|
| Status |
Public on Dec 09, 2022 |
| Title |
Brain.ThalamusAndHypothalamus.Middle.Nile_T3F |
| Sample type |
SRA |
| |
|
| Source name |
Brain.ThalamusAndHypothalamus.Middle.Nile
|
| Organism |
Arvicanthis niloticus |
| Characteristics |
tissue: Brain
treatment: No treatment - healthy tissue
|
| Growth protocol |
Nile grass rat biopsy samples
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNAs from 28 Nile grass rat vascular samples were isolated using trizol (ThermoFisher #15596018) and chloroform phase separations followed by the RNeasy mini protocol (Qiagen #74106) with optional on-column DNase digestion (Qiagen #79254).
Illumina truSeq Protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Biopsy - tissue
|
| Data processing |
RSEM: Reads were mapped to the human genome using Bowtie 0.12.8 (Langmead et al. 2009) allowing up to 2-mismatches. The gene expression values are estimated by RSEM tool
CRSP: we used CRSP tool to estimate the gene expression values. The CRSP tool allows estimation of gene expression values from RNA-seq data for species lacking a sequenced genome or corresponding gene annotations.
Assembly: NaN
Supplementary files format and content: text and gene expression values
|
| |
|
| Submission date |
Oct 11, 2022 |
| Last update date |
Dec 09, 2022 |
| Contact name |
Peng Jiang |
| E-mail(s) |
p.jiang@csuohio.edu
|
| Organization name |
Cleveland State University
|
| Street address |
2121 Euclid Ave
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44115 |
| Country |
USA |
| |
|
| Platform ID |
GPL32739 |
| Series (1) |
| GSE215233 |
A Nile Rat Transcriptomic Landscape Across 22 Organs By Ultra-deep Sequencing and Comparative RNA-seq pipeline (CRSP) |
|
| Relations |
| BioSample |
SAMN31242788 |
| SRA |
SRX17850533 |
