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Sample GSM2230013 Query DataSets for GSM2230013
Status Public on Dec 15, 2017
Title Primary human hepatocyte 8 days control replicate 3
Sample type RNA
 
Source name RNA from human primary hepatocytes exposed to 1% ethanol for 5 days daily and subsequently to 3 days medium
Organism Homo sapiens
Characteristics cell type: Primary human hepatocytes
treatment: exposed to 1% ethanol for 5 days daily and subsequently to 3 days medium
Treatment protocol PHH were exposed to 15 mM of VPA in a 24 hour repeat-dose testing regime. Medium was changed daily thereby providing a new dose of VPA to the PHH each day. A bi-phasic treatment regime was applied, combining a 5-day VPA exposure with a subsequent 3-days washout period during which the PHH were exposed to medium only. 1% Ethanol was used as solvent control.
Growth protocol Cryopreserved primary human hepatocytes (PHH) and culture media were purchased from Life Technologies (Bleiswijk, The Netherlands), unless otherwise stated.PHH were cultured in pre-coated multi-well plates in a 2-layer collagen sandwich.PHH were thawed for 1 min at 37°C. Three vials (one per donor) were poured in 50 ml Thawing Medium (CHRM CM7000) and centrifuged at 4°C for 10 min at 100g. The cell pellet was dissolved in plating medium (CM9000) at a concentration of 1*10E6 cells/ml. After seeding, PHH were incubated in the pre-coated multi-well plates for 4 hours at 37°C. Next, debris was removed by shaking and washing the cells twice with Williams’ Medium E medium. Subsequently, PHH were covered by a collagen layer (containing DMEM, NaOH and rat tail Collagen type 1 (BD biosciences, Breda, The Netherlands)), incubated for 30 min at 37°C, and covered with incubation medium (CM600, CM4000).
Extracted molecule total RNA
Extraction protocol At the end of treatment, medium was removed and PHH were harvested in Qiazol (Qiagen). Total RNA was isolated using a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol and followed by DNase I (Qiagen) treatment.
Label Cy3
Label protocol MicroRNA expression profiling was performed using Agilent Sureprint G3 Unrestricted Human miRNA V16 8 × 60 K microarrays. The hybridization was performed following standard protocols, after which the microarray slides were washed and scanned using a DNA microarray scanner (Agilent Technologies).
 
Hybridization protocol MicroRNA expression profiling was performed using Agilent Sureprint G3 Unrestricted Human miRNA V16 8 × 60 K microarrays. The hybridization was performed following standard protocols, after which the microarray slides were washed and scanned using a DNA microarray scanner (Agilent Technologies).
Scan protocol MicroRNA expression profiling was performed using Agilent Sureprint G3 Unrestricted Human miRNA V16 8 × 60 K microarrays. The hybridization was performed following standard protocols, after which the microarray slides were washed and scanned using a DNA microarray scanner (Agilent Technologies).
Data processing The scanned images were converted into TXT files using the Feature Extraction Software v10.7.3.1 from Agilent Technologies, which were imported in R 2.15.3 (http://www.r-project.org) for quality control with an in-house developed pipeline (26). Filtering and normalization was performed using AgiMicroRna (27), which applies a LIMMA approach for selection of differentially expressed microRNAs (DE-miRs). Total gene signals were log2-transformed and quantile-normalized. DE-miRs with an absolute FC of 1.5 or higher (i.e., average log2 ratio of < −0.58 or > 0.58) and an FDR-corrected p-value < 0.05 were considered statistically significant.
 
Submission date Jul 11, 2016
Last update date Dec 15, 2017
Contact name Simone G van Breda
E-mail(s) s.vanbreda@maastrichtuniversity.nl
Phone 0031433882127
Organization name Maastricht University
Department Toxicogenomics
Street address Universiteitssingel 50
City Maastricht
State/province Limburg
ZIP/Postal code 6229 ER
Country Netherlands
 
Platform ID GPL16770
Series (2)
GSE84239 Induction of miRNA changes in primary human hepatocytes by valproic acid
GSE84250 Induction of changes in primary human hepatocytes by valproic acid

Data table header descriptions
ID_REF
VALUE log2 signal intensity

Data table
ID_REF VALUE
ebv-miR-BART1-3p -1
hsa-miR-4256 -1
ebv-miR-BART17-3p -1
hsa-miR-1279 -1
hsa-miR-3616-5p -1
hsa-miR-17 4.571554376
hsa-miR-1286 -1
hsa-miR-484 -1
hsa-miR-4323 3.352938709
hsa-miR-372 -1
hsa-miR-1537 -1
hsa-miR-548j -1
hsa-miR-151-5p 3.477793101
hsa-miR-200b -1
hsa-miR-4287 -1
hsa-miR-296-3p -1
hsa-miR-30d 7.745423574
hsa-miR-1264 -1
hsa-miR-2278 3.503609516
hsa-miR-519b-3p -1

Total number of rows: 1368

Table truncated, full table size 24 Kbytes.




Supplementary file Size Download File type/resource
GSM2230013_US10063773_253118113914_S01_miRNA_107_Sep09_1_2.txt.gz 6.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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