EPIC-CoGe and iAnimal: Difference between revisions

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== iAnimal genomes in CoGe  ==
== iAnimal genomes in CoGe<br> ==


<br>
{| border="1" cellpadding="1" cellspacing="1" align="left"
 
{| width="200" border="1" cellpadding="1" cellspacing="1" align="left"
|-
|-
! scope="col" | Organism  
! scope="col" | Organism  
Line 22: Line 20:
| Ensembl  
| Ensembl  
| 2014-08-06 17:18:24  
| 2014-08-06 17:18:24  
| 293
| 82
| None  
| None  
| James Koltes (jekoltes)<br>Sabarinath Subramaniam (shabari)  
| James Koltes (jekoltes), Sabarinath Subramaniam (shabari)  
| 24423  
| 24423  
| https://coge.iplantcollaborative.org/CoGe/GenomeInfo.pl?gid=24423
| https://genomevolution.org/coge/NotebookView.pl?nid=801
|  
|  
|-
|-
| Bos taurus (cattle)<br>
| Bos taurus (cattle
| btau 4.6.1  
| btau 4.6.1  
| unmasked  
| unmasked  
Line 38: Line 36:
| Everyone  
| Everyone  
| 24465  
| 24465  
| https://coge.iplantcollaborative.org/CoGe/GenomeInfo.pl?gid=24465
| https://genomevolution.org/coge/NotebookView.pl?nid=801
|  
|  
|-
|-
| Gallus gallus (Chicken)<br>
| Gallus gallus (Chicken)
| 4.75  
| 4.75  
| unmasked  
| unmasked  
| Ensembl  
| Ensembl  
| 2014-08-01 15:11:11  
| 2014-08-01 15:11:11  
| 10
| 2
| None  
| None  
| James Koltes (jekoltes)<br>Sabarinath Subramaniam (shabari)  
| James Koltes (jekoltes), Sabarinath Subramaniam (shabari)  
| 24371  
| 24371  
| https://coge.iplantcollaborative.org/CoGe/GenomeInfo.pl?gid=24371
| https://genomevolution.org/coge/NotebookView.pl?nid=801
|  
|  
|-
|-
| Sus scrofa (pig)  
| Sus scrofa (pig)  
| 10.2.75<br>
| 10.2.75  
| unmasked  
| unmasked  
| Ensembl  
| Ensembl  
Line 60: Line 58:
| 5  
| 5  
| None  
| None  
| James Koltes (jekoltes)<br>Sabarinath Subramaniam (shabari)  
| James Koltes (jekoltes), Sabarinath Subramaniam (shabari)  
| 24374  
| 24374  
| https://coge.iplantcollaborative.org/CoGe/GenomeInfo.pl?gid=24374
| https://genomevolution.org/coge/NotebookView.pl?nid=801
|  
|  
|}
|}


<br>


<br>  
<br><br>


<br>


<br>


<br>


<br>
== iAnimal experiments in CoGe==


<br>  
{| border="1" cellpadding="1" cellspacing="1" align="left"
|-
! scope="col" | Name of experiment
! scope="col" | Type
! scope="col" | Source
! scope="col" | Groups with access<br>  
! scope="col" | Users with access<br>
! scope="col" | Genome
! scope="col" | Organism
! scope="col" | Link
! scope="col" | Notes
|-
|
Bovine Kidney Heart and Pelvic Fat RNAseq


<br>
| scope="col" | RNAseq
| scope="col" | Jim Reesy
| scope="col" | Restricted
| scope="col" | Sabarinath Subramaniam, James Koltes
| scope="col" | Bos taurus (cattle) (vUMD3.1, id24423): unmasked
| scope="col" | Bos taurus
| scope="col" | https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=3032
|-
|
Bovine Kidney Heart and Pelvic Fat miRNAseq


<br>
| scope="col" | RNAseq
| scope="col" | Jim Reesy
| scope="col" | Restricted
| scope="col" | Sabarinath Subramaniam, James Koltes
| scope="col" | Bos taurus (cattle) (vUMD3.1, id24423): unmasked
| scope="col" | Bos taurus
| scope="col" | https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=3027
|-
|
Bovine Liver miRNAseq


<br>
| scope="col" | RNAseq
| scope="col" | Jim Reesy
| scope="col" | Restricted
| scope="col" | Sabarinath Subramaniam, James Koltes
| scope="col" | Bos taurus (cattle) (vUMD3.1, id24423): unmasked
| scope="col" | Bos taurus
| scope="col" | https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=3028
|-
|
Bovine Subcutaneous fat RNAseq


<br>
| scope="col" | RNAseq
| scope="col" | Jim Reesy
| scope="col" | Restricted
| scope="col" | Sabarinath Subramaniam, James Koltes
| scope="col" | Bos taurus (cattle) (vUMD3.1, id24423): unmasked
| scope="col" | Bos taurus
| scope="col" | https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=3025
|-
|
Bovine Subcutaneous fat miRNAseq


