Personal tools

FF:11498-119F4: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(22 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|id=FF:11498-119F4
|DRA_sample_Accession=CAGE@SAMD00005819
|name=Schwann Cells, donor1
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00005819
|sample_id=11498
|accession_numbers=CAGE;DRX008444;DRR009316;DRZ000741;DRZ002126;DRZ012091;DRZ013476
|rna_tube_id=119F4
|accession_numbers_RNASeq=sRNA-Seq;DRX037115;DRR041481;DRZ007123
|rna_box=119
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0004121,UBERON:0011216,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0000010,UBERON:0001016
|rna_position=F4
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000095,CL:0000243,CL:0000325,CL:0000215,CL:0000630,CL:0000217,CL:0000328,CL:0002573,CL:0000125,CL:0000255,CL:0002376,CL:0000218,CL:0000692,CL:0002377
|sample_cell_lot=N/A
|sample_cell_catalog=N/A
|sample_company=Sciencell/3H
|rna_lot_number=lot:5951
|rna_catalog_number=SC1705
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=peripheral nervous system
|sample_donor(cell lot)=
|sample_sex=
|sample_age=
|sample_ethnicity=
|rna_rin=9.7
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=schwann cell
|sample_cell_line=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_weight_ug=10
|rna_concentration=1.375
|sample_note=
|profile_hcage=CNhs12073,LSID838,release011,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=SRhi10008,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000030,CL:0000055,CL:0000095,CL:0000123,CL:0000125,CL:0000133,CL:0000144,CL:0000215,CL:0000217,CL:0000218,CL:0000219,CL:0000220,CL:0000221,CL:0000243,CL:0000255,CL:0000325,CL:0000328,CL:0000333,CL:0000339,CL:0000548,CL:0000630,CL:0000692,CL:0002319,CL:0002321,CL:0002371,CL:0002375,CL:0002376,CL:0002377,CL:0002573
|ancestors_in_anatomy_facet=UBERON:0000010,UBERON:0000061,UBERON:0000073,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001016,UBERON:0001062,UBERON:0002050,UBERON:0002532,UBERON:0004121,UBERON:0005423
|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:0000159
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|fantom_cat=http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0002573
|ffid_belonging_in_development=CL:0000133,CL:0000339,CL:0000221
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 42:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Schwann%2520Cells%252c%2520donor1.CNhs12073.11498-119F4.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Schwann%2520Cells%252c%2520donor1.CNhs12073.11498-119F4.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Schwann%2520Cells%252c%2520donor1.CNhs12073.11498-119F4.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Schwann%2520Cells%252c%2520donor1.CNhs12073.11498-119F4.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Schwann%2520Cells%252c%2520donor1.CNhs12073.11498-119F4.hg38.nobarcode.ctss.bed.gz
|id=FF:11498-119F4
|is_a=EFO:0002091;;FF:0000159
|is_obsolete=
|library_id=CNhs12073
|library_id_phase_based=2:CNhs12073
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11498
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10008.GATCAG.11498
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11498
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10008.GATCAG.11498
|name=Schwann Cells, donor1
|namespace=FANTOM5
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12073,LSID838,release011,COMPLETED
|profile_rnaseq=
|profile_srnaseq=SRhi10008,,,
|rna_box=119
|rna_catalog_number=SC1705
|rna_concentration=1.375
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_lot_number=lot:5951
|rna_od260/230=
|rna_od260/280=
|rna_position=F4
|rna_rin=9.7
|rna_sample_type=total RNA
|rna_tube_id=119F4
|rna_weight_ug=10
|rnaseq_library_id=SRhi10008.GATCAG
|sample_age=
|sample_category=primary cells
|sample_cell_catalog=N/A
|sample_cell_line=
|sample_cell_lot=N/A
|sample_cell_type=schwann cell
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=Sciencell/3H
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=11498
|sample_note=
|sample_sex=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=peripheral nervous system
|top_motifs=
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:11498-119F4;search_select_hide=table117:FF:11498-119F4
}}
}}

Latest revision as of 18:04, 4 June 2020

Name:Schwann Cells, donor1
Species:Human (Homo sapiens)
Library ID:CNhs12073
Sample type:primary cells
Genomic View: UCSC
FANTOM CAT:1
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueperipheral nervous system
dev stageNA
sexNA
ageNA
cell typeschwann cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberlot:5951
catalog numberSC1705
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005819
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12073 CAGE DRX008444 DRR009316
Accession ID Hg19

Library idBAMCTSS
CNhs12073 DRZ000741 DRZ002126
Accession ID Hg38

Library idBAMCTSS
CNhs12073 DRZ012091 DRZ013476
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00005819
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10008.GATCAG sRNA-Seq DRX037115 DRR041481
Accession ID Hg19

Library idBAMCTSS
SRhi10008.GATCAG DRZ007123





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: CNhs12073This 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: CNhs12073This 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: CNhs12073


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)
0002371 (somatic cell)
0002319 (neural cell)
0000095 (neuron associated cell)
0000243 (glial cell (sensu Vertebrata))
0000325 (stuff accumulating cell)
0000215 (barrier cell)
0000630 (supportive cell)
0000217 (insulating cell)
0000328 (myelin accumulating cell)
0002573 (Schwann cell)
0000125 (glial cell)
0000255 (eukaryotic cell)
0002376 (non-myelinating Schwann cell)
0000218 (myelinating Schwann cell;;Schwann cell)
0000692 (terminal Schwann cell)
0002377 (immature Schwann cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0004121 (ectoderm-derived structure)
0011216 (organ system subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0000010 (peripheral nervous system)
0001016 (nervous system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000159 (human Schwann cell 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:0000133 (neurectodermal cell)
CL:0000339 (glioblast (sensu Vertebrata))
CL:0000221 (ectodermal cell)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:11498-119F4&oldid=4576512"