NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1306225 Query DataSets for GSM1306225
Status Public on Jun 16, 2014
Title Ctrl 24h_R2
Sample type RNA
 
Source name Control 24h_R2
Organism Rattus norvegicus
Characteristics strain background: Wistar
develpmetal stage: E18 rat embryos
tissue: Primary hippocampal neurons
exposed to: none (non-stimulated control)
time point: after 24h recovery
Treatment protocol For the OGD challenge, hippocampal cultures were incubated in a glucose-free saline buffer (in mM: 10 HEPES, 116 NaCl, 5.4 KCl, 0.8 MgSO4, 1 NaH2PO4, 1.8 CaCl2, 25 NaHCO3, 25 sucrose, pH 7.3) in an anaerobic chamber (Forma Anaerobic System, Thermo Fisher Scientific), at 37C, for the indicated times. Control neurons were placed in a similar saline buffer with 25 mM glucose instead of sucrose and kept in an air/CO2 incubator, at 37C, for the same period of time. After the stimulus periods, the saline buffers were replaced by conditioned medium and the cultures returned to the air/CO2 incubator, where they were kept to recover for the indicated times.
Growth protocol The cultures were maintained in Neurobasal medium in a humidified incubator with 5% CO2/95% air, at 37°C, for 14-15 days.
Extracted molecule total RNA
Extraction protocol Total RNA from three rat hippocampal neuronal cultures submitted to control or OGD conditions were collected after 7h and 24h of recovery
Label Cy3
Label protocol Equal amounts of RNA extract (200 ng) from each replicate were amplified and Cy-3-labeled using the Low Input Quick Amp Labeling kit (Agilent Technologies)
 
Hybridization protocol Hybridizations were carried out following Agilent Technologies instructions for One-Color Microarray-Based Gene Expression Analysis (Agilent Technologies, Santa Clara, CA, USA), using whole-genome Rat GE 4x44K v3 Microarrays.
Scan protocol Images were obtained using Agilent G2565AA microarray scanner and fluorescence quantization was performed using Agilent Feature Extraction 10.5.1.1 software and GE1_105_Dec08 protocol.
Description Gene expression of non-stimulated neurons after 24h
Data processing The signal intensity was aligned and normalized between microarrays by centering the median of the signal distribution using BRB-ArrayTools v3.8.1.
 
Submission date Jan 13, 2014
Last update date Jun 16, 2014
Contact name Joana Filipa Fernandes
E-mail(s) [email protected]
Organization name Center for Neuroscience and Cell Biology
Department Life Sciences
Lab Neurobiology and Disease
Street address Rua Larga, Faculdade de Medicina 2º andar, lab 206A Coimbra
City Coimbra
State/province -- Please Select --
ZIP/Postal code 3004-504
Country Portugal
 
Platform ID GPL14746
Series (1)
GSE54037 In vitro ischemia triggers a transcriptional response to down-regulate synaptic proteins in hippocampal neurons.

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner 15.77947807
DarkCorner 1.211578488
A_64_P076162 1.353095293
A_64_P002176 7.49022913
A_42_P664913 8.81007576
A_43_P13320 2.239969015
A_64_P126523 6.205497265
A_64_P038045 4.875637531
A_43_P11804 13.98132324
A_44_P808710 5.552203655
A_64_P142111 9.155849457
A_64_P095642 8.620744705
A_42_P735279 12.30708313
A_44_P902822 5.553418636
A_42_P563843 1.020037055
A_42_P610788 10.39687157
A_44_P242429 9.056879044
A_64_P020571 8.803510666
A_42_P518462 12.69999886
A_42_P469751 5.260260582

Total number of rows: 30423

Table truncated, full table size 738 Kbytes.




Supplementary file Size Download File type/resource
GSM1306225_UA_252828210636_Ctrl_24h_R2.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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