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Status |
Public on Aug 01, 2016 |
Title |
RnESF2 |
Sample type |
SRA |
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Source name |
endometrial stromal fibroblasts from rat
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Organism |
Rattus norvegicus |
Characteristics |
culture type: primary rat endometrial stromal fibroblasts grown in culture cell type: endometrial stromal fibroblast
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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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.
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Submission date |
Apr 08, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Koryu Kin |
Organization name |
Yale University
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Department |
EEB
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Lab |
Gunter Wagner Lab
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Street address |
840 West Campus Drive
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City |
West Haven |
State/province |
CT |
ZIP/Postal code |
06516 |
Country |
USA |
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Platform ID |
GPL14844 |
Series (1) |
GSE67659 |
Comparative transcriptomics of endometrial stromal fibroblasts |
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Relations |
BioSample |
SAMN03465361 |
SRA |
SRX982569 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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