FF:10618-108G6: Difference between revisions
From FANTOM5_SSTAR
No edit summary |
No edit summary |
||
Line 1: | Line 1: | ||
{{f5samples | {{f5samples | ||
|id= | |id=FF:10618-108G6 | ||
|name= | |name=choriocarcinoma cell line:T3M-3 | ||
|sample_id= | |sample_id=10618 | ||
|rna_tube_id= | |rna_tube_id=108G6 | ||
|rna_box= | |rna_box=108 | ||
|rna_position= | |rna_position=G6 | ||
|sample_cell_lot= | |sample_cell_lot= | ||
|sample_cell_catalog= | |sample_cell_catalog=RCB1018 | ||
|sample_company= | |sample_company=RIKEN Bioresource centre | ||
|rna_lot_number= | |rna_lot_number= | ||
|rna_catalog_number= | |rna_catalog_number= | ||
|sample_species= | |sample_species=Human (Homo sapiens) | ||
|sample_strain= | |sample_strain= | ||
|sample_dev_stage= | |sample_dev_stage= | ||
|sample_tissue= | |sample_tissue=chorioamniotic membrane | ||
|sample_donor(cell lot)= | |sample_donor(cell lot)= | ||
|sample_sex= | |sample_sex=unknown | ||
|sample_age= | |sample_age=fetal | ||
|sample_ethnicity= | |sample_ethnicity=J | ||
|rna_rin= | |rna_rin= | ||
|rna_od260/230= | |rna_od260/230=2.12 | ||
|rna_od260/280= | |rna_od260/280=2.04 | ||
|sample_cell_type= | |sample_cell_type=trophoblast cell | ||
|sample_cell_line= | |sample_cell_line=T3M-3 | ||
|sample_collaboration= | |sample_collaboration=Yukio Nakamura (RIKEN BRC) | ||
|sample_experimental_condition= | |sample_experimental_condition= | ||
|sample_disease= | |sample_disease=choriocarcinoma | ||
|rna_sample_type= | |rna_sample_type=total RNA | ||
|rna_extraction_protocol= | |rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | ||
|rna_weight_ug= | |rna_weight_ug=181.29 | ||
|rna_concentration= | |rna_concentration=2.4172 | ||
|sample_note= | |sample_note= | ||
|profile_hcage=,,, | |profile_hcage=CNhs11820,LSID829,release010,COMPLETED | ||
|profile_cagescan=,,, | |profile_cagescan=,,, | ||
|profile_srnaseq=,,, | |profile_srnaseq=,,, | ||
Line 40: | Line 40: | ||
|ancestors_in_disease_facet= | |ancestors_in_disease_facet= | ||
|sample_description= | |sample_description= | ||
|fonse_cell_line=FF:0101575 | |fonse_cell_line=FF:0101575 | ||
|fonse_cell_line_closure=FF:0101575 | |fonse_cell_line_closure=FF:0101575 | ||
Line 67: | Line 66: | ||
|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|top_motifs= | |||
}} | }} |
Revision as of 17:27, 27 February 2012
Name: | choriocarcinoma cell line:T3M-3 |
---|---|
Species: | Human (Homo sapiens) |
Library ID: | {{{library_id}}} |
Sample type: | {{{sample_category}}} |
Genomic View: | UCSC |
CAGEd-oPOSSUM: | link |
ExpandAdditional information |
---|
ExpandDownload raw sequence, BAM & CTSS |
---|
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: CNhs11820
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: CNhs11820
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: CNhs11820
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
{{{is_a}}}
part_of relathionship
{{{part_of}}}
has_quality relathionship
{{{has_quality}}}
Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data
FF: FANTOM5
NA
Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA