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Sample GSM672541 Query DataSets for GSM672541
Status Public on Mar 03, 2011
Title brain_RNAseq_Tdp43-oligo_rep2.1
Sample type SRA
 
Source name Striatum
Organism Mus musculus
Characteristics strain: C57BL/6
age: 8-10 weeks
treatment: Tdp-43 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 The RNA-seq libraries were constructed as described previously (Parkhomchuk, 2009) with slight modifications. Briefly, 7mg of total RNA was used for polyadenylated RNA selection using oligo-dT paramagnetic beads (Invitrogen). First-strand synthesis was prepared using a combination of oligodT primers and random hexamers with SuperScript III reverse transcriptase (Invitrogen), using gradually increasing temperature. dNTPs were then removed from the reaction by gel filtration through Sephadex G-50 (GE-health care) spin columns equilibrated with 1mM TrisHCl, pH 7.0. Second strand was then synthesized by a 2hr-incubation for 16oC with a dUTP-containing nucleotide mixture, 100mM MgCl2, 0.1M DTT, and a combination of ligase (NEB), DNA polymerase I (NEB) and RNase H (Invitrogen) in second strand synthesis buffer (Invitrogen). Double-stranded cDNA was then purified through spin columns (QIAGEN) and fragmented by ultrasonic digestion (Bioruptor, Diagenode) with continuous cooling at 1oC, using repeated cycles of 30 sec sonication with 100% amplitude and 30 sec breaks for 2-3 hrs. 1-2 mL of the material was used to check the level of fragmentation on a FlashGel DNA Cassette 1.2% (LONZA). End repair, A-tailing and adaptor ligation were all performed according to the Illumina protocol and libraries were subjected to electrophoresis on a 2% Low Range Ultra Agarose gel (BioRad). Fragments with a size range of 150-200 bp were cut out of the gel and libraries were gel purified on spin columns (QIAGEN) according to the manufacturer’s instructions. Prior to amplification, libraries were incubated with Uracil N-Glycosylase (Applied Biosystems) to digest the dUTP-containing strand, thereby ensuring a single orientation of our RNA-seq libraries. 8 pM of amplified libraries was used for sequencing on the Illumina GA2 for 72 cycles.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Description strand-specific RNAseq
Data processing Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
 
Submission date Feb 10, 2011
Last update date May 15, 2019
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 GPL9250
Series (2)
GSE27218 Disrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43 (RNA-seq)
GSE27394 Disrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43
Relations
SRA SRX043757
BioSample SAMN00216120

Supplementary file Size Download File type/resource
GSM672541_MP15_2_brainTDP43KD19.mm8.bowtie.gz 397.5 Mb (ftp)(http) BOWTIE
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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