T-DNA Express|AtTome: Data Sources, Details and Summary ( Aug. 2, 2016 )

1. Data Sources :
    

a. Genome : AGI sequenced and assemblied pseudo-molecules, and Arabidopsis Information Portal annotated v 11 (final. Jun, 2016).

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!

    Josť 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]

  • 1.1 Salk T-DNA lines, HM & FST by Next Generation Sequencing.
  • 1.2 Salk, SAIL, GABI and Wisc T-DNA Seq Targets (Next Generation Sequencing).
  • 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. Saskatoon SK Lines.
  • 11. 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 :

2. Data Details :
Salk T-DNA Columbia137,259 lines 166,127 mapped 10/28/2009
Salk T-DNA Homozygous 38,333 lines 41,905 mapped 04/10/2012
Salk T-DNA HM by
Next Generation Seq
5,022 lines 5,022 mapped 03/31/2016
Salk T-DNASeq Targets   89,879 peaks 01/16/2013
SAIL FST   62,041 mapped 10/28/2009
SAIL T-DNA Homozygous 5,124 lines 5,409 mapped 04/10/2012
Sail T-DNA HM by
Next Generation Seq
1,244 lines 1,244 mapped 03/31/2016
Wisc FST 32,607 (22,089) 21,406 mapped 09/30/2009
Wisc HM by Salk
& by NG Seq
2,724 lines 2,724 mapped 03/31/2016
NextG Seqs for SALK,
SAIL, GABI and Wisc lines
by Salk group
161,298 12/18/2014
FLAGdb FST Wassilevskija 41,369 37,142 mapped 06/23/2009
GABI-Kat FST Columbia 130,654 98,559 mapped (70,578 lines) 06/29/2011
GABI-Kat Confirmed 7,656 lines 11,030 mapped 04/12/2010
GABI-Kat HM by Salk
& by NG Seq
1,250 lines 1,536 mapped 03/31/2016
RIKEN FST N^ssen   18,622 mapped 06/23/2009
JIC SM FST Landsberg 22,664 w seeds 24,206 mapped 10/28/2009
CSHL FST 24,444
(17,689 lines)
23,998 mapped 10/25/2010
IMA FST 488 lines 808 mapped 10/28/2009
Saskatoon FST Col-415,507 lines 14,941 mapped 08/17/2009
Other FST     175 mapped 06/23/2009
Total     455,145 mapped 04/06/2012

Invitrogen/Salk Gateway Clone12,042 (11,985) 06/23/2009
Salk, Stanford, PGEC (SSP) full-length cDNAs 11,732 (11,704) 06/23/2009, completed
SSP gold standard ORF clones 10,592 (10,536) 06/23/2009, completed
Salk (2010 Project) full-length cDNAs 1,278 (1,272) 06/23/2009
Salk (2010 Project) gold standard ORF clones 4,019 (3,988) 06/23/2009
RIKEN full-length cDNAs 11,497 (11,376) 07/07/2009
TIGR hypothetical genes (DNAs/cDNAs)1,054 (1,041)06/23/2009
TIGR ORFs3,095 (3,040)06/23/2009
Arabidopsis research community cDNAs (mRNA)11,553 (11,537) 08/16/2013
Arabidopsis research community Genes (DNA)1,079 (1,079)06/23/2009
Peking Yale Transcription factor reads2,057 (1,282 clones)06/23/2009
GSLT cDNA single reads 28,85906/23/2009
Orphan Transcripts63106/23/2009
ESTs on the Transcriptome1,449,016 (1,527,298)06/23/2009
Affymetrix GeneChip (GPL198) Probe Sets: 2281006/23/2009
Expts Series: 227
Expts Samples: 2987
MPSS mRNA Targets Transcriptome 80,481 (94,260) 06/25/2009
MPSS sRNA Contigs Transcriptome 148,449 06/25/2009
ASRP sRNA Transcriptome 117,14206/25/2009
JAtY TAC Transcriptome 8,29606/25/2009

3. Download Data : http://signal.salk.edu/database/.

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