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Sample GSM1310401 Query DataSets for GSM1310401
Status Public on Mar 01, 2015
Title HSPC-MA9.6_treated_6h.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: 6h 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 15.3878574
A_33_P3246448 8.060820343
A_33_P3318220 7.216726711
A_33_P3236322 8.014427972
A_33_P3319925 8.001678556
A_21_P0000509 16.45263697
A_21_P0000744 14.63833963
A_24_P215804 12.40720084
A_23_P110167 15.31829912
A_33_P3211513 10.62090529
A_23_P103349 8.082670797
A_32_P61480 8.384343541
A_33_P3788124 7.710792839
A_33_P3414202 10.97226043
A_33_P3316686 12.16046961
A_33_P3300975 9.844584987
A_33_P3263061 14.55512521
A_33_P3261373 8.078140269
A_24_P278460 12.79398893
A_21_P0013109 7.039994037

Total number of rows: 50599

Table truncated, full table size 1256 Kbytes.

Supplementary file Size Download File type/resource
GSM1310401_MA9_6_6h_2.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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