wiki:TrackRelabelling

Version 32 (modified by mah79, 6 years ago) (diff)

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Track labels for genome browser

Each track should have a label with five components: data type, method, track details, strand (optional) and citation.

We should get enough details via the submission form (http://www.pombase.org/submit-data/data-submission-form) to generate a label for each track; email submitters if necessary. Include the labels in the Jira ticket for the submission.

componentmore infoexample
AData typethe biological datatype; also indicate whether the track is an average/consensus/combination of replicatestranscripts
BMethodthe experimental technique usedtiling microarray
CTrack detailsthe experimental features that distinguish each track from others in the same experimentmitosis, 972h-, haploid
DStrandforward or reverse (or leave blank if not relevant)reverse strand
ECitationFirst author (year)Soriano(2013)

Note: a number of specific track labels were stored here temporarily. Most have been deleted (but can be seen in the page history); a few have been retained as illustrative examples:

Soriano 2013
Soriano 2013 MN_Mit nucleosome positioning NGS mitosis, 972 h-, haploid - Soriano (2013)
Soriano 2013 MN_Mit-pat1.114 nucleosome positioning NGS mitosis, pat1.114, diploid- Soriano (2013)
Soriano 2013 MN_Mei0h nucleosome positioning NGS meiosis 0h, pat1.114, diploid - Soriano (2013)
Soriano 2013 MN_Mei3h nucleosome positioning NGS meiosis 3h, pat1.114, diploid - Soriano (2013)
Soriano 2013 MN_Mei5h nucleosome positioning NGS meiosis 5h, pat1.114, diploid - Soriano (2013)
Soriano 2013 MN Mit nucleosome positioning tiling microarray mitosis, 972 h-, haploid - Soriano (2013)
Soriano 2013 MN_pcr1D nucleosome positioning tiling microarray mitosis, pcr1(delta), haploid - Soriano (2013)
Soriano 2013 MN_atf1D nucleosome positioning tiling microarray mitosis, atf1(delta), haploid - Soriano (2013)
Soriano 2013 - RNA_Mit (Reverse Strand) transcripts tiling microarray mitosis, 972h-, haploid reverse strand Soriano (2013)
Soriano 2013 - RNA_Mit (Forward Strand) transcripts tiling microarray mitosis, 972h-, haploid forward strand Soriano (2013)
Soriano 2013 - RNA_Mit_pat1.114 (Reverse Strand) transcripts tiling microarray mitosis, pat1.114, diploid reverse strand Soriano (2013)
Soriano 2013 - RNA_Mit_pat1.114 (Forward Strand) transcripts tiling microarray mitosis, pat1.114, diploid forward strand Soriano (2013)
Soriano 2013 - RNA_Mei0h (Reverse Strand) transcripts tiling microarray meiosis 0h, pat1.114, diploid reverse strand Soriano (2013)
Soriano 2013 - RNA_Mei0h (Forward Strand) transcripts tiling microarray meiosis 0h, pat1.114, diploid forward strand Soriano (2013)
Soriano 2013 - RNA_Mei3h (Reverse Strand) transcripts tiling microarray meiosis 3h, pat1.114, diploid reverse strand Soriano (2013)
Soriano 2013 - RNA_Mei3h (Forward Strand) transcripts tiling microarray meiosis 3h, pat1.114, diploid forward strand Soriano (2013)
Soriano 2013 - RNA_Mei5h (Reverse Strand) transcripts tiling microarray meiosis 5h, pat1.114, diploid reverse strand Soriano (2013)
Soriano 2013 - RNA_Mei5h (Forward Strand) transcripts tiling microarray meiosis 5h, pat1.114, diploid forward strand Soriano (2013)
