|
| Status |
Public on Jun 01, 2014 |
| Title |
Control NSC34 cells treated with shGFP 3 |
| Sample type |
RNA |
| |
|
| Source name |
cultured NSC34 cells, shGFP
|
| Organism |
Mus musculus |
| Characteristics |
cell line: NSC34
treatment: shGFP
|
| Growth protocol |
NSC34 cells were transfected using lipofectamine 2000 with Tardbp-specific short hairpin (sh) RNA and two control shRNAs using the pSUPERIOR (oligoengine) vector and stable clones isolated following puromycin selection. The hairpin targeted the Tardbp sequence TCTAAGCAAAGCCCCAGACGAGCCT. Oligonucleotides were annealed and ligated into the vector using the BglII and HindIII sites and the constructs generated were verified by sequencing. NSC34 control lines were established using GFP-shRNA and Renilla-shRNA (henceforth shGFP and shLuciferase) constructs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the cells using the Qiagen RNeasy Mini Kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
The Ambion WT Expression Kit was used to amplify the RNA and convert it to cDNA. The cDNA was then fragmented and biotin-labelled using the Affymetrix GeneChip WT Terminal Labelling Kit.
|
| |
|
| Hybridization protocol |
Hybridized to GeneChip Mouse Exon 1.0 ST Arrays, washed and stained using the Affymetrix GeneChip Hybridization, Wash and Stain Kit and an Affymetrix Fluidics Station 450.
|
| Scan protocol |
Scanned on an Affymetrix® GeneChip Scanner 3000 according to manufacturer's protocols.
|
| Description |
C3
Control NSC34 cells treated with shGFP.
|
| Data processing |
The Partek Genomics Suite was used to normalize (by GC RMA) and then analyse the microarray data following Affymetrix guidelines. Core probesets only were used.
|
| |
|
| Submission date |
Apr 03, 2014 |
| Last update date |
Jun 01, 2014 |
| Contact name |
Paul Roy Heath |
| E-mail(s) |
[email protected]
|
| Phone |
+44 114 2222254
|
| Organization name |
University of Sheffield
|
| Department |
Academic Neurology Unit
|
| Lab |
Heath
|
| Street address |
SITraN, 385a Glossop Road
|
| City |
Sheffield |
| State/province |
S. Yorks |
| ZIP/Postal code |
S10 2HQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL6193 |
| Series (2) |
| GSE56503 |
Loss of nuclear TDP-43 in ALS causes altered expression of splicing machinery and widespread dysregulation of RNA splicing in motor neurons [NSC34] |
| GSE56504 |
Loss of nuclear TDP-43 in ALS causes altered expression of splicing machinery and widespread dysregulation of RNA splicing in motor neurons |
|
