Gene expression in the gut of keratin-feeding clothes moths (Tineola) and keratin beetles (Trox) revealed by subtracted cDNA libraries

Abstract With the goal of creating a resource for in-depth study of myelopoiesis, we have executed a 2-pronged strategy to obtain a complementary DNA (cDNA) clone set enriched in hematopoietic genes. One aspect is a library subtraction to enrich for underrepresented transcripts present at early stages of hematopoiesis. For this, a hematopoietic cDNA library from primary murine bone marrow cells enriched for primitive progenitors was used as tester. The subtraction used 10 000 known genes and expressed sequence tags (ESTs) as driver. The 2304 randomly picked clones from the subtracted cDNA libraries represent 1255 distinct genes, of which 622 (50%) are named genes, 386 (30%) match uncharacterized ESTs, and 247 (20%) are novel. The second aspect of our strategy was to complement this subtracted library with genes known to be involved in myeloid cell differentiation and function. The resulting cDNAs were arrayed on polylysine-coated glass slides. The microarrays were used to analyze gene expression in primary and cultured murine bone marrow–derived progenitors. We found expression of various types of genes, including regulatory cytokines and their receptors, signal transduction genes, and transcription factors. To assess gene expression during myeloid differentiation, we examined patterns of change during induced differentiation of EML cells. Several hundred of the genes underwent fluctuations in expression level during myeloid cell differentiation. The complete database, accessible on the World Wide Web at http://yale130132115135.med.yale.edu/, allows for retrieval of information regarding these genes. Our microarray allows for genomewide expression analysis of myeloid stem cells, which will help in defining the regulatory mechanisms of stem cell differentiation.

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Analysis of gene expression during bud burst initiation in Norway spruce via ESTs from subtracted cDNA libraries

Tree Genetics & Genomes ◽

10.1007/s11295-005-0031-z ◽

2006 ◽

Vol 2 (1) ◽

pp. 39-52 ◽

Cited By ~ 42

Author(s):

Igor A. Yakovlev ◽

Carl-Gunnar Fossdal ◽

Øystein Johnsen ◽

Olavi Junttila ◽

Tore Skrøppa

Keyword(s):

Gene Expression ◽

Norway Spruce ◽

Cdna Libraries ◽

Bud Burst ◽

Subtracted Cdna Libraries

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Gene expression profiling of bovine endometrium during the oestrous cycle: detection of molecular pathways involved in functional changes

Journal of Molecular Endocrinology ◽

10.1677/jme.1.01799 ◽

2005 ◽

Vol 34 (3) ◽

pp. 889-908 ◽

Cited By ~ 92

Author(s):

S Bauersachs ◽

S E Ulbrich ◽

K Gross ◽

S E M Schmidt ◽

H H D Meyer ◽

...

Keyword(s):

Molecular Mechanisms ◽

Transforming Growth Factor ◽

Cdna Array ◽

Transforming Growth Factor Β ◽

Early Embryo ◽

Oestrous Cycle ◽

Cdna Libraries ◽

Functional Changes ◽

Retinoic Acid Signalling ◽

Subtracted Cdna Libraries

The endometrium plays a central role among the reproductive tissues in the context of early embryo–maternal communication and pregnancy. It undergoes typical changes during the sexual/oestrous cycle, which are regulated by the ovarian hormones progesterone and oestrogen. To identify the underlying molecular mechanisms we have performed the first holistic screen of transcriptome changes in bovine intercaruncular endometrium at two stages of the cycle – end of day 0 (late oestrus, low progesterone) and day 12 (dioestrus, high progesterone). A combination of subtracted cDNA libraries and cDNA array hybridisation revealed 133 genes showing at least a 2-fold change of their mRNA abundance, 65 with higher levels at oestrus and 68 at dioestrus. Interestingly, genes were identified which showed differential expression between different uterine sections as well. The most prominent example was the UTMP (uterine milk protein) mRNA, which was markedly upregulated in the cranial part of the ipsilateral uterine horn at oestrus. A Gene Ontology classification of the genes with known function characterised the oestrus time by elevated expression of genes, for example related to cell adhesion, cell motility and extracellular matrix and the dioestrus time by higher expression of mRNAs encoding for a variety of enzymes and transport proteins, in particular ion channels. Searching in pathway databases and literature data-mining revealed physiological processes and signalling cascades, e.g. the transforming growth factor-β signalling pathway and retinoic acid signalling, which are potentially involved in the regulation of changes of the endometrium during the oestrous cycle.