Soriano 2013 - RNA_atf1D (Reverse Strand) transcripts tiling microarray mitosis, atf1(delta), haploid reverse strand Soriano (2013)
Soriano 2013 - RNA_atf1D (Forward Strand) transcripts tiling microarray mitosis, atf1(delta), haploid forward strand Soriano (2013)
Soriano 2013 - RNA_pcr1D (Reverse Strand) transcripts tiling microarray mitosis, pcr1(delta), haploid reverse strand Soriano (2013)
Soriano 2013 - RNA_pcr1D (Forward Strand) transcripts tiling microarray mitosis, pcr1(delta), haploid forward strand Soriano (2013)
Mata 2013
Mata, 2013 (Forward Strand) poly(A) sites mRNA end sequencing 972 h- forward strand Mata (2013)
Mata, 2013 (Reverse Strand) poly(A) sites mRNA end sequencing 972 h- reverse strand Mata (2013)
Schlackow 2013
Schlackow 2013 All Combined (Forward Strand) poly(A) sites RNA-Seq all data forward strand Schlackow (2013)
Schlackow 2013 All Combined (Reverse Strand) poly(A) sites RNA-Seq all data reverse strand Schlackow (2013)
Schlackow 2013 All Strand Specific Combined (Forward Strand) poly(A) sites RNA-Seq all strand-specific data forward strand Schlackow (2013)
Schlackow 2013 All Strand Specific Combined (Reverse Strand) poly(A) sites RNA-Seq all strand-specific data reverse strand Schlackow (2013)
Schlackow 2013 Non-strand Specific Cycling (Forward Strand) poly(A) sites RNA-Seq cycling, non-strand-specific, 972 h- forward strand Schlackow (2013)
Schlackow 2013 Non-strand Specific Cycling (Reverse Strand) poly(A) sites RNA-Seq cycling, non-strand-specific, 972 h- reverse strand Schlackow (2013)
Schlackow 2013 Meiosis Arrested (Forward Strand) poly(A) sites RNA-Seq meiotic arrest, pat1-114 diploid forward strand Schlackow (2013)
Schlackow 2013 Meiosis Arrested (Reverse Strand) poly(A) sites RNA-Seq meiotic arrest, pat1-114 diploid reverse strand Schlackow (2013)
Schlackow 2013 Quiescence Arrested 24hours Nitrogen Depletion (Forward Strand) poly(A) sites RNA-Seq quiescence 24h, 972 h- forward strand Schlackow (2013)
Schlackow 2013 Quiescence Arrested 24hours Nitrogen Depletion (Reverse Strand) poly(A) sites RNA-Seq quiescence 24h, 972 h- reverse strand Schlackow (2013)
Schlackow 2013 Quiescence Arrested 7days Nitrogen Depletion (Forward Strand) poly(A) sites RNA-Seq quiescence 7d, 972 h- forward strand Schlackow (2013)
Schlackow 2013 Quiescence Arrested 7days Nitrogen Depletion (Reverse Strand) poly(A) sites RNA-Seq quiescence 7d, 972 h- reverse strand Schlackow (2013)
Xu 2012 [note: called "Rhind 2012" in test browser, but J. Xu is 1st author]
Rhind 2012 WT elutriated HUreplication origins HT sequencing wild type, elutriation, +HU Xu (2012)
Rhind 2012 cdc25 release HU replication origins HT sequencing cdc25-ts, block/release, +HU Xu (2012)
Rhind 2012 dfp1-3A elutriated HU replication origins HT sequencing dfp1-3A, elutriation, +HU Xu (2012)
Rhind 2011
72 features from 'Rhind 2011 - All Data (Forward Strand)' omitted transcripts RNA-seq all data forward strand Rhind (2011)
547 features from 'Rhind 2011 - All Data (Reverse Strand)' omitted transcripts RNA-seq all data reverse strand Rhind (2011)
[none] transcripts RNA-seq log phase forward strand Rhind (2011)
[none] transcripts RNA-seq log phase reverse strand Rhind (2011)
[none] transcripts RNA-seq glucose depletion forward strand Rhind (2011)
50 features from 'Rhind 2011 - Glucose Depletion (Reverse Strand)' omitted transcripts RNA-seq glucose depletion reverse strand Rhind (2011)
