Characterization of an Atlantic cod (Gadus morhua) embryonic stem cell cDNA library
Abstract Background The Atlantic cod is an ecologically and economically important North Atlantic fish species and also an emerging aquaculture species. To study gene expression in Atlantic cod embryonic stem (ES) cells, our goal was to generate and analyze expressed sequence tags (ESTs) from an ES...
Main Authors: | , |
---|---|
Format: | Other/Unknown Material |
Language: | English |
Published: |
BioMed Central Ltd.
2009
|
Subjects: | |
Online Access: | http://www.biomedcentral.com/1756-0500/2/74 |
id |
ftbiomed:oai:biomedcentral.com:1756-0500-2-74 |
---|---|
record_format |
openpolar |
spelling |
ftbiomed:oai:biomedcentral.com:1756-0500-2-74 2023-05-15T15:26:46+02:00 Characterization of an Atlantic cod (Gadus morhua) embryonic stem cell cDNA library Olsvik, Pål A Holen, Elisabeth 2009-05-06 http://www.biomedcentral.com/1756-0500/2/74 en eng BioMed Central Ltd. http://www.biomedcentral.com/1756-0500/2/74 Copyright 2009 Olsvik et al; licensee BioMed Central Ltd. Short Report 2009 ftbiomed 2009-06-27T01:35:25Z Abstract Background The Atlantic cod is an ecologically and economically important North Atlantic fish species and also an emerging aquaculture species. To study gene expression in Atlantic cod embryonic stem (ES) cells, our goal was to generate and analyze expressed sequence tags (ESTs) from an ES cell cDNA library of mRNA consisting of approximately 3,900 ESTs. Results We sequenced 3,935 EST clones using a directional cDNA library made from pooled ES cells harvested at the blastula stage. Quality filtering of these ESTs allowed identification of 2,719 high-quality sequences with an average length of 442 bp containing 368 contigs and 1,276 singletons (1,644 unique sequences). BLASTX searches produced 889 significant (E-value < 10 -3 ) hits, of which 698 (42.5%) were annotated with Gene Ontology terms (E-value < 10 -6 ). The number of unknown unique sequences was 946 (57.5%). All the high-quality EST sequences have been deposited in GenBank (GenBank: 2,719 sequences in UniGene library dbEST id: 22,021). Gene discovery and annotations are presented and discussed. Conclusion This set of ESTs represents one of the first attempts to describe mRNA in ES cells from a marine cold-water fish species, and provides a basis for gene expression studies of Atlantic cod ES cells. Other/Unknown Material atlantic cod Gadus morhua North Atlantic BioMed Central |
institution |
Open Polar |
collection |
BioMed Central |
op_collection_id |
ftbiomed |
language |
English |
description |
Abstract Background The Atlantic cod is an ecologically and economically important North Atlantic fish species and also an emerging aquaculture species. To study gene expression in Atlantic cod embryonic stem (ES) cells, our goal was to generate and analyze expressed sequence tags (ESTs) from an ES cell cDNA library of mRNA consisting of approximately 3,900 ESTs. Results We sequenced 3,935 EST clones using a directional cDNA library made from pooled ES cells harvested at the blastula stage. Quality filtering of these ESTs allowed identification of 2,719 high-quality sequences with an average length of 442 bp containing 368 contigs and 1,276 singletons (1,644 unique sequences). BLASTX searches produced 889 significant (E-value < 10 -3 ) hits, of which 698 (42.5%) were annotated with Gene Ontology terms (E-value < 10 -6 ). The number of unknown unique sequences was 946 (57.5%). All the high-quality EST sequences have been deposited in GenBank (GenBank: 2,719 sequences in UniGene library dbEST id: 22,021). Gene discovery and annotations are presented and discussed. Conclusion This set of ESTs represents one of the first attempts to describe mRNA in ES cells from a marine cold-water fish species, and provides a basis for gene expression studies of Atlantic cod ES cells. |
format |
Other/Unknown Material |
author |
Olsvik, Pål A Holen, Elisabeth |
spellingShingle |
Olsvik, Pål A Holen, Elisabeth Characterization of an Atlantic cod (Gadus morhua) embryonic stem cell cDNA library |
author_facet |
Olsvik, Pål A Holen, Elisabeth |
author_sort |
Olsvik, Pål A |
title |
Characterization of an Atlantic cod (Gadus morhua) embryonic stem cell cDNA library |
title_short |
Characterization of an Atlantic cod (Gadus morhua) embryonic stem cell cDNA library |
title_full |
Characterization of an Atlantic cod (Gadus morhua) embryonic stem cell cDNA library |
title_fullStr |
Characterization of an Atlantic cod (Gadus morhua) embryonic stem cell cDNA library |
title_full_unstemmed |
Characterization of an Atlantic cod (Gadus morhua) embryonic stem cell cDNA library |
title_sort |
characterization of an atlantic cod (gadus morhua) embryonic stem cell cdna library |
publisher |
BioMed Central Ltd. |
publishDate |
2009 |
url |
http://www.biomedcentral.com/1756-0500/2/74 |
genre |
atlantic cod Gadus morhua North Atlantic |
genre_facet |
atlantic cod Gadus morhua North Atlantic |
op_relation |
http://www.biomedcentral.com/1756-0500/2/74 |
op_rights |
Copyright 2009 Olsvik et al; licensee BioMed Central Ltd. |
_version_ |
1766357244481372160 |