Personal tools

Difference between revisions of "FF:14335-155F6"

From FANTOM5_SSTAR

Jump to: navigation, search
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
 
{{f5samples
 
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000479,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0000467,UBERON:0001062,UBERON:0005291,UBERON:0000925,UBERON:0006598,UBERON:0002532,UBERON:0000065,UBERON:0001004,UBERON:0006595
+
|DRA_sample_Accession=CAGE@SAMD00022307
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000144,CL:0000548,CL:0000012,CL:0002321,CL:0000063,CL:0000066,CL:0002371,CL:0000220,CL:0000004,CL:0000255,CL:0002076,CL:0002368,CL:0000223
+
|accession_numbers=CAGE;DRX022780;DRR025119;DRZ003544;DRZ004427;DRZ008285;DRZ009168
 +
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0000065,UBERON:0001004
 +
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0000255,CL:0002076,CL:0002368
 
|ancestors_in_disease_facet=
 
|ancestors_in_disease_facet=
 +
|ancestors_in_ff_facet=FF:0000102,FF:0000210,FF:0000002,FF:0000101,FF:0000001,FF:0000408,FF:0000350,FF:0000166,FF:0000406,FF:0000673
 
|comment=
 
|comment=
 
|created_by=
 
|created_by=
 
|creation_date=
 
|creation_date=
 +
|data_phase=2
 +
|datafreeze_phase=2
 
|def=
 
|def=
 +
|ffid_belonging_in_development=CL:0000223
 
|fonse_cell_line=
 
|fonse_cell_line=
 
|fonse_cell_line_closure=
 
|fonse_cell_line_closure=
Line 34: Line 40:
 
|fonse_treatment_closure=
 
|fonse_treatment_closure=
 
|has_quality=
 
|has_quality=
 +
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.fractionation.hCAGE/Small%2520Airway%2520Epithelial%2520Cells%2520donor2%2520%2528nuclear%2520fraction%2529.CNhs14565.14335-155F6.hg19.nobarcode.bam
 +
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.fractionation.hCAGE/Small%2520Airway%2520Epithelial%2520Cells%2520donor2%2520%2528nuclear%2520fraction%2529.CNhs14565.14335-155F6.hg19.ctss.bed.gz
 +
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.fractionation.hCAGE/Small%2520Airway%2520Epithelial%2520Cells%2520donor2%2520%2528nuclear%2520fraction%2529.CNhs14565.14335-155F6.hg19.nobarcode.rdna.fa.gz
 +
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.fractionation.hCAGE/Small%2520Airway%2520Epithelial%2520Cells%2520donor2%2520%2528nuclear%2520fraction%2529.CNhs14565.14335-155F6.hg38.nobarcode.bam
 +
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.fractionation.hCAGE/Small%2520Airway%2520Epithelial%2520Cells%2520donor2%2520%2528nuclear%2520fraction%2529.CNhs14565.14335-155F6.hg38.nobarcode.ctss.bed.gz
 
|id=FF:14335-155F6
 
|id=FF:14335-155F6
 
|is_a=EFO:0002091;;FF:0000673
 
|is_a=EFO:0002091;;FF:0000673
|name=
+
|is_obsolete=
 +
|library_id=CNhs14565
 +
|library_id_phase_based=2:
 +
|microRNAs=
 +
|microRNAs_nn=
 +
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;14335
 +
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;14335
 +
|name=Small Airway Epithelial Cells donor2 (nuclear fraction)
 
|namespace=FANTOM5
 
|namespace=FANTOM5
 
|part_of=
 
|part_of=
 
|profile_cagescan=
 
|profile_cagescan=
|profile_hcage=,,,IN_LIBRARIAN
+
|profile_hcage=CNhs14565,LSID1334,,COMPLETED
 
|profile_rnaseq=
 
|profile_rnaseq=
 
|profile_srnaseq=
 
|profile_srnaseq=
 
|rna_box=155
 
|rna_box=155
|rna_catalog_number=N/A
+
|rna_catalog_number=
 
|rna_concentration=0.15254
 
|rna_concentration=0.15254
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
+
|rna_extraction_protocol=
 
|rna_lot_number=
 
|rna_lot_number=
|rna_od260/230=1.36
+
|rna_od260/230=
|rna_od260/280=1.91
+
|rna_od260/280=
 
|rna_position=F6
 
|rna_position=F6
 
|rna_rin=
 
|rna_rin=
Line 55: Line 73:
 
|rna_tube_id=155F6
 
|rna_tube_id=155F6
 
|rna_weight_ug=8.3897
 
|rna_weight_ug=8.3897
|sample_age=58
+
|sample_age=
|sample_cell_catalog=CC-2547
+
|sample_category=fractionations and perturbations
|sample_cell_line=
+
|sample_cell_catalog=
|sample_cell_lot=lot:5F0380J
+
|sample_cell_line=UNDEFINED_CELL_LINE
 +
|sample_cell_lot=
 
|sample_cell_type=pneumocyte
 
|sample_cell_type=pneumocyte
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
+
|sample_collaboration=UNDEFINED_COLLABORATION
|sample_company=Lonza
+
|sample_company=
 
|sample_description=
 
|sample_description=
 
|sample_dev_stage=58 years old adult
 
|sample_dev_stage=58 years old adult
 
|sample_disease=
 
|sample_disease=
 
|sample_donor(cell lot)=
 
|sample_donor(cell lot)=
|sample_ethnicity=C
+
|sample_ethnicity=
 
|sample_experimental_condition=nuclear RNA
 
|sample_experimental_condition=nuclear RNA
 
|sample_id=14335
 
|sample_id=14335
Line 72: Line 91:
 
|sample_sex=male
 
|sample_sex=male
 
|sample_species=Human (Homo sapiens)
 
|sample_species=Human (Homo sapiens)
|sample_strain=
+
|sample_strain=UNDEFINED_STRAIN
 
|sample_tissue=lung
 
|sample_tissue=lung
 
|top_motifs=
 
|top_motifs=
 +
|xref=
 +
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:14335-155F6;search_select_hide=table117:FF:14335-155F6
 
}}
 
}}

Latest revision as of 10:07, 4 June 2020


Name:Small Airway Epithelial Cells donor2 (nuclear fraction)
Species:Human (Homo sapiens)
Library ID:CNhs14565
Sample type:fractionations and perturbations
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainUNDEFINED_STRAIN
tissuelung
dev stage58 years old adult
sexmale
ageNA
cell typepneumocyte
cell lineUNDEFINED_CELL_LINE
companyNA
collaborationUNDEFINED_COLLABORATION
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00022307
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs14565 CAGE DRX022780 DRR025119
Accession ID Hg19

Library idBAMCTSS
CNhs14565 DRZ003544 DRZ004427
Accession ID Hg38

Library idBAMCTSS
CNhs14565 DRZ008285 DRZ009168
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload





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>dataNo results for this sample

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: CNhs14565This 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: CNhs14565This 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: CNhs14565


FANTOM5 (FF) ontology


Direct parent terms


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)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0002076 (endo-epithelial cell)
0002368 (respiratory epithelial cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0004119 (endoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0000065 (respiratory tract)
0001004 (respiratory system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000408 (cellular fractionation sample)
0000350 (experimentally modified sample)
0000166 (human small airway epithelial cell sample)
0000406 (nuclear fraction sample)
0000673 (human Small Airway Epithelial Cells, nuclear fraction sample)

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
CL:0000223 (endodermal cell)