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Sample GSM1079552 Query DataSets for GSM1079552
Status Public on Dec 31, 2013
Title immortalized erythroblasts (donor b) at day 40 of expansion culture (after viral transduction)
Sample type RNA
 
Source name immortalized erythroblasts at day 40 of expansion culture (after viral transduction)
Organism Homo sapiens
Characteristics tissue of origin: cord blood
expansion days: 19+40 days
genetic factors: Sox2, Klf4, c-Myc and p53shRNA
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 immortalized erythroblasts at day 40 of expansion culture (after viral transduction) in serum-free medium supplemented with SCF, IL-3, IGF-1, EPO and Dexamethasone
iE2(d40)
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 7.60582
7892502 6.34727
7892503 3.81489
7892504 8.64445
7892505 4.71483
7892506 7.97939
7892507 5.55799
7892508 8.78197
7892509 12.8494
7892510 5.11927
7892511 5.3319
7892512 7.5782
7892513 4.46214
7892514 11.7731
7892515 9.93218
7892516 5.34066
7892517 7.12829
7892518 4.18254
7892519 7.89367
7892520 10.1489

Total number of rows: 257430

Table truncated, full table size 3993 Kbytes.




Supplementary file Size Download File type/resource
GSM1079552_XHua-IEC-ie2d40-1a-HuGene-1_0_HuGene-1_0-st-v1_.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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