NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5260775 Query DataSets for GSM5260775
Status Public on Apr 23, 2021
Title 00078A1863_IL
Sample type SRA
 
Source name Brain region: Infralimbic cortex
Organism Rattus norvegicus
Characteristics population: Heterogeneous Stock
Sex: M
rat batch: Batch03
brain region: Infralimbic cortex
Treatment protocol All rats were naïve to behavioral or pharmacology treatment.
Growth protocol All rats were group housed under standard laboratory conditions.
Extracted molecule polyA RNA
Extraction protocol 1) Brain region dissection: Brains were taken out of a minus 80 degree freezer and cryosectioned into 60um sections, which were mounted onto RNase-free glass slides. Slides were stored in minus 80 degree until dissection. During dissection, slides were placed on a minus 20 degree cold plate. One drop (approximately 50 ul) of RNAlater was placed on the brain region of interest. Each brain region then was dissected out under a dissecting video camera by using a pair of fine tipped forceps with the assistance of an 18 gauge needle with a bent tip. Bilateral tissue of the same brain region from each rat was immediately transferred into 350 ul Buffer RLT (containing beta-mercaptoethanol) and placed on dry ice. Tissue was stored in minus 80 degree before RNA extraction. 2) RNA extraction: Tissue was thawed on ice and homogenized by using a clean stainless steel bead using Qiagen TissueLyser (40Hz, 3 min). AllPrep DNA/RNA mini kit (Qiagen) was used to extract RNA. Samples were processed by using the QIAcube robot following standard protocols. The optional DNase digestion step was included for RNA samples.
RNA libraries were prepared for sequencing using standard Illumina protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Reads were first trimmed for adapter and poor-quality base calls using cutadapt
Reads were then aligned to the Ensembl Rat Transcriptome using RSEM
Upper quantile adjusted was applied to estimated gene read counts using DESeq2
Samples were filtered based on low reads counts, mismatched genotypes, and expression PCA outliers
Genes were eliminated if less than 25% of libraries had more than one read or if the total number of reads among all libraries for the gene was less than 100
Read counts were log base 2 transformed after the addition of 1 to each read count (to avoid taking the log of zero)
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Tab-separated table with row names (Ensembl gene IDs) and column names (sample IDs) containing log2(read count + 1) values
 
Submission date Apr 22, 2021
Last update date Apr 23, 2021
Contact name Daniel Munro
E-mail(s) dmunro@scripps.edu
Organization name UC San Diego
Department Psychiatry
Lab Palmer Lab
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platform ID GPL22396
Series (2)
GSE173137 Mapping genotype-expression associations in Heterogeneous Stock rat brains to advance behavioral genetics research [Infralimbic cortex]
GSE173141 Mapping genotype-expression associations in Heterogeneous Stock rat brains to advance behavioral genetics research
Relations
BioSample SAMN18835902
SRA SRX10660028

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