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{{f5samples
{{f5samples
|id=FF:10245-104B2
|DRA_sample_Accession=CAGE@SAMD00021153
|name=visual cortex - Mecp knockout, neonate N15, donor2
|accession_numbers=CAGE;DRX024357;DRR026762;DRZ006014;DRZ006794;DRZ010629;DRZ011287
|sample_id=10245
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0002021,UBERON:0000411,UBERON:0000956,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0003528,UBERON:0002791,UBERON:0000467,UBERON:0002619,UBERON:0001062,UBERON:0000480,UBERON:0002616,UBERON:0002780,UBERON:0002020,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001869,UBERON:0001893,UBERON:0001890,UBERON:0000203,UBERON:0001950
|rna_tube_id=104B2
|rna_box=104
|rna_position=B2
|sample_cell_lot=N/A
|sample_cell_catalog=N/A
|sample_company=N/A
|rna_lot_number=N/A
|rna_catalog_number=N/A
|sample_species=mus musculus
|sample_strain=
|sample_dev_stage=postnatal day 15
|sample_tissue=Visual cortex
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=P15
|sample_ethnicity=N/A
|rna_rin=
|rna_od260/230=2.06
|rna_od260/280=2.1
|sample_cell_type=mixed
|sample_cell_line=N/A
|sample_collaboration=Michela Fagiolini/Alka Saxena/Piero Carninci
|sample_experimental_condition=age matched P15 mecp2 ko-2
|sample_disease=Rett Syndrome
|rna_sample_type=Visual cortex tissue
|rna_extraction_protocol=Total RNA Trizol Qiagen minElute
|rna_weight_ug=11.292
|rna_concentration=0.941
|sample_note=
|profile_hcage=CNhs13041,LSID999,release012,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:0000064,UBERON:0000073,UBERON:0000153,UBERON:0000411,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000955,UBERON:0000956,UBERON:0001016,UBERON:0001017,UBERON:0001049,UBERON:0001062,UBERON:0001869,UBERON:0001890,UBERON:0001893,UBERON:0002050,UBERON:0002346,UBERON:0002532,UBERON:0002616,UBERON:0002619,UBERON:0002780,UBERON:0002791,UBERON:0003056,UBERON:0003075,UBERON:0003080,UBERON:0004121,UBERON:0005068,UBERON:0005291,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:0000004,FF:0000303,FF:0000316,FF:0011271
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|donor= donor2
|ffid_belonging_in_development=UBERON:0002532,UBERON:0006601,UBERON:0010316,FF:0000294
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 40:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|id=FF:10245-104B2
|is_a=EFO:0002091;;FF:0011271
|is_obsolete=
|library_id=CNhs13041
|library_id_phase_based=2:CNhs13041
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;10245
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;10245
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520Mecp%2520knockout%252c%2520neonate%2520N15%252c%2520donor2.CNhs13041.10245-104B2.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520Mecp%2520knockout%252c%2520neonate%2520N15%252c%2520donor2.CNhs13041.10245-104B2.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520Mecp%2520knockout%252c%2520neonate%2520N15%252c%2520donor2.CNhs13041.10245-104B2.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520Mecp%2520knockout%252c%2520neonate%2520N15%252c%2520donor2.CNhs13041.10245-104B2.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520Mecp%2520knockout%252c%2520neonate%2520N15%252c%2520donor2.CNhs13041.10245-104B2.mm9.nobarcode.rdna.fa.gz
|name=visual cortex - Mecp knockout
|namespace=FANTOM5
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs13041,LSID999,release012,COMPLETED
|profile_rnaseq=
|profile_srnaseq=,,,
|rna_box=104
|rna_catalog_number=N/A
|rna_concentration=0.941
|rna_extraction_protocol=Total RNA Trizol Qiagen minElute
|rna_lot_number=N/A
|rna_od260/230=2.06
|rna_od260/280=2.1
|rna_position=B2
|rna_rin=
|rna_sample_type=Visual cortex tissue
|rna_tube_id=104B2
|rna_weight_ug=11.292
|sample_age=P15
|sample_category=tissues
|sample_cell_catalog=N/A
|sample_cell_line=N/A
|sample_cell_lot=N/A
|sample_cell_type=mixed
|sample_collaboration=Michela Fagiolini/Alka Saxena/Piero Carninci
|sample_company=N/A
|sample_description=
|sample_dev_stage=postnatal day 15
|sample_disease=Rett Syndrome
|sample_donor(cell lot)=
|sample_ethnicity=N/A
|sample_experimental_condition=age matched P15 mecp2 ko-2
|sample_id=10245
|sample_note=
|sample_sex=male
|sample_species=Mouse (Mus musculus)
|sample_strain=
|sample_tissue=Visual cortex
|time= neonate N15
|timecourse=Visual_cortex_development
|top_motifs=
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:10245-104B2;search_select_hide=table117:10245-104B2
}}
}}

Latest revision as of 13:57, 3 June 2020


Name:visual cortex - Mecp knockout
Species:Mouse (Mus musculus)
Library ID:CNhs13041
Sample type:tissues
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueVisual cortex
dev stagepostnatal day 15
sexmale
ageP15
cell typemixed
cell lineN/A
companyN/A
collaborationMichela Fagiolini/Alka Saxena/Piero Carninci
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberN/A
catalog numberN/A
sample typeVisual cortex tissue
extraction protocol (Details)Total RNA Trizol Qiagen minElute

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00021153
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13041 CAGE DRX024357 DRR026762
Accession ID Mm9

Library idBAMCTSS
CNhs13041 DRZ006014 DRZ006794
Accession ID Mm10

Library idBAMCTSS
CNhs13041 DRZ010629 DRZ011287
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

CNhs13041



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: CNhs13041This 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: CNhs13041This 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: CNhs13041


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)
0000955 (brain)
0002021 (occipital lobe)
0000411 (visual cortex)
0000956 (cerebral cortex)
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)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0002619 (regional part of cerebral cortex)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)
0001950 (neocortex)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000316 (mouse neonate N15 sample)
0011271 (mouse visual cortex from Mecp knockout- neonate N15 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:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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