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Sample GSM1591960 Query DataSets for GSM1591960
Status Public on Aug 31, 2015
Title AHLCL_VPA_1mM_30min_rep3
Sample type RNA
 
Source name AH LCL, 1mM VPA, 30min
Organism Homo sapiens
Characteristics gender: Male
Treatment protocol Cells were treated with 0.2mM, 1mM or 5mM valproic acid (VPA) or 0.5, 2.5 or 12.5µM suberoylanilide hydroxamic acid (SAHA) for 0, 30, 60 and 120 minutes
Growth protocol Immortalized, EBV-transformed lymphoblastoid cell lines (AH LCL) from healthy, karyotypically normal individuals were established in house. GM12878 Lymphoblastoid cells were purchased from the Coriell Institute. Both cell lines were maintained at 37°C, 5% CO2 in RPMI 1640 medium, 10% foetal bovine serum, supplemented with L-glutamine (2mM) and penicillin/streptomycin (all additives from Gibco).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Mini kit (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA was converted to double-stranded cDNA using cDNA synthesis kit (Roche Nimblegen, 11 117 831 001)
Label Cy3
Label protocol Samples were labelled with Cy3 using a Nimblegen One Colour Labeling Kit (Roche Nimblegen, 06 370 438 001)
 
Hybridization protocol Samples were hybridised using a Nimblegen Hybridisation Kit (05 583 934 001), including Sample Tracking Controls (05 223 512 001)
Scan protocol Slides were scanned on a Nimblegen MS200 microarray scanner at a resolution of 2µm with balanced Speed/Sensitivity and 100% laser intensity using autogain
Description Gene expression data following treatment of lymphoblastoid cells with histone deacetylase inhibitors
Data processing Data were extracted using DEVA (Roche Nimblegen) and normalised by robust multichip average in R.
 
Submission date Jan 26, 2015
Last update date Aug 31, 2015
Contact name John Halsall
E-mail(s) j.halsall@bham.ac.uk
Organization name University of Birmingham
Department Cancer and Genomic Sciences
Lab Chromatin & Gene Expression Group
Street address Medical School, Vincent Drive
City Birmingham
ZIP/Postal code B15 2TT
Country United Kingdom
 
Platform ID GPL16025
Series (1)
GSE65297 Transcriptional response to histone deacetylase inhibitors

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
AB000409 11.20304781
AB000463 11.03739941
AB000781 5.521825602
AB001328 2.862904822
AB002294 11.20421295
AB002308 12.55109086
AB002311 11.47136665
AB002313 13.63441855
AB002360 3.641571853
AB002377 11.75232913
AB002381 12.18974743
AB002382 11.87544741
AB002384 10.55222007
AB003177 12.46685385
AB003333 12.80480774
AB006589 7.159646717
AB006590 7.470593759
AB006621 3.533007636
AB006625 2.965211858
AB007457 12.74327822

Total number of rows: 45033

Table truncated, full table size 952 Kbytes.




Supplementary file Size Download File type/resource
GSM1591960_555175A06_2013-12-13_2013-12-16T102743_532.xys.gz 789.8 Kb (ftp)(http) XYS
Processed data included within Sample table

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