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Sample GSM2200538 Query DataSets for GSM2200538
Status Public on Jun 15, 2016
Title LCL10_control_21days
Sample type RNA
Source name LCL10_control_21days
Organism Homo sapiens
Characteristics disease state: depressive disorder
cell line: LCL10
treatment: control
clinical treatment outcome: non-responder
Treatment protocol LCLs were treated with 0.5µg/ml fluoxetine (dissolved in DMSO) for 21 days. MOCK treated control cultures were grown in parallel.
Growth protocol LCLs were grown in RPMI medium supplemented with 15% heat-inactivated fetal bovine serum, antibiotics (100 µg/ml penicillin, 100 µg/ml streptomycin) and a final concentration of 4 mM L-glutamine. Medium exchanging was done every second day.
Extracted molecule total RNA
Extraction protocol RNA was extracted using the NucleoSpin® RNA Kit (Macherey-Nagel, Germany) according to the manufacturer instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Germany). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 0.025ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 0.025ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner using one color scan setting .
Data processing The scanned images were analyzed with Feature Extraction Software 10 (Agilent) using default parameters (protocol GE1_1100 and Grid: 039494_D_F_20120411) to obtain background subtracted and spatially detrended Processed Signal intensities.
Submission date Jun 15, 2016
Last update date Jun 15, 2016
Contact name Julia Carolin Stingl
Organization name Federal Institute for Drugs and Medical Devices
Department Research
Street address Kurt-Georg-Kiesinger Allee 3
City Bonn
ZIP/Postal code 53175
Country Germany
Platform ID GPL17077
Series (1)
GSE83386 Gene expression of Lymphoblastoid Cell Lines (LCLs) from Depressed Patients after in-vitro treatment with fluoxetine

Data table header descriptions
VALUE Normalized signal intensity

Data table
A_23_P117082 283.80
A_33_P3246448 19.63
A_33_P3318220 6.05
A_33_P3236322 16.59
A_33_P3319925 76.31
A_21_P0000509 6987.03
A_21_P0000744 1320.42
A_24_P215804 206.24
A_23_P110167 1017.80
A_33_P3211513 361.86
A_23_P103349 10.11
A_32_P61480 3.68
A_33_P3788124 4.48
A_33_P3414202 746.30
A_33_P3316686 448.06
A_33_P3300975 618.43
A_33_P3263061 4122.15
A_33_P3261373 19.48
A_24_P278460 197.40
A_21_P0013109 3.68

Total number of rows: 50737

Table truncated, full table size 995 Kbytes.

Supplementary file Size Download File type/resource
GSM2200538_LCL10_control.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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