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Sample GSM1359241 Query DataSets for GSM1359241
Status Public on Mar 28, 2014
Title G1_2
Sample type RNA
 
Source name FL-HSPCs, transduced with LeGO-iG-Gata1/shG1, grown 4 days in myeloid differentiation medium, duplicate 2
Organism Homo sapiens
Characteristics cell line: wild-type CD34+-hematopoietic stem and progenitor cells
genotype/variation (vector): LeGO-iG-Gata1/shG1
days: 4
Treatment protocol FL-HSPCs were transduced with the indicated virus.
Growth protocol FL-HSPCs cells were grown in RPMI, 20% FCS, 1% P/S, SCF (5ng/ml), GM-CSF (10ng/ml), G-SCF (10ng/ml), IL-3 (5ng/ml)
Extracted molecule total RNA
Extraction protocol RNeasy Mini Kit (Qiagen)
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent 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), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Data processing The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Mar 28, 2014
Last update date Mar 28, 2014
Contact name Jan-Henning Klusmann
E-mail(s) jan-henning.klusmann@kgu.de
Organization name Goehte University Frankfurt
Department Pediatric Hematology and Oncology
Street address Theodor-Stern-Kai 7
City Frankfurt
ZIP/Postal code 60590
Country Germany
 
Platform ID GPL6480
Series (1)
GSE56332 GATA1s induces hyperproliferation of eosinophil precursors in Down syndrome transient leukemia

Data table header descriptions
ID_REF
VALUE log2 transformed, scaled to mean of all samples

Data table
ID_REF VALUE
GE_BrightCorner 16.283556
DarkCorner 3.6579983
A_24_P66027 8.678417
A_32_P77178 4.754305
A_23_P212522 8.270145
A_24_P934473 5.274167
A_24_P9671 10.967798
A_32_P29551 3.6155689
A_24_P801451 6.5421066
A_32_P30710 15.463582
A_32_P89523 3.8204412
A_24_P704878 3.5995455
A_32_P86028 15.731281
A_24_P470079 6.1173115
A_23_P65830 10.896317
A_23_P109143 12.132243
A_24_P595567 4.172606
A_24_P391591 9.102333
A_24_P799245 3.5675526
A_24_P932757 3.5634828

Total number of rows: 41093

Table truncated, full table size 891 Kbytes.




Supplementary file Size Download File type/resource
GSM1359241_251485076630_Emmrich7011_S01_GE1_107_Sep09_1_3.txt.gz 2.1 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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