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Transcriptome analysis of monocytic leukemia cell differentiation

ABSTRACT: The human leukemia cell line U937 is a well-established model for studying monocytic cell differentiation. We used a modified protocol (SADE) of serial analysis of gene expression (SAGE) and developed a SADE linker-anchored PCR assay to investigate the pattern of expression of known genes and to identify new transcripts in proliferating cells and during cell growth arrest and differentiation. We implemented new informatic tools to compare expression profiles before and after exposure of cells to differentiation inducers. From the analysis of 47,388 tags, we identified 13,806 distinct transcripts, 265 of which showed significant variations (P<0.01). Among 1219 well-identified genes, major changes concerned transcription and translation components, cytoskeleton, and macrophage-specific genes. Nearly half of the tags, some of them expressed at high levels, matched partially characterized genes or ESTs, or revealed yet-unknown transcripts, providing a wealth of new candidate genes that may reveal novel aspects of terminal monocytic differentiation. Keywords = 12213207 Keywords: other

ORGANISM(S): Homo sapiens

PROVIDER: GSE1865 | GEO | 2004/10/23

SECONDARY ACCESSION(S): PRJNA90491

REPOSITORIES: GEO

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Transcriptome analysis of monocytic leukemia cell differentiation

Project description:The human leukemia cell line U937 is a well-established model for studying monocytic cell differentiation. We used a modified protocol (SADE) of serial analysis of gene expression (SAGE) and developed a SADE linker-anchored PCR assay to investigate the pattern of expression of known genes and to identify new transcripts in proliferating cells and during cell growth arrest and differentiation. We implemented new informatic tools to compare expression profiles before and after exposure of cells to differentiation inducers. From the analysis of 47,388 tags, we identified 13,806 distinct transcripts, 265 of which showed significant variations (P<0.01). Among 1219 well-identified genes, major changes concerned transcription and translation components, cytoskeleton, and macrophage-specific genes. Nearly half of the tags, some of them expressed at high levels, matched partially characterized genes or ESTs, or revealed yet-unknown transcripts, providing a wealth of new candidate genes that may reveal novel aspects of terminal monocytic differentiation. Keywords = 12213207 Keywords: other

2004-10-23 | E-GEOD-1865 | biostudies-arrayexpress

Confirmation of the gene expression pattern in Mxi1-deficient mouse (time course)

Project description:For final aim to completes network map between gene that is concerned in cystogenesis, verifies meaning genes connected with cyst formation analyzing gene pattern in time-dependent Mxi1 KO mouse that have phenotype of polycystic kidney disease. Monitoring meaning genes through microarray analysis, and confirm the function of these genes. Also, find pathway including meaning genes and new pathway related with PKD. Completes network map concerned in time-dependent cystogenesis through integrates knowing pathway and predicting pathway. Develope diagnostic of cyst disease and cure target through such completed network map, and wish to clear new role of cyst formation connection gene through in vivo model and examine closely control system of cyst formation mechanism. Keywords: time course

2008-03-31 | GSE10941 | GEO

Confirmation of the gene expression pattern in Mxi1-deficient mouse

Project description:For final aim to completes network map between gene that is concerned in cystogenesis, verifies meaning genes connected with cyst formation analyzing gene pattern in Mxi1 KO mouse that have phenotype of polycystic kidney disease. Monitoring meaning genes through microarray analysis, and confirm the function of these genes. Also, find pathway including meaning genes and new pathway related with PKD. Completes network map concerned in cystogenesis through integrates knowing pathway and predicting pathway. Develope diagnostic of cyst disease and cure target through such completed network map, and wish to clear new role of cyst formation connection gene through in vivo model and examine closely control system of cyst formation mechanism. Keywords: Cystogenesis

2008-04-29 | GSE11053 | GEO

Digital Gene Expression Analysis Based on Integrated De Novo Transcriptome Assembly of Sweet Potato [Ipomoea batatas (L.) Lam.]

Project description:More than 3.5 million raw DGE tags were obtained in each library. The clean tags in each sample ranged from 3.35 to 3.63 million, and the distinct clean tags ranged from 93,593 to 139,389. The 21 bp DGE clean tags were mapped to sweet potato transcripts. Then, we compared 7 libraries pair-wisely so that 21 pairs of comparisons were implemented. Among these comparisons, we found that 4,721 to 12,151 transcripts had significant changes in expression, and the average number was 9,657. We also observed a large number of specifically expressed transcripts between each two libraries. The expression profiles of those genes involved in root development and carbohydrates accumulation were characterized. Moreover, other genes of interest, such as potentially abiotic stress tolerance and insect resistance, were also characterized.

