|
| Status |
Public on Aug 29, 2014 |
| Title |
013/09_hippocampus |
| Sample type |
RNA |
| |
|
| Source name |
post-mortem brain tissue, individual ID 013/09, hippocampus
|
| Organism |
Homo sapiens |
| Characteristics |
individual id: 013/09
brain region: hippocampus
disease status: neurologically and neuropathologically normal
brain bank: MRC Sudden Death Brain & Tissue Bank in Edinburgh
Cause of death: Ischaemic heart disease
Sex: Female
age at death (in years): 79
post-mortem interval (in hours): 45
ancestry: European
brain ph: 6.34
rin: 5
|
| Treatment protocol |
Not applicable.
|
| Growth protocol |
Not applicable.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the miRNeasy kit (Qiagen, UK). cDNA synthesis and amplification were performed using the Ambion®WT Expression Kit (Ambion, UK).
|
| Label |
biotin
|
| Label protocol |
Samples were enzymatically fragmented and biotinylated using the WT Terminal labelling kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 95° for 5 minutes, then 45° for 5 minutes. • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001.
|
| Scan protocol |
Affymetrix GeneChip Scanner 3000 7G.
|
| Description |
This entry supercedes previous accession: GSM1135414
|
| Data processing |
Data were processed using Affymetrix Power Tools 1.14.3. Arrays were pre-processed using RMA quantile normalization with background correction. Gene level summary signals were generated by calculating the Winsorized mean (10% and 90%) of all probe sets annotated to a transcript.
Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: Core_adapted_from_netaffyx31
Transcript assignments are based on genome build hg19
Core exons only are included in this analysis
|
| |
|
| Submission date |
Aug 27, 2014 |
| Last update date |
Aug 29, 2014 |
| Contact name |
Mina Ryten |
| E-mail(s) |
mina.ryten@ucl.ac.uk
|
| Organization name |
UCL Institute of Neurology
|
| Department |
Department of Molecular Neuroscience
|
| Street address |
Queen Square
|
| City |
London |
| ZIP/Postal code |
WC1N 3BG |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL5175 |
| Series (2) |
| GSE46706 |
Expression data generated from post-mortem human brain tissue originating from neurologically and neuropathologically control individuals |
| GSE60862 |
Gene-level analysis of 1231 samples originating from 134 Caucasian individuals |
|
