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Sample GSM311354 Query DataSets for GSM311354
Status Public on Oct 03, 2008
Title Human CD15+ myeloid progenitor cells
Sample type SAGE
Anchor NlaIII
Tag Count 104993
Tag Length 10
Source name Primary human CD15+ myeloid progenitor cells
Organism Homo sapiens
Characteristics Human bone-marrow mononuclear cells were obtained from the Poietics Company (Gaithersburg, MD).
Extracted molecule total RNA
Extraction protocol Human bone-marrow mononuclear cells were isolated from bone marrow with FicollyPaque solution and stored in liquid nitrogen. Cells from three donors were thawed at 37°C, pooled, and used immediately for the isolation of myeloid progenitor cells with CD15 magnetic beads (Dynal, Oslo, Norway). The cells isolated by CD15 magnetic beads were lysed directly with TRIzol reagent for isolation of total RNA. mRNA was purified from 5 mg of total RNA with oligo(dT)25 beads. cDNA was synthesized with a cDNA synthesis kit, and SAGE was performed according to the SAGE protocol with the exceptions described in the original paper. SAGE-tag sequences were collected with the Big-Dye sequencing kit and ABI377 sequencer, and tag sequences were extracted with SAGE 300 software.
Description Lee S, Zhou G, Clark T, Chen J, Rowley JD, Wang SM. The pattern of gene expression in human CD15+ myeloid progenitor cells. Proc Natl Acad Sci U S A. 98(6):3340-5, 2001;
Lee S, Chen J, Zhou G, Shi RZ, Bouffard GG, Kocherginsky M, Ge X, Sun M, Jayathilaka N, Kim YC, Emmanuel N, Bohlander SK, Minden M, Kline J, Ozer O, Larson RA, LeBeau MM, Green ED, Trent J, Karrison T, Liu PP, Wang SM, Rowley JD. Gene expression profiles in acute myeloid leukemia with common translocations using SAGE. Proc Natl Acad Sci U S A. 103(4):1030-5, 2006;
We performed a genome-wide analysis of gene expression in primary human CD151 myeloid progenitor cells. By using the serial analysis of gene expression (SAGE) technique, we obtained quantitativetinformation for the expression of 37,519 unique SAGE-tag sequences. Of these unique tags, (i) 25% were detected at high and intermediate levels, whereas 75% were present as single copies, (ii) 53% of the tags matched known expressed sequences, 34% of which were matched to more than one known expressed sequence, and (iii) 47% of the tags had no matches and represent potentially novel genes. The correct genes were confirmed by application of the generation of longer cDNA fragments from SAGE tags for gene identification (GLGI) technique for high-copy tags with multiple matches. A set of genes known to be important in myeloid differentiation were expressed at various levels and used different spliced forms. This study provides a normal baseline for comparison of gene expression in myeloid diseases. The strategy of using SAGE and GLGI techniques in this study has broad applications to the genome-wide identification of expressed genes.
Submission date Aug 11, 2008
Last update date Nov 19, 2008
Contact name San Ming Wang
Phone 224-364-7491
Fax 224-364-5003
Organization name ENH Research Institute, Northwestern University
Department Center for Functional Genomics
Street address 1001 University Place
City Evanston
State/province IL
ZIP/Postal code 60062
Country USA
Platform ID GPL4
Series (1)
GSE13007 The pattern of gene expression in human CD15+ myeloid progenitor cells

Data table header descriptions
TPM tags per million

Data table
GTGACCACGG 2866 27297.06
TGTGTTGAGA 900 8572.00
CCCATCGTCC 876 8343.41
TACCTGCAGA 864 8229.12
GTTGTGGTTA 802 7638.60
GTGGCCACGG 769 7324.30
CTAAGACTTC 745 7095.71
AGCCCTACAA 686 6533.77
ACTAACACCC 673 6409.95
TTCATACACC 550 5238.44
ATGTAAAAAA 544 5181.30
CACCTAATTG 502 4781.27
CTCATAAGGA 477 4543.16
GCAAGCCAAC 457 4352.67
GTGAAGGCAG 407 3876.45
ATTTGAGAAG 395 3762.16
TTGGGGTTTC 394 3752.63
ATGGCTGGTA 379 3609.76
ACCCTTGGCC 358 3409.75
CCACTGCACT 356 3390.70

Total number of rows: 38869

Table truncated, full table size 695 Kbytes.

Supplementary data files not provided

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