|
| Status |
Public on May 01, 2023 |
| Title |
Retrotrapezoid Nucleus, 14 days, Mild CH, Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Brain (Medulla)
|
| Organism |
Capra hircus |
| Characteristics |
tissue: Brain (Medulla)
treatment (co2 condition): Mild CH
tissue region: Retrotrapezoid Nucleus
Sex: Female
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated on-column using Direct-Zol RNA Miniprep plus (Zymo Research, Irvine, CA, USA) per manufacture instructions
RNA libraries were prepared using SMARTer® Universal Low Input RNA Kit for Sequencing (Takara Bio, San Jose, CA, USA), per manufacturing recommendations
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
matrix column name: RTN-14d-6p_rep2
|
| Data processing |
MAP-RSeq3 workflow
Initial quality control and preprocessing of raw reads was completed with FASTQC and Trimmomatic
Alignment of preprocssed raw sequence reads were mapped to goat reference genome (GCA_001704415.1) using STAR package
Read counts were generated with featureCounts function of MAP-RSeq3 workflow and normalization values provided by MAP-RSeq3 workflow
Assembly: GCA_001704415.1
Supplementary files format and content: tab-delimited text files include raw RPKM values for each sample for each nuclei
Supplementary files format and content: xlsx file containing results from EdgeR DEG pairwaise analysis with each separate file representing comparison between RA vs CO2 condition across different nuclei
|
| |
|
| Submission date |
Apr 29, 2023 |
| Last update date |
May 01, 2023 |
| Contact name |
Kirstyn J Grams |
| E-mail(s) |
kgrams@mcw.edu
|
| Organization name |
Medical College of Wisconsin
|
| Department |
Physiology
|
| Lab |
Forster
|
| Street address |
8701 W Watertown Plank Road
|
| City |
Milwaukee |
| State/province |
Wisconsin |
| ZIP/Postal code |
53226 |
| Country |
USA |
| |
|
| Platform ID |
GPL27106 |
| Series (1) |
| GSE231308 |
Chronic hypercapnia-induced gene expression profiles in the brain |
|
| Relations |
| BioSample |
SAMN34441334 |
| SRA |
SRX20144515 |
