Personal tools

FF:10144-102H9: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{f5samples |id=FF:10144-102H9 |name=cerebellum, embryo E17, biol_rep3 (E17R3) |sample_id=10144 |rna_tube_id=102H9 |rna_box=102 |rna_position=H9 |sample_cell_lot= |sam...")
 
No edit summary
 
(20 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|id=FF:10144-102H9
|DRA_sample_Accession=CAGE@SAMD00021141
|name=cerebellum, embryo E17, biol_rep3 (E17R3)
|accession_numbers=CAGE;DRX024350;DRR026755;DRZ006007;DRZ006787;DRZ010622;DRZ011280
|sample_id=10144
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000955,UBERON:0002037,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002680,UBERON:0002616,UBERON:0004733,UBERON:0004732,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001895,UBERON:0002028
|rna_tube_id=102H9
|rna_box=102
|rna_position=H9
|sample_cell_lot=
|sample_cell_catalog=NA
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_dev_stage=17 days embryo
|sample_tissue=cerebellum
|sample_donor(cell lot)=
|sample_sex=
|sample_age=
|sample_ethnicity=
|rna_rin=9.80000
|rna_od260/230=1.63000
|rna_od260/280=1.94000
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_line=
|sample_collaboration=Dan Goldowitz(University of British Columbia Canada)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=
|rna_extraction_protocol=
|rna_weight_ug=55.08000
|rna_concentration=0.61200
|sample_note=
|profile_hcage=CNhs13020,LSID999,,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000063,UBERON:0000064,UBERON:0000073,UBERON:0000153,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000955,UBERON:0001016,UBERON:0001017,UBERON:0001049,UBERON:0001062,UBERON:0001895,UBERON:0002028,UBERON:0002037,UBERON:0002050,UBERON:0002346,UBERON:0002532,UBERON:0002616,UBERON:0002680,UBERON:0003057,UBERON:0003075,UBERON:0003076,UBERON:0004121,UBERON:0004732,UBERON:0004733,UBERON:0005068,UBERON:0005423,UBERON:0005743,UBERON:0006598,UBERON:0007135,UBERON:0007284
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000999,FF:0000292,FF:0000004,FF:0000300,FF:0011188
 
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|donor= biol_rep3 (E17R3)
|ffid_belonging_in_development=UBERON:0002532,UBERON:0006601,UBERON:0006215,UBERON:0010316,FF:0000294
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 67: Line 40:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|id=FF:10144-102H9
|is_a=EFO:0002091;;FF:0011188
|is_obsolete=
|library_id=CNhs13020
|library_id_phase_based=2:CNhs13020
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;10144
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;10144
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/cerebellum%252c%2520embryo%2520E17%252c%2520biol_rep3%2520%2528E17R3%2529.CNhs13020.10144-102H9.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/cerebellum%252c%2520embryo%2520E17%252c%2520biol_rep3%2520%2528E17R3%2529.CNhs13020.10144-102H9.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/cerebellum%252c%2520embryo%2520E17%252c%2520biol_rep3%2520%2528E17R3%2529.CNhs13020.10144-102H9.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/cerebellum%252c%2520embryo%2520E17%252c%2520biol_rep3%2520%2528E17R3%2529.CNhs13020.10144-102H9.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/cerebellum%252c%2520embryo%2520E17%252c%2520biol_rep3%2520%2528E17R3%2529.CNhs13020.10144-102H9.mm9.nobarcode.rdna.fa.gz
|name=cerebellum
|namespace=FANTOM5
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs13020,LSID999,release012,COMPLETED
|profile_rnaseq=
|profile_srnaseq=,,,
|rna_box=102
|rna_catalog_number=
|rna_concentration=0.612
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=1.63
|rna_od260/280=1.94
|rna_position=H9
|rna_rin=9.8
|rna_sample_type=
|rna_tube_id=102H9
|rna_weight_ug=55.08
|sample_age=
|sample_category=developmental
|sample_cell_catalog=NA
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=Dan Goldowitz(University of British Columbia Canada)
|sample_company=
|sample_description=
|sample_dev_stage=17 days embryo
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=10144
|sample_note=
|sample_sex=
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=cerebellum
|time= embryo E17
|timecourse=Cerebellum_development
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:10144-102H9;search_select_hide=table117:10144-102H9
}}
}}

Latest revision as of 12:22, 3 June 2020


Name:cerebellum
Species:Mouse (Mus musculus)
Library ID:CNhs13020
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainC57BL/6J
tissuecerebellum
dev stage17 days embryo
sexNA
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationDan Goldowitz(University of British Columbia Canada)
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  SAMD00021141
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13020 CAGE DRX024350 DRR026755
Accession ID Mm9

Library idBAMCTSS
CNhs13020 DRZ006007 DRZ006787
Accession ID Mm10

Library idBAMCTSS
CNhs13020 DRZ010622 DRZ011280
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

CNhs13020



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: CNhs13020This 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: CNhs13020This 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: CNhs13020


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)
0000955 (brain)
0002037 (cerebellum)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002680 (regional part of metencephalon)
0002616 (regional part of brain)
0004733 (segmental subdivision of hindbrain)
0004732 (segmental subdivision of nervous system)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001895 (metencephalon)
0002028 (hindbrain)

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)
0000300 (mouse embryonic day 17 sample)
0011188 (mouse cerebellum- embryo E17 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
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0006215 (rhombic lip)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:10144-102H9&oldid=4575880"