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Sample GSM3291064 Query DataSets for GSM3291064
Status Public on Jul 26, 2018
Title saline mPFC biological rep 4
Sample type RNA
 
Source name mPFC of saline offspring at 4 mo.
Organism Mus musculus
Characteristics strain: C57BL/6J
maternal treatment: saline
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).
 
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.
 
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

Data table header descriptions
ID_REF
VALUE SST-RMA
DETECTION P-VALUE

Data table
ID_REF VALUE DETECTION P-VALUE
AFFX-BkGr-GC03_st 7.40009 0.802459
AFFX-BkGr-GC04_st 6.93128 0.974984
AFFX-BkGr-GC05_st 6.75093 0.997213
AFFX-BkGr-GC06_st 6.70178 0.998324
AFFX-BkGr-GC07_st 6.04229 0.99853
AFFX-BkGr-GC08_st 4.51176 0.997118
AFFX-BkGr-GC09_st 3.80391 0.994943
AFFX-BkGr-GC10_st 3.41726 0.991712
AFFX-BkGr-GC11_st 2.97266 0.979566
AFFX-BkGr-GC12_st 2.57501 0.937199
AFFX-BkGr-GC13_st 2.27267 0.973927
AFFX-BkGr-GC14_st 2.16837 0.971843
AFFX-BkGr-GC15_st 2.13606 0.974709
AFFX-BkGr-GC16_st 2.27267 0.933128
AFFX-BkGr-GC17_st 2.41797 0.911882
AFFX-BkGr-GC18_st 2.76109 0.819981
AFFX-BkGr-GC19_st 5.63392 0.634268
AFFX-BkGr-GC20_st 5.98643 0.622768
AFFX-BkGr-GC21_st 6.08925 0.614762
AFFX-BkGr-GC22_st 6.17278 0.60994

Total number of rows: 28846

Table truncated, full table size 1058 Kbytes.




Supplementary file Size Download File type/resource
GSM3291064_Mouse_Saline_PFC_4.CEL.gz 1.1 Mb (ftp)(http) CEL
GSM3291064_Mouse_Saline_PFC_4.sst-rma-gene-full.chp.gz 320.4 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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