|
| Status |
Public on Apr 25, 2016 |
| Title |
BlCa_4 - FFPE Input |
| Sample type |
SRA |
| |
|
| Source name |
Primary bladder cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: FFPE
|
| Treatment protocol |
sections of 10 μm thickness were scraped into plastic tubes , FiT-Seq protocol was performed no antibody was used. Libraries were prepared with ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a Nextseq 500 instrument (Illumina)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIPseq:ThruPLEX-FD kits (Rubicon Genomics) was used and 75 bp single-end reads were sequenced on a NextSeq 500 instrument (Illumina). For RNAseq: TruSeq RNA Sample Preparation Kit (Illumina) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Alignment: For ChIPseq experiments we used Bowtie2 (2.1.0) with settings (--no-unal). For RNAseq we used Tophat, version 2.0.9, default options.
For big wiggle generation we used MACS analysis.
RNAseq analyses: normalized and differential expression: Cufflinks, version 2.2.1; settings: -b, -u, and default; Cuffmerge was used with reference gtf and default settings; Cuffquant was used with default settings; Cuffnorm was used with default settings; Cuffdiff was used with -b, -u and default settings.
Supplementary_files_format_and_content: RNAseq: Individual samples have an FPKM gene tracking file from Cufflinks, estimating transcript abundance for that sample, along with confidence intervals. There are two processed data matrices that apply to all the samples.
Genome_build: Hg19
Supplementary_files_format_and_content: Bigwiggle files
|
| |
|
| Submission date |
Sep 24, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ramesh Shivdasani |
| E-mail(s) |
ramesh_shivdasani@dfci.harvard.edu
|
| Organization name |
Dana Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Shivdasani
|
| Street address |
450 Brookline Ave. Dana 720D
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE73398 |
Fixed tissue ChIP-Seq (FiT-Seq) of archived clinical samples reveals chromatin dynamics and tumor-specific enhancer profiles |
|
| Relations |
| BioSample |
SAMN04110936 |
| SRA |
SRX1286334 |