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Cell cycle phase-specific cDNA libraries reflecting phase-specific gene expression of Ehrlich ascites cells growing in vivo

Experimental Cell Research ◽

10.1016/0014-4827(88)90155-3 ◽

1988 ◽

Vol 174 (1) ◽

pp. 199-214 ◽

Cited By ~ 12

Author(s):

Xiang Lu ◽

Marijana Kopun ◽

Dieter Werner

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Cell Cycle Phase ◽

Cdna Libraries ◽

Cycle Phase ◽

Specific Gene ◽

Specific Gene Expression ◽

Ehrlich Ascites ◽

Ehrlich Ascites Cells

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Embryo-induced transcriptome changes in bovine endometrium reveal species-specific and common molecular markers of uterine receptivity

Reproduction ◽

10.1530/rep.1.00996 ◽

2006 ◽

Vol 132 (2) ◽

pp. 319-331 ◽

Cited By ~ 146

Author(s):

Stefan Bauersachs ◽

Susanne E Ulbrich ◽

Karin Gross ◽

Susanne E M Schmidt ◽

Heinrich H D Meyer ◽

...

Keyword(s):

Molecular Markers ◽

Molecular Mechanisms ◽

Cdna Array ◽

Early Embryo ◽

Cdna Libraries ◽

Control Group ◽

Regulation Of Transcription ◽

Uterine Receptivity ◽

Subtracted Cdna Libraries ◽

Species Specific

The endometrium plays a central role among the reproductive tissues in the context of early embryo–maternal communication and pregnancy. This study investigated transcriptome profiles of endometrium samples from day 18 pregnant vs non-pregnant heifers to get insight into the molecular mechanisms involved in conditioning the endometrium for embryo attachment and implantation. Using a combination of subtracted cDNA libraries and cDNA array hybridisation, 109 mRNAs with at least twofold higher abundance in endometrium of pregnant animals and 70 mRNAs with higher levels in the control group were identified. Among the mRNAs with higher abundance in pregnant animals, at least 41 are already described as induced by interferons. In addition, transcript levels of many new candidate genes involved in the regulation of transcription, cell adhesion, modulation of the maternal immune system and endometrial remodelling were found to be increased. The different expression level was confirmed with real-time PCR for nine genes. Localisation of mRNA expression in the endometrium was shown byin situhybridisation forAGRN,LGALS3BP,LGALS9,USP18,PARP12andBST2. A comparison with similar studies in humans, mice, and revealed species-specific and common molecular markers of uterine receptivity.

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Transcriptome analysis ofSchistosoma mansonilarval development using serial analysis of gene expression (SAGE)

Parasitology ◽

10.1017/s0031182009005733 ◽

2009 ◽

Vol 136 (5) ◽

pp. 469-485 ◽

Cited By ~ 22

Author(s):

A. S. TAFT ◽

J. J. VERMEIRE ◽

J. BERNIER ◽

S. R. BIRKELAND ◽

M. J. CIPRIANO ◽

...

Keyword(s):

Gene Expression ◽

Sequence Data ◽

Subsequent Development ◽

Differentially Expressed ◽

Cdna Libraries ◽

Genome Wide ◽

A Genome ◽

Genome Wide Expression ◽

Cell Conditioned Medium

SUMMARYInfection of the snail,Biomphalaria glabrata, by the free-swimming miracidial stage of the human blood fluke,Schistosoma mansoni, and its subsequent development to the parasitic sporocyst stage is critical to establishment of viable infections and continued human transmission. We performed a genome-wide expression analysis of theS. mansonimiracidia and developing sporocyst using Long Serial Analysis of Gene Expression (LongSAGE). Five cDNA libraries were constructed from miracidia andin vitrocultured 6- and 20-day-old sporocysts maintained in sporocyst medium (SM) or in SM conditioned by previous cultivation with cells of theB. glabrataembryonic (Bge) cell line. We generated 21 440 SAGE tags and mapped 13 381 to theS. mansonigene predictions (v4.0e) either by estimating theoretical 3′ UTR lengths or using existing 3′ EST sequence data. Overall, 432 transcripts were found to be differentially expressed amongst all 5 libraries. In total, 172 tags were differentially expressed between miracidia and 6-day conditioned sporocysts and 152 were differentially expressed between miracidia and 6-day unconditioned sporocysts. In addition, 53 and 45 tags, respectively, were differentially expressed in 6-day and 20-day cultured sporocysts, due to the effects of exposure to Bge cell-conditioned medium.

