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Sample GSM1077394 Query DataSets for GSM1077394
Status Public on Apr 27, 2013
Title B6 brown SVF 1
Sample type RNA
 
Source name stromal-vascular fraction of interscapular brown adipose tissue
Organism Mus musculus
Characteristics strain: C57BL/6
gender: male
developmental stage: young adult
tissue: interscapular brown adipose
fraction: stromal-vascular
Treatment protocol For cellular separation, dissected adipose tissues were minced and incubated in 2.0 ml 0.2% collagenase type II in collagenase buffer (25 mM KHCO3, 12 mM KH2PO4, 1.2 mM MgSO4, 4.8 mM KCl, 120 NaCl, 1.2 mM CaCl2, 5 mM glucose, 2.5% BSA, 1% Pen/Strep, pH 7.4) rocking for 50 min at 37°C with occasional resuspension. 10 ml 90% PBS were added and samples centrifuged 5 min at 200 g. The adipocyte fraction was removed from the top and filtered through 100 µm cell strainers (BD). Filters were washed with 10 ml PBS and sample centrifuged as above. The adipocyte fraction was spun 2 min at 200 g and buffer removed from below the adipocytes with a 40 mm 20 G needle. The SVF pellet from the initial centrifugation was aspirated, resuspended in 2 ml erythrocyte lysis buffer (154 mM NH4lC, 10 mM KHCO3, 0.1 mM EDTA, pH 7.4) and incubated for 4 min. After addition of 2 ml PBS samples were filtered through 40 µm cell strainers. Filters were rinsed with 8 ml buffer and samples centrifuged for 5 min at 200 g.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cells using Trizol reagent (Invitrogen) and Phase Lock Gel tubes (5prime) according to the manufacturer's instructions. Final RNA samples were re-precipitated with NaOAc and ethanol and washed with 70% ethanol before analysis on a NanoDrop-2000 spectrophotometer and Bioanalyzer 2100 (Agilent).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 600 ng RNA using the One-Color Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol Agilent Gene Expression kit for oligo microarrays (Agilent, order number 5188-5242, protocol G4140-90050).
Scan protocol Agilent Feature Extraction software 9.5.3.1.
Data processing GeneSpring GX10 default loading and analysis.
 
Submission date Feb 04, 2013
Last update date Apr 27, 2013
Contact name Christian Wolfrum
E-mail(s) christian-wolfrum@ethz.ch
Organization name ETH Zürich
Street address Schorenstrasse 16
City Schwerzenbach
ZIP/Postal code 8603
Country Switzerland
 
Platform ID GPL7202
Series (1)
GSE44059 Gene expression of adipocyte and stromal-vascular fractions

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
E1A_r60_1 17.10
E1A_r60_a104 5.97
E1A_r60_a107 6.22
E1A_r60_a135 7.30
E1A_r60_a20 8.11
E1A_r60_a22 10.22
E1A_r60_a97 11.91
E1A_r60_n11 13.92
E1A_r60_n9 15.09
EQC 6.19
A_51_P100034 13.65
A_51_P100063 12.64
A_51_P100084 6.52
A_51_P100099 9.68
A_51_P100155 11.49
A_51_P100174 8.21
A_51_P100181 8.65
A_51_P100227 10.13
A_51_P100246 11.06
A_51_P100289 11.84

Total number of rows: 31201

Table truncated, full table size 555 Kbytes.




Supplementary file Size Download File type/resource
GSM1077394_FGCZ_B6_brown_svf_1.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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