An encyclopedia of mouse genes

Marra, Marco A.; Hillier, La Deana W.; Kucaba, Tamara A.; Allen, Melissa; Barstead, Robert; Beck, Catherine D.; Blistain, Angela; Bonaldo, Maria F.; Bowers, Yvette; Bowles, Louise; Cardenas, Marco; Chamberlain, Ann; Chappell, Julie A.; Clifton, Sandra W.; Favello, Anthony; Geisel, Steve; Gibbons, Marilyn; Harvey, Njata; Hill, Francesca; Jackson, Yo; Kohn, Sophie; Lennon, Greg; Mardis, Elaine R.; Martin, John; Mila, Lee Anne; McCann, Rhonda; Morales, Richard; Pape, Deana; Person, Barry; Prange, Christa; Ritter, Erika; Soares, Marcelo B.; Schurk, Rebecca; Shin, Tanya; Steptoe, Michele; Swaller, Timothy; Theising, Brenda; Underwood, Keith D.; Wylie, Todd; Yount, Tamara; Wilson, Richard K.; Waterston, Robert H.

doi:10.1038/5976

Cited by 107 publications

(55 citation statements)

References 29 publications

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“…This is in accordance with the results obtained in the mouse EST project (Marra et al, 1999). This collection of 237,954 ESTs provides us with a preliminary view into the gene expression profile of sugarcane.…”

Section: Quality Controlsupporting

confidence: 89%

The libraries that made SUCEST

et al. 2001

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A large-scale sequencing of sugarcane expressed sequence tags (ESTs) was carried out as a first step in depicting the genome of this important tropical crop. Twenty-six unidirectional cDNA libraries were constructed from a variety of tissues sampled from thirteen different sugarcane cultivars. A total of 291,689 cDNA clones were sequenced in their 5' and 3'end regions. After trimming low-quality sequences and removing vector and ribosomal RNA sequences, 237,954 ESTs potentially derived from protein-encoding messenger RNA (mRNA) remained. The average insert size in all libraries was estimated to be 1,250bp with the insert length varying from 500 to 5,000 bp. Clustering the 237,954 sugarcane ESTs resulted in 43,141clusters, from which 38% had no matches with existing sequences in the public databases. Around 53% of the clusters were formed by ESTs expressed in at least two libraries while 47% of the clusters are formed by ESTs expressed in only one library. A global analysis of the ESTs indicated that around 33% contain cDNA clones with full-length insert.

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Section: Quality Controlsupporting

confidence: 89%

The libraries that made SUCEST

et al. 2001

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“…The limitations of a priori genome annotation dictate that the transcriptome needs to be identified experimentally via cDNA cloning and sequencing. Although expressed sequence tags (ESTs) (Adams et al 1991(Adams et al , 1995Hillier et al 1996;Marra et al 1999;Kargul et al 2001) and ORESTES (Camargo et al 2001) have been extremely valuable for new gene discovery, these approaches have not allowed highthroughput recovering of full-length cDNA clones nor definition of protein sequence derived from actual cDNA clones. To overcome such problems, we undertook from the year 1995, a strategic project aimed at the comprehensive collection of at least one full-length cDNA derived from each mouse gene, a strategy that is recently becoming useful in similar projects to collect full-length gene collections (Stapleton et al 2002;Strausberg et al 2002).…”

mentioning

confidence: 99%

Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia

Carninci¹,

Waki²,

Shiraki³

et al. 2003

Genome Res.

