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Sample GSM4116557 Query DataSets for GSM4116557
Status Public on Nov 17, 2019
Title CTV-1_PU.1mRNA_FA_FLAG-ChIP_12
Sample type SRA
 
Source name T cell leukemia cell line
Organism Homo sapiens
Characteristics cell type: CTV-1
chip antibody: FLAG M2 (Sigma, #F3165)
transfected ivt mrna: PU.1
fixation method: FA
preperation batch: 12
Treatment protocol Cells were transfected with the indicated in vitro transcribed mRNA transcripts (PU1-IVT-mRNA, PU1mut-IVT-mRNA, PU1-delA-IVT-mRNA, PU1-delQ-IVT-mRNA, PU1-delP-IVT-mRNA, PU1-delAQP-IVT-mRNA) and cultured for 8 hours prior to chromatin extraction
Growth protocol CTV-1 and HEP-G2 cells were cultured in RPMI 1640 (Gibco; routinely supplemented with 2 mM L-glutamine (Biochrom), 1 mM sodium pyruvate (Sigma), 50 U/ml penicillin/streptomycin, 0.4x vitamins (Sigma), 1x non-essential amino acids (Sigma), 50 μM b-mercaptoethanol (Gibco)) supplemented with 10% heat inactivated fetal bovine serum; For TALL-1 cells the culture medium was supplemented with 15% heat inactivated fetal bovine serum was used; adherent HEP-G2 cells were detached using Trypsin-EDTA (Gibco)
Extracted molecule genomic DNA
Extraction protocol Lysates were preparated from sonicated nuclei and protein/histone-DNA complexes were isolated with antibody.
ChIP construction was essentially done as described (Pham et al. 2012) with slight modifications for BRG1, ETS1 and FLI1 samples, which were prepared using dual crosslinking with 2 mM DSG (Thermo Fisher Scientific) and 1% formaldehyde. Libraries for sequencing were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer’s instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model NextSeq 550
 
Description Chromatin IP against FLAG-epitope, 8h after mRNA transfection
Data processing Raw data were aligned to the human genome (GRCh37/hg19) using bowtie2 (Langmead and Salzberg, 2012) in very sensitive mode, keeping only reads that map to a single unique genomic location for further analysis (MAPQ > 10).
Bigwigs of ChIPseq data sets were generated using HOMER v4.9 (Heinz et al, 2010) and standard settings. For cancer cell lines, we used the Control-FREEC v11.0 program to determine allelic imbalances from low-depth whole genome sequencing data and corrected ChIP-seq read counts accordingly to generate CNV-corrected bigWigs.
ChIP-seq peaks were called using HOMER?s findPeaks program in ??factor?? mode using default parameters (standard) or with -fdr 0.00001 (stringent) to identify focal peaks. Stringent peaks were further filtered for a minimal normalized tag count of 15 tags per peak. All peak sets were filtered by subtracting blacklisted genomic regions 49, and by filtering out regions with a mappability <0.8. The latter was annotated to peak regions from mappability tracks generated with the GEM package using HOMER?s annotatePeaks.pl.
Genome_build: hg19
Supplementary_files_format_and_content: ChIPseq tracks in bigWig format (before and after CNV normalization
Supplementary_files_format_and_content: ChIPseq peaks (called using standard or stringent parameters)
 
Submission date Oct 10, 2019
Last update date Nov 18, 2019
Contact name Michael Rehli
E-mail(s) michael.rehli@klinik.uni-r.de
Organization name University Hospital Regensburg
Department Internal Med III
Street address F.-J.-Strauss-Allee 11
City Regensburg
ZIP/Postal code 93042
Country Germany
 
Platform ID GPL21697
Series (2)
GSE128835 The hematopoietic master transcription factor PU.1 requires its interaction with the SWI/SNF remodeler to access chromatin de novo [CTV1_TALL_HELP ChIP-seq]
GSE128837 The hematopoietic master transcription factor PU.1 requires its interaction with the SWI/SNF remodeler to access chromatin de novo
Relations
BioSample SAMN13012507
SRA SRX6976257

Supplementary file Size Download File type/resource
GSM4116557_CTV-1_PU.1mRNA_FA_FLAG-ChIP_12.bigwig 352.3 Mb (ftp)(http) BIGWIG
GSM4116557_CTV-1_PU.1mRNA_FA_FLAG-ChIP_12.filtered.standard.peaks.bed.gz 2.1 Mb (ftp)(http) BED
GSM4116557_CTV-1_PU.1mRNA_FA_FLAG-ChIP_12.filtered.stringent.peaks.bed.gz 643.0 Kb (ftp)(http) BED
GSM4116557_CTV-1_PU.1mRNA_FA_FLAG-ChIP_12_CNVnormRefChr.bigwig 352.1 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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