells were treated with 100nM mithramycin for 8-hours or 18-hours continous treatment then collected.
Growth protocol BT12 cells were grown in RPMI-1640 medium (Invitrogen) supplemented with 10% fetal bovine serum (Gemini Bio-Products), 2 mM L-glutamine (Invitrogen), 100 U/mL penicillin and 100 μg/mL streptomycin (Invitrogen). Cell lines were maintained at less than 80% confluency at 37°C and 5% CO2 and confirmed to be mycoplasma negative every 6-months.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Sequencing libraries were prepared using the Kapa Biosystems Hyper Prep kit for the Illumina platform.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing Libraries were sequenced using 2x50 bp sequencing on the Illumina NovaSeq platform at the Van Andel Research Institute. Data were demultplexed using bcl2fastq v2.20.0.
Reads were aligned using bwa mem, duplicate marked with samblaster, and filtered and converted to BAM format using samtools. Aligned reads were retained if they were aligned and had a minimum mapping quality of 20 (e.g. -F 4 -q 20 flags in samtools). BAMs were ingested into R (v3.6.1) and processed using csaw (v1.18.0). Briefly, a 150 bp sliding window with a 50 bp step-size was used to summarize the read counts with a maximum fragment size set to 800 bp. Next, the background was estimated using a 5kb sliding window where reads were binned and summarized. Regions were excluded if they overlapped known blacklist regions in hg19. Regions having signal greater than log2(3) fold-change over background were retained for differential binding analysis. The first principal component was regressed out of the data due to a batch effect being present prior to downstream analysis. Differential binding analysis was carried out using csaw and edgeR, fitting a quasi-likelihood (QL) negative binomial generalized log-linear model that estimates the prior QL dispersion distribution robustly. Differences were tested using an anova-like test or individual contrasts to generate initial differentially bound regions (DBR). Windows were merged with a maximum width of 5kb and a tolerance of 100bp between adjacent windows to consider being combined. Next, p-values were combined across clustered sites using Simes’ method to control the cluster false discovery rate as implemented in the combineTests function in csaw. Finally, clustered DBRs were defined as having a q < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files for raw and lambda corrected (pc1_corrected) peaks from all samples.
 
Submission date Sep 13, 2019
Last update date Nov 16, 2020
Contact name Patrick Grohar
E-mail(s) groharp@email.chop.edu
Phone 2674250494
Organization name Children's Hospital of Philadelphia
Street address 3501 Civic Center Blvd
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL24676
Series (2)
GSE137399 SWI/SNF inhibition leads to epigenetic reprogramming in rhabdoid tumor [ChIP-seq]
GSE137404 SWI/SNF inhibition leads to epigenetic reprogramming in rhabdoid tumor
Relations
BioSample SAMN12742366
SRA SRX6845069

Supplementary file Size Download File type/resource
GSM4078561_IPAcSolvF.pc1_corrected.bkgfilt.bw 816.0 Mb (ftp)(http) BW
GSM4078561_IPAcSolvF.raw.bw 166.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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