NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1006489 Query DataSets for GSM1006489
Status Public on Sep 20, 2012
Title Salt IP/Input #1
Sample type RNA
 
Channel 1
Source name Salt IP #1
Organism Mus musculus
Characteristics tissue: Hypothalamus
strain: C57Bl/6J
ip antibody: pS6 244/247 IP [Cell Signaling #2215 lot 10]
Treatment protocol Mice were given an injection of vehicle (PBS) or 2M NaCl solution (325 uL), water was removed, and mice were sacrificed 2h later
Growth protocol Mice were maintained on a 12h light dark cycle and sacrificed at 12 weeks of age at approximately CT6
Extracted molecule total RNA
Extraction protocol RNA was purified using the RNAeasy Micro kit.
Label Biotin
Label protocol RNA was amplified using the Ovation RNA Amplification System V2 and labelled using the Nugen Biotin Labelling Protocol.
 
Channel 2
Source name Salt Input #1
Organism Mus musculus
Characteristics tissue: Hypothalamus
strain: C57Bl/6J
ip antibody: none
Treatment protocol Mice were given an injection of vehicle (PBS) or 2M NaCl solution (325 uL), water was removed, and mice were sacrificed 2h later
Growth protocol Mice were maintained on a 12h light dark cycle and sacrificed at 12 weeks of age at approximately CT6
Extracted molecule total RNA
Extraction protocol RNA was purified using the RNAeasy Micro kit.
Label Biotin
Label protocol RNA was amplified using the Ovation RNA Amplification System V2 and labelled using the Nugen Biotin Labelling Protocol.
 
 
Hybridization protocol Hybridization followed Nugen's recommendation and temperature in their biotin labelling protocol
Scan protocol The standard DirectHyb Illumina expression array protocol was used.
Data processing Raw Data was exported using illumina Genomestudio software without normalization. The raw data was transformed in Excel as follows: The ratio IP/Input (the fold-enrichment) was calculated for the Salt and Control samples for replicates #1 and #2. The replicates were then averaged and the differential fold-enrichment was determined by dividing the average Salt (IP/Input) by the average Control (IP/Input). The log2 of this differential fold-enrichment was then calculated and these values were plotted. These caculations are shown in the Matrix normalized worksheet.
 
Submission date Sep 19, 2012
Last update date Sep 20, 2012
Contact name Zachary Knight
Organization name Rockefeller University
Street address 1230 York Ave
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL6885
Series (2)
GSE40994 Molecular profiling of activated neurons by phosphorylated ribosome capture [Illumina BeadArray]
GSE40995 Molecular profiling of activated neurons by phosphorylated ribosome capture

Data table header descriptions
ID_REF
VALUE ratio IP/Input (the fold-enrichment)

Data table
ID_REF VALUE
ILMN_1250052 1.31678293
ILMN_3122480 1.12
ILMN_2599935 1.06452581
ILMN_2675543 0.869724771
ILMN_2686883 1.405356683
ILMN_2751818 0.872382851
ILMN_2728634 0.775735294
ILMN_3040515 1.095862765
ILMN_2711608 0.906844106
ILMN_1232875 1.202228412
ILMN_1258507 3.124233983
ILMN_2746142 0.942909761
ILMN_1252690 1.027314112
ILMN_2655499 0.919110212
ILMN_1252870 0.85659824
ILMN_1248179 0.970072239
ILMN_2649955 0.982005141
ILMN_2628708 0.987962963
ILMN_3024781 0.878514056
ILMN_2705628 0.91084855

Total number of rows: 25697

Table truncated, full table size 623 Kbytes.




Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table
Processed data are available on Series record

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