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Sample GSM1079557 Query DataSets for GSM1079557
Status Public on Dec 31, 2013
Title Human induced pluripotent stem cells derived from adult blood cells
Sample type RNA
 
Source name Human induced pluripotent stem cells derived from adult blood cells
Organism Homo sapiens
Characteristics tissue of origin: adult blood
expansion days: passage 37
genetic factors: OCT4, SOX2, KLF4, C-MYC, LIN28
Treatment protocol no treatment
Growth protocol pCBE19: After thawing, frozen CB MNCs (5x106/ml) were cultivated in serum-free medium (SFM; 50% IMDM with 50% Ham’s F12 (Invitrogen), synthetic lipids (Invitrogen), insulin-transferrin-selenium supplement (Invitrogen) and 5 mg/ml BSA (Sigma), 50 ug/ml of ascorbic acid (Sigma) and 2 mM glutamax ) supplemented with Epo (2 U/mL; R&D systems), Dexamethasone (1 µM; Sigma), insulin-like growth factor 1 (IGF-1; 40 ng/mL), stem cell factor (SCF; 100 ng/mL), and holo-transferrin (100 µg/ml; Sigma), termed “erythroblast expansion medium” in gelatin-coated wells. Primary cultures of erythroblasts established after several days were kept less than 1x106 cells/ml by daily cell counting and partial medium changes. iE2: Grow in the erythroblast expansion medium. After the culture cells become proliferating constantly, only partial medium change and cell passaging every 2 or 3 days are performed to keep cell density at or below 5 × 105 cells/ml. CD34+: primary cells isolated by magenetic beads binding to CD34 cell surface marker. TF-1: RPMI-1640+10% FBS+ 3U/ml hEPO. iPSC and ESC: standard ESC medium and on MEF feeder.
Extracted molecule total RNA
Extraction protocol RNeasy according to manufacture's protocol
Label biotin
Label protocol One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter engineered random primers for cDNA synthesis, and Ambion® WT Expression Kit (www.affymetrix.com).
 
Hybridization protocol 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip® Expression Wash, Stain and Scan User Manual (www.affymetrix.com).
Scan protocol Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.
Description Human induced pluripotent stem cells derived from adult blood cells
iPSC1
Data processing Image analysis used the Affymetrix Command Console version 3 (AGCC v3.0) software, processed with the Expression Console PLIER algorithm and the manufacturer’s specifications.
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.na33.1.hg19.probeset.csv, HuGene-1_0-st-v1.na33.1.hg19.transcript.csv
RMA Log2 values from the Partek Genomics Suite, using all probesets, were summarized for gene-level analysis.
 
Submission date Feb 07, 2013
Last update date Dec 31, 2013
Contact name Xiaosong Huang
E-mail(s) xhuang18@jhmi.edu
Organization name Johns Hopkins University
Department Medicine/Hematology
Lab Linzhao Cheng
Street address 733 North Broadway, Rm780
City Baltimore
State/province Maryland
ZIP/Postal code 21205
Country USA
 
Platform ID GPL10739
Series (1)
GSE44136 Expression data from primary CB erythroblasts, immortalized/induced erythroblasts, Fetal liver CD34+ blood stem cells, adult CD34+ blood stem cells, erythroleukemia cell line (TF-1) and human ESC and iPSCs

Data table header descriptions
ID_REF
VALUE RMA Log2 values

Data table
ID_REF VALUE
7892501 5.71442
7892502 6.50522
7892503 3.203
7892504 8.25335
7892505 4.57497
7892506 6.55243
7892507 5.99721
7892508 8.55832
7892509 12.734
7892510 5.52434
7892511 5.32331
7892512 6.97427
7892513 4.68191
7892514 11.1243
7892515 10.2775
7892516 6.25114
7892517 6.84872
7892518 4.06011
7892519 6.54875
7892520 9.61344

Total number of rows: 257430

Table truncated, full table size 3993 Kbytes.




Supplementary file Size Download File type/resource
GSM1079557_KTsa-PSC-BC1-1a-HuGene1.0ST_HuGene-1_0-st-v1_.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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