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Sample GSM999604 Query DataSets for GSM999604
Status Public on Sep 09, 2012
Title Ctrl shRNA
Sample type RNA
 
Source name Bone marrow CD34+ cells, ctrl shRNA
Organism Homo sapiens
Characteristics disease state: healthy
tissue: bone marrow
cell type: CD34+ cells
treatment: ctrl shRNA
Treatment protocol CD34+ hematopoietic cells were transduced with lenitvirus-based RFP-expressed shRNA constructs targeting HCLS1 mRNA (two different shRNA constructs were used simultaneously) or scrambled control shRNA. On day 4 after transduction, transduced RFP+ cells were sorted and total RNA was isolated.
Growth protocol Cells were cultured in ex-vivo medium supplemented with 10% HSA, 20 ng/ml IL-3, 20 ng/ml IL-6, 20 ng/ml TPO, 50 ng/ml SCF and 50 ng/ml Flt-3L.
Extracted molecule total RNA
Extraction protocol Extraction of total RNA was performed using the RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.
Label biotin
Label protocol The GeneChip WT cDNA Synthesis and Amplification Kit was used to make double-stranded cDNA from total RNA, which was then labeled with biotin (GeneChip WT Terminal Labeling Kit).
 
Hybridization protocol After chemical fragmentation of the biotin-labeled cRNA targets, they were hybridized to Affymetrix Human Exome microarrays using the Fluidics Station 450.
Scan protocol Microarrays were scanned using the Affymetrix Genechip Scanner 3000 with Genechip Operating Software 1.4 (Affymetrix, Santa Clara, CA).
Description shRNA_CTL
Gene expression data from CD34+ cells transduced with ctrl shRNA.
Data processing The data were analyzed with Affymetrix Expression Console software with RMA-sketch exon-level analysis settings.
 
Submission date Sep 09, 2012
Last update date Sep 09, 2012
Contact name Siarhei Kandabarau
E-mail(s) kandabarau.siarhei@mh-hannover.de
Organization name Hannover Medical School
Street address Carl-Neuberg-Str 1
City Hannover
ZIP/Postal code 30625
Country Germany
 
Platform ID GPL10739
Series (1)
GSE40712 Expression data from CD34+ hematopoietic cells transduced with control or anti-HCLS1 shRNA

Data table header descriptions
ID_REF
VALUE RMA log2 intensity

Data table
ID_REF VALUE
7892501 6.700584
7892502 6.539212
7892503 5.503216
7892504 9.011186
7892505 4.855461
7892506 5.469156
7892507 6.113296
7892508 8.016815
7892509 12.25874
7892510 6.146144
7892511 4.051857
7892512 7.750323
7892513 4.866564
7892514 10.85618
7892515 9.786484
7892516 6.072908
7892517 7.515214
7892518 3.754692
7892519 6.329803
7892520 10.33892

Total number of rows: 257430

Table truncated, full table size 4244 Kbytes.




Supplementary file Size Download File type/resource
GSM999604_shRNA_CTL.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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