Personal tools

Template:F5samples: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 30: Line 30:
<tr><th scope="row" align="right">[[Property:Sample_species|Species]]:</th><td>[[sample_species::{{{sample_species}}}]]</td></tr>
<tr><th scope="row" align="right">[[Property:Sample_species|Species]]:</th><td>[[sample_species::{{{sample_species}}}]]</td></tr>
<tr><th scope="row" align="right">Genomic View:</th><td>[https://fantom5-collaboration.gsc.riken.jp/zenbu/dex/#section=Experiments;search={{#replace:{{{id}}}|FF:|}} zenbu] , [https://fantom5-collaboration.gsc.riken.jp/ucsc/cgi-bin/hgTracks?db={{#ifeq: {{{sample_species}}} | Human (Homo sapiens) | hg19 | }}{{#ifeq: {{{sample_species}}} | Mouse (Mus musculus) | mm9 | }}{{#ifeq: {{{sample_species}}} | Rat (Rattus rattus) |  rn4 | }}{{#ifeq: {{{sample_species}}} | Dog (Canis lupus familaris) | canFam2 | }}{{#ifeq: {{{sample_species}}} | Chicken (Gallus gallus) | galGal3 | }}&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&tsName={{#replace:{{{id}}}|FF:|}} UCSC] </td></tr>
<tr><th scope="row" align="right">Genomic View:</th><td>[https://fantom5-collaboration.gsc.riken.jp/zenbu/dex/#section=Experiments;search={{#replace:{{{id}}}|FF:|}} zenbu] , [https://fantom5-collaboration.gsc.riken.jp/ucsc/cgi-bin/hgTracks?db={{#ifeq: {{{sample_species}}} | Human (Homo sapiens) | hg19 | }}{{#ifeq: {{{sample_species}}} | Mouse (Mus musculus) | mm9 | }}{{#ifeq: {{{sample_species}}} | Rat (Rattus rattus) |  rn4 | }}{{#ifeq: {{{sample_species}}} | Dog (Canis lupus familaris) | canFam2 | }}{{#ifeq: {{{sample_species}}} | Chicken (Gallus gallus) | galGal3 | }}&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&tsName={{#replace:{{{id}}}|FF:|}} UCSC] </td></tr>
<tr><th scope="row" align="right">Sample accession:</th><td><span>{{SampleAccession|[[Sample Accession Number::{{{DRA_sample_Accession}}}]]}}</span></td></tr>
<tr><th scope="row" align="right">[[Property:Sample accession|Sample accession number]]:</th><td><span>{{SampleAccession|{{{DRA_sample_Accession}}}}}</span></td></tr>
</table>
</table>
</div>
</div>

Revision as of 18:07, 18 October 2013

Name:{{{name}}}
Species:{{{sample_species}}}
Genomic View:zenbu , UCSC
Sample accession number:

{{{DRA_sample_Accession}}} 





Details

Transcriptome profiling

hCAGE: {{{profile_hcage}}}
RNA-seq: {{{profile_rnaseq}}}
smallRNA seq: {{{profile_srnaseq}}}
nanoCAGEscan:{{{profile_cagescan}}}

Sample info

strain: {{{sample_strain}}}
tissue:{{{sample_tissue}}}
dev_stage:{{{sample_dev_stage}}}
sex:{{{sample_sex}}}
age:{{{sample_age}}}
ethnicity:{{{sample_ethnicity}}}
cell_type: {{{sample_cell_type}}}
cell_line:{{{sample_cell_line}}}
collaboration: {{{sample_collaboration}}}
Experimental condition:{{{sample_experimental_condition}}}
disease:{{{sample_disease}}}
cell_lot;{{{sample_cell_lot}}}
cell_catalog: {{{sample_cell_catalog}}}
company: {{{sample_company}}}
donor(cell lot): {{{sample_donor(cell lot)}}}
Note:{{{sample_note}}}

RNA info

sample_id: {{{sample_id}}}
tube_id:{{{rna_tube_id}}}
box:{{{rna_box}}}
position: {{{rna_position}}}
lot_number: {{{rna_lot_number}}}
catalog_number:{{{rna_catalog_number}}}
RIN:{{{rna_rin}}}
OD260/230:{{{rna_od260/230}}}
OD260/280:{{{rna_od260/280}}}
sample_type:{{{rna_sample_type}}}
extraction_protocol: {{{rna_extraction_protocol}}}
weight_ug:{{{rna_weight_ug}}}
concentration:{{{rna_concentration}}}

Parent ontology

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

Ancestors in ontology (non-development)

Connected ontology terms with is_a, part_of or located_in relathionship <br>Analyst: Hideya Kawaji

CL: Cell type

DOID: Disease
Property "Ancestors in disease facet" (as page type) with input value "{{{ancestors_in_disease_facet}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.

UBERON: Anatomy

FF: FANTOM5

Ancestors in ontology (development)

Connected ontology terms with develops_from, derives_from or preceded_by relathionship <br>Analyst: Hideya Kawaji



De novo Motif

<b>Homer de novo Motifs</b><br>Analyst: Michael Rehli


Related Novel Motifs

The values shown are the p-values of novel motifs in FANTOM5 samples. <br>Analyst: Michiel de Hoon

CAGE Library ID:{{{profile_hcage}}}


This sample isn't target for the analysis


Related JASPAR Motifs

The values shown are the p-values of jaspar motifs in FANTOM5 samples. <br>Analyst: Michiel de Hoon

CAGE Library ID:{{{profile_hcage}}}


This sample isn't target for the analysis



Repeat Enrichment

<br>Analyst:

no result for this sample


Relative expression of the co-expression cluster

<br>Analyst:




Data accession details

{{{DRA_sample_Accession}}} Accession numbers
MethodSample accession id
{{{accession_numbers}}} 
Library accession numbers

Library idMethodExp. accession idRun accession id
{{{4}}} {{{library_id}}}
Accession ID

Library idBAMCTSS
{{{4}}}