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Sample GSM1652953 Query DataSets for GSM1652953
Status Public on Aug 01, 2016
Title MdESF1
Sample type SRA
 
Source name endometrial stromal fibroblasts from opossum
Organism Monodelphis domestica
Characteristics culture type: primary opossum endometrial stromal fibroblasts grown in culture
cell type: endometrial stromal fibroblast
Extracted molecule polyA RNA
Extraction protocol Cells grown in cluture were treated with trypsin and detached from flasks, and RNA was isolated using the RNeasy Micro RNA extraction kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Basecalls performed using CASAVA version 1.4
mRNA-seq reads were aligned to the human (GRCh37.69), rabbit (OryCun2.0.75), cow (UMD3.1.75), ferret (MusPutFur1.0.75), opossum (MonDom5.75) and rat (Rnor_5.0.75) cDNA builds using Tophat2 version 2.0.5
Number of times reads overlapped with known features (gene counts) was counted using HTSeq
transcripts per million (TPM) values were calculated according to Wagner et al (2012) Theor. Biosci.
Genome_build: Human (GRCh37.69), Rabbit (OryCun2.0.75), Cow (UMD3.1.75), Ferret (MusPutFur1.0.75), Opossum (MonDom5.75), Rat (Rnor_5.0.75)
Supplementary_files_format_and_content: Comma-delimited csv files include read counts for each Sample as well as a comma-delimited csv file which contains TPM values corrected by using only genes which have 1-to-1 orthologues in all species. All csv files can be found in the tar archive on the series record.
 
Submission date Apr 08, 2015
Last update date May 15, 2019
Contact name Koryu Kin
Organization name Yale University
Department EEB
Lab Gunter Wagner Lab
Street address 840 West Campus Drive
City West Haven
State/province CT
ZIP/Postal code 06516
Country USA
 
Platform ID GPL15381
Series (1)
GSE67659 Comparative transcriptomics of endometrial stromal fibroblasts
Relations
BioSample SAMN03465358
SRA SRX982566

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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