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Sample GSM1260325 Query DataSets for GSM1260325
Status Public on Feb 07, 2014
Title ST-HSC_rep1 [expression]
Sample type RNA
 
Source name sorted ST-HSC from human bone marrow
Organism Homo sapiens
Characteristics cell type: Lin (CD2, CD3, CD4, CD7, CD10, CD11b, CD14, CD15, CD19, CD20, CD56, and Glycophorin A )-, CD34+, CD38-, CD90- cells
disease status: healthy
Treatment protocol No treatment.
Growth protocol Uncultured primary cells.
Extracted molecule total RNA
Extraction protocol Cells were sorted into RLT buffer (Qiagen, Valencia, CA), homogenized by passing five times through a needle. Simultaneous harvest of RNA and genomic DNA was achieved with the AllPrep kit (Qiagen, Valencia, CA) following the instructions of the manufacturer. Total RNA was linearly amplified and transcribed with the MessageAmp Kit AM1751 (Ambion/ Life Technologies, Carlsbad, CA) prior to microarray gene expression analysis following the NimbleGen Arrays User's Guide (NimbleGen, Madison, WI). Integrity of RNA and cDNA was verified at each step of amplification using the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA).
Label Cy5
Label protocol See manufacturer's web site (www.nimblegen.com).
 
Hybridization protocol Labeling and hybridization onto the NimbleGen Homo sapiens HG18 60mer expr (385k) was carried out by Roche/NimblGen (Madison, WI) according to the manufacturer's protocols (see manufacturer's website (www.nimblegen.com)).
Scan protocol See manufacturer's web site (www.nimblegen.com).
Description 0084STHSC
Data processing Gene expression profiling was performed on NimbleGen HG18 arrays (design name 2006-08-03_HG18_60mer_expr, Roche-NimbleGen Inc., Madison, WI). The raw data (.pair file) was analyzed by the NimbleScan software package (Roche NimbleGen, Inc.). The data was normalized using the RMA algorithm.
 
Submission date Nov 06, 2013
Last update date Feb 07, 2014
Contact name Boris Bartholdy
Organization name Albert Einstein College of Medicine
Department Cell Biology
Street address 1300 Morris Park Ave
City Bronx
State/province NY
ZIP/Postal code 10461
Country USA
 
Platform ID GPL11219
Series (2)
GSE52150 Analysis of RNA expression changes in normal human hematopoietic stem and progenitor cells
GSE52152 Analysis of RNA expression and DNA cytosine methylation in healthy human hematopoietic stem and progenitor cells

Data table header descriptions
ID_REF
VALUE Log2-transformed RMA expression value

Data table
ID_REF VALUE
AB000409 8.7746
AB000461 12.7023
AB000463 8.5696
AB000781 5.8475
AB001025 5.9858
AB001328 4.7656
AB002294 6.8175
AB002308 13.2384
AB002311 12.1719
AB002313 7.9453
AB002360 5.5605
AB002372 6.9346
AB002377 8.881
AB002381 13.6831
AB002382 6.6363
AB002384 10.6444
AB003177 11.1294
AB003333 12.5273
AB004885 12.3794
AB006589 7.1835

Total number of rows: 47633

Table truncated, full table size 786 Kbytes.




Supplementary file Size Download File type/resource
GSM1260325_326071_Usteidl_635.pair.gz 7.6 Mb (ftp)(http) PAIR
Processed data included within Sample table

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