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Sample GSM3686905 Query DataSets for GSM3686905
Status Public on Nov 17, 2019
Title CTV1_PU1mut_3
Sample type SRA
 
Source name CTV1_PU1mut
Organism Homo sapiens
Characteristics cell type: CTV-1
cell type: T cell leukemia cell line
transfected ivt mrna: PU.1mut
molecule subtype: transposed, nuclear DNA
Treatment protocol Cells were transfected with the indicated in vitro transcribed mRNA transcripts (PU1-IVT-mRNA, PU1mut-IVT-mRNA, PU1-delA-IVT-mRNA) and cultured for 8 hours prior to lysis procedure.
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 Cells were treated with DNase I directly in culture medium prior to nuclear transposition procedure.
ATACseq was essentially done as described (Corces et al. 2017).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model NextSeq 550
 
Description Cells were transfected with IVT mRNA and transposition was carried out 8 hours after transfection
Data processing Raw data were aligned to the human genome (GRCh37/hg19) using bowtie2 in very-sensitive and no-discordant modes, keeping only reads that map to a single unique genomic location for further analysis (MAPQ > 10). Read positions were adjusted to move the ends proximal to the Tn5 binding site (for reads on the positive strand, the start is shifted +4 bp and its partner reads start -5 bp, for reads on the negative strand, the start is shifted -5 bp and its partner reads start +4 bp) using a custom script.
Bigwigs of ChIPseq data sets were generated using HOMER v4.9 (Heinz et al, 2010) and a fixed fragment length of 65 bp. 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.
ATAC-seq peak regions were called by combining two different approaches: The basic peak region set was called using HOMER?s findPeaks program in ?region?? mode using parameters ?-size 150 -minDist 250 -L 2 -fdr 0.00001? to identify regions of variable length by stitching nucleosome-size peaks. To exclude shallow peak regions, only those were kept that overlapped a second peak set that was generated in ??factor?? mode using parameters ?-size 250 -minDist 250 -L 2 -fdr 0.00001? to identify focal peaks.
Genome_build: hg19hg19
Supplementary_files_format_and_content: coverage tracks in bigWig format (before and after CNV normalization
Supplementary_files_format_and_content: ATACseq peaks (open chromatin regions)
 
Submission date Mar 25, 2019
Last update date Nov 19, 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)
GSE128833 The hematopoietic master transcription factor PU.1 requires its interaction with the SWI/SNF remodeler to access chromatin de novo [ATAC-seq]
GSE128837 The hematopoietic master transcription factor PU.1 requires its interaction with the SWI/SNF remodeler to access chromatin de novo
Relations
BioSample SAMN11252778
SRA SRX5574402

Supplementary file Size Download File type/resource
GSM3686905_CTV1_PU1mut_3_CNVnormRefChr.ATACpeaks.bed.gz 534.8 Kb (ftp)(http) BED
GSM3686905_CTV1_PU1mut_3_CNVnormRefChr.bigwig 15.8 Mb (ftp)(http) BIGWIG
GSM3686905_CTV1_PU1mut_R3.bigwig 235.2 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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