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Sample GSM313481 Query DataSets for GSM313481
Status Public on Sep 15, 2009
Title P43_TGFB_T12 (12 hours TGFB treatment, SSc FBs)
Sample type RNA
 
Channel 1
Source name P43_TGFB_T12
Organism Homo sapiens
Characteristics primary fibroblasts from 41yo male, 1 year diagnosed with dSSc, forearm biopsy taken in 2000
Biomaterial provider Kari Connolly UCSF
Treatment protocol 12 hours of 24 hour timecourse of 50pM TGFB treatment
Growth protocol Plated at 4x10e4 - grown for 48 hours in DMEM + Pen/Strep + 10% FBS (37C 5% CO2)
Grown for 24 hours in low serum conditions (DMEM + Pen/Strep + 0.1%FBS, 37C 5%CO2)
- then either treated with 50pM TGFB or sample taken for baseline measurement.
Extracted molecule total RNA
Extraction protocol RNeasy mini columns with on column DNaseI digestion (Qiagen)
Label Cy3
Label protocol Agilent Low RNA Input Linear Amplification protocol: 200 ng of total RNA from each time point sample was converted to Cy3-CTP (Perkin Elmer) labeled cRNA, and Universal Human Reference (UHR) RNA (Stratagene) was converted to Cy5-CTP (Perkin Elmer) using a low input linear amplification kit (Agilent Technologies) as per manufacturers protocols. Labeled cRNA targets were then purified using RNeasy columns (Qiagen).
 
Channel 2
Source name Universal Human Reference RNA
Organism Homo sapiens
Characteristics pool of RNA from 10 different human cell lines, commercially available from Stratagene.
Biomaterial provider purchased from Stratagene
Extracted molecule total RNA
Extraction protocol Stratagene's protocol
Label Cy5
Label protocol Agilent Low RNA Input Linear Amplification protocol: 200 ng of total RNA from each time point sample was converted to Cy3-CTP (Perkin Elmer) labeled cRNA, and Universal Human Reference (UHR) RNA (Stratagene) was converted to Cy5-CTP (Perkin Elmer) using a low input linear amplification kit (Agilent Technologies) as per manufacturers protocols. Labeled cRNA targets were then purified using RNeasy columns (Qiagen).
 
 
Hybridization protocol Agilent Gene Expression Hybridization kit was used for hybridization. Cy3- and Cy5-labeled cRNA was hybridized to stripped 4 x 44K Agilent Whole Human genome oligo-array. Hybridization was carried out for 17 hours at 65oC with rotation.
Scan protocol Microarrays were scanned using a dual laser GenePix 4000B scanner (Axon Instruments). The pixel intensities of the acquired images were then quantified using GenePix Pro 5.1 software.
Description Comparison of dermal fibroblasts from healthy and dSSc patients treated and untreated with TGFB.
Data processing Arrays were visually inspected for defects or technical artifacts, and poor quality spots were manually flagged and excluded from further analysis. Only spots with fluorescent signal at least 1.5 fold greater than local background in both Cy3- Cy5- channels were included in the analysis. Genes missing more than 20% of their data points were excluded, resulting in 18,695 probes that passed the filtering criteria.
 
Submission date Aug 18, 2008
Last update date Aug 03, 2009
Contact name Jennifer L Sargent
E-mail(s) jennifer.sargent@gmail.com
Organization name Dartmouth Medical School
Department Genetics
Lab Whitfield
Street address Dartmouth College; HB7400
City Hanover
State/province NH
ZIP/Postal code 03755
Country USA
 
Platform ID GPL6480
Series (1)
GSE12493 A TGFB Responsive Gene Expression Signature is Associated With More Severe Skin and Lung Disease in Diffuse Scleroderma

Data table header descriptions
ID_REF
VALUE Data is displayed as log2 of the LOWESS-normalized Cy5/Cy3 ratio

Data table
ID_REF VALUE
A_23_P100001 0.841
A_23_P100074 -1.551
A_23_P100092 0.416
A_23_P100103 -1.641
A_23_P100141 0.609
A_23_P100156 -1.882
A_23_P100196 0.285
A_23_P100203 -0.078
A_23_P100263 0.084
A_23_P100292 -0.61
A_23_P100315 0.368
A_23_P100326 -0.082
A_23_P100341 2.598
A_23_P100344 2.635
A_23_P100355 -0.368
A_23_P100392 0.398
A_23_P100413 -0.304
A_23_P100420 -0.735
A_23_P100441 0.039
A_23_P100455 0.13

Total number of rows: 18696

Table truncated, full table size 342 Kbytes.




Supplementary file Size Download File type/resource
GSM313481.gpr.gz 5.7 Mb (ftp)(http) GPR
Processed data included within Sample table

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