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Sample GSM1310398 Query DataSets for GSM1310398
Status Public on Mar 01, 2015
Title HSPC-MA9.1_treated_6h.rep1
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
E-mail(s) salvarez@nimgenetics.com
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
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_23_P117082 16.86351176
A_33_P3246448 7.545721511
A_33_P3318220 6.849224001
A_33_P3236322 8.041511457
A_33_P3319925 8.636617465
A_21_P0000509 17.84517668
A_21_P0000744 15.20010733
A_24_P215804 11.10747736
A_23_P110167 15.05167195
A_33_P3211513 11.44169823
A_23_P103349 8.215280723
A_32_P61480 7.336265764
A_33_P3788124 7.003917296
A_33_P3414202 10.74995155
A_33_P3316686 12.62346957
A_33_P3300975 8.151513978
A_33_P3263061 14.35879184
A_33_P3261373 7.403634365
A_24_P278460 12.86382775
A_21_P0013109 6.681562072

Total number of rows: 50599

Table truncated, full table size 1255 Kbytes.




Supplementary file Size Download File type/resource
GSM1310398_MA9_1_6h_1.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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