XENLA Genome

From Marcotte Lab
Revision as of 10:30, 8 May 2014 by TaejoonKwon (Talk | contribs)

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search

Contents

Genome browser

Genome version

In here, 'N50' is calculated based on the combination of 'Scaffolds' and 'Contigs', so it may be slightly different to official report of 'Scaffolds N50'.

Sequences 'in public' are available at ftp://ftp.xenbase.org/pub/Genomics/JGI/

Name Release Date Concat. Length (bp) N50 (bp) Scaffolds > 10kbp Remarks
JGIv1 2010 Dec. 2.30 Gbp 8 kbp 385,933 Internal Use Only.
JGIv5 2011 Oct. 2.84 Gbp 0.28 Mbp 16,625 Released in Xenopus PI Meeting.
JGIv6 2012 Jul. 2.75 Gbp 0.70 Mbp 8,426 Officially released in XenBase.
JGIv6a 2012 Jul. 2.75 Gbp 0.70 Mbp 8,426 Officially released in XenBase;
Minor update of JGIv6.
NIGv1 2012 Nov. 2.88 Gbp 0.34 Mbp 14,260 Original name is 'xl.v1soap';
Internal Use Only.
NIGv1ap 2012 Nov. 3.27 Gbp 0.17 Mbp 39,283 Original name is 'xl.v3ap'(AllPath?);
Internal Use Only.
NIGv1m 2012 Nov. 2.84 Gbp 0.28 Mbp 82,132 Original name is 'xl.v5m';
Internal Use Only.
NIGv2 2013 Feb. 2.89 Gbp 0.72 Mbp 5,394 Original name is 'xl.v2soap';
Internal Use Only.
NIGv2c 2013 Feb. 2.88 Gbp 0.71 Mbp 5,377 Original name is 'xl.v2soap,GapClosed';
Can browse at NIG gbrowser.
JGIv7a 2013 Mar. 2.72 Gbp 1.15 Mbp 5,714 JGI7;Released in public.
JGIv7b 2013 May 2.78 Gbp 3.49 Mbp 2,598 JGI7.1;Released in public. Minor updates of 7.0.

J-strain Genomic Data Summary

Whole genome shotgun sequencing, JGI/UC Berkeley, USA

J strain

  • JBL_009 Illumina paired-end (225 bp insertion), 2x150: 320 M reads, 48 G bases
  • JBL_010 Illumina paired-end (450 bp insertion), 2x150: 264 M reads, 40 G bases
  • JBL_011 Illumina paired-end (900 bp insertion), 2x150: 424 M reads, 64 G bases
  • JBL_012 Illumina mate-pair (1,500 bp insertion), 2x100: 320 M reads, 32 G bases
  • JBL_013 Illumina mate-pair (4,000 bp insertion), 2x100: 328 M reads, 33 G bases

F strain

  • JBL_005 Illumina paired-end, 2x100: 416 M reads, 42 G bases
  • JBL_005b Illumina paired-end, 2x150: 464 M reads, 70 G bases

F/J hybrid

  • JBL_007 Illumina paired-end, 2x150: 344 M reads, 52 G bases

Whole genome shotgun sequencing, NIG/U Tokyo, Japan

J strain

  • Illumina paired-end (207 bp insertion): 1,004 M reads, 105 G bases
  • Illumina paired-end (425 bp insertion): 672 M reads, 78 G bases
  • Illumina paired-end (900 bp insertion): 695 M reads, 60 G bases
  • Illumina mate-pair (1,387 bp insertion): 188 M reads, 15 G bases
  • Illumina mate-pair (3,762 bp insertion): 188 M reads, 15 G bases
  • Illumina mate-pair (9,850 bp insertion): 239 M reads, 18 G bases

Whole genome shotgun sequencing, UT Austin, USA

  • SOLiD v3 mate-pair (1,500 bp insertion): 608 M reads, 30 G bases

Fosmid-end sequencing, JGI/Berkeley + UW, USA

  • Illumina paired-end (? bp insertion): 18 M reads, 1.35 G bases

BAC-end sequencing, NIG/U Tokyo, Japan

  • Sanger sequencing
  • SceI BACs: 720,384 sequences in total. 458,392 sequences with good pairs (233 k pairs; mean length 1,061 bp)
  • HindIII BACs: 38,400 sequences in total. 34,044 sequences with good pairs (17 k pairs; mean length 1,125 bp)

Fosmid-end sequencing, NIG/U Tokyo, Japan

  • Sanger sequencing
  • 119,808 sequences in total. 99,652 sequences with good pairs (50 k pairs; mean length 1,106 bp).

BAC full sequencing, NIG/U Tokyo, Japan

  • Sanger sequencing.
  • 30 BACs (mean length 112 kb).

Fosmid shotgun sequencing, JGI/Berkeley + UW, USA

  • Illumina single-end: 102 M reads, 3.5 G bases

BAC shotgun sequencing, UT Austin, USA

  • One plate of CHORI-210 (96 BACs).
  • SOLiD v3 mate-pair (2,000 bp insertion): 70 M reads, 3.5 G bases
  • SOLiD v3 mate-pair (5,000 bp insertion): 56 M reads, 2.8 G bases

FISH, NIG/U Tokyo, Japan

See Also

XENLA_Transcriptome, XENLA_Proteome