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! Additional information
! Additional information
|-
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|<div class="left">Transcriptome profiling<table cellspacing="0" border="1">
|<div><div class="left">Transcriptome profiling<table cellspacing="0" border="1">
<tr><th>[[Property:profile_hcage|hCAGE]]:</th><td>{{#switch: {{{profile_hcage}}}|,,,=NA| =NA |{{{profile_hcage}}}}}</td></tr>
<tr><th>[[Property:profile_hcage|hCAGE]]:</th><td>{{#switch: {{{profile_hcage}}}|,,,=NA| =NA |{{{profile_hcage}}}}}</td></tr>
<tr><th>[[Property:profile_rnaseq|RNA-seq]]:</th><td>{{#switch: {{{profile_rnaseq}}}|,,,=NA| =NA |{{{profile_rnaseq}}}}}</td></tr>
<tr><th>[[Property:profile_rnaseq|RNA-seq]]:</th><td>{{#switch: {{{profile_rnaseq}}}|,,,=NA| =NA |{{{profile_rnaseq}}}}}</td></tr>
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<tr><th>[[Property:rna_concentration|concentration]]:</th><td>{{#switch:{{{rna_concentration}}}|,,,=NA| =NA |{{{rna_concentration}}}}}</td></tr>
<tr><th>[[Property:rna_concentration|concentration]]:</th><td>{{#switch:{{{rna_concentration}}}|,,,=NA| =NA |{{{rna_concentration}}}}}</td></tr>
<tr><th>[[Property:rna_extraction_protocol|extraction_protocol]]:<span style="background-color:white">[[Protocols:RNA_extraction|(Details)]]</span></th><td>{{#switch:{{{rna_extraction_protocol}}}|,,,=NA| =NA |{{{rna_extraction_protocol}}}}}</td></tr></table></div>
<tr><th>[[Property:rna_extraction_protocol|extraction_protocol]]:<span style="background-color:white">[[Protocols:RNA_extraction|(Details)]]</span></th><td>{{#switch:{{{rna_extraction_protocol}}}|,,,=NA| =NA |{{{rna_extraction_protocol}}}}}</td></tr></table></div>
<br style="clear: left;" /></div>
|}{{#if:{{#pos:{{{DRA_sample_Accession}}}|@|0}}|{{DRAAccessionNumbers|{{{DRA_sample_Accession}}}|{{{accession_numbers}}}|{{{library_id}}}}}|}}{{#vardefine:species_temp|{{#switch: {{{sample_species}}} | Human (Homo sapiens) = Hg19 | Mouse (Mus musculus) = Mm9 }}}}
|}{{#if:{{#pos:{{{DRA_sample_Accession}}}|@|0}}|{{DRAAccessionNumbers|{{{DRA_sample_Accession}}}|{{{accession_numbers}}}|{{{library_id}}}}}|}}{{#vardefine:species_temp|{{#switch: {{{sample_species}}} | Human (Homo sapiens) = Hg19 | Mouse (Mus musculus) = Mm9 }}}}



Revision as of 15:22, 7 April 2014

Name:{{{name}}}
Species:{{{sample_species}}}
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View:zenbu , UCSC
Additional information
Transcriptome profiling
hCAGE:{{{profile_hcage}}}
RNA-seq:{{{profile_rnaseq}}}
smallRNA seq:{{{profile_srnaseq}}}
nanoCAGEscan:{{{profile_cagescan}}}
Sample information
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}}}
company:{{{sample_company}}}
collaboration:{{{sample_collaboration}}}
Experimental condition:{{{sample_experimental_condition}}}
disease:{{{sample_disease}}}
cell_lot;{{{sample_cell_lot}}}
cell_catalog:{{{sample_cell_catalog}}}
donor(cell lot):{{{sample_donor(cell lot)}}}
company:{{{sample_company}}}
Note:{{{sample_note}}}
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
sample_id:{{{sample_id}}}
tube_id:{{{rna_tube_id}}}
box:{{{rna_box}}}
position:{{{rna_position}}}
tube_id:{{{rna_tube_id}}}
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}}}
weight_ug:{{{rna_weight_ug}}}
concentration:{{{rna_concentration}}}
extraction_protocol:(Details){{{rna_extraction_protocol}}}




Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data
Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data

no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: {{{profile_hcage}}}This sample isn't target for the analysis

FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data
library id: {{{profile_hcage}}}This sample isn't target for the analysis



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: {{{profile_hcage}}}


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