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Sample GSM1515955 Query DataSets for GSM1515955
Status Public on Oct 27, 2014
Title TALL_JS_29
Sample type RNA
 
Source name bone marrow
Organism Homo sapiens
Characteristics disease state: T-ALL
sample type: bone marrow sample
Extracted molecule total RNA
Extraction protocol Total RNA was harvested with the miRNeasy mini kit (Qiagen) with Dnase treatment on-column.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labling kit (Agilent) according to the manufacturer's instructions, followed by miRNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to the array for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner with SureScan High-Resolution Technology using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green).
Description Gene expression of T-ALL patient bone marrow sample
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 041648_D_F_20120615) to obtain background subtracted and spatially detrended Processed Signal intensities.
 
Submission date Sep 29, 2014
Last update date Oct 28, 2014
Contact name Annelynn Wallaert
E-mail(s) [email protected]
Organization name UGent
Street address De Pintelaan 185
City Gent
ZIP/Postal code 9000
Country Belgium
 
Platform ID GPL19197
Series (2)
GSE61866 Development of gene expression signatures with lncRNAs for 64 T-ALL patient samples
GSE62006 The Notch driven long non-coding RNA repertoire in T-cell acute lymphoblastic leukemia

Data table header descriptions
ID_REF
VALUE Normalized signal intensity.

Data table
ID_REF VALUE
A_23_P100001 5.132367298
A_23_P100022 3.076645465
A_23_P100056 4.96560384
A_23_P100074 8.58975117
A_23_P100127 9.205339401
A_23_P100141 7.618600825
A_23_P100189 3.957382445
A_23_P100196 10.71277458
A_23_P100203 9.708902273
A_23_P100220 5.631174883
A_23_P100240 2.46526396
A_23_P10025 5.948183952
A_23_P100292 13.09679111
A_23_P100315 10.85820603
A_23_P100326 10.94389194
A_23_P100344 7.074176115
A_23_P100355 11.20349246
A_23_P100386 2.770111457
A_23_P100392 8.826758031
A_23_P100420 9.034178561

Total number of rows: 57176

Table truncated, full table size 1609 Kbytes.




Supplementary file Size Download File type/resource
GSM1515955_TALL_JS_29.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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