|
| Status |
Public on Jun 16, 2020 |
| Title |
ATAC_DF_2038_T |
| Sample type |
SRA |
| |
|
| Source name |
Patient localized prostate tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: localized prostate tissue
chip antibody: ATAC
chip antibody vendor: NA
chip antibody cat.#: NA
chip antibody lot/batch#: NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
One (histone ChIP) or three (transcription factor ChIP) 2 mm2 frozen cores were pulverized using the Covaris CryoPrep system. Tissue was fixed using 1% formaldehyde and chromatin sheared to 300-500 bp in size using the Covaris E220 ultrasonicator. Resulting chromatin was incubated overnight with indicated antibodies. Purified immunoprecipitates were isolated and quantified by Qubit fluorometer.
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep kit (Rubicon Genomics). Libraries were sequenced using 75-bp reads on the Illumina platform at the Dana-Farber Cancer Institute.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ATAC_2038-6_T
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline
|
| |
|
| Submission date |
May 27, 2020 |
| Last update date |
Jun 16, 2020 |
| Contact name |
Matthew Freedman |
| E-mail(s) |
freedman@broadinstitute.org
|
| Organization name |
Dana Faber Cancer Institute
|
| Street address |
450 Brookline Avenue
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE130408 |
Charting the prostate epigenomic landscape from transformation to progression |
|
| Relations |
| BioSample |
SAMN15032610 |
| SRA |
SRX8406475 |
