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Sample GSM6911634 Query DataSets for GSM6911634
Status Public on May 30, 2023
Title 316_3_NAIVE_10115 (PN7 Pups)
Sample type RNA
 
Source name Amygdala
Organism Rattus norvegicus
Characteristics treatment: NAIVE
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 6.215192311
24157_at 8.986870425
24158_at 8.566108704
24159_at 11.45513938
24162_at 9.995271703
24163_at 6.963194126
24165_at 7.009069109
24166_at 9.42058674
24167_at 10.65677322
24170_at 11.41518552
24171_at 10.8024619
24172_at 7.64167131
24173_at 8.43511432
24174_at 7.051752013
24175_at 9.451548009
24176_at 6.821694808
24177_at 6.274632428
24179_at 8.86281717
24180_at 6.959833951
24182_at 5.503578316

Total number of rows: 19357

Table truncated, full table size 414 Kbytes.




Supplementary file Size Download File type/resource
GSM6911634_316_3_NAIVE_RatGene1ST_RaGene-1_0-st-v1_.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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