Personal tools

FF:11270-116H1: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
(11 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008157
|DRA_sample_Accession=CAGE@SAMD00004854
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00004854
|accession_numbers=CAGE;DRX008265;DRR009137;DRZ000562;DRZ001947;DRZ011912;DRZ013297
|accession_numbers_RNASeq=sRNA-Seq;DRX037035;DRR041401;DRZ007043
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002048,UBERON:0002100,UBERON:0002384,UBERON:0000479,UBERON:0004119,UBERON:0000466,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000025,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0005178,UBERON:0005177,UBERON:0000117,UBERON:0000171,UBERON:0000464,UBERON:0005181,UBERON:0010317,UBERON:0000065,UBERON:0000170,UBERON:0001004,UBERON:0002224,UBERON:0000915
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002048,UBERON:0002100,UBERON:0002384,UBERON:0000479,UBERON:0004119,UBERON:0000466,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000025,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0005178,UBERON:0005177,UBERON:0000117,UBERON:0000171,UBERON:0000464,UBERON:0005181,UBERON:0010317,UBERON:0000065,UBERON:0000170,UBERON:0001004,UBERON:0002224,UBERON:0000915
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002320,CL:0002371,CL:0000255,CL:0000057,CL:0002553
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002320,CL:0002371,CL:0000255,CL:0000057,CL:0002553
Line 8: Line 11:
|created_by=
|created_by=
|creation_date=
|creation_date=
|datafreeze_phase=1
|data_phase=2
|datafreeze_phase=2
|def=
|def=
|ffid_belonging_in_development=CL:0000134
|ffid_belonging_in_development=CL:0000134
Line 38: Line 42:
|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Fibroblast%2520-%2520Lung%252c%2520donor1.CNhs12500.11270-116H1.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Fibroblast%2520-%2520Lung%252c%2520donor1.CNhs12500.11270-116H1.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Fibroblast%2520-%2520Lung%252c%2520donor1.CNhs12500.11270-116H1.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Fibroblast%2520-%2520Lung%252c%2520donor1.CNhs12500.11270-116H1.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Fibroblast%2520-%2520Lung%252c%2520donor1.CNhs12500.11270-116H1.hg38.nobarcode.ctss.bed.gz
|id=FF:11270-116H1
|id=FF:11270-116H1
|is_a=EFO:0002091;;FF:0000064
|is_a=EFO:0002091;;FF:0000064
|is_obsolete=
|is_obsolete=
|library_ids=CNhs12500
|library_id=CNhs12500
|library_id_phase_based=2:CNhs12500
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11270
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10004.ACAGTG.11270
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11270
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10004.ACAGTG.11270
|name=Fibroblast - Lung, donor1
|name=Fibroblast - Lung, donor1
|namespace=FANTOM5
|namespace=FANTOM5
Line 47: Line 63:
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_hcage=CNhs12500,LSID916,release011,COMPLETED
|profile_hcage=CNhs12500,LSID916,release011,COMPLETED
|profile_rnaseq=,,,
|profile_rnaseq=
|profile_srnaseq=SRhi10004,,,
|profile_srnaseq=SRhi10004,,,
|rna_box=116
|rna_box=116
Line 61: Line 77:
|rna_tube_id=116H1
|rna_tube_id=116H1
|rna_weight_ug=10
|rna_weight_ug=10
|rnaseq_library_id=SRhi10004.ACAGTG
|sample_age=embryo 20week
|sample_age=embryo 20week
|sample_category=primary cells
|sample_category=primary cells
Line 83: Line 100:
|top_motifs=
|top_motifs=
|xref=
|xref=
}} {{DRAAccessionNumbers
|DRA_sample_Accession=CAGE@DRS008157
|accession_numbers=DRX008265;DRR009137;DRZ000562;DRZ001947;CAGE
|library_id=CNhs12500
}}
}}

Revision as of 15:20, 17 October 2017


Name:Fibroblast - Lung, donor1
Species:Human (Homo sapiens)
Library ID:CNhs12500
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuelung
dev stage20 weeks old fetus
sexfemale
ageembryo 20week
cell typefibroblast
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1432
catalog numberCA506-R10f
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004854
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12500 CAGE DRX008265 DRR009137
Accession ID Hg19

Library idBAMCTSS
CNhs12500 DRZ000562 DRZ001947
Accession ID Hg38

Library idBAMCTSS
CNhs12500 DRZ011912 DRZ013297
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00004854
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10004.ACAGTG sRNA-Seq DRX037035 DRR041401
Accession ID Hg19

Library idBAMCTSS
SRhi10004.ACAGTG DRZ007043





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: CNhs12500This 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: CNhs12500This 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: CNhs12500


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)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0000057 (fibroblast)
0002553 (lung fibroblast)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002048 (lung)
0002100 (trunk)
0002384 (connective tissue)
0000479 (tissue)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000025 (tube)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0005178 (thoracic cavity element)
0005177 (trunk region element)
0000117 (respiratory tube)
0000171 (respiration organ)
0000464 (anatomical space)
0005181 (thoracic segment organ)
0010317 (germ layer / neural crest derived structure)
0000065 (respiratory tract)
0000170 (pair of lungs)
0001004 (respiratory system)
0002224 (thoracic cavity)
0000915 (thoracic segment of trunk)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000057 (fibroblast sample)
0000001 (sample)
0000064 (human fibroblast of lung 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:0000134 (mesenchymal cell)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:11270-116H1&oldid=4346073"