Personal tools

FF:10101-102D3: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(9 intermediate revisions by 2 users not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00021109
|accession_numbers=CAGE;DRX023717;DRR026112;DRZ005364;DRZ006154!CAGE;DRX023718;DRR026113;DRZ005365;DRZ006155!CAGE;DRX023719;DRR026114;DRZ005366;DRZ006156!CAGE;DRX023720;DRR026115;DRZ005367;DRZ006157!CAGE;DRX023721;DRR026116;DRZ005368;DRZ006158!CAGE;DRX023722;DRR026117;DRZ005369;DRZ006159!CAGE;DRX023736;DRR026135;DRZ005387;DRZ006173!CAGE;DRX023737;DRR026136;DRZ005388;DRZ006174!CAGE;DRX023739;DRR026138;DRZ005390;DRZ006176
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
Line 7: Line 9:
|created_by=
|created_by=
|creation_date=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|def=
|expression_enrichment_score=
|expression_enrichment_score=
|ffid_belonging_in_development=FF:0000294
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 36: Line 41:
|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|has_quality=
|id=
|id=FF:10101-102D3
|is_a=EFO:0001461;;FF:0011374
|is_a=EFO:0001461;;FF:0011374
|is_obsolete=
|is_obsolete=
|name=
|library_id=CNhs13928!CNhs13929!CNhs13930!CNhs13931!CNhs13932!CNhs13933!CNhs13934!CNhs13935!CNhs13967
|library_id_phase_based=2:CNhs13928,CNhs13929,CNhs13930,CNhs13931,CNhs13932,CNhs13933,CNhs13934,CNhs13935,CNhs13967
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.qualitycontrol.hCAGE/whole%2520body%252c%2520embryo%2520E17%252e5%252c%2520pool1%2520%2528internal%2520control%2529.CNhs13967.10101-102D3.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.qualitycontrol.hCAGE/whole%2520body%252c%2520embryo%2520E17%252e5%252c%2520pool1%2520%2528internal%2520control%2529.CNhs13967.10101-102D3.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.qualitycontrol.hCAGE/whole%2520body%252c%2520embryo%2520E17%252e5%252c%2520pool1%2520%2528internal%2520control%2529.CNhs13967.10101-102D3.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.qualitycontrol.hCAGE/whole%2520body%252c%2520embryo%2520E17%252e5%252c%2520pool1%2520%2528internal%2520control%2529.CNhs13967.10101-102D3.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.qualitycontrol.hCAGE/whole%2520body%252c%2520embryo%2520E17%252e5%252c%2520pool1%2520%2528internal%2520control%2529.CNhs13967.10101-102D3.mm9.nobarcode.rdna.fa.gz
|name=whole body, embryo E17.5, pool1 (internal control)
|namespace=
|namespace=
|part_of=
|part_of=
Line 46: Line 58:
|profile_rnaseq=
|profile_rnaseq=
|profile_srnaseq=
|profile_srnaseq=
|rna_box=
|rna_box=102
|rna_catalog_number=
|rna_catalog_number=NA
|rna_concentration=
|rna_concentration=109
|rna_extraction_protocol=
|rna_extraction_protocol=1
|rna_lot_number=
|rna_lot_number=NA
|rna_od260/230=
|rna_od260/230=2.1
|rna_od260/280=
|rna_od260/280=2
|rna_position=
|rna_position=D3
|rna_rin=
|rna_rin=8.5
|rna_sample_type=
|rna_sample_type=total RNA
|rna_tube_id=
|rna_tube_id=102D3
|rna_weight_ug=
|rna_weight_ug=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|sample_age=
|sample_age=
|sample_cell_catalog=
|sample_category=control
|sample_cell_catalog=NA
|sample_cell_line=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_lot=NA
|sample_cell_type=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=
|sample_company=NA
|sample_description=
|sample_description=
|sample_dev_stage=
|sample_dev_stage=17.5 days embryo
|sample_disease=
|sample_disease=normal
|sample_donor(cell lot)=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_ethnicity=
|sample_experimental_condition=
|sample_experimental_condition=
|sample_id=
|sample_id=10101
|sample_note=
|sample_note=
|sample_sex=
|sample_sex=
|sample_species=
|sample_species=Mouse (Mus musculus)
|sample_strain=
|sample_strain=C57BL/6J
|sample_tissue=
|sample_tissue=whole body
|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:10101-102D3;search_select_hide=table117:10101-102D3
}}
}}

Latest revision as of 12:21, 3 June 2020


Name:whole body, embryo E17.5, pool1 (internal control)
Species:Mouse (Mus musculus)
Library ID:CNhs13928,CNhs13929,CNhs13930,CNhs13931,CNhs13932,CNhs13933,CNhs13934,CNhs13935,CNhs13967
Sample type:control
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainC57BL/6J
tissuewhole body
dev stage17.5 days embryo
sexNA
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)1

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00021109
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13928 CAGE DRX023717 DRR026112
CNhs13929 CAGE DRX023718 DRR026113
CNhs13930 CAGE DRX023719 DRR026114
CNhs13931 CAGE DRX023720 DRR026115
CNhs13932 CAGE DRX023721 DRR026116
CNhs13933 CAGE DRX023722 DRR026117
CNhs13934 CAGE DRX023736 DRR026135
CNhs13935 CAGE DRX023737 DRR026136
CNhs13967 CAGE DRX023739 DRR026138
Accession ID Mm9

Library idBAMCTSS
CNhs13928 DRZ005364 DRZ006154
CNhs13929 DRZ005365 DRZ006155
CNhs13930 DRZ005366 DRZ006156
CNhs13931 DRZ005367 DRZ006157
CNhs13932 DRZ005368 DRZ006158
CNhs13933 DRZ005369 DRZ006159
CNhs13934 DRZ005387 DRZ006173
CNhs13935 DRZ005388 DRZ006174
CNhs13967 DRZ005390 DRZ006176
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload





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>data

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



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



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>


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

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000301 (mouse embryonic day 17.5 sample)
0011374 (mouse whole body- embryo E17.5 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
FF:0000294 (mouse embryonic day 11 sample)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:10101-102D3&oldid=4575848"