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BDGP
EST Submitted Collections
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CK
EST Project |
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Project
to screen for novel secreted and transmembrane proteins during development.
1,600 ESTs Completed 1997. |
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Non-BDGP
Fly EST Projects |
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7297 ESTs
from the Brian Oliver laboratory at the National Institute of Diabetes
and Digestive and Kidney Diseases. |
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| 2001
EST Project |
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We have finished another EST project at the Drosophila Sequencing
Center at Lawrence Berkeley National Laboratory. Our primary goal
was to expand the Drosophila
Gene Collection by sequencing an additional 160,000 ESTs. The
ESTs for this project were generated from existing as well as newly
constructed cDNA libraries.
We sequenced cDNA clones from the old GM
and SD libraries,
as well a new AT
Drosophila testes library, which is in the new plasmid vector
pOTB7.
Clones from new normalized embryonic (RE)
and head (RH)
Drosophila cDNA libraries made at Riken
have also been sequenced.
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| 1999
EST Project |
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Our first EST project was motivated by the short-term goal of producing
at least 80,000 Drosophila ESTs from several different cDNA libraries.
We completed our goal ahead of schedule in March, 1999
These ESTs were then clustered by sequence similarity in order
to choose the best cDNA clones for the Drosophila
Gene Collection.
All BDGP ESTs are available at dbEST
All of the cDNA clones that are submitted to dbEST are available
from Research
Genetics.
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| CK
EST Project |
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The goal of the CK library EST project aimed to characterize secreted
and transmembrane proteins involved in intercellular communication
during development. The project was conducted both at the BDGP and
in the laboratory of Corey Goodman at U.C. Berkeley.
The CK library - named for its primary author Casey Kopczynski
- consists of clones made from rough endoplasmic reticulum-bound
mRNA, and is therefore enriched in clones encoding membrane and
secreted proteins. To increase the representation of rare cDNAs
in the library, the library was normalized using a novel
method based on cDNA hybridization to genomic DNA-coated beads.
cDNAs were chosen for sequencing using a specialized screen
that involves whole
embryo in situ hybridization. A total of 2518 individual cDNAs
from the normalized library were screened by in situ hybridization,
and 917 of these cDNAs represent genes differentially expressed
during embryonic development.
Sequence analysis of 1001 cDNAs revealed that 811 represent
genes not previously described in Drosophila. Expression pattern
photographs and partial DNA sequences have been assembled in a
database and are publicly available from this web site. A total
of 1691 CK ESTs have been submitted to dbEST.
The work of Kopczynski et al. is reported in PNAS 95(17):9973-8.
You can read it [HERE].
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| Notice:
Chimeric cDNA Clones |
Cautionary note on the presence of chimeric clones in some libraries.
During synthesis of the cDNA libraries the linkers used to clone
the double-stranded cDNA into the pOT2 vector are cleaved with restriction
enzymes. It appears that this reaction did not go to completion
during synthesis of the GH and LP libraries. The result is that
blunt end ligations between 2 different cDNAs can occur. We estimate
that about one-quarter of the clones in the LP and GH libraries
contain cDNAs derived from two distinct transcripts ligated together
into a single pOT2 plasmid. In contrast, such chimeric cDNA are
much less frequent in other libraries.
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