| Version 32 (modified by , 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.
| component | more info | example | |
| A | Data type | the biological datatype; also indicate whether the track is an average/consensus/combination of replicates | transcripts |
| B | Method | the experimental technique used | tiling microarray |
| C | Track details | the experimental features that distinguish each track from others in the same experiment | mitosis, 972h-, haploid |
| D | Strand | forward or reverse (or leave blank if not relevant) | reverse strand |
| E | Citation | First 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 HU | replication 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 array | Swi6 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 array | Swi6 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 array | Swi6 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 array | Swi6 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 array | Swi6 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 array | Swi6 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 array | Swi6 binding sites, clr4(delta), repeat 1 | - | Woolcock (2011) | |
| Woolcock 2011 - DamSwi6_clr4D_SPB483_2_vs_Damonly_clr4D_SPB482_2 (12795472615) | chromatin binding | DamID / tiling array | Swi6 binding sites, clr4(delta), repeat 2 | - | Woolcock (2011) | |
| Woolcock 2011 - DamSwi6_clr4D_SPB483_3_vs_Damonly_clr4D_SPB482_3 (12795473018) | chromatin binding | DamID / tiling array | Swi6 binding sites, clr4(delta), repeat 3 | - | Woolcock (2011) | |
| Woolcock 2011 - DamSwi6_dcr1D_SPB491_1_vs_DamSwi6_clr4D_SPB483_4 (127954732710) | chromatin binding | DamID / tiling array | Swi6 binding sites, dcr1(delta), repeat 1 | - | Woolcock (2011) | |
| Woolcock 2011 - DamSwi6_dcr1D_SPB491_2_vs_DamSwi6_clr4D_SPB483_5 (127954734011) | chromatin binding | DamID / tiling array | Swi6 binding sites, dcr1(delta), repeat 2 | - | Woolcock (2011) | |
| Woolcock 2011 - DamDcr1_SPB381_1_vs_Damonly_SPB492_1 (127954735412) | chromatin binding | DamID / tiling array | Dcr1 binding sites, repeat 1 | - | Woolcock (2011) | |
| Woolcock 2011 - DamDcr1_SPB381_2_vs_Damonly_SPB492_2 (127954739315) | chromatin binding | DamID / tiling array | Dcr1 binding sites, repeat 2 | - | Woolcock (2011) | |
| Woolcock 2011 - DamDcr1_SPB381_3_vs_Damonly_SPB492_3 (127954743318) | chromatin binding | DamID / tiling array | Dcr1 binding sites, repeat 3 | - | Woolcock (2011) | |
| Woolcock 2011 - DamArb1_SPB382_1_vs_Damonly_SPB492_1 (127954736713) | chromatin binding | DamID / tiling array | Arb1 binding sites, repeat 1 | - | Woolcock (2011) | |
| Woolcock 2011 - DamArb1_SPB382_2_vs_Damonly_SPB492_2 (127954740616) | chromatin binding | DamID / tiling array | Arb1 binding sites, repeat 2 | - | Woolcock (2011) | |
| Woolcock 2011 - DamArb1_SPB382_3_vs_Damonly_SPB492_3 (127954744619) | chromatin binding | DamID / tiling array | Arb1 binding sites, repeat 3 | - | Woolcock (2011) | |
| Woolcock 2011 - DamRdp1_SPB494_1_vs_Damonly_SPB492_1 (127954738014) | chromatin binding | DamID / tiling array | Rdp1 binding sites, repeat 1 | - | Woolcock (2011) | |
| Woolcock 2011 - DamRdp1_SPB494_2_vs_Damonly_SPB492_2 (127954742017) | chromatin binding | DamID / tiling array | Rdp1 binding sites, repeat 2 | - | Woolcock (2011) | |
| Woolcock 2011 - DamRdp1_SPB494_3_vs_Damonly_SPB492_3 (127954745920) | chromatin binding | DamID / tiling array | Rdp1 binding sites, repeat 3 | - | Woolcock (2011) | |
| Woolcock 2011 - DamDcr1_clr4D_SPB433_1_vs_Damonly_clr4D_SPB432_1 (127954747221) | chromatin binding | DamID / tiling array | Dcr1 binding sites, clr4(delta), repeat 1 | - | Woolcock (2011) | |
| Woolcock 2011 - DamDcr1_clr4D_SPB709_2_vs_Damonly_clr4D_SPB711_2 (127954749923) | chromatin binding | DamID / tiling array | Dcr1 binding sites, clr4(delta), repeat 2 | - | Woolcock (2011) | |
| Woolcock 2011 - DamDcr1_clr4D_SPB709_3_vs_Damonly_clr4D_SPB711_3 (127954753826) | chromatin binding | DamID / tiling array | Dcr1 binding sites, clr4(delta), repeat 3 | - | Woolcock (2011) | |
| Woolcock 2011 - DamArb1_clr4D_SPB434_1_vs_Damonly_clr4D_SPB432_1 (127954748522) | chromatin binding | DamID / tiling array | Arb1 binding sites, clr4(delta), repeat 1 | - | Woolcock (2011) | |
| Woolcock 2011 - DamArb1_clr4D_SPB710_2_vs_Damonly_clr4D_SPB711_2 (127954751224) | chromatin binding | DamID / tiling array | Arb1 binding sites, clr4(delta), repeat 2 | - | Woolcock (2011) | |
| Woolcock 2011 - DamArb1_clr4D_SPB710_3_vs_Damonly_clr4D_SPB711_3 (127954755127) | chromatin binding | DamID / tiling array | Arb1 binding sites, clr4(delta), repeat 3 | - | Woolcock (2011) | |
| Woolcock 2011 - DamRdp1_clr4D_SPB712_1_vs_Damonly_clr4D_SPB711_2 (127954752525) | chromatin binding | DamID / tiling array | Rdp1 binding sites, clr4(delta), repeat 1 | - | Woolcock (2011) | |
| Woolcock 2011 - DamRdp1_clr4D_SPB712_2_vs_Damonly_clr4D_SPB711_3 (127954756428) | chromatin binding | DamID / tiling array | Rdp1 binding sites, clr4(delta), repeat 2 | - | Woolcock (2011) | |
| Woolcock 2011 - DamRdp1_clr4D_SPB712_3_vs_Damonly_clr4D_SPB711_4 (127954757729) | chromatin binding | DamID / tiling array | Rdp1 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
- "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)"
- 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
