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Series GSE104047 Query DataSets for GSE104047
Status Public on Jun 14, 2019
Title AGO CLIP reveals an activated network for acute regulation of brain glutamate homeostasis in ischemic stroke [dataset 5]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Cortical cultures treated with OGD (oxygen glucose deprivation) in the presence of miR-29 expressing lenti-virus were analyzed by RNAseq to assess differences in miR-29 target gene expression.
 
Overall design DIV6 cortical cultures were infected with virus expressing miR-29 or empty control virus at (MOI=1) two times, for total MOI of 2. On DIV14, cultures were first rinsed twice with warm OGD buffer (125 mM NaCl, 5 mM KCl, 1.2 mM Na2PO4, 26 mM NaHCO3, 1.8 mM CaCl2, 0.9 mM MgCl2, 10 mM Hepes, pH 7.4) plus 10 mM glucose and incubated for 30 min with the same rinsing buffer. The cultures were then rinsed with OGD buffer twice and transferred to an OGD chamber (Billups-Rothenberg, San Diego, CA) and flushed with anoxic gas (95% N2 and 5% CO2) at 21 L/min for 5 min. The chamber was then sealed and placed into 37°C incubator for 3 hrs. Controls (sham) were rinsed with OGD buffer but incubated in a normoxia conditions. After OGD treatment, the cultures were transferred to normal culture medium and incubated for 4 hrs, cells harvested and RNA extracted for library construction. Each set of biological replicates represent cultures dissected on distinct days. Complete protocol detailed in referenced publication.
 
Contributor(s) Kobayashi M
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Submission date Sep 20, 2017
Last update date Jun 14, 2019
Contact name Mariko Kobayashi
E-mail(s) mkobayashi@rockefeller.edu
Organization name Rockefeller University
Department Molecular Neuro-Oncology
Lab Robert B. Darnell
Street address 1230 York Avenue
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (12)
GSM2788315 sham, empty virus, replicate 1
GSM2788316 sham, miR-29 virus, replicate 1
GSM2788317 OGD, empty virus, replicate 1
This SubSeries is part of SuperSeries:
GSE104053 AGO CLIP reveals an activated network for acute regulation of brain glutamate homeostasis in ischemic stroke
Relations
BioProject PRJNA408121
SRA SRP118327

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE104047_EdgeR_OEvsSE.txt.gz 501.2 Kb (ftp)(http) TXT
GSE104047_EdgeR_OMvsSE.txt.gz 473.2 Kb (ftp)(http) TXT
GSE104047_OGD-RNAseq_count.txt.gz 195.8 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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