[none] transcripts RNA-seq heat shock forward strand Rhind (2011)
[none] transcripts RNA-seq heat shock reverse strand Rhind (2011)
[none] transcripts RNA-seq stationary phase forward strand Rhind (2011)
159 features from 'Rhind 2011 - Stationary Phase (Reverse Strand)' omitted transcripts RNA-seq stationary phase reverse strand Rhind (2011)
Woolcock 2011
Woolcock 2011 - DamSwi6_SPB330_1_vs_Damonly_SPB380_1 (12795472081) chromatin binding DamID / tiling arraySwi6 binding sites, unfused Dam used as experimental control, repeat 1 - Woolcock (2011)
Woolcock 2011 - DamSwi6_SPB330_2_vs_Damonly_SPB380_2 (12795472484) chromatin binding DamID / tiling arraySwi6 binding sites, unfused Dam used as experimental control, repeat 2 - Woolcock (2011)
Woolcock 2011 - DamSwi6_SPB330_3_vs_Damonly_SPB380_3 (12795472877) chromatin binding DamID / tiling arraySwi6 binding sites, unfused Dam used as experimental control, repeat 3 - Woolcock (2011)
Woolcock 2011 - DamSwi6_SPB330_1_vs_DamSwi6_clr4D_SPB483_1 (12795472353) chromatin binding DamID / tiling arraySwi6 binding sites, clr4(delta) used as experimental control, repeat 1 - Woolcock (2011)
Woolcock 2011 - DamSwi6_SPB330_2_vs_DamSwi6_clr4D_SPB483_2 (12795472746) chromatin binding DamID / tiling arraySwi6 binding sites, clr4(delta) used as experimental control, repeat 2 - Woolcock (2011)
Woolcock 2011 - DamSwi6_SPB330_3_vs_DamSwi6_clr4D_SPB483_3 (12795473149) chromatin binding DamID / tiling arraySwi6 binding sites, clr4(delta) used as experimental control, repeat 3 - Woolcock (2011)
Woolcock 2011 - DamSwi6_clr4D_SPB483_1_vs_Damonly_clr4D_SPB482_1 (12795472222) chromatin binding DamID / tiling arraySwi6 binding sites, clr4(delta), repeat 1 - Woolcock (2011)
Woolcock 2011 - DamSwi6_clr4D_SPB483_2_vs_Damonly_clr4D_SPB482_2 (12795472615) chromatin binding DamID / tiling arraySwi6 binding sites, clr4(delta), repeat 2 - Woolcock (2011)
Woolcock 2011 - DamSwi6_clr4D_SPB483_3_vs_Damonly_clr4D_SPB482_3 (12795473018) chromatin binding DamID / tiling arraySwi6 binding sites, clr4(delta), repeat 3 - Woolcock (2011)
Woolcock 2011 - DamSwi6_dcr1D_SPB491_1_vs_DamSwi6_clr4D_SPB483_4 (127954732710) chromatin binding DamID / tiling arraySwi6 binding sites, dcr1(delta), repeat 1 - Woolcock (2011)
Woolcock 2011 - DamSwi6_dcr1D_SPB491_2_vs_DamSwi6_clr4D_SPB483_5 (127954734011) chromatin binding DamID / tiling arraySwi6 binding sites, dcr1(delta), repeat 2 - Woolcock (2011)
Woolcock 2011 - DamDcr1_SPB381_1_vs_Damonly_SPB492_1 (127954735412) chromatin binding DamID / tiling arrayDcr1 binding sites, repeat 1 - Woolcock (2011)
Woolcock 2011 - DamDcr1_SPB381_2_vs_Damonly_SPB492_2 (127954739315) chromatin binding DamID / tiling arrayDcr1 binding sites, repeat 2 - Woolcock (2011)
Woolcock 2011 - DamDcr1_SPB381_3_vs_Damonly_SPB492_3 (127954743318) chromatin binding DamID / tiling arrayDcr1 binding sites, repeat 3 - Woolcock (2011)
Woolcock 2011 - DamArb1_SPB382_1_vs_Damonly_SPB492_1 (127954736713) chromatin binding DamID / tiling arrayArb1 binding sites, repeat 1 - Woolcock (2011)
Woolcock 2011 - DamArb1_SPB382_2_vs_Damonly_SPB492_2 (127954740616) chromatin binding DamID / tiling arrayArb1 binding sites, repeat 2 - Woolcock (2011)
Woolcock 2011 - DamArb1_SPB382_3_vs_Damonly_SPB492_3 (127954744619) chromatin binding DamID / tiling arrayArb1 binding sites, repeat 3 - Woolcock (2011)
