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(Created page with "{{f5samples |id=FF:10281-104F2 |name=skeletal muscle - lateralis muscle, donor1 |sample_id=10281 |rna_tube_id= |rna_box=104 |rna_position=F2 |sample_cell_lot= |sample_...")
 
 
(6 intermediate revisions by one other user not shown)
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{{f5samples
 
{{f5samples
|id=FF:10281-104F2
+
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0001379,UBERON:0000479,UBERON:0000062,UBERON:0000026,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003663,UBERON:0005090,UBERON:0001630,UBERON:0004708,UBERON:0002101,UBERON:0004709,UBERON:0003661,UBERON:0010890,UBERON:0010317,UBERON:0010707,UBERON:0002204,UBERON:0002103,UBERON:0000383,UBERON:0001377,UBERON:0000154,UBERON:0010709
|name=skeletal muscle - lateralis muscle, donor1
 
|sample_id=10281
 
|rna_tube_id=
 
|rna_box=104
 
|rna_position=F2
 
|sample_cell_lot=
 
|sample_cell_catalog=
 
|sample_company=
 
|rna_lot_number=1-Sm1
 
|rna_catalog_number=
 
|sample_species=Human (Homo sapiens)
 
|sample_strain=
 
|sample_dev_stage=
 
|sample_tissue=skeletal muscle - lateralis muscle
 
|sample_donor(cell lot)=
 
|sample_sex=male
 
|sample_age=
 
|sample_ethnicity=
 
|rna_rin=8.00000
 
|rna_od260/230=1.43000
 
|rna_od260/280=2.06000
 
|sample_cell_type=CELL MIXTURE - tissue sample
 
|sample_cell_line=
 
|sample_collaboration=Alessandro Bonetti
 
|sample_experimental_condition=
 
|sample_disease=
 
|rna_sample_type=total RNA
 
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
 
|rna_weight_ug=19.61415
 
|rna_concentration=
 
|sample_note=
 
|profile_hcage=,LSID1024,,SEQUENCING QUEUE
 
|profile_cagescan=,,,
 
|profile_srnaseq=,,,
 
|profile_rnaseq=,,,
 
 
|ancestors_in_cell_lineage_facet=
 
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000026,UBERON:0000061,UBERON:0000062,UBERON:0000154,UBERON:0000383,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001048,UBERON:0001062,UBERON:0001377,UBERON:0001379,UBERON:0001630,UBERON:0002050,UBERON:0002101,UBERON:0002103,UBERON:0002204,UBERON:0002532,UBERON:0003081,UBERON:0003102,UBERON:0003661,UBERON:0003663,UBERON:0004120,UBERON:0004347,UBERON:0004357,UBERON:0004708,UBERON:0004709,UBERON:0005090,UBERON:0005423,UBERON:0005732,UBERON:0005733,UBERON:0007023
 
 
|ancestors_in_disease_facet=
 
|ancestors_in_disease_facet=
|sample_description=
+
|ancestors_in_ff_facet=FF:0000102,FF:0000210,FF:0000101,FF:0000001,FF:0000998,FF:0000004,FF:0011172
 
+
|comment=
 +
|created_by=
 +
|creation_date=
 +
|def=
 +
|f5samples=
 +
|ffid_belonging_in_development=UBERON:0002532,UBERON:0006603,UBERON:0010316
 
|fonse_cell_line=
 
|fonse_cell_line=
 
|fonse_cell_line_closure=
 
|fonse_cell_line_closure=
Line 67: Line 36:
 
|fonse_treatment=
 
|fonse_treatment=
 
|fonse_treatment_closure=
 
|fonse_treatment_closure=
 +
|has_quality=
 +
|id=FF:10281-104F2
 +
|is_a=EFO:0002091;;FF:0011172
 +
|is_obsolete=
 +
|name=
 +
|namespace=
 +
|part_of=
 +
|profile_cagescan=,,,
 +
|profile_hcage=,LSID1024,,SEQUENCING QUEUE
 +
|profile_rnaseq=,,,
 +
|profile_srnaseq=,,,
 +
|rna_box=104
 +
|rna_catalog_number=
 +
|rna_concentration=
 +
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
 +
|rna_lot_number=1-Sm1
 +
|rna_od260/230=1.43000
 +
|rna_od260/280=2.06000
 +
|rna_position=F2
 +
|rna_rin=8.00000
 +
|rna_sample_type=total RNA
 +
|rna_tube_id=
 +
|rna_weight_ug=19.61415
 +
|sample_age=
 +
|sample_cell_catalog=
 +
|sample_cell_line=
 +
|sample_cell_lot=
 +
|sample_cell_type=CELL MIXTURE - tissue sample
 +
|sample_collaboration=Alessandro Bonetti
 +
|sample_company=
 +
|sample_description=
 +
|sample_dev_stage=
 +
|sample_disease=
 +
|sample_donor(cell lot)=
 +
|sample_ethnicity=
 +
|sample_experimental_condition=
 +
|sample_id=10281
 +
|sample_note=
 +
|sample_sex=male
 +
|sample_species=Human (Homo sapiens)
 +
|sample_strain=
 +
|sample_tissue=skeletal muscle - lateralis muscle
 +
|top_motifs=
 +
|xref=
 
}}
 
}}

Latest revision as of 06:43, 11 July 2012


Name:
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueskeletal muscle - lateralis muscle
dev stageNA
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationAlessandro Bonetti
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1-Sm1
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} 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.
Analyst:NA

link to dataset.
data


Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data
no result for this sample


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


JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data



FANTOM5 phase1 novel unique motifsSummary: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 in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data



de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
data

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0001379 (vastus lateralis)
0000479 (tissue)
0000062 (organ)
0000026 (appendage)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003663 (hindlimb muscle)
0005090 (muscle structure)
0001630 (muscle organ)
0004708 (paired limb/fin)
0002101 (limb)
0004709 (pelvic appendage)
0003661 (limb muscle)
0010890 (pelvic complex muscle)
0010317 (germ layer / neural crest derived structure)
0010707 (appendage girdle complex)
0002204 (musculoskeletal system)
0002103 (hindlimb)
0000383 (musculature of body)
0001377 (quadriceps femoris)
0000154 (posterior region of body)
0010709 (pelvic complex)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011172 (skeletal muscle - lateralis muscle)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)