<br>
| scope="col" | RNAseq
 
| scope="col" | Jim Reesy
<br>
| scope="col" | Restricted
 
| scope="col" | Sabarinath Subramaniam, James Koltes
<br>
| scope="col" | Bos taurus (cattle) (vUMD3.1, id24423): unmasked
 
| scope="col" | Bos taurus
<br>
| scope="col" | https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=3029
 
! scope="col" |
== iAnimal datasets in CoGe ==
|-
| Bovine skeletal muscle miRNAseq
| scope="col" | RNAseq
| scope="col" | Jim Reesy
| scope="col" | Restricted
| scope="col" | Sabarinath Subramaniam, James Koltes
| scope="col" | Bos taurus (cattle) (vUMD3.1, id24423): unmasked
| scope="col" | Bos taurus
| scope="col" | https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=3020
! scope="col" |
|-
| Gallus Gallus DNA methylation data
| scope="col" | Methylation
| scope="col" | Jin Reesy
| scope="col" | Restricted
| scope="col" | Sabarinath Subramaniam, James Koltes
| scope="col" | Gallus gallus (Chicken) (v4.75, id24371): unmasked
| scope="col" | Gallus gallus
| scope="col" | https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=3031
! scope="col" |
|-
| Gallus Gallus skeletal muscle ChIP-seq
| scope="col" | ChIP-seq
| scope="col" | Jim Reesy
| scope="col" | Restricted
| scope="col" | Sabarinath Subramaniam, James Koltes
| scope="col" | Gallus gallus (Chicken) (v4.75, id24371): unmasked
| scope="col" | Gallus gallus
| scope="col" | https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=3030
! scope="col" |
|-
| Sus scrofa adipose RNAseq
| scope="col" | RNAseq
| scope="col" | Jim Reesy
| scope="col" | Restricted
| scope="col" | Sabarinath Subramaniam, James Koltes
| scope="col" | Sus scrofa (pig) (v10.2.75, id24374): unmasked
| scope="col" | Sus scrofa
| scope="col" | https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=4351
! scope="col" |
|-
| Sus scrofa iPS ChIP-seq
| scope="col" | ChIP-seq
| scope="col" | Jim Reesy
| scope="col" | Restricted
| scope="col" | Sabarinath Subramaniam, James Koltes
| scope="col" | Sus scrofa (pig) (v10.2.75, id24374): unmasked
| scope="col" | Sus scrofa
| scope="col" | https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=4352
! scope="col" |
|-
| Sus scrofa liver RNAseq
| scope="col" | RNAseq
| scope="col" | Jim Reesy
| scope="col" | Restricted
| scope="col" | Sabarinath Subramaniam, James Koltes
| scope="col" | Sus scrofa (pig) (v10.2.75, id24374): unmasked
| scope="col" | Sus scrofa
| scope="col" | https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=4353
! scope="col" |
|-
| Sus scrofa muscle RNAseq sample 1
| scope="col" | RNAseq
| scope="col" | Jim Reesy
| scope="col" | Restricted
| scope="col" | Sabarinath Subramaniam, James Koltes
| scope="col" | Sus scrofa (pig) (v10.2.75, id24374): unmasked
| scope="col" | Sus scrofa
| scope="col" | https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=4354
! scope="col" |
|-
| Sus scrofa muscle RNAseq sample 2
| scope="col" | RNAseq
| scope="col" | Jim Reesy
| scope="col" | Restricted
| scope="col" | Sabarinath Subramaniam, James Koltes
| scope="col" | Sus scrofa (pig) (v10.2.75, id24374): unmasked
| scope="col" | Sus scrofa
| scope="col" | https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=4355
! scope="col" |
|-
| iAnimal Bovine Variants (Notebook with 72 experiments)
| scope="col" | SNPs
| scope="col" | Jim Reesy
| scope="col" | Restricted
| scope="col" | Sabarinath Subramaniam, James Koltes
| scope="col" | Bos taurus (cattle) (vUMD3.1, id24423): unmasked
| scope="col" | Bos taurus
| scope="col" | https://coge.iplantcollaborative.org/CoGe/NotebookView.pl?nid=845
! scope="col" |
|-
| iAnimal Bovine QTL data
| scope="col" | QTL data
| scope="col" | animalgenome.org
| scope="col" | Public
| scope="col" | All
| scope="col" | Bos taurus (cattle) (vbtau 4.6.1, id24465): unmasked
| scope="col" | Bos taurus
| scope="col" | https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?embed=&amp;eid=4578
! scope="col" |
|}
<br><br>

