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a. Genome :
AGI sequenced and assemblied pseudo-molecules, and TAIR updated and annotated v 8 (Apr-28-2008)  . By comparison with Version 7, the version 8 masks 37,624 bps of vector sequences and makes 1,412 single point changes.
Below is a summary of confirmation of these changes by the third party high quality SSP, Salk, TIGR, RIKEN and Community full-length/ORF sequences.
|
changes
|
3rd Party
|
Support
|
Not support
|
Either
|
Total
|
1,412
|
178
|
104
|
66
|
8
|
chr1
|
267
|
18
|
13
|
5
|
0
|
chr2
|
156
|
19
|
8
|
10
|
1
|
chr3
|
237
|
30
|
17
|
10
|
3
|
chr4
|
544
|
93
|
59
|
32
|
2
|
chr5
|
208
|
18
|
7
|
9
|
2
|
b. T-DNA/Ds FSTs :
- 1. Salk T-DNA lines. [About Salk T-DNA] [FAQs]
We requested that users include this reference in publications describing the use of Salk lines obtained from ABRC or NASC. Thanks!
José M. Alonso, Anna N. Stepanova, Thomas J. Leisse, Christopher J. Kim, Huaming
Chen, Paul Shinn, Denise K. Stevenson, Justin Zimmerman, Pascual Barajas, Rosa
Cheuk, Carmelita Gadrinab, Collen Heller, Albert Jeske, Eric Koesema, Cristina C.
Meyers, Holly Parker, Lance Prednis, Yasser Ansari, Nathan Choy, Hashim Deen,
Michael Geralt, Nisha Hazari, Emily Hom, Meagan Karnes, Celene Mulholland, Ral
Ndubaku, Ian Schmidt, Plinio Guzman, Laura Aguilar-Henonin, Markus Schmid, Detlef
Weigel, David E. Carter, Trudy Marchand, Eddy Risseeuw, Debra Brogden, Albana Zeko,
William L. Crosby, Charles C. Berry, and Joseph R. Ecker (2003)
Genome-Wide Insertional Mutagenesis of Arabidopsis thaliana
Science 301: 653-657.
[Abstract]
[Full Text]
- 2. SAIL T-DNA lines. [About the SAIL lines] [Order from ABRC].
- 3. GABI-Kat lines.
- 4. FLAGdb/FST.
- 5. Wisconsin T-DNA lines.
- 6. CSHL genetrap lines.
- 7. RIKEN T-DNA & Ds lines. [Order from RIKEN BRC]
- 8. JIC SM lines. [About the SM lines] [NASC]
- 9. IMA Ds lines.
- 10. other FSTs from NCBI.
c. cDNAs :
- 1. SSP (Salk, Stanford and PGEC) Consortium.
We requested that users include this reference (below) in publications describing the use
of SSP gold standard cDNA ORF clones obtained from ABRC. Thanks!
Kayoko Yamada, Jun Lim, Joseph M. Dale, Huaming Chen, Paul Shinn, Curtis J. Palm, Audrey M.
Southwick, Hank C. Wu, Christopher Kim, Michelle Nguyen, Paul Pham, Rosa Cheuk, George
Karlin-Newmann, Shirley X. Liu, Bao Lam, Hitomi Sakano, Troy Wu, Guixia Yu, Molly Miranda,
Hong L. Quach, Matthew Tripp, Charlie H. Chang, Jeong M. Lee, Mitsue Toriumi, Marie M. H.
Chan, Carolyn C. Tang, Courtney S. Onodera, Justine M. Deng, Kenji Akiyama, Yasser Ansari,
Takahiro Arakawa, Jenny Banh, Fumika Banno, Leah Bowser, Shelise Brooks, Piero Carninci,
Qimin Chao, Nathan Choy, Akiko Enju, Andrew D. Goldsmith, Mani Gurjal, Nancy F. Hansen,
Yoshihide Hayashizaki, Chanda Johnson-Hopson, Vickie W. Hsuan, Kei Iida, Meagan Karnes,
Shehnaz Khan, Eric Koesema, Junko Ishida, Paul X. Jiang, Ted Jones, Jun Kawai, Asako Kamiya,
Cristina Meyers, Maiko Nakajima, Mari Narusaka, Motoaki Seki, Tetsuya Sakurai, Masakazu
Satou, Racquel Tamse, Maria Vaysberg, Erika K. Wallender, Cecilia Wong, Yuki Yamamura,
Shiaulou Yuan, Kazuo Shinozaki, Ronald W. Davis, Athanasios Theologis, and Joseph R. Ecker
(2003) Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome Science 302: 842-846.
