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Sample GSM1085011 Query DataSets for GSM1085011
Status Public on Sep 13, 2016
Title Cord Blood CD34+ progenitors Day zero, Sample 3 [FigS4]
Sample type RNA
 
Source name Cord Blood CD34+ Day Zero progenitors, treated as described, Sample 3
Organism Homo sapiens
Characteristics cell type: Cord Blood CD34+ Day Zero progenitors, Sample 3
sample type: Cord blood CD34+ cells expanded from day -3 to day zero with Flt3L, SCF, and TPO, and then harvested
Extracted molecule total RNA
Extraction protocol Total RNA was prepared as described in the RNeasy Mini Kit (Qiagen) with on-column DNase I digestion. RNA quality was assessed by Nanodrop-1000 spectrometer for OD260/280 and OD260/230 ratio and Bioanalyzer (Agilent Technologies).
Label Cy3
Label protocol 500 ng total RNA from each sample was amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (AMIL1791, Ambion, Austin, TX) as described in the instruction manual.
 
Hybridization protocol For array assay, 750 ng biotin-labeled cRNA was combined with hybridization buffer and hybridized to the array at 58°C for 16-20 hours. After hybridization, the hybridization cartridge was disassembled and the array was washed with buffer at 55C and blocked at room temperature. Bound biotinylated cRNA was stained with streptavidin-Cy3 and then washed. Illumina HumanHT-12 V4.0 expression beadchips were used for all analyses in this series.
Scan protocol Fluorescent signals were obtained by scanning with the iScan System.
Description Individual sample
Data processing Data were extracted with Gene Expression Module 1.0.6 in GenomeStudio 1.0.2 and signal intensities from multiple chips comprising this single series were quantile normalized without background subtraction to obtain normalized data as deposited.
 
Submission date Feb 20, 2013
Last update date Sep 13, 2016
Contact name Elias Thomas Zambidis
Organization name Johns Hopkins School of Medicine
Department Oncology
Street address 733 N. Broadway
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
 
Platform ID GPL10904
Series (2)
GSE44427 Global gene expression analysis of donor cells, low passage episomal stromal and non-stromal primed myeloid iPSC, and hESC
GSE44430 Comprehensive microarray analysis of reprogramming fidelity in a library of non-integrated induced pluripotent stem cell lines prepared with various derivation methods

Data table header descriptions
ID_REF
VALUE Signal intensity

Data table
ID_REF VALUE
7A5 98.9
A1BG 104.5
A1CF 102.4
A26C3 99
A2BP1 94.4
A2LD1 156.9
A2M 93.9
A2ML1 81.9
A3GALT2 99.8
A4GALT 87.8
A4GNT 97.1
AAA1 93.1
AAAS 135.3
AACS 249.7
AACSL 147.1
AADAC 89.2
AADACL1 167.3
AADACL2 94.9
AADACL3 96.5
AADACL4 90.9

Total number of rows: 34682

Table truncated, full table size 460 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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