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Sample GSM1652946

Query DataSets for GSM1652946

Status

Public on Aug 01, 2016

Title

HsESF2

Sample type

SRA

Source name

endometrial stromal fibroblasts from human

Organism

Homo sapiens

Characteristics

culture type: primary human 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 Genome Analyzer II

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