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{{f5samples
{{f5samples
|id=FF:13455-144G8
|DRA_sample_Accession=CAGE@SAMD00022073
|name=
|accession_numbers=CAGE;DRX023384;DRR025779;DRZ004204;DRZ005031;DRZ008945;DRZ009772
|sample_id=13455
|rna_tube_id=144G8
|rna_box=144
|rna_position=G8
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=
|sample_donor(cell lot)=C11-CCL54
|sample_sex=male
|sample_age=unknown
|sample_ethnicity=
|rna_rin=7.7
|rna_od260/230=2
|rna_od260/280=1.82
|sample_cell_type=iPS-derived neurospheres
|sample_cell_line=
|sample_collaboration=Christine Wells (University of Queensland)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=5
|rna_concentration=0.2
|sample_note=
|profile_hcage=CNhs13952,LSID1138,release015,SEQUENCING QUEUE
|profile_cagescan=
|profile_srnaseq=
|profile_rnaseq=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_disease_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000540,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000393,CL:0000211,CL:0000404,CL:0000255
|sample_description=
|ancestors_in_disease_facet=DOID:4,DOID:630,DOID:0050177,DOID:0080014,DOID:14250
|ancestors_in_ff_facet=FF:0000210,FF:0000101,FF:0000001,FF:0200005,FF:0200004
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|donor= rep3
|ffid_belonging_in_development=CL:0000133,CL:0000031,CL:0000221
|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=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/iPS%2520differentiation%2520to%2520neuron%252c%2520down-syndrome%2520donor%2520C11-CCL54%252c%2520day12%252c%2520rep3.CNhs14058.13455-144G8.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/iPS%2520differentiation%2520to%2520neuron%252c%2520down-syndrome%2520donor%2520C11-CCL54%252c%2520day12%252c%2520rep3.CNhs14058.13455-144G8.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/iPS%2520differentiation%2520to%2520neuron%252c%2520down-syndrome%2520donor%2520C11-CCL54%252c%2520day12%252c%2520rep3.CNhs14058.13455-144G8.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/iPS%2520differentiation%2520to%2520neuron%252c%2520down-syndrome%2520donor%2520C11-CCL54%252c%2520day12%252c%2520rep3.CNhs14058.13455-144G8.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/iPS%2520differentiation%2520to%2520neuron%252c%2520down-syndrome%2520donor%2520C11-CCL54%252c%2520day12%252c%2520rep3.CNhs14058.13455-144G8.hg38.nobarcode.ctss.bed.gz
|id=FF:13455-144G8
|is_a=FF:0000210;;FF:0200004;;PR:00000349
|is_obsolete=
|library_id=CNhs14058
|library_id_phase_based=2:CNhs14058
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;13455
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;13455
|name=iPS differentiation to neuron, down-syndrome donor C18-CCL54
|namespace=
|part_of=
|profile_cagescan=
|profile_hcage=CNhs14058,LSID1158,release016,COMPLETED
|profile_rnaseq=
|profile_srnaseq=
|rna_box=144
|rna_catalog_number=
|rna_concentration=0.2
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=2
|rna_od260/280=1.82
|rna_position=G8
|rna_rin=7.7
|rna_sample_type=total RNA
|rna_tube_id=144G8
|rna_weight_ug=5
|sample_age=unknown
|sample_category=time courses
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=iPS-derived neurospheres
|sample_collaboration=Christine Wells (University of Queensland)
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=C11-CCL54
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=13455
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=
|time= day12
|timecourse=Human_iPS_to_neuron_(Down's_syndrome)_1
|top_motifs=
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:13455-144G8;search_select_hide=table117:FF:13455-144G8
}}
}}

Latest revision as of 18:59, 4 June 2020


Name:iPS differentiation to neuron, down-syndrome donor C18-CCL54
Species:Human (Homo sapiens)
Library ID:CNhs14058
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexmale
ageunknown
cell typeiPS-derived neurospheres
cell lineNA
companyNA
collaborationChristine Wells (University of Queensland)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00022073
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs14058 CAGE DRX023384 DRR025779
Accession ID Hg19

Library idBAMCTSS
CNhs14058 DRZ004204 DRZ005031
Accession ID Hg38

Library idBAMCTSS
CNhs14058 DRZ008945 DRZ009772
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
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>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: CNhs14058This 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: CNhs14058This 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: CNhs14058


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000540 (neuron)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)

DOID: Disease
4 (disease)
630 (genetic disease)
0050177 (monogenic disease)
0080014 (chromosomal disease)
14250 (Down syndrome)

FF: FANTOM5
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0200005 (iPS differentiation to neuron sample)
0200004 (iPS differentiation to neuron, down-syndrome donor 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
CL:0000133 (neurectodermal cell)
CL:0000031 (neuroblast)
CL:0000221 (ectodermal cell)

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