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{{f5samples
{{f5samples
|id=FF:11424-118G2
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00035592
|name=Neural stem cells, donor3
|accession_numbers_RNASeq=sRNA-Seq;DRX037187;DRR041553;DRZ007195
|sample_id=11424
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0004121,UBERON:0011216,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0001017,UBERON:0001016
|rna_tube_id=118G2
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000047,CL:0000003,CL:0000723,CL:0000048,CL:0000548,CL:0002371,CL:0002319,CL:0000255,CL:0000034
|rna_box=118
|rna_position=G2
|sample_cell_lot=N/A
|sample_cell_catalog=N/A
|sample_company=Cell Applications
|rna_lot_number=2654.00000
|rna_catalog_number=custom
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=18 weeks old fetus
|sample_tissue=brain
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=embryo 18 week
|sample_ethnicity=M
|rna_rin=
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=neural stem cell
|sample_cell_line=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_weight_ug=10.00000
|rna_concentration=0.40000
|sample_note=
|profile_hcage=,LSID837,release011,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=SRhi10012,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000047,CL:0000048,CL:0000133,CL:0000144,CL:0000220,CL:0000221,CL:0000255,CL:0000548,CL:0000723,CL:0002319,CL:0002321,CL:0002371
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000073,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001016,UBERON:0001017,UBERON:0001062,UBERON:0002050,UBERON:0002532,UBERON:0004121,UBERON:0005423,UBERON:0005743
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|ancestors_in_ff_facet=FF:0000102,FF:0000210,FF:0000002,FF:0000101,FF:0000001,FF:0000120
 
|comment=
|created_by=
|creation_date=
|def=
|ffid_belonging_in_development=CL:0000133,CL:0000221
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 67: Line 37:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|id=FF:11424-118G2
|is_a=EFO:0002091;;FF:0000120
|is_obsolete=
|name=
|namespace=FANTOM5
|part_of=
|profile_cagescan=,,,
|profile_hcage=,LSID837,release011,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=SRhi10012,,,
|rna_box=118
|rna_catalog_number=custom
|rna_concentration=0.40000
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_lot_number=2654.00000
|rna_od260/230=
|rna_od260/280=
|rna_position=G2
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=118G2
|rna_weight_ug=10.00000
|rnaseq_library_id=SRhi10012.CAGATC
|sample_age=embryo 18 week
|sample_cell_catalog=N/A
|sample_cell_line=
|sample_cell_lot=N/A
|sample_cell_type=neural stem cell
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=Cell Applications
|sample_description=
|sample_dev_stage=18 weeks old fetus
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=M
|sample_experimental_condition=
|sample_id=11424
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=brain
|top_motifs=
|xref=
}}
}}

Latest revision as of 15:41, 17 October 2017


Name:
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebrain
dev stage18 weeks old fetus
sexmale
ageembryo 18 week
cell typeneural stem cell
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number2654.00000
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00035592
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10012.CAGATC sRNA-Seq DRX037187 DRR041553
Accession ID Hg19

Library idBAMCTSS
SRhi10012.CAGATC DRZ007195





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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000047 (neuronal stem cell)
0000003 (native cell)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000255 (eukaryotic cell)
0000034 (stem cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0004121 (ectoderm-derived structure)
0011216 (organ system subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000120 (human neural stem cell 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:0000221 (ectodermal cell)

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