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Sample GSM1975478 Query DataSets for GSM1975478
Status Public on Jan 27, 2016
Title PCLS_subject 3_DMSO_rep1
Sample type RNA
Source name precision-cut liver slices, after 24h incubation with vehicle
Organism Homo sapiens
Characteristics tissue: liver
treatment: vehicle (0.1% DMSO)
time point: 24h
patient_id: 3
gender: female
age (yr): 39
bmi: 34.9
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 obeticholic acid (OCA, INT-747, 6α-ethyl-chenodeoxycholic acid) (1 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_B11_05_3_DMSO.CEL
Data processing Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.30.0).
Submission date Dec 18, 2015
Last update date Jan 27, 2016
Contact name Guido Hooiveld
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 (2)
GSE76161 Gene expression profiling in human precision-cut liver slices upon treatment with the FXR agonist obeticholic acid [human]
GSE76163 Gene expression profiling in human precision-cut liver slices upon treatment with the FXR agonist obeticholic acid
Reanalysis of GSM1844303

Data table header descriptions
VALUE RMA signal (as log2)

Data table
7892501 5.71999728
7892502 4.667870393
7892503 2.762005433
7892504 7.834405662
7892505 1.696592641
7892506 4.649316345
7892507 4.955942887
7892508 6.023001341
7892509 10.79855765
7892510 4.971842976
7892511 3.784950099
7892512 4.627953461
7892513 4.749902846
7892514 10.3882919
7892515 8.475705794
7892516 6.314085814
7892517 5.478901021
7892518 1.62001211
7892519 4.621210949
7892520 8.280753427

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.

Supplementary file Size Download File type/resource
GSM1975478_G173_B11_05_3_DMSO.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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