|
| Status |
Public on Jul 31, 2017 |
| Title |
Opossum Non-pregnant 4 |
| Sample type |
SRA |
| |
|
| Source name |
cervix
|
| Organism |
Monodelphis domestica |
| Characteristics |
tissue: cervix
gestation stage: Non-pregnant
strain: NA
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tissues were harvested and kept in RNAlater until extraction of RNA using Qiagen RNeasy extraction kit.
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 |
| |
|
| Description |
Md_NP_4
|
| Data processing |
Basecalls performed using CASAVA
mRNA-seq reads were aligned to the rabbit (OryCun2.0), opossum (MonDom5.69) mouse (Mus38.69) and armadillo (DasNov3.0) cDNA builds using Tophat2
Number of 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: Genome_build: rabbit (OryCun2.0), opossum (MonDom5.69) mouse (Mus38.69) and armadillo (DasNov3.0)
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Comma-delimited csv files include read counts for each sample.
|
| |
|
| Submission date |
Aug 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Gunter Wagner |
| E-mail(s) |
[email protected]
|
| Organization name |
Yale University
|
| Department |
Systems Biology Institute, EEB
|
| Lab |
Gunter Wagner
|
| Street address |
300 Heffernan Drive, ISTC 108
|
| City |
West Haven |
| State/province |
CT |
| ZIP/Postal code |
06516 |
| Country |
USA |
| |
|
| Platform ID |
GPL15381 |
| Series (1) |
| GSE85815 |
Evolution of Gene Expression in the Uterine Cervix related to Steroid Signaling: Conserved features in the regulation of cervical remodeling. |
|
| Relations |
| BioSample |
SAMN05591635 |
| SRA |
SRX2034653 |
