|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Mar 09, 2020 |
Title |
Dog_7_CD5-CD21+ |
Sample type |
SRA |
|
|
Source name |
lymph node
|
Organism |
Canis lupus |
Characteristics |
animal: Dog_7_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 |
WUY5223A111
|
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 |
SAMN13321596 |
SRA |
SRX7176315 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|