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Sample GSM4556982 Query DataSets for GSM4556982
Status Public on May 19, 2020
Title canine tissue from C349
Sample type SRA
 
Source name canine splenic HSA
Organism Canis lupus familiaris
Characteristics breed: Ches Bay ret
age: 13
Sex: female
tissue: spleen
disease state: HSA
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 SAMN14938348
SRA SRX8353482

Supplementary file Size Download File type/resource
GSM4556982_C349_HSA_minus.bw 15.1 Mb (ftp)(http) BW
GSM4556982_C349_HSA_plus.bw 15.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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