Latest revision as of 18:59, 5 November 2015

iAnimal genomes in CoGe

Organism Version Type Source Created Experiments Groups with access Users with access Genome id Link Notes
Bos taurus (cattle) UMD3.1 Unmasked Ensembl 2014-08-06 17:18:24 82 None James Koltes (jekoltes), Sabarinath Subramaniam (shabari) 24423 https://genomevolution.org/coge/NotebookView.pl?nid=801
Bos taurus (cattle btau 4.6.1 unmasked animalgenome.org 2014-08-19 14:15:26 0 None Everyone 24465 https://genomevolution.org/coge/NotebookView.pl?nid=801
Gallus gallus (Chicken) 4.75 unmasked Ensembl 2014-08-01 15:11:11 2 None James Koltes (jekoltes), Sabarinath Subramaniam (shabari) 24371 https://genomevolution.org/coge/NotebookView.pl?nid=801
Sus scrofa (pig) 10.2.75 unmasked Ensembl 2014-08-02 08:39:46 5 None James Koltes (jekoltes), Sabarinath Subramaniam (shabari) 24374 https://genomevolution.org/coge/NotebookView.pl?nid=801






iAnimal experiments in CoGe

Name of experiment Type Source Groups with access
 Users with access
 Genome Organism Link Notes

Bovine Kidney Heart and Pelvic Fat RNAseq

RNAseq Jim Reesy Restricted Sabarinath Subramaniam, James Koltes Bos taurus (cattle) (vUMD3.1, id24423): unmasked Bos taurus https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=3032

Bovine Kidney Heart and Pelvic Fat miRNAseq

RNAseq Jim Reesy Restricted Sabarinath Subramaniam, James Koltes Bos taurus (cattle) (vUMD3.1, id24423): unmasked Bos taurus https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=3027

Bovine Liver miRNAseq

RNAseq Jim Reesy Restricted Sabarinath Subramaniam, James Koltes Bos taurus (cattle) (vUMD3.1, id24423): unmasked Bos taurus https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=3028

Bovine Subcutaneous fat RNAseq

RNAseq Jim Reesy Restricted Sabarinath Subramaniam, James Koltes Bos taurus (cattle) (vUMD3.1, id24423): unmasked Bos taurus https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=3025

Bovine Subcutaneous fat miRNAseq

RNAseq Jim Reesy Restricted Sabarinath Subramaniam, James Koltes Bos taurus (cattle) (vUMD3.1, id24423): unmasked Bos taurus https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=3029
Bovine skeletal muscle miRNAseq RNAseq Jim Reesy Restricted Sabarinath Subramaniam, James Koltes Bos taurus (cattle) (vUMD3.1, id24423): unmasked Bos taurus https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=3020
Gallus Gallus DNA methylation data Methylation Jin Reesy Restricted Sabarinath Subramaniam, James Koltes Gallus gallus (Chicken) (v4.75, id24371): unmasked Gallus gallus https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=3031
Gallus Gallus skeletal muscle ChIP-seq ChIP-seq Jim Reesy Restricted Sabarinath Subramaniam, James Koltes Gallus gallus (Chicken) (v4.75, id24371): unmasked Gallus gallus https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=3030
Sus scrofa adipose RNAseq RNAseq Jim Reesy Restricted Sabarinath Subramaniam, James Koltes Sus scrofa (pig) (v10.2.75, id24374): unmasked Sus scrofa https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=4351
Sus scrofa iPS ChIP-seq ChIP-seq Jim Reesy Restricted Sabarinath Subramaniam, James Koltes Sus scrofa (pig) (v10.2.75, id24374): unmasked Sus scrofa https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=4352
Sus scrofa liver RNAseq RNAseq Jim Reesy Restricted Sabarinath Subramaniam, James Koltes Sus scrofa (pig) (v10.2.75, id24374): unmasked Sus scrofa https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=4353
Sus scrofa muscle RNAseq sample 1 RNAseq Jim Reesy Restricted Sabarinath Subramaniam, James Koltes Sus scrofa (pig) (v10.2.75, id24374): unmasked Sus scrofa https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=4354
Sus scrofa muscle RNAseq sample 2 RNAseq Jim Reesy Restricted Sabarinath Subramaniam, James Koltes Sus scrofa (pig) (v10.2.75, id24374): unmasked Sus scrofa https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?eid=4355
iAnimal Bovine Variants (Notebook with 72 experiments) SNPs Jim Reesy Restricted Sabarinath Subramaniam, James Koltes Bos taurus (cattle) (vUMD3.1, id24423): unmasked Bos taurus https://coge.iplantcollaborative.org/CoGe/NotebookView.pl?nid=845
iAnimal Bovine QTL data QTL data animalgenome.org Public All Bos taurus (cattle) (vbtau 4.6.1, id24465): unmasked Bos taurus https://coge.iplantcollaborative.org/CoGe/ExperimentView.pl?embed=&eid=4578



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