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Sample GSM315232 Query DataSets for GSM315232
Status Public on Aug 23, 2008
Title Day 5 (H1 hEB cells)
Sample type RNA
 
Source name Human stem cells differentiated under conditions
Organism Homo sapiens
Characteristics Human stem cells differentiated under conditions
Growth protocol The hESC line H1 (NIH code: WA01) was maintained on irradiated primary murine embryonic feeders (PMEF), and hEB were formed from hESC clumps in semisolid, serum-supplemented medium, exactly as previously described (Zambidis et al., 2005). Twenty-four hours after hESC plating, (Day 2) simple hEB were harvested, washed, re-suspended in PBS in 50-ml conical tubes, and collected by gentle gravity settling for 2-3 minutes. Formed hEB were re-suspended into 6-well ultra-non-adherent plates (Corning) at ~100-200 hEB/ml in SF liquid differentiation medium (SF LDM), consisting of serum-free expansion medium (SFEM, StemCell Technologies) supplemented with 50 ug/ml ascorbic acid (SIGMA), 1% EXCYTE, 0.5% insulin/transferrin/selenium (Invitrogen), 3% PFHM-II (Invitrogen), and penicillin/streptomycin (SIGMA). Various combinations of human growth factors (all from R&D Systems, Peprotech, or Invitrogen) were added directly into SF LDM at 2-20 days of hEB development: BMP4 (50 ng/ml), VEGF (50 ng/ml), FGF1 (50 ng/ml+ 5ug/ml heparin sulfate, SIGMA), FGF2 (50 ng/ml+ 5 ug/ml heparin sulfate), murine Nodal (50 ng/ml), IGF-II (50 ng/ml), murine wnt3a (50 ng/ml), and activin A (50 ng/ml). hEB cultures were fed by hemi-depletion and replacement of medium every 2-3 days with fresh SF LDM and GFs. To expand hEB-derived hematopoietic progenitors, enzymatically-digested (Accutase, SIGMA) day 9-10 hEB clumps, differentiated as above, were transferred into SF LDM and allowed to adhere to gelatinized tissue culture plates. SF cultures were supplemented with various hematopoietic inductive factors including: BMP4 (50 ng/ml), SCF (50 ng/ml), Flt3L (50 ng/ml), TPO (50 ng/ml), GM-CSF (50 ng/ml), G-CSF (50 ng/ml), IL-3 (20 ng/ml), IL-6 (20 ng/ml), VEGF (20 ng/ml), EPO (2 units/ml), FGF1 (10 ng/ml) and FGF2 (10 ng/ml).
Extracted molecule total RNA
Extraction protocol Total RNA are isolated from cell pellets using TriZol reagent(Invitrogen) followed by Rneasy mini kit (Qiagen) clean-up.
Label Cy3
Label protocol 400 ng total Rna is amplified and labeled using Agilent low in put RNA amplification and labeling kit and Cy3-CTP (Perkin Elmer) following manufacturer's protocol.
 
Hybridization protocol Using Agilent hybridization chambers and oven following manufacturer's protocol (65oC for 17 hours)
Scan protocol Scanned on an Agilent G2565AA scanner.
Description Individual sample
Data processing Processed signal intensities are imported into GeneSpring Gx 7.3 and normalized to the median signal intensities of each arrays. Intensities of replicate probes are represented as single value of average.
 
Submission date Aug 22, 2008
Last update date Aug 22, 2008
Contact name Wayne Yu
E-mail(s) wyu8@jhmi.edu
Phone (410)502-7970
Fax (410)955-8780
Organization name Johns Hopkins University
Department Cancer Center
Street address 417 N. Caroline St.
City Baltimore
State/province MD
ZIP/Postal code 21231
Country USA
 
Platform ID GPL6480
Series (1)
GSE12531 Global gene expression analysis of undifferentiated H1 hESC, and hEB cells differentiated with SF BVF2H conditions

Data table header descriptions
ID_REF
VALUE Ratio of processed signal intensity over median signal intensity of the array

Data table
ID_REF VALUE
A_23_P100001 6.827
A_23_P100011 0.602
A_23_P100022 1.135
A_23_P100056 8.309
A_23_P100074 13.9
A_23_P100092 1.608
A_23_P100103 0.507
A_23_P100111 3.711
A_23_P100127 1.04
A_23_P100133 1.108
A_23_P100141 2.306
A_23_P100156 3.912
A_23_P100177 0.472
A_23_P100189 0.575
A_23_P100196 15.52
A_23_P100203 15.1
A_23_P100220 14.63
A_23_P100240 0.322
A_23_P10025 2.992
A_23_P100263 6.794

Total number of rows: 41000

Table truncated, full table size 748 Kbytes.




Supplementary file Size Download File type/resource
GSM315232.txt.gz 7.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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