|
| Status |
Public on Oct 20, 2016 |
| Title |
14277.Yeo.14.sh_(HTA-2_0) |
| Sample type |
RNA |
| |
|
| Source name |
iPSC-MNs
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: hnRNP A2/B1 D290V
treatment: nontarget ASO
disease: MSP
tissue type: iPSC-MN
|
| Treatment protocol |
iPSC-MNs were treated with ASO against hnRNP A2/B1 or nontarget ASO for 28 days
|
| Growth protocol |
iPSC-MNs were differentiated from MSP and control individuals
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by standard Trizol extraction.
|
| Label |
biotin
|
| Label protocol |
WT Terminal Labeling Kit, Affymetrix
|
| |
|
| Hybridization protocol |
Hybridization cocktails containing ~5.5 ug of fragmented and labeled DNA target were prepared and applied to GeneChip Human Splice Junction arrays. Hybridization was performed for 16 hours using the Fluidics 450 station.
|
| Scan protocol |
Arrays were scanned using the Affymetrix 3000 7G scanner and GeneChip Operating Software version 1.4 to produce .CEL intensity files.
|
| Data processing |
Cel files were analyzed using Expression Console (build 1.4.1.46, Affymetrix), with RMA normalization and DABG probe-level detection. Only probesets with detection p-value ≤ 0.05 in more than half of the microarray samples were considered for downstream analysis. All probes corresponding to cassette exons profiled on the microarray (comprising exclusion junction, upstream and downstream inclusion junction, and inclusion exonic probes) were identified and normalized against the average signal on a per-gene basis to remove gene expression changes. Student’s t-test was performed on residuals for inclusion probes and exclusion probes separately to identify robust splicing changes, which were quantified by SepScore ( defined as the normalized change in exclusion minus the normalized change in inclusion).
HTA-2_0.r1.pgf
HTA-2_0.r1.Psrs.mps
|
| |
|
| Submission date |
Aug 30, 2016 |
| Last update date |
Oct 20, 2016 |
| Contact name |
Gene Yeo |
| E-mail(s) |
geneyeo@ucsd.edu
|
| Organization name |
UCSD
|
| Street address |
2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL17585 |
| Series (2) |
| GSE86223 |
HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_Arrays_human_iPSC_MN_ASO] |
| GSE86464 |
HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons |
|
