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Sample GSM1319104 Query DataSets for GSM1319104
Status Public on May 16, 2014
Title MDD matched sample pair brain dorsolateral prefrontal cortex BA9_F #19
Sample type RNA
Source name MDD sample, brain dorsolateral prefrontal cortex
Organism Homo sapiens
Characteristics tissue: brain dorsolateral prefrontal cortex
disease state: MDD case
Treatment protocol not applicable
Growth protocol not applicable
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from frozen samples stored in TRIzol (Invitrogen, Carlsbad, Calif.) and processed for microarray analysis according to the microarray manufacturer’s protocol (Affymetrix, Santa Clara, Calif.)
Label biotin
Label protocol According to standard affymetrix protocol: • 10ul Purified cDNA10ul • DEPC H2O • 4ul 10x IVT Labeling Buffer • 12ul IVT Labeling NTP mix • 4ul IVT Labeling Enzyme mix - Incubate at 37C 16 hour in an incubating oven or thermal cycler with heated lid to avoid condensation. - Purify labeled cRNA generated from either IVT labeling reaction using RNeasy RNA Purification Mini kit (Qiagen) using the RNA Cleanup Protocol according to manufacturers instructions. - Quantitate Biotin labeled cRNA using 260nm/280nm spectrophotometric assay.
Hybridization protocol Samples were hybridized using Affymetrix hybridization kit materials: • Heat the hybridization cocktail to 99°C for 5 minutes in a heat block • Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation • Transfer the hybridization cocktail that has been heated at 99°C, to a 45°C heat block for 5 minutes • Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture • Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube • Place probe array into the hybridization oven, set to 45°C • To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm • Hybridize for 16 hours • During the latter part of the 16-hour hybridization, proceed to the GeneChip® Expression Wash, Stain and Scan User Manual, P/N 702731, to prepare reagents for the washing and staining steps required immediately after completion of hybridization
Scan protocol Affymetrix GeneChIP Scanner 3000 7G
Description dissected from frozen coronal blocks ~2–3 cm caudal to the temporal pole
Data processing Probeset signals (i.e., transcript levels) were extracted with the Affymetrix GCOS software. For statistical analysis, log2- transformed probeset signal intensities were extracted and normalized with the robust multiarray average (GC-RMA) algorithm
Submission date Jan 30, 2014
Last update date May 30, 2014
Contact name Etienne Sibille
Phone 412-624-0804
Organization name University of Pittsburgh
Department Psychiatry
Street address 450 Technology Drive, Suite 231
City Pittsburgh
State/province PA
ZIP/Postal code 15219
Country USA
Platform ID GPL570
Series (1)
GSE54568 Expression data from human brain dorsolateral prefrontal cortex - including control samples and samples with major depression disorders (30 samples BA9_F)

Data table header descriptions
VALUE Signal estimates from Affymetrix GCOS software

Data table
1007_s_at 10.45571366
1053_at 6.786390626
117_at 5.123632408
121_at 8.277963691
1255_g_at 6.042338131
1294_at 6.496952123
1316_at 6.626897011
1320_at 4.821883996
1405_i_at 4.299842028
1431_at 5.73611919
1438_at 6.563824078
1487_at 7.940178847
1494_f_at 6.15064871
1552256_a_at 7.454206872
1552257_a_at 8.042371115
1552258_at 4.220487228
1552261_at 4.948913068
1552263_at 3.524636354
1552264_a_at 8.15193928
1552266_at 4.40144543

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.

Supplementary file Size Download File type/resource
GSM1319104_19-d.CEL.gz 5.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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