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Sample GSM465845 Query DataSets for GSM465845
Status Public on Dec 07, 2009
Title Mouse_+il-3 replicate 1 time 0
Sample type RNA
 
Source name FDM, +il-3
Organism Mus musculus
Characteristics cell type: myeloid progenitor cells
cell line: WT
Extracted molecule total RNA
Extraction protocol Mouse total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.
Label biotin
Label protocol A total of 500ng was labelled using the Ambion Total Prep RNA amplification kit (Cat. No. – IL1791). The quantity of labelled product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.
 
Hybridization protocol A total of 1.5ug of labelled cRNA was then prepared for hybridisation to the MouseWG-6_V1_1_R3 by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes GEX-HYB Hybridisation Buffer (supplied with the beadchip). A total hybridisation volume of 30ul is prepared for each sample and 30ul loaded into a single array on the MouseWG-6_V1_1_R3. A total of 6 different labelled samples can be loaded into 6 individual arrays per beadchip. The chip is hybridised at 58C for 16 hours in an oven with a rocking platform. After hybridisation, the chip is washed using the appropriate protocols as outlined in the illumina manual.
Scan protocol Upon completion of the washing, the chips are then coupled with Cy3 and scanned in the illumina BeadArray Reader. The scanner operating software, BeadStudio, converts the signal on the array into a TXT file for analysis.
Description IL-3 study.
Data processing The Bioconductor/R package lumi was used to perform variance stabilizing transformation and quantile normalization
 
Submission date Oct 27, 2009
Last update date Nov 06, 2009
Contact name Anissa Jabbour
E-mail(s) jabbour@wehi.edu.au
Organization name Walter and Eliza Hall Institute
Department Cell Signalling and Cell Death
Lab Cell Biology Laboratory
Street address 1G Royal Parade
City Parkville
State/province Victoria
ZIP/Postal code 3052
Country Australia
 
Platform ID GPL6105
Series (1)
GSE18770 Myeloid progenitor cells lacking p53 exhibit delayed upregulation of Puma, prolonged survival after cytokine deprivation

Data table header descriptions
ID_REF
VALUE Processed log2 expression data
Detection Pval The detectable probe ratio

Data table
ID_REF VALUE Detection Pval
ILMN_1212602 8.153345836 0.81938
ILMN_1212603 8.091973805 0.412
ILMN_1212605 9.774156695 1
ILMN_1212607 8.107372082 0.55834
ILMN_1212608 8.077423803 0.26961
ILMN_1212610 8.113040458 0.60448
ILMN_1212612 8.0655432 0.18853
ILMN_1212614 8.0971541 0.46276
ILMN_1212616 8.218421955 0.96638
ILMN_1212619 8.126398168 0.70138
ILMN_1212623 8.11845428 0.64799
ILMN_1212625 10.30854105 1
ILMN_1212626 8.843108992 1
ILMN_1212628 8.062467968 0.17007
ILMN_1212632 8.055703043 0.13382
ILMN_1212633 8.3823304 1
ILMN_1212636 11.58334069 1
ILMN_1212637 10.01842252 1
ILMN_1212639 8.086052615 0.35531
ILMN_1212644 8.054089658 0.12788

Total number of rows: 46632

Table truncated, full table size 1411 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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