FF:14383-156B9: Difference between revisions
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{{f5samples | {{f5samples | ||
| | |DRA_sample_Accession=CAGE@SAMD00011636 | ||
| | |accession_numbers=CAGE;DRX016550;DRR018323;DRZ003164;DRZ003170;DRZ008228;DRZ008234 | ||
|ancestors_in_anatomy_facet= | |ancestors_in_anatomy_facet= | ||
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000723,CL:0002371,CL:0000034,CL:0002248 | |||
|ancestors_in_disease_facet= | |ancestors_in_disease_facet= | ||
| | |ancestors_in_ff_facet=FF:0000210,FF:0000101,FF:0000001,FF:0300101 | ||
|comment= | |||
|created_by= | |||
|creation_date= | |||
|data_phase=2 | |||
|datafreeze_phase=2 | |||
|def= | |||
|fonse_cell_line= | |fonse_cell_line= | ||
|fonse_cell_line_closure= | |fonse_cell_line_closure= | ||
Line 66: | Line 38: | ||
|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|has_quality= | |has_quality= | ||
|is_a= | |hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/hIPS%2520%252bCCl2%252c%2520biol_rep1.CNhs14217.14383-156B9.hg19.nobarcode.bam | ||
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/hIPS%2520%252bCCl2%252c%2520biol_rep1.CNhs14217.14383-156B9.hg19.ctss.bed.gz | |||
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/hIPS%2520%252bCCl2%252c%2520biol_rep1.CNhs14217.14383-156B9.hg19.nobarcode.rdna.fa.gz | |||
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/hIPS%2520%252bCCl2%252c%2520biol_rep1.CNhs14217.14383-156B9.hg38.nobarcode.bam | |||
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/hIPS%2520%252bCCl2%252c%2520biol_rep1.CNhs14217.14383-156B9.hg38.nobarcode.ctss.bed.gz | |||
|id=FF:14383-156B9 | |||
|is_a=FF:0000210;;FF:0300101 | |||
|is_obsolete= | |||
|library_id=CNhs14217 | |||
|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;14383 | |||
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;14383 | |||
|name=hIPS +CCl2, biol_rep1 | |||
|namespace= | |namespace= | ||
|part_of= | |part_of= | ||
|profile_cagescan= | |||
|profile_hcage=CNhs14217,LSID1178,release016,COMPLETED | |||
|profile_rnaseq= | |||
|profile_srnaseq= | |||
|rna_box=156 | |||
|rna_catalog_number= | |||
|rna_concentration=0.5583 | |||
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-RNeasy_Mini-v1.0 | |||
|rna_lot_number= | |||
|rna_od260/230= | |||
|rna_od260/280=2.16 | |||
|rna_position=B9 | |||
|rna_rin= | |||
|rna_sample_type=total RNA | |||
|rna_tube_id=156B9 | |||
|rna_weight_ug=8.4 | |||
|sample_age= | |||
|sample_category=time courses | |||
|sample_cell_catalog= | |||
|sample_cell_line= | |||
|sample_cell_lot= | |||
|sample_cell_type=iPS | |||
|sample_collaboration=Yuki Hasegawa | |||
|sample_company= | |||
|sample_description= | |||
|sample_dev_stage= | |||
|sample_disease= | |||
|sample_donor(cell lot)= | |||
|sample_ethnicity= | |||
|sample_experimental_condition= | |||
|sample_id=14383 | |||
|sample_note= | |||
|sample_sex= | |||
|sample_species=Human (Homo sapiens) | |||
|sample_strain= | |||
|sample_tissue= | |||
|top_motifs= | |||
|xref= | |||
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:14383-156B9;search_select_hide=table117:FF:14383-156B9 | |||
}} | }} |
Latest revision as of 19:08, 4 June 2020
Name: | hIPS +CCl2, biol_rep1 |
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Species: | Human (Homo sapiens) |
Library ID: | CNhs14217 |
Sample type: | time courses |
Genomic View: | UCSC |
CAGEd-oPOSSUM: | link |
ZENBU report : | link |
Additional information | ||||||||||||||||||||||||||||
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Sample information
RNA information
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CAGE Accession numbers | ||||||||||||||||||||||||||||||||||||||||||||||
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Download raw sequence, BAM & CTSS | ||||||||||||||
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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: CNhs14217This 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: CNhs14217This 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: CNhs14217
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
FF:0000210 human sample
FF:0300101 hIPS sample
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)
0000723 (somatic stem cell)
0002371 (somatic cell)
0000034 (stem cell)
0002248 (pluripotent stem cell)
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