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Sample GSM6911671 Query DataSets for GSM6911671
Status Public on May 30, 2023
Title 917_2 SHOCK_NoMOM (PN12 Pups)
Sample type RNA
 
Source name Amygdala
Organism Rattus norvegicus
Characteristics treatment: SHOCKnoMOM
tissue: Amygdala
Sex: Male
age: PN12 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 PN12 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 5.394557914
24157_at 8.263708012
24158_at 8.495924461
24159_at 10.72606645
24162_at 9.438794523
24163_at 5.748765853
24165_at 6.625765651
24166_at 8.855033263
24167_at 10.13188723
24170_at 10.75142726
24171_at 10.12072729
24172_at 8.291016059
24173_at 8.079889496
24174_at 6.385906056
24175_at 8.589332855
24176_at 6.373033899
24177_at 5.229250957
24179_at 10.01343531
24180_at 5.886491186
24182_at 5.55501459

Total number of rows: 19357

Table truncated, full table size 414 Kbytes.




Supplementary file Size Download File type/resource
GSM6911671_917-2_SHOCKnoMOM_RaGene-1_0-st-v1_.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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