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Sample GSM6911640 Query DataSets for GSM6911640
Status Public on May 30, 2023
Title V62_1_SHOCKplusMOM (PN7 Pups)
Sample type RNA
 
Source name Amygdala
Organism Rattus norvegicus
Characteristics treatment: SHOCKplusMOM
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 6.17749306
24157_at 8.855805194
24158_at 8.241319272
24159_at 11.45621768
24162_at 10.00707377
24163_at 6.803595085
24165_at 6.693416644
24166_at 8.723479494
24167_at 10.67828547
24170_at 11.43473283
24171_at 10.86057322
24172_at 7.599805164
24173_at 8.1559737
24174_at 7.226431304
24175_at 9.373158373
24176_at 6.697609082
24177_at 6.075734938
24179_at 8.75439711
24180_at 6.385797005
24182_at 5.277721041

Total number of rows: 19357

Table truncated, full table size 414 Kbytes.




Supplementary file Size Download File type/resource
GSM6911640_V62_1_SHOCKplusMOM_RaGene-1_0-st-v1_.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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