2012-02-18 | GSE35929 | GEO

Confirmation of the gene expression pattern in Mxi1-deficient mouse

Project description:For final aim to completes network map between gene that is concerned in cystogenesis, verifies meaning genes connected with cyst formation analyzing gene pattern in Mxi1 KO mouse that have phenotype of polycystic kidney disease. Monitoring meaning genes through microarray analysis, and confirm the function of these genes. Also, find pathway including meaning genes and new pathway related with PKD. Completes network map concerned in cystogenesis through integrates knowing pathway and predicting pathway. Develope diagnostic of cyst disease and cure target through such completed network map, and wish to clear new role of cyst formation connection gene through in vivo model and examine closely control system of cyst formation mechanism. Keywords: Cystogenesis Use 1 mouse at each experiment and control. Indirect labeling of 10g cRNA, using bacterial control mRNA.

2008-04-29 | E-GEOD-11053 | biostudies-arrayexpress

Detecting novel low-abundant transcripts in Drosophila

Project description:Increasing evidence suggests that low-abundant transcripts may play fundamental roles in biological processes. In an attempt to estimate the prevalence of low-abundant transcripts in eukaryotic genomes, we performed a transcriptome analysis in Drosophila using the SAGE technique. We collected 244,313 SAGE tags from transcripts expressed in Drosophila embryonic, larval, pupae, adult, and testicular tissue. From these SAGE tags, we identified 40,823 unique SAGE tags. Our analysis showed that 55% of the 40,823 unique SAGE tags are novel without matches in currently known Drosophila transcripts, and most of the novel SAGE tags have low copy numbers. Further analysis indicated that these novel SAGE tags represent novel low-abundant transcripts expressed from loci outside of currently annotated exons including the intergenic and intronic regions, and antisense of the currently annotated exons in the Drosophila genome. Our study reveals the presence of a significant number of novel low-abundant transcripts in Drosophila, and highlights the need to isolate these novel low-abundant transcripts for further biological studies. Keywords: other

2005-06-03 | GSE2347 | GEO

Confirmation of the gene expression pattern in Mxi1-deficient mouse (time course)

2008-03-31 | E-GEOD-10941 | biostudies-arrayexpress

LongSAGE analysis significantly improves genome annotation

Project description:Owing to its increased tag length, LongSAGE tags are expected to be more reliable in direct assignment to genome sequences. Therefore, we evaluated the use of LongSAGE data in genome annotation by using our LongSAGE dataset of 202 015 tags (consisting of 41 718 unique tags), experimentally generated from mouse embryonic tail libraries. RESULTS: A fraction of LongSAGE tags could not be unambiguously assigned to its gene, due to the presence of widely conserved sequences downstream of particular CATG anchor sites. The presence of alternative forms of transcripts was confirmed in 45% of all detected genes. Surprisingly, a large fraction of LongSAGE tags with hits to the genome (66%) could not be assigned to any gene annotated in EnsEMBL. Among such cases, 2098 LongSAGE tags fell into a region containing a putative gene predicted by GenScan, providing experimental evidence for the presence of real genes, while 9112 genes were found out to be left out or wrongly annotated by the EnsEMBL pipeline. CONCLUSIONS: LongSAGE transcriptome data can significantly improve the genome annotation by identifying novel genes and alternative transcripts, even in the case of thus far best-characterized organisms like the mouse. Keywords: other

2005-07-20 | GSE2967 | GEO

Characterization of mRNA transcripts in spermatozoa of fertile men

Project description:Accumulated evidence proves that mature spermatozoa contain a complex yet specific mRNA, which could provide information of the past events of spermatogenesis. Our aim was to quantitatively microdissect these mRNA transcripts by a digital approach. SAGE was used to study the mRNA transcripts from ejaculate of an individual and of a pool of 10 fertile men. SAGE library from individual produced 20237 raw tags representing 2459 unique tags (those tags that show at least twice in the library), and that from pooled 10 men generated 21052 raw tags representing 2712 unique tags. The SAGE view of ejaculate of fertile men has revealed a large number of transcripts, which occur in steady frequencies and probably have important implications in the spermatogenesis and fertilization. Keywords: normal gene expression profile

2005-11-11 | GSE3587 | GEO

Somatic cells in testes

Project description:Gene expression profiles of somatic cells of fetal and adult testis. To identify genes developmentally regulated in the somatic cells of the testis, serial analysis of gene expression (SAGE) has been used to generate gene expression profiles from these cells in the fetal and adult mouse. To avoid germ cell transcripts, a fetal SAGE library was generated from germ cell-free fetal Wv/Wv mice, and an adult SAGE library was generated from adult testes depleted of germ cells with busulfan. The combined SAGE libraries contained 147570 tags identifying 12976 unique transcripts. Of these transcripts, 3607 were present in only the fetal library and 3941 were present in only the adult library. Most of the abundant differentially expressed tags in the adult testis library were from characterized genes, whereas 3' rapid amplification of complementary ends was required to identify most differentially expressed tags in the fetal library. These fetal tags were mostly associated with uncharacterized UniGene clusters. These data provide a comprehensive and quantitative analysis of gene expression in the somatic cells of the fetal and adult testis (including unknown transcripts) and identify genes differentially expressed in these cells during testis development. These differentially regulated genes are likely to provide insight into mechanisms regulating testis function both during development and in the adult animal. Keywords: other

2003-05-06 | GSE366 | GEO

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