|
Status |
Public on May 01, 2023 |
Title |
Nucleus Tractus Solitarii, 7 days 6%-7 days 8%, Moderate CH, Replicate 5 |
Sample type |
SRA |
|
|
Source name |
Brain (Medulla)
|
Organism |
Capra hircus |
Characteristics |
tissue: Brain (Medulla) treatment (co2 condition): Moderate CH tissue region: Nucleus Tractus Solitarii 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 SMARTerĀ® 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: NTS-7d-6p-8p_rep5
|
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 |
SAMN34441343 |
SRA |
SRX20144506 |