Details about Libraries
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|sHA|sHB|sMA|sMY|sMC|sML|sZO|sZS|sZG|iMY|gHA|gHB|

 

Vector, adaptor information
Library : sHA,sHB,sMA,sMY,sZO,sZS,gHA,gHB iMY,sMC,sML,sZG
Vector pBK-CMV(Stratagene) pCMV*SPORT6.1 (Invitrogen)
5'_cloning_site_name EcoRI [3' and 5' can be the same] SalI
5'_cloning_site_seq G/AATTC G/TCGAC
3'_cloning_site_name XhoI NotI
3'_cloning_site_seq C/TCGAG GC/GGCCGC
5'_cloning_adapter AATTCGGCACGAGG TCGACCCACGCGTCCG
3'_cloning_adapter CTCGA GGGCGGCC

 

Information on the Libraries
Library sHA
Project Start Date 01/01/1998
Library type cDNA
Target species Soybean
Cell line P6497
Possible contaminations Vector and Soybean
Treatments 48 hrs post infection
Project Description 48 hr post-infection. Harsosoy cultivar hypocotyl
Publication
Qutob, D., Hraber, P., Sobral, B. and Gijzen, M. (2000) Comparative Analysis of Expressed Sequences in Phytophthora Sojae. Plant Phys., 123, 243-253
Library sHB
Project Start Date 10/01/2000
Library type cDNA
Target species Soybean
Cell line P6497
Possible contaminations Vector and Soybean
Treatments 48 hrs post infection: Same as sHA, but sequenced at a different sequencing center
Project Description 48 hr post-infection. Harsosoy cultivar hypocotyl. sequenced at:
Publication Qutob, D., Hraber, P., Sobral, B. and Gijzen, M. (2000) Comparative Analysis of Expressed Sequences in Phytophthora Sojae. Plant Phys., 123, 243-253
Library sMA
Project Start Date 10/01/2000
Library type cDNA
Target species -
Cell line P6497
Possible contaminations Vector and Soybean
Treatments Mycelia grown in defined media
Project Description Mycelia tissue taken for sequencing. Sequencing done at USDA-IFAFS
Publication -
Library sMY
Project Start Date 01/01/1998
Library type cDNA
Target species -
Cell line P6497
Possible contaminations Vector
Treatments Mycelia grown in defined media
Project Description Same as library sMA, but sequenced at a different sequencing center
Publication Qutob, D., Hraber, P., Sobral, B. and Gijzen, M. (2000) "Comparative Analysis of Expressed Sequences in Phytophthora Sojae." Plant Phys. 123, 243-253.
Library sMC
Project Start Date 10/01/2000
Library type cDNA
Target species -
Cell line P6497
Possible contaminations Vector
Treatments Mycelium grown in complex medium
Project Description Mycelium grown in complex medium.  RNA in equal amounts from mycelia grown in V8 broth, lima bean broth or soybean broth. sequenced at USDA-IFAFS:
Publication -
Library sML
Project Start Date 10/01/2000
Library type cDNA
Target species -
Cell line P6497
Possible contaminations vector
Treatments Mycelium grown in nutrient limited medium
Project Description Mycelium grown in nutrient limited medium.  RNA in equal amounts from mycelium grown first in V8 broth then transferred to water, 1/5 soybean both or 1/10 V8 broth.sequenced at USDA-IFAFS:
Publication -
Library sZO
Project Start Date 01/01/1998
Library type cDNA
Target species -
Cell line P6497
Possible contaminations vector
Treatments swimming zoospore
Project Description ZO and ZS. Same library. Different sequencing center. Swimming zoospores
Publication -
Library sZS
Project Start Date 10/01/2000
Library type cDNA
Target species -
Cell line P6497
Possible contaminations vector
Treatments swimming zoospore
Project Description ZO and ZS. Same library. Different sequencing center. Swimming zoospores
Publication -
Library sZG
Project Start Date 10/01/2000
Library type cDNA
Target species -
Cell line P6497
Possible contaminations vector
Treatments germinating zoospore
Project Description Germinated Zoospores. RNA in equal amounts from zoospores germinated for 3 hours in V8 broth or soybean seed exudate.
Publication -
Library iMY
Project Start Date 01/01/1997
Library type cDNA
Target species -
Cell line -
Possible contaminations vector
Treatments -
Project Description -
Publication -
Library gHA
Project Start Date 01/16/2003
Library type cDNA
Target species -
Cell line -
Possible contaminations Phytophthora sojae, vector
Treatments -
Project Description This is a virtual project, where the sHA libraries were filtered of the soybean sequences using a set of strategies. Some of them are: primary separation on the basis of strong blast hits to Soybean ESTs. Then the sequences were screened with TA/CG dinucleotide frequency, followed by codon usage screening. The doubtful sequences were separated by perfect matches to the Phytophthora genome sequences and final manual inspection.
Publication Not yet published
Library gHB
Project Start Date 01/16/2003
Library type cDNA
Target species -
Cell line -
Possible contaminations Phytophthora sojae
Treatments -
Project Description This is a virtual project, where the sHB libraries were filtered of the soybean sequences using a set of strategies. Some of them are: primary separation on the basis of strong blast hits to Soybean ESTs. Then the sequences were screened with TA/CG dinucleotide frequency, followed by codon usage screening. The doubtful sequences were separated by perfect matches to the Phytophthora genome sequences and final manual inspection. This library contains some sequences from the sMA library.
Publication Not yet published
Library Public P.infestans Sequences
Project Start Date -
Library type -
Target species -
Cell line -
Possible contaminations -
Treatments -
Project Description -
Publication -

 

 

Nomeclature of Libraries:

The library names are typically of 12 characters in length.
They can be split into 6 different fields
e.g; p|sZS|001|x|A01|f 

1. First part  'p'   stands for Phytophthora
2. Second part 'sZS' stands for library
3. Third part  '001' stands for row positions
4. Fourth part 'x'   stands for the lab code
5. fifth part  'A01' stands for column position
6. sixth part  'f'   stands for forward or reverse primer

The Clone ids are 9 characters in length
e.g; sZS001A01 These are devoid of the first part, the fourth part 
and the sixth part.

 

 

 





Oomycetes Soybean EST Database Version 3.0
For questions and comments email: sutripa@vbi.vt.edu