Template:F5samples: Difference between revisions
From FANTOM5_SSTAR
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Its transcriptome profile can be found in Genome Browsers ( [https://fantom5-collaboration.gsc.riken.jp/zenbu/dex/#section=Experiments;search={{#replace:{{{id}}}|FF:|}} zenbu] and [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] ) | Its transcriptome profile can be found in Genome Browsers ( [https://fantom5-collaboration.gsc.riken.jp/zenbu/dex/#section=Experiments;search={{#replace:{{{id}}}|FF:|}} zenbu] and [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] ) | ||
= Motifs = | |||
== Top activities with MARA == | |||
{{TopMotifsInMaraPhase1|top_motifs={{{top_motifs}}}}}|}} | {{TopMotifsInMaraPhase1|top_motifs={{{top_motifs}}}}}|}} | ||
== De-novo motifs == | |||
= Specific genes = | |||
= Facet (from FONSE) = | |||
{{#if: {{{ancestors_in_cell_lineage_facet}}} | {{#show:{{PAGENAME}}|?ancestors_in_cell_lineage_facet|intro='''Cell_lineage'''<br>|sep = <br> }} |}} | {{#if: {{{ancestors_in_cell_lineage_facet}}} | {{#show:{{PAGENAME}}|?ancestors_in_cell_lineage_facet|intro='''Cell_lineage'''<br>|sep = <br> }} |}} | ||
{{#if: {{{ancestors_in_disease_facet}}} | {{#show:{{PAGENAME}}|?ancestors_in_disease_facet|intro='''Disease'''<br>|sep = <br> }} |}} | {{#if: {{{ancestors_in_disease_facet}}} | {{#show:{{PAGENAME}}|?ancestors_in_disease_facet|intro='''Disease'''<br>|sep = <br> }} |}} |
Revision as of 02:12, 23 February 2012
{{{name}}}
{{{id}}} | |
---|---|
name | {{{name}}} |
species | {{{sample_species}}} |
Transcriptome | |
Genomic view | zenbu , UCSC |
hCAGE | {{{profile_hcage}}} |
RNA-seq | {{{profile_rnaseq}}} |
smallRNA seq | {{{profile_srnaseq}}} |
nanoCAGEscan | {{{profile_cagescan}}} |
sample detail | |
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}}} |
Its transcriptome profile can be found in Genome Browsers ( zenbu and UCSC )
Motifs
Top activities with MARA
{{#top_motifs_table01: {{{top_motifs}}}}}|}}
De-novo motifs
Specific genes
Facet (from FONSE)
{{#if: {{{top_motifs}}} |