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Sample GSM998844 Query DataSets for GSM998844
Status Public on Sep 30, 2012
Title Fus/Tls anti-sense oligo rep2
Sample type RNA
 
Source name Striatum
Organism Mus musculus
Characteristics tissue: brain striatum
genetic background: C57BL/6
age: 8-10 weeks
treatment: Fus/Tls anti-sense oligo
Treatment protocol 8-10 week old female C57Bl/6 mice were anesthetized with 2.5-3% isofluorane, and a midline incision of approximately 1cm was made on their heads. Using stereotaxic guides, 3 mL of antisense oligonucleotide (ASO) solution targeting Tdp-43 or a control – corresponding to a total of 75 mg or 100 mg ASOs – or saline buffer was injected using a Hamilton syringe directly into their striatum. The incision was closed with sutures and the mice were allowed to recover in their cages. They were monitored for any adverse effects for the next two weeks until they were sacrificed. The striatum and adjacent cortex area were dissected, placed in separate tubes containing 1 mL Trizol (Invitrogen) and were frozen at -80oC until use.
Extracted molecule total RNA
Extraction protocol Trizol extraction of RNA and protein was performed according to the manufacturer’s instructions. In summary, tissues were homogenized in Trizol using a Polytron homogenizer (Company) for 15 sec. Homogenates were then incubated at room temperature for 5min. Chloroform was added to the homogenates (200 l per 1 mL of Trizol) and tubes were shaken vigorously for 15 sec. After incubation at room temperature for 2-10 min, samples were centrifuged at 12,000 g for 15 min at 4oC. The RNA-containing aqueous phase was transferred to fresh tubes and after the addition of glycogen and isopropanol, RNA was precipitated at -20oC overnight. The next day, samples were centrifuged for 10 mins at maximum speed in a microcentrifuge at 4oC. RNA pellets were washed with 75% Ethanol twice, dried at room temperature and reconstituted in DEPC-treated water.
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 Data processed using Affymetrix package (Affy Power Tools) apt-probeset-summarize. Iter-plier algorithm used to quantify probesets.
 
Submission date Sep 06, 2012
Last update date Sep 30, 2012
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 GPL13185
Series (2)
GSE40649 Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs (microarray)
GSE40653 Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs

Data table header descriptions
ID_REF
VALUE Quantile normalized and gc background corrected.

Data table
ID_REF VALUE
127219 168.04566
58017 565.87182
28336 238.10012
564321 307.77446
544357 619.52793
342596 482.16060
81834 910.39032
67525 62.43135
474416 1364.39317
598631 741.71749
403345 3930.91325
440294 130.90812
296021 5636.90549
150275 224.66680
624353 398.94784
564868 184.50259
658553 1029.82357
287374 301.98615
198359 46.50867
399155 156.54531

Total number of rows: 527499

Table truncated, full table size 8598 Kbytes.




Supplementary file Size Download File type/resource
GSM998844_GY10081908.CEL.gz 26.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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