The pattern of gene expression in human CD15<sup>+</sup>myeloid progenitor cells

Lee, Sanggyu; Zhou, Guolin; Clark, Terry; Chen, Jianjun; Rowley, Janet D.; Wang, San Ming

doi:10.1073/pnas.051013798

Cited by 36 publications

(34 citation statements)

References 22 publications

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“…Sequences from 32 novel tags matched known expressed sequences, and reactions for 49 novel tags did not generate qualified sequences. This result, as well as our earlier study on CD15 ϩ cells (11), indicates that the novel SAGE tags we have identified truly represent a large number of novel genes. The conversion of novel SAGE tags into 3Ј ESTs provides an efficient way to identify novel genes on a large scale.…”

Section: Conversion Of Novel Sage Tags Into Novel 3 Estssupporting

confidence: 83%

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The pattern of gene expression in human CD34 ⁺ stem/progenitor cells

Zhou

Chen

Lee

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

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We have analyzed the pattern of gene expression in human primary CD34 ؉ stem͞progenitor cells. We identified 42,399 unique serial analysis of gene expression (SAGE) tags among 106,021 SAGE tags collected from 2.5 ؋ 10 6 CD34 ؉ cells purified from bone marrow. Of these unique SAGE tags, 21,546 matched known expressed sequences, including 3,687 known genes, and 20,854 were novel without a match. The SAGE tags that matched known sequences tended to be at higher levels, whereas the novel SAGE tags tended to be at lower levels. By using the generation of longer sequences from SAGE tags for gene identification (GLGI) method, we identified the correct gene for 385 of 440 high-copy SAGE tags that matched multiple genes and we generated 198 novel 3 expressed sequence tags from 138 high-copy novel SAGE tags. We observed that many different SAGE tags were derived from the same genes, reflecting the high heterogeneity of the 3 untranslated region in the expressed genes. We compared the quantitative relationship for genes known to be important in hematopoiesis. The qualitative identification and quantitative measure for each known gene, expressed sequence tag, and novel SAGE tag provide a base for studying normal gene expression in hematopoietic stem͞progenitor cells and for studying abnormal gene expression in hematopoietic diseases.

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Section: Conversion Of Novel Sage Tags Into Novel 3 Estssupporting

confidence: 83%

“…SAGE Performance. SAGE was performed with our modified SAGE protocol (10), and the data were processed by use of our procedure (11).…”

Section: Methodsmentioning

confidence: 99%

The pattern of gene expression in human CD34 ⁺ stem/progenitor cells

Zhou

Chen

Lee

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

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“…The result revealed a similar distribution of genes between the two studies in various abundance classes, with minor variation largely due to sampling depth (Table III). In most of the SAGE studies, over 80% of unique tags were found present at low copy numbers (#5 tags), and around 50% of them were detected only once in a genome (Chrast et al, 2000;Lee et al, 2001;Fizames et al, 2004).…”

Section: Distribution Of Sage Tags In Rice Genomementioning

confidence: 99%

“…Poly(A 1 ) RNA isolation, cDNA synthesis, and SAGE library construction were performed according to a published protocol (Lee et al, 2001). Briefly, mRNAs were purified with the Oligotex mRNA Mini kit (Qiagen USA, Valencia, CA) and double-stranded cDNAs were synthesized from the fractioned poly(A 1 )-containing mRNAs with 5#-biotinylated 3#-anchored oligo(dT) primers (5#-biotin-ATCTAGAGCGGCCGCdT16[A/G/CA/CG/ CC]-3#).…”

Section: Plant Materials and Sage Library Constructionmentioning

confidence: 99%

Serial Analysis of Gene Expression Study of a Hybrid Rice Strain (LYP9) and Its Parental Cultivars

et al. 2005

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Using the serial analysis of gene expression technique, we surveyed transcriptomes of three major tissues (panicles, leaves, and roots) of a super-hybrid rice (Oryza sativa) strain, LYP9, in comparison to its parental cultivars, 93-11 (indica) and PA64s (japonica). We acquired 465,679 tags from the serial analysis of gene expression libraries, which were consolidated into 68,483 unique tags. Focusing our initial functional analyses on a subset of the data that are supported by full-length cDNAs and the tags (genes) differentially expressed in the hybrid at a significant level (P , 0.01), we identified 595 up-regulated (22 tags in panicles, 228 in leaves, and 345 in roots) and 25 down-regulated (seven tags in panicles, 15 in leaves, and three in roots) in LYP9. Most of the tag-identified and up-regulated genes were found related to enhancing carbon-and nitrogen-assimilation, including photosynthesis in leaves, nitrogen uptake in roots, and rapid growth in both roots and panicles. Among the downregulated genes in LYP9, there is an essential enzyme in photorespiration, alanine:glyoxylate aminotransferase 1. Our study adds a new set of data crucial for the understanding of molecular mechanisms of heterosis and gene regulation networks of the cultivated rice.

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“…TMSBX4 is an actin sequestering peptide that is highly expressed in CD15 þ myeloid progenitor cells, 33 and is involved in the differentiation of lymphocytes, macrophages, and granulocytes. 34 TMSBX4 has been shown to inhibit growth of AML cell lines, 35 suggesting that decreased expression in AMKL cells may promote proliferation compared to TL cells.…”

Section: Resultsmentioning

confidence: 99%

Distinct gene signatures of transient and acute megakaryoblastic leukemia in Down syndrome

et al. 2004

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Approximately 10% of newborns with Down syndrome develop Transient Leukemia (TL), a disorder that is unique to infants with constitutional trisomy 21 (or trisomy 21 mosaicism). TL blasts disappear spontaneously within the first 3 months of life in the majority of cases. Despite the resolution of TL, 20-30% of these newborns will go on to develop acute megakaryoblastic leukemia (AMKL) later in life. In this study, samples from both TL and AMKL patients were examined using cDNA microarrays to study the pathogenic progression from TL to AMKL. TL and AMKL samples partition separately by cluster analysis, and AMKL samples had substantial increases in apolipoprotein C-I, transporter 1, myosin alkali light chain 4, and spermidine/ spermine N-acetyltransferase, compared to TL samples. Although these findings will require validation in an independent series of TL and AMKL samples, they indicate that TL and AMKL have distinct gene signatures, and provide a basis for studies of the different mechanisms underlying either the resolution of TL or its progression to AMKL.

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The pattern of gene expression in human CD15⁺myeloid progenitor cells

Cited by 36 publications

References 22 publications

The pattern of gene expression in human CD34 ⁺ stem/progenitor cells

The pattern of gene expression in human CD34 ⁺ stem/progenitor cells

Serial Analysis of Gene Expression Study of a Hybrid Rice Strain (LYP9) and Its Parental Cultivars

Distinct gene signatures of transient and acute megakaryoblastic leukemia in Down syndrome

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The pattern of gene expression in human CD15+myeloid progenitor cells

Cited by 36 publications

References 22 publications

The pattern of gene expression in human CD34 + stem/progenitor cells

The pattern of gene expression in human CD34 + stem/progenitor cells

Serial Analysis of Gene Expression Study of a Hybrid Rice Strain (LYP9) and Its Parental Cultivars

Distinct gene signatures of transient and acute megakaryoblastic leukemia in Down syndrome

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The pattern of gene expression in human CD15⁺myeloid progenitor cells

The pattern of gene expression in human CD34 ⁺ stem/progenitor cells

The pattern of gene expression in human CD34 ⁺ stem/progenitor cells