|
| Status |
Public on Dec 31, 2013 |
| Title |
Mid-term cervix tissue rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Mid-term cervix tissue
|
| Organism |
Cavia porcellus |
| Characteristics |
strain: Hartley
gestation stage: mid-term (43.6 ± 0.5 days)
tissue: cervical tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy extraction kit (Qiagen, cat# 75142) following manufactures instructions that included an in-column DNAse digestion. Poly A RNA sselection. Quality of the RNA was then confirmed using Agilent 2100 Bioanalyzer.
RNA library preparation and high-throughput sequencing were performed on an Illumina HiSeq 2000 sequencing system following the protocol recommended by Illumina for sequencing total RNA samples. Strand-specific library prep. Sequencing was done for each biological replicates at 1 x 75bp strand specific by the Yale Center for Genome Analysis
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
GpMT586
replicate 1
|
| Data processing |
Basecalls performed using CASAVA 1.8.2 according to the manufacturer’s protocols
Sequence reads were aligned to the Cavia porcellus reference genome (cavPor3.69) using the splice junction mapper for RNA-seq reads TopHat2
After alignment, read counts were determined with HTSeq-count v0.5.4p1 as described by the authors
Relative RNA abundance was measured as Transcripts Per Million Transcripts (TPM) as recommended in (Li, Ruotti et al. 2010; Wagner, Kin et al. 2012) rather than RPKM or FPKM. The reason is that units of RPKM are not consistent between samples and are thus problematic when comparing RNA abundance between samples of different transcript composition
Genome_build: Cavpor3.0
Supplementary_files_format_and_content: Matrix (linked as supplementary file on Series record) of TPM and HTSeq counts for each sample. Columns labled by sample name.
|
| |
|
| Submission date |
Jun 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Mauris Chukwudebelu Nnamani |
| E-mail(s) |
mnnamani@gmail.com
|
| Organization name |
Yale University
|
| Department |
Systems Biology institute, EEB
|
| Lab |
Gunter Wagner
|
| Street address |
300 heffernan drive B31-ABC/rm269
|
| City |
west Haven |
| State/province |
CT |
| ZIP/Postal code |
06512 |
| Country |
USA |
| |
|
| Platform ID |
GPL17296 |
| Series (1) |
| GSE47986 |
Evidence for the independent evolution of "functional progesterone withdrawal" in primates and guinea pigs: a comparative transcriptomic study |
|
| Relations |
| BioSample |
SAMN02204325 |
| SRA |
SRX306491 |