[ Abstract ]
[ Full Text ]
[ Supporting data ]
[ Supplementary GEO Analysis Files ]
- 2. Salk (2010 Project).
- 3. Invitrogen/Salk Gateway Clone. [pENTR223 Seq] [pENTR223 Map]and SSP Gateway Clones [pENTR_TOPO].
- 4. About TIGR Hypo ORFs.
- 5. RIKEN full-length cDNAs.
- 6. community cDNA/DNA from NCBI.
- 7. RIKEN RAFL clone end sequences.
- 8. Arabidopsis ESTs from NCBI.
- 9. About GSLT cDNA.
- 10. Peking/Yale TF clones.
- 11. Orphan Transcripts.
d. Gene Expression Atlas :
- 1. Salk Tome : L+: Light-grown seedlings AN: Anthers FL: Flowers-mixed stages RT: Roots SC: Suspension cell culture
- 2. NASA Tome: GSM41324-GSM41336 from GEO, NCBI.
- 3. Gene expression data from GEO, NCBI.
e. Others :
|
|
| Salk T-DNA | Columbia | | 151,534 mapped | 07/09/2007 |
| Salk T-DNA Homozygous | 19,851 lines | 22,260 mapped | 05/01/2008 |
Other T-DNA Homozygous
(SAIL)
(Wisc)
| 25 lines | 27mapped | 03/12/2007 |
| SAIL FST | | 57,242 mapped | 03/12/2007 |
| Wisc FST | | 10,470 mapped | 07/09/2007 |
| FLAGdb FST | Wassilevskija | 36,287 | 31,744 mapped | 07/09/2007 |
| GABI-Kat FST | Columbia | 110,197 | 63,887 mapped | 07/09/2007 |
| GABI-Kat Confirmed | | 5,446 mapped | 10/08/2007 |
| JIC SM FST | Landsberg | 22,664 w seeds | 23,573 mapped | 07/09/2007 |
| RIKEN FST | N^ssen | | 18,566 mapped | 07/09/2007 |
| CSHL FST | Columbia | 22,084
(16,018 lines) | 21,661 mapped | 07/09/2007 |
| IMA FST | Landsberg | 488 lines | 822 mapped | 07/09/2007 |
| Other FST | | | 175 mapped | 07/09/2007 |
| Total | | | 379,674 mapped | 07/09/2007 |
| Invitrogen/Salk Gateway Clone | 12,143 (12,090) | 02/08/2008 |
| Salk, Stanford, PGEC (SSP) full-length cDNAs | 11,727 (11,704) | 03/12/2007, completed |
| SSP gold standard ORF clones | 10,586 (10,537) | 03/12/2007, completed |
| Salk (2010 Project) full-length cDNAs | 1,280 (1,272) | 03/12/2007 |
| Salk (2010 Project) gold standard ORF clones | 3,774 (3,749) | 04/15/2008 |
| RIKEN full-length cDNAs | 9,934 (9,864) | 03/12/2007 |
| TIGR hypothetical genes (DNAs/cDNAs) | 1,055 (1,041) | 04/04/2008 |
| TIGR ORFs | 3,070 (3,041) | 04/04/2008 |
| Arabidopsis research community cDNAs (mRNA) | 11,176 (11,0386 | 05/07/2008 |
| Arabidopsis research community Genes (DNA) | 1,080 (1,080) | 03/12/2007 |
| Peking Yale Transcription factor reads | 2,057 (1,282 clones) | 03/12/2007 |
| RIKEN cDNA end sequences | 19,606 | 03/12/2007 |
| GSLT cDNA single reads | 28,816 | 03/12/2007 |
| Orphan Transcripts | 591 | 03/12/2007 |
| ESTs on the Transcriptome | 713,598 (730,932) | 03/12/2007 |
| Affymetrix GeneChip (GPL198) | Probe Sets: 22810 | 08/30/2007 |
| Expts Series: 227 |
| Expts Samples: 2987 |
| MPSS mRNA Targets Transcriptome | 80,486 (94,265) | 03/12/2007 |
| MPSS sRNA Contigs Transcriptome | 148,456 | 03/12/2007 |
| ASRP sRNA Transcriptome | 262,742 | 03/12/2007 |
| JAtY TAC Transcriptome | 9,314 | 03/12/2007 |
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