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Sample GSM693856 Query DataSets for GSM693856
Status Public on Mar 22, 2011
Title HMC1 17h SerumStarv 4h Imatinib versus HMC1 17h SerumStarv 4h Imatinib 0.5h NGF
Sample type RNA
 
Channel 1
Source name HMC1 17h SerumStarv 4h Imatinib
Organism Homo sapiens
Characteristics cell line: HMC-1
Treatment protocol HMC-1(V560G c-Kit) cells were serum starved for 17 h, then treated with dimethyl sulfoxide (DMSO) or 5 μM Imatinib for 4 hours prior to stimulation with 100 ng/ml mouse recombinant NGF. After 30 or 120 min the stimulation was stopped in ice-cold PBS. Samples from cells grown in medium supplemented with 10% FCS were analyzed in parallel.
Growth protocol HMC-1(V560G c-Kit) cells were grown in RPMI1640 medium supplemented with 10% FCS.
Extracted molecule total RNA
Extraction protocol RNA was isolated using RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. Residual DNA contamination was removed with DNAseI (Invitrogen GmbH, Darmstadt, Germany) according to the manufacturer’s recommendations, and the RNA was again purified with RNeasy Mini kit (Qiagen).
Label Cy3
Label protocol 1000ng of total RNA per condition were used to prepare Cy3-, or Cy5-labeled cRNA with the “Low RNA Input Linear Amplification Kit PLUS, Two-Color” (#5188-5340, Agilent Technologies) according to the manufacturer’s recommendations.
 
Channel 2
Source name HMC1 17h SerumStarv 4h Imatinib 0.5h NGF
Organism Homo sapiens
Characteristics cell line: HMC-1
Treatment protocol HMC-1(V560G c-Kit) cells were serum starved for 17 h, then treated with dimethyl sulfoxide (DMSO) or 5 μM Imatinib for 4 hours prior to stimulation with 100 ng/ml mouse recombinant NGF. After 30 or 120 min the stimulation was stopped in ice-cold PBS. Samples from cells grown in medium supplemented with 10% FCS were analyzed in parallel.
Growth protocol HMC-1(V560G c-Kit) cells were grown in RPMI1640 medium supplemented with 10% FCS.
Extracted molecule total RNA
Extraction protocol RNA was isolated using RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. Residual DNA contamination was removed with DNAseI (Invitrogen GmbH, Darmstadt, Germany) according to the manufacturer’s recommendations, and the RNA was again purified with RNeasy Mini kit (Qiagen).
Label Cy5
Label protocol 1000ng of total RNA per condition were used to prepare Cy3-, or Cy5-labeled cRNA with the “Low RNA Input Linear Amplification Kit PLUS, Two-Color” (#5188-5340, Agilent Technologies) according to the manufacturer’s recommendations.
 
 
Hybridization protocol cRNA fragmentation, hybridization and washing steps were performed exactly as recommended by the manufacturer “Two-Color Microarray-Based Gene Expression Analysis Protocol V5.5” except that 4 µg of each labeled cRNA were used for hybridization.
Scan protocol Slides were scanned on the Agilent Micro Array Scanner G2505 B at two different PMT settings (100 % and 5 %) to increase the dynamic range of the measurements (extended dynamic range mode).
Data processing Data extraction and normalization were performed with the “Feature Extraction Software V9.5.3.1” by using the recommended default extraction protocol file: GE2-v5_95_Feb07.xml.
 
Submission date Mar 18, 2011
Last update date Mar 22, 2011
Contact name Oliver Dittrich-Breiholz
E-mail(s) dittrich.oliver@mh-hannover.de
Organization name Medical School Hannover
Department Research Core Unit Genomics
Street address Carl-Neuberg-Str. 1
City Hannover
ZIP/Postal code 30625
Country Germany
 
Platform ID GPL4133
Series (1)
GSE28045 Identification of novel target genes of nerve growth factor (NGF) in human mastocytoma cell line (HMC-1 (V560G c-Kit)) by transcriptome analysis

Data table header descriptions
ID_REF
VALUE log2 ratios (test sample / common reference sample)

Data table
ID_REF VALUE
1 -0.025438982
2 0
3 0
4 0
5 0
6 0
7 0
8 0
9 0
10 0
11 0
12 0.051206038
13 0.833971726
14 -0.193393278
15 0.800626406
16 -0.201713215
17 0.023372597
18 -0.159329905
19 0.252146688
20 -0.201278229

Total number of rows: 45015

Table truncated, full table size 745 Kbytes.




Supplementary file Size Download File type/resource
GSM693856.txt.gz 15.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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