|
| Status |
Public on May 19, 2020 |
| Title |
canine tissue from B297NM |
| Sample type |
SRA |
| |
|
| Source name |
canine splenic normal tissue
|
| Organism |
Canis lupus familiaris |
| Characteristics |
breed: Boxer
age: 8
Sex: male
tissue: spleen
disease state: healthy normal
rna fraction: nascent RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nascent RNA were extracted as chromatin complex following ChRO-seq protocol (Mahat DB et al, Nat Protoc. 2016).
ChRO-seq libraries were prepared following ChRO-seq protocol (Mahat DB et al, Nat Protoc. 2016).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Library strategy: ChRO-seq
Single-read sequencing data were preprocessed and mapped to the canine genome assembly by proseq 2.0 pipeline (https://github.com/Danko-Lab/proseq2.0).
Single-read sequencing data were preprocessed to remove the adapter sequences and trim based on base quality, and deduplicating the reads based on unique molecular identifiers in RNA adapters.
Sequencing reads were mapped into a canine genome assembly (CanFam 3.1) using the Burrows-Wheeler Aligner software package.
Aligned BAM files were converted into bigWig format.
Genome_build: CanFam3.1
Supplementary_files_format_and_content: BigWig files were generated from aligned BAM files by proseq 2.0 pipeline (https://github.com/Danko-Lab/proseq2.0).
|
| |
|
| Submission date |
May 16, 2020 |
| Last update date |
May 20, 2020 |
| Contact name |
Scott Coonrod |
| E-mail(s) |
sac269@cornell.edu
|
| Organization name |
Cornell University
|
| Department |
Baker Institute for Animal Health
|
| Lab |
Coonrod lab
|
| Street address |
235 Hungerford Hill Road
|
| City |
Ithaca |
| State/province |
New York |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL21400 |
| Series (1) |
| GSE150705 |
Genome-wide analysis of hemangiosarcoma tumor tissue using ChRO-seq finds ECM remodeling plays an important role in canine hemangiosarcoma pathogenesis. |
|
| Relations |
| BioSample |
SAMN14938359 |
| SRA |
SRX8353471 |
