NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3842070 Query DataSets for GSM3842070
Status Public on Sep 21, 2019
Title CD4+CD25neg_1
Sample type SRA
 
Source name peripheral blood
Organism Canis lupus
Characteristics sorted cell: CD4+CD25neg
animal: healthy dog_1
Extracted molecule total RNA
Extraction protocol CD4+CD25high and CD4+CD25neg cells were sorted from peripheral blood mononuclear 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 GAR3761A1-13_tpm_gene_count_table.txt [GAR3761A9]
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 Jun 02, 2019
Last update date Sep 21, 2019
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)
GSE132068 Phenotypic characterisation of regulatory T cells in dogs reveals signature transcripts conserved in humans and mice
Relations
BioSample SAMN11935532
SRA SRX5951750

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap