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| Status |
Public on Nov 15, 2016 |
| Title |
BPDCN Patient-1 ATAC-Seq |
| Sample type |
SRA |
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| Source name |
BPDCN Patient-1
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| Organism |
Homo sapiens |
| Characteristics |
cell type: primary PBMCs from BPDCN-Patients
disease state: blastic plasmacytoid dendritic cell neoplasm (BPDCN)
individual: Patient 1
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| 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.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
Jul 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Louis M. Staudt |
| E-mail(s) |
lstaudt@mail.nih.gov
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| Phone |
301-402-1892
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| Organization name |
National Cancer Institute
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| Department |
Lymphoid Malignancies Branch
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| Lab |
Louis M Staudt
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| Street address |
9000 Rockville Pike, Bldg 10, Rm 4N114
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE84623 |
A Druggable TCF4- and BRD4-dependent Transcriptional Network Sustains Malignancy in Blastic Plasmacytoid Dendritic Cell Neoplasm (ATAC-Seq) |
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| Relations |
| BioSample |
SAMN05420605 |
| SRA |
SRX1962082 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2243041_BPDCN_Patient-1_ATAC-Seq.wig.gz |
9.0 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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