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Sample GSM1844305 Query DataSets for GSM1844305
Status Public on Nov 23, 2015
Title PCLS_subject 4_DMSO
Sample type RNA
 
Source name precision-cut liver slices, after 24h incubation with vehicle (0.1% DMSO)
Organism Homo sapiens
Characteristics tissue: liver
treatment: vehicle (0.1% DMSO)
time point: 24h
patient_id: 4
gender: female
age (yr): 41
bmi: 37.7
Treatment protocol Liver slices were incubated in William's E Medium in 6-well plates at 37°C/5% CO2/80% O2 under continuous shaking (70 rpm). Duplicate wells were used per donor with 3 liver slices per well. After 1 hour the media was replaced with fresh William's E Medium in the presence or absence of Wy14643 (100 μM) dissolved in dimethyl sulfoxide (DMSO, final concentration 0.1%). After 24 h incubation, liver slices were snap-frozen in liquid nitrogen and stored in -80°C for RNA isolation.
Growth protocol Liver biopsies were collected from obese patients undergoing bariatric surgery. After collection, biopsies were immediately placed in ice-cold oxygenated Belzer UW Cold Storage Solution and quickly transferred to the laboratory for further processing. 5 mm cylindrical liver cores were prepared with a surgical biopsy punch and sectioned to 200 μm slices using a Krumdieck tissue slicer.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from the liver slices using TRIzol reagent and purified using Qiagen RNeasy columns. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
Label Biotin
Label protocol One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).
 
Hybridization protocol Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.
Scan protocol Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).
Description G173_D10_10_4_DMSO.CEL
Data processing Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.30.0).
 
Submission date Aug 04, 2015
Last update date Dec 18, 2015
Contact name Guido Hooiveld
E-mail(s) [email protected]
Organization name Wageningen University
Department Div. Human Nutrition & Health
Lab Nutrition, Metabolism & Genomics Group
Street address HELIX, Stippeneng 4
City Wageningen
ZIP/Postal code NL-6708WE
Country Netherlands
 
Platform ID GPL11532
Series (1)
GSE71731 The impact of PPARα activation on whole genome gene expression in human precision-cut liver slices
Relations
Reanalyzed by GSM1975480

Data table header descriptions
ID_REF
VALUE RMA signal (as log2)

Data table
ID_REF VALUE
7892501 7.346001488
7892502 4.84845588
7892503 4.664884747
7892504 7.785667227
7892505 2.330374154
7892506 4.717607737
7892507 4.186015759
7892508 6.941847489
7892509 10.95107869
7892510 4.795759529
7892511 3.84161897
7892512 5.175101518
7892513 2.260643694
7892514 10.11138393
7892515 8.989665784
7892516 6.156758882
7892517 5.402912554
7892518 1.662459504
7892519 4.689435786
7892520 8.550587022

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM1844305_G173_D10_10_4_DMSO.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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