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Single pass cDNA sequencing - a powerful tool to analyse gene expression in preparasitic juveniles of the southern root-knot nematode Meloidogyne incognita

Nematology ◽

10.1163/156854101750236259 ◽

2001 ◽

Vol 3 (2) ◽

pp. 129-139 ◽

Cited By ~ 38

Author(s):

Jaap Bakker ◽

Fred Gommers ◽

Geert Smant ◽

Pierre Abad ◽

Marie-Noëlle Rosso ◽

...

Keyword(s):

Gene Expression ◽

Cdna Library ◽

Meloidogyne Incognita ◽

Sequence Data ◽

Homo Sapiens ◽

Large Fraction ◽

Nematode Species ◽

Cdna Libraries ◽

Parasitic Nematodes ◽

Root Knot Nematode

AbstractExpressed sequence tags (EST) have been widely used to assist in gene discovery in various organisms (e.g., Arabidopsis thaliana, Caenorhabditis elegans, Mus musculus, and Homo sapiens). In this paper we describe an EST project, which aims to investigate gene expression in Meloidogyne incognita at the onset of parasitism. Approximately 1000 5′-end sequence tags were produced from a cDNA library made of freshly hatched preparasitic second stage juveniles (J2). The EST were identified in the primary transformants of the cDNA library, and assigned to nine different functional groups, including (candidate) parasitism genes. A large fraction of the EST (45%) did not have a putative homologue in public databases. Sixty five percent of the EST that could be clustered into a functional group had putative homologues in other nematode species. EST were found for virtually all parasitism related genes that have been cloned from M. incognita to date. In addition, several novel genes were tagged, including a xylanase and a chitinase gene. The efficiency of EST projects, which produce sequence data for thousands of genes in months time without any difficult pre-selections of mRNA pools, makes random sequencing cDNA libraries a superior method to identify candidates for parasitism related genes in plant-parasitic nematodes. The sequences in this paper are retrievable from Genbank with the accession numbers BE191640 to BE191741, BE217592 to BE217720, BE225324 to BE225598, BE238852 to BE239221, and BE240829 to BE240865.

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Analysis of B-L?-chain gene expression in two chicken cDNA libraries

Immunogenetics ◽

10.1007/bf00216803 ◽

1993 ◽

Vol 37 (5) ◽

pp. 381-385 ◽

Cited By ~ 12

Author(s):

G. T. Pharr ◽

Larry D. Bacon ◽

Jerry B. Dodgson

Keyword(s):

Gene Expression ◽

Cdna Libraries ◽

Chain Gene

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Effect of protein synthesis inhibition on gene expression during early development of Dictyostelium discoideum

Molecular and Cellular Biology ◽

10.1128/mcb.8.1.10-16.1988 ◽

1988 ◽

Vol 8 (1) ◽

pp. 10-16

Author(s):

C K Singleton ◽

S S Manning ◽

Y Feng

Keyword(s):

Gene Expression ◽

Protein Synthesis ◽

Dictyostelium Discoideum ◽

Cdna Libraries ◽

Mrna Levels ◽

Protein Synthesis Inhibition ◽

Mutant Strains ◽

V Genes ◽

Steady State Levels ◽

Development Proceeds

Several genes which are deactivated on the initiation of development of Dictyostelium discoideum were identified by differential screening of various cDNA libraries. These genes have in common a decrease in the steady-state levels of their corresponding mRNAs on the onset of development and as development proceeds. When development was carried out in the absence of protein synthesis by inhibition with cycloheximide, the decrease in mRNA levels for most genes (V genes) was normal or slightly accelerated. For about 5% of the genes (H genes), however, cycloheximide caused an apparent induction of expression, as revealed by a slight or dramatic increase in mRNA levels, instead of the normal decrease. This effect was due to inhibition of protein synthesis and not to cycloheximide per se. The induction was found to be due to an enhancement of the transcription rate; normal rates of transcription for the H genes were dependent on continued protein synthesis during vegetative growth and development. Thus, two general regulatory classes exist for deactivation of gene expression on initiation of development, one of which is dependent on and one of which is independent of protein synthesis. Analysis of expression of these genes in mutant strains which are aggregation deficient allowed the classes to be subdivided further. Taken together, these characterizations allow several distinct regulatory mechanisms to be identified that are involved in the deactivation of gene expression on the onset of development in D. discoideum.

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