|
| Status |
Public on Jan 03, 2024 |
| Title |
Short-14 |
| Sample type |
RNA |
| |
|
| Source name |
Lymphoblastoid cell line RNA
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For mRNA extraction, 75 µl LCL suspension containing approximately 5x10^6 cells was taken through the QIAGEN RNeasy Mini Kit protocol following the manufacturer’s instructions, with total RNA eluted in 40μL RNase-free water
|
| Label |
biotin
|
| Label protocol |
300 ng of extracted RNA was processed using the Ambion Whole Transcript (WT) Expression Kit (Thermo Fisher Scientific, UK) producing fragmented biotin-labelled sense-stranded copy DNA that was hybridised onto Human Exon 1.0ST GeneChip microarrays
|
| |
|
| Hybridization protocol |
Post-hybridisation array washing, and staining were performed in the GeneChip Fluidics station and arrays scanned using the GeneChip 3000 7G scanner.
|
| Scan protocol |
standard Affymetrix protocol
|
| Data processing |
Individual sample .CEL files quantifying gene transcripts were uploaded into Expression Console (Thermo Fisher Scientific, UK) and several quality control (QC) parameters were checked for each sample including poly-A RNA labelling controls, hybridisation controls, positive vs. negative area under the curve (AUC) and signal intensity. Qlucore Omics Explorer (Qlucore, Lund, Switzerland) was used to identify differentially expressed genes between successfully QC’d samples with long vs. short disease duration (FC ≥ ±1.20, p-value 0.05). Both Metascape (http://metascape.org) 14 and Ingenuity Pathway Analysis (IPA) (Qiagen, UK) were used to interrogate the data further.
|
| |
|
| Submission date |
Aug 26, 2022 |
| Last update date |
Jan 03, 2024 |
| Contact name |
Rachel Waller |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of Sheffield
|
| Department |
Neuroscience
|
| Street address |
SITraN, 385A Glossop Road
|
| City |
SHEFFIELD |
| State/province |
South Yorkshire |
| ZIP/Postal code |
S102HQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL5175 |
| Series (2) |
| GSE212131 |
Establishing mRNA and miRNA interactions driving disease heterogeneity in ALS patient survival (microarray) |
| GSE212134 |
Establishing mRNA and microRNA interactions driving disease heterogeneity in Amyotrophic lateral sclerosis |
|