Woolcock 2011 - DamRdp1_SPB494_1_vs_Damonly_SPB492_1 (127954738014) chromatin binding DamID / tiling arrayRdp1 binding sites, repeat 1 - Woolcock (2011)
Woolcock 2011 - DamRdp1_SPB494_2_vs_Damonly_SPB492_2 (127954742017) chromatin binding DamID / tiling arrayRdp1 binding sites, repeat 2 - Woolcock (2011)
Woolcock 2011 - DamRdp1_SPB494_3_vs_Damonly_SPB492_3 (127954745920) chromatin binding DamID / tiling arrayRdp1 binding sites, repeat 3 - Woolcock (2011)
Woolcock 2011 - DamDcr1_clr4D_SPB433_1_vs_Damonly_clr4D_SPB432_1 (127954747221) chromatin binding DamID / tiling arrayDcr1 binding sites, clr4(delta), repeat 1 - Woolcock (2011)
Woolcock 2011 - DamDcr1_clr4D_SPB709_2_vs_Damonly_clr4D_SPB711_2 (127954749923) chromatin binding DamID / tiling arrayDcr1 binding sites, clr4(delta), repeat 2 - Woolcock (2011)
Woolcock 2011 - DamDcr1_clr4D_SPB709_3_vs_Damonly_clr4D_SPB711_3 (127954753826) chromatin binding DamID / tiling arrayDcr1 binding sites, clr4(delta), repeat 3 - Woolcock (2011)
Woolcock 2011 - DamArb1_clr4D_SPB434_1_vs_Damonly_clr4D_SPB432_1 (127954748522) chromatin binding DamID / tiling arrayArb1 binding sites, clr4(delta), repeat 1 - Woolcock (2011)
Woolcock 2011 - DamArb1_clr4D_SPB710_2_vs_Damonly_clr4D_SPB711_2 (127954751224) chromatin binding DamID / tiling arrayArb1 binding sites, clr4(delta), repeat 2 - Woolcock (2011)
Woolcock 2011 - DamArb1_clr4D_SPB710_3_vs_Damonly_clr4D_SPB711_3 (127954755127) chromatin binding DamID / tiling arrayArb1 binding sites, clr4(delta), repeat 3 - Woolcock (2011)
Woolcock 2011 - DamRdp1_clr4D_SPB712_1_vs_Damonly_clr4D_SPB711_2 (127954752525) chromatin binding DamID / tiling arrayRdp1 binding sites, clr4(delta), repeat 1 - Woolcock (2011)
Woolcock 2011 - DamRdp1_clr4D_SPB712_2_vs_Damonly_clr4D_SPB711_3 (127954756428) chromatin binding DamID / tiling arrayRdp1 binding sites, clr4(delta), repeat 2 - Woolcock (2011)
Woolcock 2011 - DamRdp1_clr4D_SPB712_3_vs_Damonly_clr4D_SPB711_4 (127954757729) chromatin binding DamID / tiling arrayRdp1 binding sites, clr4(delta), repeat 3 - Woolcock (2011)

Note: For the Mata poly(A) data, col C is blank because the only difference is strand, and col D covers that.

Lists of track component content used to date (last updated 2014-10-20):

Biological data types

  • chromatin binding
  • nucleosome positioning
  • poly(A) sites
  • replication origins
  • transcripts

Methods

  • DamID / tiling array
  • HT sequencing
  • NGS
  • RNA-seq
  • tiling microarray

Historical record of additional global changes requested and implemented

  1. "Configure this page" dialog
    • Descriptions for track selection should be replaced by columns E,B,C,D
    • e.g. Soriano 2013 MN_atf1D will become "Soriano 2013, tiling microarray, mitosis, pcr1(delta)"
  1. Mouseover
    • The text visible upon mousing over the (i) icon (e.g. "Data served from a BigWig file: Nucleosome_Seq: Diploid pat1.114 Mitosis pat1.114 as described by Soriano et al 2013") isn't necessary or useful. Most of this information is provided in the track label, and the rest is superfluous for our users (or is inherently excess verbiage).
    • Instead, change this to provide only 2 things:
      • A link to this data set in the public repositories (e.g. GEO, ArrayExpress)
      • A link to the publication