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Sample GSM3686913 Query DataSets for GSM3686913
Status Public on Nov 17, 2019
Title TALL1_PU1mut_2
Sample type SRA
Source name TALL1_PU1mut
Organism Homo sapiens
Characteristics cell type: TALL-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
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
BioSample SAMN11252770
SRA SRX5574410

Supplementary file Size Download File type/resource
GSM3686913_TALL1_PU1mut_2_CNVnormRefChr.ATACpeaks.bed.gz 855.8 Kb (ftp)(http) BED
GSM3686913_TALL1_PU1mut_2_CNVnormRefChr.bigwig 1.2 Gb (ftp)(http) BIGWIG
GSM3686913_TALL1_PU1mut_R2.bigwig 1.1 Gb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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