Personal tools

FF:12249-129H8: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{f5samples |id=FF:12249-129H8 |name=natural helper cells, IL2 treated, day15, biol_rep3 |sample_id=12249 |rna_tube_id=129H8 |rna_box=129 |rna_position=H8 |sample_cell_...")
 
No edit summary
Line 9: Line 9:
|sample_cell_catalog=
|sample_cell_catalog=
|sample_company=
|sample_company=
|rna_lot_number=3.00000
|rna_lot_number=3
|rna_catalog_number=
|rna_catalog_number=
|sample_species=Mouse (Mus musculus)
|sample_species=Mouse (Mus musculus)
Line 20: Line 20:
|sample_ethnicity=
|sample_ethnicity=
|rna_rin=
|rna_rin=
|rna_od260/230=2.21000
|rna_od260/230=2.21
|rna_od260/280=1.92000
|rna_od260/280=1.92
|sample_cell_type=natural helper cells
|sample_cell_type=natural helper cells
|sample_cell_line=
|sample_cell_line=
Line 29: Line 29:
|rna_sample_type=total RNA
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
|rna_weight_ug=2.96800
|rna_weight_ug=2.968
|rna_concentration=0.11872
|rna_concentration=0.11872
|sample_note=Jan 20 librarian
|sample_note=Jan 20 librarian
|profile_hcage=CNhs12509,LSID918,release012,MAPPING
|profile_hcage=CNhs12509,LSID918,release012,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=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 67: Line 66:
|fonse_treatment=EFO:0000369,FF:0000636,FF:0011524,FF:12249-129H8
|fonse_treatment=EFO:0000369,FF:0000636,FF:0011524,FF:12249-129H8
|fonse_treatment_closure=EFO:0000369,FF:0000636,FF:0011524,FF:12249-129H8
|fonse_treatment_closure=EFO:0000369,FF:0000636,FF:0011524,FF:12249-129H8
|top_motifs=
}}
}}

Revision as of 17:49, 27 February 2012


Name:natural helper cells, IL2 treated, day15, biol_rep3
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueunclassifiable
dev stageNA
sexNA
ageNA
cell typenatural helper cells
cell lineNA
companyNA
collaborationKoyasu
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number3
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs12509



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: CNhs12509This 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: CNhs12509This 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: CNhs12509


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000051 (common lymphoid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000837 (hematopoietic multipotent progenitor cell)
0000988 (hematopoietic cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002679 (natural helper lymphocyte)

UBERON: Anatomy
0000061 (anatomical structure)
0000160 (intestine)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001007 (digestive system)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002384 (connective tissue)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007026 (primitive gut)

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