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Sample GSM2247089 Query DataSets for GSM2247089
Status Public on Feb 22, 2018
Title 1HR_LTP_ANIMAL_3 (3' READS)
Sample type SRA
 
Source name hippocampus
Organism Mus musculus
Characteristics tissue: hippocampus
condition: LTP
age: 3 month old
strain: C57BL/6
Treatment protocol To induce LTP in acute hippocampal slices we used a chemical LTP protocol: 50uM forskolin for 5 minutes followed by 5 minutes of 50uM forskolin, 30mM KCl and 10mM Ca2+ ACSF. Control samples were treated for 10 minutes with ACSF containing 0.2% DMSO. Hippocampal slices were collected directly on dry ice either 1 hour or 3 hours after the treatment. (Makhinson M., 1999; Chotiner JK., 2003)
Extracted molecule total RNA
Extraction protocol All libraries were prepared from 1ug of RNA as described in Hoque M., et al 2013.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description library strategy: 3'READS
Data processing Alligned to mm9 using bowtie-2
identifying pA site supporting reads and clustering of pA site
calculating RPM for normalized genes and analysing the changes between treatment
Genome_build: mm9
 
Submission date Jul 20, 2016
Last update date May 15, 2019
Contact name Riki Kawaguchi
E-mail(s) rkawaguchi@mednet.ucla.edu
Phone 4244424783
Organization name University of California Los Angeles
Department Department of Neurology and Department of Psychiatry
Lab Informatics Center for Neurogenetics and Neurogenomics (ICNN).
Street address 760 Westwood Plaza, Room 37-420
City Los Angeles
State/province CA
ZIP/Postal code 90095-1759
Country USA
 
Platform ID GPL17021
Series (2)
GSE84643 Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation (APA) during hippocampal Long-Term Potentiation (LTP) [3'READS]
GSE84644 Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation (APA) During Hippocampal Long-Term Potentiation (LTP)
Relations
BioSample SAMN05421394
SRA SRX1962905

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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