NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7256876 Query DataSets for GSM7256876
Status Public on May 01, 2023
Title Ventral Respiratory Column, 14 days, Room Air, Replicate 5
Sample type SRA
 
Source name Brain (Medulla)
Organism Capra hircus
Characteristics tissue: Brain (Medulla)
treatment (co2 condition): Room Air
tissue region: Ventral Respiratory Column
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: VRC-14d-NCO2_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 SAMN34441319
SRA SRX20144458

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap