GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1310397 Query DataSets for GSM1310397
Status Public on Mar 01, 2015
Title HSPC-MA9.31_treated_24h.rep2
Sample type RNA
Source name CD34+ cord blood cells transduced with MLL-AF9 fusion gene
Organism Homo sapiens
Characteristics cell type: CD34+ cord blood cells transduced with MLL-AF9 fusion gene
treatment: 24h exposure to 30nM panobinostat
Treatment protocol HSPC-MA9 cells were cultured with 30 nm panobinostat or vehicle. After 6 and 24 hr cells were harvested, PBS washed and pelleted.
Growth protocol Umbilical cord blood CD34+ cells were selected using immunomagnetic beads (Miltenyi Biotech) and stably transduced with retroviruses expressing empty vectors (HSPC control) or the MLL-AF9 (HSPC-MA9) fusion protein. Cells were cultured as described elsewhere ( Wei et al., cell 2008).
Extracted molecule total RNA
Extraction protocol RNA was extracted using Rneasy mini kit (Quiagen), quality was assessed using the Agilent 2100 Bioanalyzer.
Label Cy3
Label protocol RNA was labeled using Cyanine-3 (Cy3) with low input quick amp labeling (v6.6, Sept 2012), following the manufacturer´s specificacions.
Hybridization protocol The Agilent official protocol G4140-90040 for hybridization was used
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA, 3um resolution). We used the AgilentG3_GX_1color method (61x21.6 mm sscan area, Green dye channel, 3um).
Data processing The scanned images were analyzed with Feature Extraction Software v10.7 using default parameters (protocol GE1-107_Sept09) to obtain background subtracted and spatially detrended Processed Signal intensities
Submission date Jan 20, 2014
Last update date Mar 01, 2015
Contact name Sara Alvarez
Phone +34 672 05 98 89
Organization name NIMGenetics
Street address C/Faraday 7
City Madrid
State/province Madrid
ZIP/Postal code 28049
Country Spain
Platform ID GPL17077
Series (2)
GSE54218 Aberrant chromatin acetylation in MLL-AF9 leukemia mediates the response to HDAC inhibition (microarray)
GSE54348 Aberrant chromatin acetylation in MLL-AF9 leukemia mediates the response to HDAC inhibition

Data table header descriptions
VALUE Normalized signal intensity

Data table
A_23_P117082 16.02930515
A_33_P3246448 7.353420079
A_33_P3318220 6.845251305
A_33_P3236322 8.030286251
A_33_P3319925 8.165188253
A_21_P0000509 16.40937487
A_21_P0000744 16.04422079
A_24_P215804 10.06942422
A_23_P110167 16.28751546
A_33_P3211513 11.65353075
A_23_P103349 7.218015556
A_32_P61480 6.651496212
A_33_P3788124 6.695311414
A_33_P3414202 11.6860982
A_33_P3316686 13.2416899
A_33_P3300975 8.115464927
A_33_P3263061 14.95907736
A_33_P3261373 7.859571875
A_24_P278460 13.53466533
A_21_P0013109 7.123407241

Total number of rows: 50599

Table truncated, full table size 1255 Kbytes.

Supplementary file Size Download File type/resource
GSM1310397_MA9_31_24h_2.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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