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Sample GSM4175084 Query DataSets for GSM4175084
Status Public on Mar 09, 2020
Title Dog_2_CD5-CD21+
Sample type SRA
 
Source name lymph node
Organism Canis lupus
Characteristics animal: Dog_2_B cell lymphoma
Extracted molecule total RNA
Extraction protocol CD5-CD21+ cells were sorted from fine needle aspirated lymph node cells and sorted by FACS. Total RNA was extracted from cells using RNA Bee and Direct-zol RNA MicroPrep Kit.
RNA libraries were generated following standard Illumina protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description WUY5223A114
Data processing Sequence reads were trimmed using Skewer v0.1.125 to remove adaptor and achor sequences, then mapped to canine genome, CanFam3.1, using HISAT2 v2.0.0-beta.
The mapped read pairs were quantified using featureCounts v1.5.0, and annotated using the same canine genomic data.
Mapping matrics were generated using Picard Tools v1.92. The metrics and variants for assessing read distribution, biotype distribution and mapped transcripts were generated using R v3.4.2.
Read counts were all converted to transcripts per milllion (TPM).
Genome_build: CanFam3.1
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
 
Submission date Nov 18, 2019
Last update date Mar 09, 2020
Contact name Ying Wu
E-mail(s) juliawuu@vet.upenn.edu
Organization name University of Pennsylvania
Street address 3900 Spruce Street
City Philadelphia
State/province Pennsylvania
ZIP/Postal code 19104
Country USA
 
Platform ID GPL26727
Series (1)
GSE140603 Gene expression profiling of B cell lymphoma in dogs reveals dichotomous metabolic signatures distinguished by oxidative phosphorylation
Relations
BioSample SAMN13321605
SRA SRX7176310

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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