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Sample GSM916685 Query DataSets for GSM916685
Status Public on Jan 01, 2013
Title HaCaT_Cyt+Ino_Rep2
Sample type RNA
Source name HaCaT cells, with cytokines and Ino-C2-PAF, 24h, replicate 2
Organism Homo sapiens
Characteristics cell line: HaCaT
treatment protocol: stimulated with cytokines (each 2 ng/ml) and 5 µM Ino-C2-PAF
Treatment protocol The assay was performed in defined keratinocytes serum-free medium without growth supplement. Cells were treated with IL-1α, IL-17, IL-22, TNF-α and oncostatin-M (2 ng/ml each) in the presence or absence of 5 µM Ino-C2-PAF or left untreated (control) 24 h.
Growth protocol HaCaT cells were grown in RPMI medium supplemented with heat-inactivated fetal bovine serum (10 %), penicillin (100 U/ml), streptomycin (0.1 mg/ml) and L-glutamine (440 mg/l). One day prior to experimentation, cells were adapted to defined keratinocyte serum-free medium with growth supplement (including insulin, EGF, and FGF).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with RNeasy Mini Kit in accordance to the manufacturer instructions (Qiagen Hilden, Germany). The integrity of RNA was verified by the presence of the 28S and 18S rRNA on agarose gels and an A260/280 ratio in the range of 1.9–2.1.
Label Cy3
Label protocol 200 ng of total RNA were used for production of fluorescent (Cyanine-3) cRNA as described in the Agilent analysis instruction manual for One-Color Microarray-Based Gene Expression Analysis (Agilent Technologies, Palo Alto, USA). Amplified cRNA was purificated using RNAeasy mini spin columns and subsequently quantified using NanoDrop ND-1000 UV-VIS Spectrophotometer.
Hybridization protocol All samples were hybridized to Agilent whole human genome microarray kit 8x60K (G4851A) according to the manufacturer´s instructions (One-Color Microarray-Based Gene Expression Analysis).
Scan protocol Arrays were scanned at 5 µm resolution on an Agilent DNA Microarray Scanner (G2505C, Agilent).
Description Gene expression after 24h HaCaT cells stimulated with cytokines (each 2 ng/ml) and 5 µM Ino-C2-PAF
Data processing The signal values were extracted using the Agilent Feature Extracting Software version and protocol GE_107_Sep09.
Submission date Apr 17, 2012
Last update date Jan 01, 2013
Contact name Geo Semini
Organization name Charité - Universitätmedizin
Department Institute for Biochemie
Street address Oudenarderstrasse 16
City Berlin
ZIP/Postal code 13347
Country Germany
Platform ID GPL13607
Series (1)
GSE37361 Impact of Ino-C2-PAF on the gene expression profile of HaCaT cells after stimulation with pro-inflammatory cytokines

Data table header descriptions
VALUE processed Cy3 signal intensity (Agilent gProcessedSignal)

Data table
1 1.081522e+005
2 5.852929e+000
3 5.852804e+000
4 3.471036e+002
5 4.335063e+002
6 3.616632e+001
7 5.988740e+003
8 7.648249e+002
9 5.836808e+000
10 2.951454e+001
11 5.826429e+000
12 4.174447e+003
13 3.444502e+003
14 2.882758e+002
15 5.397136e+003
16 5.792145e+000
17 2.833138e+002
18 1.549118e+001
19 5.766898e+000
20 1.250130e+003

Total number of rows: 62976

Table truncated, full table size 1219 Kbytes.

Supplementary file Size Download File type/resource
GSM916685_US81403230_252800412025_S01_GE1_107_Sep09_2_3.txt.gz 12.1 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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