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{{f5samples
{{f5samples
|id=FF:11378-118B1
|DRA_sample_Accession=CAGE@SAMD00005028
|name=Sebocyte, donor3
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00005028
|sample_id=11378
|accession_numbers=CAGE;DRX008449;DRR009321;DRZ000746;DRZ002131;DRZ012096;DRZ013481
|rna_tube_id=118B1
|accession_numbers_RNASeq=sRNA-Seq;DRX037133;DRR041499;DRZ007141
|rna_box=118
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001003,UBERON:0002097,UBERON:0002199,UBERON:0002419,UBERON:0000483,UBERON:0000479,UBERON:0004121,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0003102,UBERON:0007376,UBERON:0010371,UBERON:0002365,UBERON:0007771,UBERON:0002530,UBERON:0003297,UBERON:0001821,UBERON:0010317,UBERON:0003487,UBERON:0001820,UBERON:0002330,UBERON:0002416
|rna_position=B1
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000151,CL:0000066,CL:0002371,CL:0000076,CL:0000150,CL:0000362,CL:0000154,CL:0002159,CL:0000255,CL:0002077,CL:0000317,CL:0000622,CL:1000448,CL:0002308,CL:0002140
|sample_cell_lot=N/A
|sample_cell_catalog=N/A
|sample_company=N/A
|rna_lot_number=
|rna_catalog_number=N/A
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=52 years old adult
|sample_tissue=skin
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=
|sample_ethnicity=A
|rna_rin=10
|rna_od260/230=1.156666667
|rna_od260/280=2.056666667
|sample_cell_type=sebocyte
|sample_cell_line=
|sample_collaboration=Weonju Lee (Kyungpook National University School of Medicine)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=19.5932
|rna_concentration=0.891
|sample_note=
|profile_hcage=CNhs11995,LSID837,release011,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=SRhi10009,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000144,CL:0000150,CL:0000151,CL:0000154,CL:0000255,CL:0000317,CL:0000548,CL:0000622,CL:0002140,CL:0002371,CL:1000448
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000119,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000483,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001003,UBERON:0001062,UBERON:0001820,UBERON:0001821,UBERON:0002050,UBERON:0002097,UBERON:0002199,UBERON:0002330,UBERON:0002365,UBERON:0002416,UBERON:0002419,UBERON:0002530,UBERON:0002532,UBERON:0003102,UBERON:0003297,UBERON:0003487,UBERON:0004121,UBERON:0005423,UBERON:0007376,UBERON:0007383,UBERON:0007771
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|ancestors_in_ff_facet=FF:0000102,FF:0000210,FF:0000002,FF:0000101,FF:0000001,FF:0000160
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|ffid_belonging_in_development=CL:0000221
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 41:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|is_a=EFO:0002091;;FF:0000002;;FF:0000160;;FF:0000210
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Sebocyte%252c%2520donor3.CNhs11995.11378-118B1.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Sebocyte%252c%2520donor3.CNhs11995.11378-118B1.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Sebocyte%252c%2520donor3.CNhs11995.11378-118B1.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Sebocyte%252c%2520donor3.CNhs11995.11378-118B1.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Sebocyte%252c%2520donor3.CNhs11995.11378-118B1.hg38.nobarcode.ctss.bed.gz
|id=FF:11378-118B1
|is_a=EFO:0002091;;FF:0000160
|is_obsolete=
|library_id=CNhs11995
|library_id_phase_based=2:CNhs11995
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11378
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10009.GATCAG.11378
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11378
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10009.GATCAG.11378
|name=Sebocyte, donor3
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11995,LSID837,release011,COMPLETED
|profile_rnaseq=
|profile_srnaseq=SRhi10009,,,
|rna_box=118
|rna_catalog_number=N/A
|rna_concentration=0.891
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=1.156666667
|rna_od260/280=2.056666667
|rna_position=B1
|rna_rin=10
|rna_sample_type=total RNA
|rna_tube_id=118B1
|rna_weight_ug=19.5932
|rnaseq_library_id=SRhi10009.GATCAG
|sample_age=
|sample_category=primary cells
|sample_cell_catalog=N/A
|sample_cell_line=
|sample_cell_lot=N/A
|sample_cell_type=sebocyte
|sample_collaboration=Weonju Lee (Kyungpook National University School of Medicine)
|sample_company=N/A
|sample_description=
|sample_dev_stage=52 years old adult
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=A
|sample_experimental_condition=
|sample_id=11378
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=skin
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:11378-118B1;search_select_hide=table117:FF:11378-118B1
}}
}}

Latest revision as of 17:56, 4 June 2020


Name:Sebocyte, donor3
Species:Human (Homo sapiens)
Library ID:CNhs11995
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueskin
dev stage52 years old adult
sexmale
ageNA
cell typesebocyte
cell lineNA
companyN/A
collaborationWeonju Lee (Kyungpook National University School of Medicine)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005028
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11995 CAGE DRX008449 DRR009321
Accession ID Hg19

Library idBAMCTSS
CNhs11995 DRZ000746 DRZ002131
Accession ID Hg38

Library idBAMCTSS
CNhs11995 DRZ012096 DRZ013481
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00005028
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10009.GATCAG sRNA-Seq DRX037133 DRR041499
Accession ID Hg19

Library idBAMCTSS
SRhi10009.GATCAG DRZ007141





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: CNhs11995This 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: CNhs11995This 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: CNhs11995


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)
0000151 (secretory cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000076 (squamous epithelial cell)
0000150 (glandular epithelial cell)
0000362 (epidermal cell)
0000154 (protein secreting cell)
0002159 (general ecto-epithelial cell)
0000255 (eukaryotic cell)
0002077 (ecto-epithelial cell)
0000317 (sebum secreting cell)
0000622 (acinar cell)
1000448 (epithelial cell of sweat gland)
0002308 (epithelial cell of skin gland)
0002140 (acinar cell of sebaceous gland)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001003 (skin epidermis)
0002097 (skin of body)
0002199 (integument)
0002419 (skin gland)
0000483 (epithelium)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0003102 (surface structure)
0007376 (outer epithelium)
0010371 (ecto-epithelium)
0002365 (exocrine gland)
0007771 (epidermis gland)
0002530 (gland)
0003297 (gland of integumental system)
0001821 (sebaceous gland)
0010317 (germ layer / neural crest derived structure)
0003487 (skin sebaceous gland)
0001820 (sweat gland)
0002330 (exocrine system)
0002416 (integumental system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000160 (human sebocyte 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:0000221 (ectodermal cell)

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