|
| Status |
Public on Aug 31, 2015 |
| Title |
AHLCL_SAHA_0.5µM_60min_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
AH LCL, 0.5µM SAHA, 60min
|
| 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 |
|
