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Sample GSM4609563 Query DataSets for GSM4609563
Status Public on Jun 01, 2021
Title KO Br male rep2
Sample type RNA
Source name KO male rest of brain
Organism Mus musculus
Characteristics gender: male
Treatment protocol mice were sacrificed and their brains removed immediately afterwards; while fresh, extracted brains were manually cleaned of brain stem tissue remnants by gross dissection, and split into cerebellum and rest-of-brain. Each sample was then placed inside an individual 15-ml conical, put dry-ice to snap-freeze, and archived in -80degC. To prevent cross-contamination and tissue degradation due to delayed processing, mice were dissected one at a time with a single-use scalpel blade each.
Growth protocol Animals were maintained under regular housing conditions prior to sampling
Extracted molecule total RNA
Extraction protocol RNA was extracted using Trizol from 50-100 mg of tissue
Label biotin
Label protocol One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Plus kit protocol.
Hybridization protocol 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification per the GeneChip Hybridization, Wash and Stain Kit and user manual.
Scan protocol Arrays were scanned in an Affymetrix Scanner 3000.
Description gene expression data from male rest of brain (whole brain minus the cerebellum)
Data processing Data was obtained using the TAC 4.0 Software using the MAS5 algorithm to generate .CHP files.
Submission date Jun 10, 2020
Last update date Jun 02, 2021
Contact name NIEHS Microarray Core
Organization name NIEHS
Department DIR
Lab Microarray Core
Street address 111 T.W. Alexander Drive
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
Platform ID GPL1261
Series (1)
GSE152224 Mutations on a novel brain-specific isoform of PGC1α leads to extensive upregulation of neurotransmitter-related genes and sexually dimorphic motor deficits in mice

Data table header descriptions
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)

Data table
AFFX-BioB-5_at 9.40395e-38 0.000296708
AFFX-BioB-M_at 9.40395e-38 4.42873e-05
AFFX-BioB-3_at 9.40395e-38 4.42873e-05
AFFX-BioC-5_at 9.40395e-38 5.16732e-05
AFFX-BioC-3_at 9.40395e-38 4.42873e-05
AFFX-BioDn-5_at 9.40395e-38 4.42873e-05
AFFX-BioDn-3_at 9.40395e-38 8.14279e-05
AFFX-CreX-5_at 9.40395e-38 5.16732e-05
AFFX-CreX-3_at 9.40395e-38 4.42873e-05
AFFX-DapX-5_at 9.40395e-38 4.42873e-05
AFFX-DapX-M_at 9.40395e-38 0.000224668
AFFX-DapX-3_at 9.40395e-38 5.16732e-05
AFFX-LysX-5_at 9.40395e-38 0.000258358
AFFX-LysX-M_at 9.40395e-38 0.00255552
AFFX-LysX-3_at 9.40395e-38 4.42873e-05
AFFX-PheX-5_at 9.40395e-38 0.00227496
AFFX-PheX-M_at 9.40395e-38 0.000340305
AFFX-PheX-3_at 9.40395e-38 6.02111e-05
AFFX-ThrX-5_at 9.40395e-38 0.00227496
AFFX-ThrX-M_at 9.40395e-38 0.00255552

Total number of rows: 45101

Table truncated, full table size 1364 Kbytes.

Supplementary file Size Download File type/resource
GSM4609563_20314_1178_KO_Male_Br_2_Rep_2_Mouse430_2_.CEL.gz 3.6 Mb (ftp)(http) CEL
GSM4609563_20314_1178_KO_Male_Br_2_Rep_2_Mouse430_2_.mas5.chp.gz 385.5 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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