|
| Status |
Public on Jul 26, 2018 |
| Title |
poly(I:C) mPFC biological rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
mPFC of poly(I:C) offspring at 4 mo.
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
maternal treatment: poly(I:C)
tissue: brain (mPFC region)
Sex: female
|
| Treatment protocol |
On E12.5, pregnant (as ascertained by weight gain) females were injected intraperitoneally with a single dose of poly(I:C) (20 mg/kg, Invivogen) or saline. Each dam was subsequently returned its cage and left undisturbed until the birth of its litter. Pups were weaned between postnatal day 21-23 (P21-P23). Offspring were group-housed at maximum of 5 per cage with same-sex littermates.
|
| Growth protocol |
To obtain control and MIA offspring, C57BL6/J mice (7-8 weeks old, Jackson Laboratory, stock no. 000664) were mated overnight and seminal plugs were examined daily, indicated as embryonic day (E0.5). Females with detectable plugs were weighed and individually housed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At 4 months of age, brains were harvested from poly(I:C) and saline offspring and the mPFC region was dissected out. Dissected cortices were homogenized and total RNA was isolated according to the manufacturer’s instructions using the RNAeasy Mini Kit (Qiagen, Stanford Translational Applications Service Center (TASC)).
|
| Label |
biotin
|
| Label protocol |
Microarray was performed at the Protein and Nuclei Acid (PAN) Facility at Stanford University. The RNA integrity was examined on a Agilent 2100 bioanalyzer (Agilent Technologies). Only high quality RNA samples (RNA integrity number > 9) were used to generate double strand cDNA, which was fragmented and biotin labeled according to the Affymetrix GeneChip Pico Reagent Kit manual (Thermo Fisher Scientific).
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| |
|
| Hybridization protocol |
Fragmented and labeled cDNA was hybridized to the Mouse Clariom S array for 16 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven 640. Arrays were washed and stained with Streptavidin Phycoerythrin in an Affymetrix Fluidics Station 450 according to Affymetrix GeneChip Pico Reagent Kit guide ((Thermo Fisher Scientific).
|
| Scan protocol |
Arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G and .CEL files were generated by Affymetrix GeneChip Command Console Software (Thermo Fisher Scientific).
|
| Data processing |
Microarrays were analyzed using Transcriptome Analysis Console (TAC) 4.0 software (Thermo Fisher Scientific) with the SST-RMA algorithm. Default parameters were applied for assessment of differential expression. TAC 4.0 implements a linear mixed model analysis (LIMMA) package to identify differentially expressed genes. The significant genes were ranked by fold-change with a cutoff of 2 and ANOVA p-value less than 0.05.
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| |
|
| Submission date |
Jul 18, 2018 |
| Last update date |
Jul 26, 2018 |
| Contact name |
John Huguenard |
| E-mail(s) |
huguenar@stanford.edu
|
| Organization name |
Stanford University
|
| Street address |
1050A Arastradero Rd., Room A250
|
| City |
Palo Alto |
| State/province |
CA |
| ZIP/Postal code |
94304 |
| Country |
USA |
| |
|
| Platform ID |
GPL23038 |
| Series (1) |
| GSE117327 |
Persistent transcriptomic alterations in medial prefrontal cortex after prenatal exposure to maternal inflammation |
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