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Sample GSM6911648 Query DataSets for GSM6911648
Status Public on May 30, 2023
Title V63_12_SHOCKnoMOM (PN7 Pups)
Sample type RNA
 
Source name Amygdala
Organism Rattus norvegicus
Characteristics treatment: SHOCKnoMOM
tissue: Amygdala
age: PN7 Pups
Treatment protocol Immediately following the acute tests of shock with and without the dam, pups were euthanized, as were Controls at the same time
Extracted molecule total RNA
Extraction protocol Dissection storage: The infant brains were rapidly frozen (-45oC - total time from decapitation to frozen ~ 2min), amygdala dissected, stored in a (-80oC) freezer
RNA processing: Total RNA (Qiagen RNeasy Micro Kit). mRNA was amplified linearly
Label biotin
Label protocol Affymetrix protocol
 
Hybridization protocol They were hybridized to Affymetrix rat 2.0 gene arrays as specified by Affymetrix (Santa Clara, CA) and NuGEN (Pico System; San Carlos, CA).
Scan protocol Affymetrix protocol
Description Gene expression data from the amydala of PN7 pups in the three conditions
Data processing Expression: Expression values were preprocessed, background-corrected, and normalized by RMA using BRAINARRAY [University of Michigan; CDF: Rat 1.0_Rn_ENTREZG] resulting in approximately 19,000 distinct genes
Significant effects: Rank Products, which simulates probabilities based on pairwise comparison differences, was used to assess differential expression in each experimental condition compared to the other.
GO: All genes were input with the fold change or pfp values (percentage of false positive predictions) calculated by the Rank Products analysis into ErmineJ using the gene score resampling method
Networks: To define networks of related probes we input probes with fold change that exceeded ±1.25, using the direct connection option. We included up- and downregulated genes together
 
Submission date Jan 02, 2023
Last update date May 30, 2023
Contact name Gordon Alfred Barr
E-mail(s) gordon_barr@mac.com
Phone 9147724698
Organization name CHOP
Department Anesthesiology
Lab Barr Lab
Street address 3615 Civic Center Blvd
City Philadelphia
State/province Pennsylvania
ZIP/Postal code 19104
Country USA
 
Platform ID GPL32992
Series (1)
GSE222012 Infant Pain Vs. Pain with Parental Suppression: Immediate and Enduring Impact on Brain, Pain and Affect

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
24152_at 6.920997843
24157_at 9.262721256
24158_at 8.736658827
24159_at 11.66030393
24162_at 10.04704631
24163_at 7.291667502
24165_at 7.635900709
24166_at 9.272518478
24167_at 10.85631989
24170_at 11.56278739
24171_at 11.00253857
24172_at 8.134277837
24173_at 8.563852539
24174_at 7.767252578
24175_at 9.488780588
24176_at 7.095145504
24177_at 6.803804854
24179_at 8.795817488
24180_at 6.909210311
24182_at 5.38585609

Total number of rows: 19357

Table truncated, full table size 414 Kbytes.




Supplementary file Size Download File type/resource
GSM6911648_V63_12_SHOCKnoMOM_RatGene1ST_RaGene-1_0-st-v1_.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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