Personal tools

FF:12626-134E7: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00021390
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00021390
|accession_numbers=CAGE;DRX022906;DRR025245;DRZ003670;DRZ004553;DRZ008411;DRZ009294
|accession_numbers_RNASeq=sRNA-Seq;DRX037270;DRR041636;DRZ007278
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002321,CL:0000255,CL:0000034,CL:0002322
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002321,CL:0000255,CL:0000034,CL:0002322
Line 8: Line 12:
|creation_date=
|creation_date=
|data_phase=2
|data_phase=2
|datafreeze_phase=2
|def=
|def=
|fantom_cat=http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0000034;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0002322
|fonse_cell_line=FF:0100669
|fonse_cell_line=FF:0100669
|fonse_cell_line_closure=FF:0100669
|fonse_cell_line_closure=FF:0100669
Line 36: Line 42:
|fonse_treatment_closure=FF:0000343,FF:0000592,FF:12626-134E7
|fonse_treatment_closure=FF:0000343,FF:0000592,FF:12626-134E7
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/H9%2520Embryonic%2520Stem%2520cells%252c%2520biol_rep1%2520%2528H9ES-1%2529.CNhs11917.12626-134E7.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/H9%2520Embryonic%2520Stem%2520cells%252c%2520biol_rep1%2520%2528H9ES-1%2529.CNhs11917.12626-134E7.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/H9%2520Embryonic%2520Stem%2520cells%252c%2520biol_rep1%2520%2528H9ES-1%2529.CNhs11917.12626-134E7.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/H9%2520Embryonic%2520Stem%2520cells%252c%2520biol_rep1%2520%2528H9ES-1%2529.CNhs11917.12626-134E7.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/H9%2520Embryonic%2520Stem%2520cells%252c%2520biol_rep1%2520%2528H9ES-1%2529.CNhs11917.12626-134E7.hg38.nobarcode.ctss.bed.gz
|id=FF:12626-134E7
|id=FF:12626-134E7
|is_a=EFO:0002091;;FF:0000592
|is_a=EFO:0002091;;FF:0000592
|is_obsolete=
|is_obsolete=
|library_id=CNhs11917
|library_id_phase_based=2:CNhs11917
|library_id_phase_based=2:CNhs11917
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;12626
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10012.ACAGTG.12626
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;12626
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10012.ACAGTG.12626
|name=H9 Embryonic Stem cells, biol_rep1 (H9ES-1)
|name=H9 Embryonic Stem cells, biol_rep1 (H9ES-1)
|namespace=FANTOM5
|namespace=FANTOM5
Line 45: Line 63:
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_hcage=CNhs11917,LSID770,release010,COMPLETED
|profile_hcage=CNhs11917,LSID770,release010,COMPLETED
|profile_rnaseq=,,,
|profile_rnaseq=
|profile_srnaseq=SRhi10012,,,
|profile_srnaseq=SRhi10012,,,
|rna_box=134
|rna_box=134
Line 57: Line 75:
|rna_rin=
|rna_rin=
|rna_sample_type=
|rna_sample_type=
|rna_tube_id=134E7
|rna_tube_id=1.34E+09
|rna_weight_ug=7.00
|rna_weight_ug=7
|rnaseq_library_id=SRhi10012.ACAGTG
|sample_age=
|sample_age=
|sample_category=time courses
|sample_category=time courses
Line 79: Line 98:
|sample_strain=
|sample_strain=
|sample_tissue=unclassifiable
|sample_tissue=unclassifiable
|timecourse=Melanocytic_differentiation
|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:12626-134E7;search_select_hide=table117:FF:12626-134E7
}}
}}

Latest revision as of 18:41, 4 June 2020

Name:H9 Embryonic Stem cells, biol_rep1 (H9ES-1)
Species:Human (Homo sapiens)
Library ID:CNhs11917
Sample type:time courses
Genomic View: UCSC
FANTOM CAT:1, 2
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueunclassifiable
dev stageNA
sexfemale
ageNA
cell typestem cell
cell lineH9
companyNA
collaborationSusan Zabierowski (Wistar Institute)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00021390
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11917 CAGE DRX022906 DRR025245
Accession ID Hg19

Library idBAMCTSS
CNhs11917 DRZ003670 DRZ004553
Accession ID Hg38

Library idBAMCTSS
CNhs11917 DRZ008411 DRZ009294
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00021390
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10012.ACAGTG sRNA-Seq DRX037270 DRR041636
Accession ID Hg19

Library idBAMCTSS
SRhi10012.ACAGTG DRZ007278





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: CNhs11917This 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: CNhs11917This 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: CNhs11917


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)
0002321 (embryonic cell)
0000255 (eukaryotic cell)
0000034 (stem cell)
0002322 (embryonic stem cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0101581 (embryonic stem cell line sample)
0000343 (control treatment sample)
0000350 (experimentally modified sample)
0000400 (H9 embryonic stem cell line sample)
0100669 (embryonic cell line sample)
0000592 (human H9 Embryonic Stem cells 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
NA

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:12626-134E7&oldid=4577140"