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Sample GSM2243033 Query DataSets for GSM2243033
Status Public on Nov 15, 2016
Title Cal-1 ATAC-Seq
Sample type SRA
Source name Cal-1
Organism Homo sapiens
Characteristics cell line: Cal-1
cell type: blastic plasmacytoid dendritic cell neoplasm (BPDCN) cell line
disease state: blastic plasmacytoid dendritic cell neoplasm (BPDCN)
Extracted molecule genomic DNA
Extraction protocol Nuclei Extraction Protocol
Other: Cells were harvested and 50,000 cells were pelleted by centrifugation for 10' at 500g. Media was removed and pelleted cells were resuspended directly in room-temperature lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.5% IGEPAL CA-630). A second centrifugation (10', 500g) isolated the nuclei.
Isolated nuclei were tagmented in 50 ul transposase reaction mix (25 uL 2X TD buffer, 10 uL transposase (Nextera DNA Library Prep Kit, Illumina) and 15 uL nuclease-free water). The transposition reaction incubated for 30 min in a 37C water bath, and then purified with the Qiagen MinElute kit. Following purification, the tagmented DNA was amplified. Depending on the sample, 8-10 total PCR cycles were necessary. After PCR amplification, the ATAC-Seq libraries were purified with the Qiagen MinElute kit and further cleaned-up with Agencourt AMPure XP beads (Beckman Coulter) at a sample to beads ratio of 1 : 1.75.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
Data processing ATAC-Seq Analysis
Calculation Method: ATAC-Seq libraries were sequenced on the High-Output Next-Seq flow cell (Illumina, 150 cycles, paired end 2 x 75 bp). To generate ATAC-Seq genome browser tracks, the reads were aligned to the human genome hg18 by Bowtie with default parameters. An in-house peak calling script was used to scan the read peaks on the alignment file with following criteria: maximum read mismatch <=4, minimum read depth >=3, bin size 25 bp, read extension 200 bp. Statistically significant peaks were selected based on a p value <= 10(6) (Poisson distribution probability) and saved in the standard WIG format for visualization in the genome browser. To perform the ATAC-Seq cluster analysis, reads were aligned to human genome hg18 by Bowtie software with mismatches up to 2 nucleotides, and extended 100 bp in each direction from the 5' start. The frequencies of aligned reads in every 100-bp-bins of chromosome regions were further summarized by an in-house script. Only the bins with the depth greater than 15 reads were used for further analysis.
Library strategy: ATAC-Seq
Supplementary_files_format_and_content: wig file
Genome_build: hg18
Submission date Jul 20, 2016
Last update date May 15, 2019
Contact name Louis M. Staudt
Phone 301-402-1892
Organization name National Cancer Institute
Department Lymphoid Malignancies Branch
Lab Louis M Staudt
Street address 9000 Rockville Pike, Bldg 10, Rm 4N114
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platform ID GPL18573
Series (1)
GSE84623 A Druggable TCF4- and BRD4-dependent Transcriptional Network Sustains Malignancy in Blastic Plasmacytoid Dendritic Cell Neoplasm (ATAC-Seq)
BioSample SAMN05420597
SRA SRX1962074

Supplementary file Size Download File type/resource
GSM2243033_Cal-1_ATAC-Seq.wig.gz 11.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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