GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2049435 Query DataSets for GSM2049435
Status Public on Mar 28, 2016
Title RBFOX2 knockdown shRNA3 Rep1
Sample type RNA
Source name RBFOX2 knockdown shRNA3
Organism Homo sapiens
Characteristics cell line: 293T
protocol: shRNA TRCN0000074543
genotype/variation: RBFOX2 knockdown
Treatment protocol Knockdowns were performed by transforming shRNA plasmid along with lentivirus packaging plasmids in 293T cells, filtering (.45 micron) supernatant, and infecting a new population of 293T cells. After 48 hours, infected cells were Puromycin selected (1 ug / mL) for 10 days, after which RNA and protein were harvested.
Growth protocol 293T cells were grown in standard media (DMEM + 10% FBS + 1X Penicillin Streptomycin).
Extracted molecule total RNA
Extraction protocol RNA was extracted by standard Trizol extraction.
Label biotin
Label protocol Microarray sample preparation was performed using Ambion WT Expression Kit (Thermo Fisher Scientific). Labeling was performed using GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).
Hybridization protocol Hybridization and washing was performed as described in the GeneChip WT PLUS Reagent Kit (Affymetrix).
Scan protocol Scanning was performed on a 7G scanner and imaged with the AGCC portal.
Data processing Cel files were analyzed using Expression Console (build, 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).
RMA probeset-level signal estimates, DABG detection flag (Absent or Present), and DABG detection p-value obtained from 'Alt Splice Analysis' performed in Affymetrix Expression Console build
Submission date Jan 28, 2016
Last update date Mar 28, 2016
Contact name Gene Yeo
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)
GSE77339 Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [array]
GSE77634 Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites

Data table header descriptions
VALUE RMA probeset-level signal

Data table
JUC01000001.hg.1 7.897103 P 0.007435679
JUC01000002.hg.1 5.732997 A 0.1867076
JUC01000003.hg.1 9.288785 P 1.439922E-05
JUC01000004.hg.1 7.313088 P 0.007243742
JUC01000005.hg.1 8.58353 P 0.001462566
JUC01000006.hg.1 8.016253 P 0.009185448
JUC01000007.hg.1 6.823001 A 0.03564736
JUC01000008.hg.1 6.544289 P 0.003587618
JUC01000009.hg.1 3.672445 A 0.04256734
JUC01000010.hg.1 3.321851 A 0.0765292
JUC01000011.hg.1 12.90879 P 4.907874E-09
JUC01000012.hg.1 9.687357 P 0.003976427
JUC01000013.hg.1 12.73056 P 4.638972E-09
JUC01000014.hg.1 10.81364 P 4.49409E-09
JUC01000015.hg.1 6.558959 P 0.004238616
JUC01000016.hg.1 9.098352 P 3.552407E-05
JUC01000017.hg.1 8.815605 P 1.559891E-08
JUC01000018.hg.1 9.745193 P 0.00457624
JUC01000019.hg.1 9.472887 P 6.468493E-05
JUC01000020.hg.1 9.472887 P 6.468493E-05

Total number of rows: 914585

Table truncated, full table size 35917 Kbytes.

Supplementary file Size Download File type/resource
GSM2049435_14337.Yeo.4.sh_HTA-2_0_.CEL.gz 27.2 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap