NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5607892 Query DataSets for GSM5607892
Status Public on Oct 04, 2021
Title AH2-16
Sample type SRA
 
Source name Nucleus Accumbens (bulk tissue)
Organism Rattus norvegicus
Characteristics tissue: Nucleus Accumbens (bulk tissue)
strain: Sprague-Dawley
Sex: Male
maternal immune activation: Saline
stress: Stress
Treatment protocol We injected lipopolysaccharide (LPS) or saline on gestational days 15 and 16 to pregnant rats. Their male offspring were then subjected to unpredictable stress or handling during adolescence. At PND 90, animals were deeply anaesthetised with isoflurane and sacrificed by decapitation. Brains were extracted and, with the help of a brain matrix, 1 mm thick coronal slices were obtained between 2.28 mm and 1.08 mm, approximately, anterior from bregma. With the help of two dissecting lancet-shaped needles, the dorsolateral striatum and the nucleus accumbens were dissected according to the Paxinos and Watson atlas. The tissue samples were snap-frozen with dry ice and stored at -70º C.
Extracted molecule total RNA
Extraction protocol Samples were homogenized, and RNA extracted according to the protocol, tools and reagents provided by RNeasy Mini Kit (Qiagen).
Libraries were prepared according to the instructions of the NEBNext Ultra Directional RNA Library Prep kit for Illumina kit (New England Biolabs), as detailed in “Chapter 1: Protocol for use with NEBNext Poly(A) mRNA Magnetic Isolation Module”. The input yield of total RNA to start the protocol was 1 µg quantified by an Agilent 2100 Bioanalyzer using an RNA 6000 nano LabChip kit. We performed the library amplification included in the cited protocol using a PCR of 14 cycles. The obtained libraries were validated and quantified by an Agilent 2100 Bioanalyzer using a DNA7500 LabChip kit and an equimolecular pool of libraries were titrated by quantitative PCR using the “Kapa-SYBR FAST qPCR kit forLightCycler480” (Kapa BioSystems) and a reference standard for quantification.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing We used the Illumina Basespace workflow version. 2.1.0. The BAM summary method was BamStats. The alligner software used was STAR (version 2.6.25.17) and the software for the analysis was Isis (2.6.25.17 version).
Differential expression analysis was carried out using the CUFFDIFF tool (2.2.1 version).
Genome_build: UCSC Rn5
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
 
Submission date Oct 02, 2021
Last update date Oct 04, 2021
Contact name Alejandro Higuera-Matas
E-mail(s) ahiguera@psi.uned.es
Phone 913989689
Organization name Universidad Nacional de Educación a Distancia (UNED)
Department Psychobiology
Street address Calle Juan del Rosal 10
City Madrid
State/province Madrid
ZIP/Postal code 28040
Country Spain
 
Platform ID GPL20084
Series (1)
GSE185195 Gene expression profiling of the nucleus accumbens and dorsolateral striatum in a two-hit model combining maternal immune activation and peripubertal stress in rats
Relations
BioSample SAMN22014092
SRA SRX12453486

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