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Sample GSM999605 Query DataSets for GSM999605
Status Public on Sep 09, 2012
Title HCLS1 shRNA
Sample type RNA
Source name Bone marrow CD34+ cells, HCLS1 shRNA
Organism Homo sapiens
Characteristics disease state: healthy
tissue: bone marrow
cell type: CD34+ cells
treatment: HCLS1 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_HS1
Gene expression data from CD34+ cells transduced with HCLS1 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
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
VALUE RMA log2 intensity

Data table
7892501 6.364873
7892502 6.478615
7892503 5.013471
7892504 9.504943
7892505 3.793557
7892506 6.141212
7892507 5.957695
7892508 7.213246
7892509 12.31838
7892510 6.310814
7892511 4.221735
7892512 8.318389
7892513 4.722036
7892514 9.499735
7892515 9.480768
7892516 5.854609
7892517 7.50892
7892518 2.674103
7892519 6.723379
7892520 10.37233

Total number of rows: 257430

Table truncated, full table size 4243 Kbytes.

Supplementary file Size Download File type/resource
GSM999605_shRNA_HS1.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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