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Sample GSM7874359 Query DataSets for GSM7874359
Status Public on Nov 05, 2023
Title mPFC, Control + Vehicle treatment, rep2
Sample type SRA
Source name Brain
Organism Rattus norvegicus
Characteristics tissue: Brain
treatment: Control + Vehicle treatment
Treatment protocol The mPFC was dissected out from the sections after electrophysiology, and the tissue was flash frozen in liquid nitrogen and stored at -80 °C until further use.
Growth protocol N/A (rat brain tissue)
Extracted molecule total RNA
Extraction protocol RNA was extracted using Qiagen RNeasy mini kit (Qiagen, Hilden, GER). RNA quality was checked using Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, US), RNA concentration was measured with Nanodrop (Thermo Fisher Scientific, Waltham, US).
500 ng of RNA was used as input for library preparation using the Illumina TruSeq Stranded mRNA library prep kit (Illumina, San Diego, US) according to the manufacturer's instructions. Libraries were quality checked on a Fragment Analyzer (Agilent Technologies) and concentration was measured with Qubit dsDNA HS Assay kit (Thermo Fisher Scientific). Libraries were pooled and sequenced on a HiSeq4000 (Illumina).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
Description C2_Ctrl_Veh
Data processing Basecalls and sample de-multiplexing performed by bcl2fastq conversion with default parameters
Sequenced reads were quality check with fastqc default parameters and then mapped with STAR using default algorithm parameters against rn6
The resulting BAM files were processed with SAMtools to yield count data for RefSeq transcript annotations
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. In short, the number of reads mapping to transcripts were counted and normalized by the size of the longest transcript of a gene and by the size of the library.
RefSeq annotations from ref_Rnor_6.0_top_level.gff3.gz
Assembly: rn6
Supplementary files format and content: counts.gct contains raw read counts per RefSeq gene in gct format
Supplementary files format and content: rpkms.gct contains normalized read counts per RefSeq gene in gct format
Submission date Oct 31, 2023
Last update date Nov 05, 2023
Contact name Roland Schmucki
Organization name F. Hoffmann - La Roche AG
Street address Grenzacherstrase
City Basel
ZIP/Postal code 4058
Country Switzerland
Platform ID GPL22396
Series (1)
GSE246666 Selective oxytocin receptor activation prevents prefrontal circuit dysfunction and social behavioral alterations in response to chronic prefrontal cortex activation in rats
BioSample SAMN38051397
SRA SRX22319134

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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