Personal tools

FF:10101-102D4: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(11 intermediate revisions by 3 users not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00021110
|accession_numbers=CAGE;DRX023727;DRR026126;DRZ005378;DRZ006164!CAGE;DRX023728;DRR026127;DRZ005379;DRZ006165!CAGE;DRX023731;DRR026130;DRZ005382;DRZ006168!CAGE;DRX023732;DRR026131;DRZ005383;DRZ006169!CAGE;DRX023733;DRR026132;DRZ005384;DRZ006170!CAGE;DRX023734;DRR026133;DRZ005385;DRZ006171!CAGE;DRX023735;DRR026134;DRZ005386;DRZ006172!CAGE;DRX023738;DRR026137;DRZ005389;DRZ006175!CAGE;DRX023740;DRR026139;DRZ005391;DRZ006177!CAGE;DRX023741;DRR026140;DRZ005392;DRZ006178!CAGE;DRX023742;DRR026141;DRZ005393;DRZ006179!CAGE;DRX023743;DRR026142;DRZ005394;DRZ006180!CAGE;DRX023744;DRR026143;DRZ005395;DRZ006181!CAGE;DRX023745;DRR026144;DRZ005396;DRZ006182!CAGE;DRX023748;DRR026147;DRZ005399;DRZ006185!CAGE;DRX023755;DRR026154;DRZ005406;DRZ006192!CAGE;DRX024299;DRR026704;DRZ005956;DRZ006736;DRZ010571;DRZ011229
|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=
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000999,FF:0000292,FF:0000004,FF:0000343,FF:0000301,FF:0011374
|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000999,FF:0000292,FF:0000004,FF:0000343,FF:0000301,FF:0011374
|data_phase=2
|datafreeze_phase=2
|ffid_belonging_in_development=FF:0000294
|ffid_belonging_in_development=FF:0000294
|id=FF:10101-102D4
|id=FF:10101-102D4
|is_a=FF:0000343;;FF:0011374
|library_id=CNhs14096!CNhs14120!CNhs14048!CNhs14072!CNhs14145!CNhs14161!CNhs14185!CNhs14209!CNhs14409!CNhs14433!CNhs14521!CNhs14545!CNhs14569!CNhs14593!CNhs14457!CNhs14377!CNhs14401
|library_id_phase_based=2:CNhs14096,CNhs14120,CNhs14048,CNhs14072,CNhs14145,CNhs14161,CNhs14185,CNhs14209,CNhs14409,CNhs14433,CNhs14521,CNhs14545,CNhs14569,CNhs14593,CNhs14457,CNhs14377,CNhs14401
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.LQhCAGE/whole%2520body%252c%2520embryo%2520E17%252e5%252c%2520pool1%2520%2528internal%2520control%2529.CNhs14401.10101-102D4.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.LQhCAGE/whole%2520body%252c%2520embryo%2520E17%252e5%252c%2520pool1%2520%2528internal%2520control%2529.CNhs14401.10101-102D4.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.qualitycontrol.LQhCAGE/whole%2520body%252c%2520embryo%2520E17%252e5%252c%2520pool1%2520%2528internal%2520control%2529.CNhs14377.10101-102D4.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.qualitycontrol.LQhCAGE/whole%2520body%252c%2520embryo%2520E17%252e5%252c%2520pool1%2520%2528internal%2520control%2529.CNhs14377.10101-102D4.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.qualitycontrol.LQhCAGE/whole%2520body%252c%2520embryo%2520E17%252e5%252c%2520pool1%2520%2528internal%2520control%2529.CNhs14377.10101-102D4.mm9.nobarcode.rdna.fa.gz
|name=whole body, embryo E17.5, pool1 (internal control)
|profile_hcage=
|profile_rnaseq=
|profile_srnaseq=
|rna_box=102
|rna_catalog_number=NA
|rna_concentration=290
|rna_extraction_protocol=1
|rna_lot_number=NA
|rna_od260/230=2.1
|rna_od260/280=2
|rna_position=D2
|rna_rin=8.5
|rna_sample_type=total RNA
|rna_tube_id=102D2
|rna_weight_ug=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|sample_age=
|sample_category=control
|sample_cell_catalog=NA
|sample_cell_line=
|sample_cell_lot=NA
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=NA
|sample_dev_stage=17.5 days embryo
|sample_disease=normal
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=10101
|sample_note=
|sample_sex=
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=whole body
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:10101-102D4;search_select_hide=table117:10101-102D4
}}
}}

Latest revision as of 12:21, 3 June 2020


Name:whole body, embryo E17.5, pool1 (internal control)
Species:Mouse (Mus musculus)
Library ID:CNhs14096,CNhs14120,CNhs14048,CNhs14072,CNhs14145,CNhs14161,CNhs14185,CNhs14209,CNhs14409,CNhs14433,CNhs14521,CNhs14545,CNhs14569,CNhs14593,CNhs14457,CNhs14377,CNhs14401
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  SAMD00021110
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs14096 CAGE DRX023727 DRR026126
CNhs14120 CAGE DRX023728 DRR026127
CNhs14048 CAGE DRX023731 DRR026130
CNhs14072 CAGE DRX023732 DRR026131
CNhs14145 CAGE DRX023733 DRR026132
CNhs14161 CAGE DRX023734 DRR026133
CNhs14185 CAGE DRX023735 DRR026134
CNhs14209 CAGE DRX023738 DRR026137
CNhs14409 CAGE DRX023740 DRR026139
CNhs14433 CAGE DRX023741 DRR026140
CNhs14521 CAGE DRX023742 DRR026141
CNhs14545 CAGE DRX023743 DRR026142
CNhs14569 CAGE DRX023744 DRR026143
CNhs14593 CAGE DRX023745 DRR026144
CNhs14457 CAGE DRX023748 DRR026147
CNhs14377 CAGE DRX023755 DRR026154
CNhs14401 CAGE DRX024299 DRR026704
Accession ID Mm9

Library idBAMCTSS
CNhs14096 DRZ005378 DRZ006164
CNhs14120 DRZ005379 DRZ006165
CNhs14048 DRZ005382 DRZ006168
CNhs14072 DRZ005383 DRZ006169
CNhs14145 DRZ005384 DRZ006170
CNhs14161 DRZ005385 DRZ006171
CNhs14185 DRZ005386 DRZ006172
CNhs14209 DRZ005389 DRZ006175
CNhs14409 DRZ005391 DRZ006177
CNhs14433 DRZ005392 DRZ006178
CNhs14521 DRZ005393 DRZ006179
CNhs14545 DRZ005394 DRZ006180
CNhs14569 DRZ005395 DRZ006181
CNhs14593 DRZ005396 DRZ006182
CNhs14457 DRZ005399 DRZ006185
CNhs14377 DRZ005406 DRZ006192
CNhs14401 DRZ005956 DRZ006736
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

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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)
0000343 (control treatment 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:10101-102D4&oldid=4575849"