156

132

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We report the construction of the mouse full-length cDNA encyclopedia, the most extensive view of a complex transcriptome, on the basis of preparing and sequencing 246 libraries. Before cloning, cDNAs were enriched in full-length by Cap-Trapper, and in most cases, aggressively subtracted/normalized. We have produced 1,442,236 successful 3Ј-end sequences clustered into 171,144 groups, from which 60,770 clones were fully sequenced cDNAs Cold Spring Harbor Laboratory Press on May 10, 2018 -Published by genome.cshlp.org Downloaded from annotated in the FANTOM-2 annotation. We have also produced 547,149 5Ј end reads, which clustered into 124,258 groups. Altogether, these cDNAs were further grouped in 70,000 transcriptional units (TU), which represent the best coverage of a transcriptome so far. By monitoring the extent of normalization/subtraction, we define the tentative equivalent coverage (TEC), which was estimated to be equivalent to >12,000,000 ESTs derived from standard libraries. High coverage explains discrepancies between the very large numbers of clusters (and TUs) of this project, which also include non-protein-coding RNAs, and the lower gene number estimation of genome annotations. Altogether, 5Ј-end clusters identify regions that are potential promoters for 8637 known genes and 5Ј-end clusters suggest the presence of almost 63,000 transcriptional starting points. An estimate of the frequency of polyadenylation signals suggests that at least half of the singletons in the EST set represent real mRNAs. Clones accounting for about half of the predicted TUs await further sequencing. The continued high-discovery rate suggests that the task of transcriptome discovery is not yet complete.[Supplemental material available online at www.genome.org.]One of the primary goals of genome sequencing projects is to identify the genome sequences that are transcribed into functional mRNAs, so that full-length cDNAs can be isolated to allow further downstream biology, and functional and structural genomics. The limitations of a priori genome annotation dictate that the transcriptome needs to be identified experimentally via cDNA cloning and sequencing. Although expressed sequence tags (ESTs) (Adams et al. 1991(Adams et al. , 1995Hillier et al. 1996;Marra et al. 1999;Kargul et al. 2001) and ORESTES (Camargo et al. 2001) have been extremely valuable for new gene discovery, these approaches have not allowed highthroughput recovering of full-length cDNA clones nor definition of protein sequence derived from actual cDNA clones. To overcome such problems, we undertook from the year 1995, a strategic project aimed at the comprehensive collection of at least one full-length cDNA derived from each mouse gene, a strategy that is recently becoming useful in similar projects to collect full-length gene collections (Stapleton et al. 2002;Strausberg et al. 2002).Because of the limited processivity of reverse transcriptase and other limitations, standard cDNA libraries generally contain a majority of truncated transcripts. The introductio...

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“…] The generation of expressed sequence tags (ESTs) provides a rapid means of gene discovery from single-pass sequencing of randomly selected cDNAs. This approach has been particularly useful for complex, model genomes including human (Hillier et al 1996), rat (Scheetz et al 2001), mouse (Marra et al 1999b), fish (Clark et al 2001), and rice (Ewing et al 1999). One of the primary advantages of ESTs is that the identification of putative genes by BLAST comparisons (Altschul et al 1990) enables researchers to begin biological analyses prior to the completion, or even initiation, of a full genome sequence.…”

mentioning

confidence: 99%

Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database

Li¹,

Brunk²,

Kissinger³

et al. 2003

Genome Res.

Self Cite

133

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Large-scale EST sequencing projects for several important parasites within the phylum Apicomplexa were undertaken for the purpose of gene discovery. Included were several parasites of medical importance (Plasmodium falciparum, Toxoplasma gondii) and others of veterinary importance (Eimeria tenella, Sarcocystis neurona, and Neospora caninum). A total of 55,192 ESTs, deposited into dbEST/GenBank, were included in the analyses. The resulting sequences have been clustered into nonredundant gene assemblies and deposited into a relational database that supports a variety of sequence and text searches. This database has been used to compare the gene assemblies using BLAST similarity comparisons to the public protein databases to identify putative genes. Of these new entries, ∼15%-20% represent putative homologs with a conservative cutoff of p < 10 −9 , thus identifying many conserved genes that are likely to share common functions with other well-studied organisms. Gene assemblies were also used to identify strain polymorphisms, examine stage-specific expression, and identify gene families. An interesting class of genes that are confined to members of this phylum and not shared by plants, animals, or fungi, was identified. These genes likely mediate the novel biological features of members of the Apicomplexa and hence offer great potential for biological investigation and as possible therapeutic targets.

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An encyclopedia of mouse genes

Cited by 107 publications

References 29 publications

The libraries that made SUCEST

The libraries that made SUCEST

Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia

Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database

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