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Status |
Public on Oct 04, 2021 |
Title |
AH2-22 |
Sample type |
SRA |
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Source name |
Nucleus Accumbens (bulk tissue)
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Organism |
Rattus norvegicus |
Characteristics |
tissue: Nucleus Accumbens (bulk tissue) strain: Sprague-Dawley Sex: Male maternal immune activation: LPS stress: Stress
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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.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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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
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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)
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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 |
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Relations |
BioSample |
SAMN22014087 |
SRA |
SRX12453491 |