Personal tools

FF:13090-140C3: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{f5samples |id=FF:13090-140C3 |name=K562 erythroblastic leukemia response to hemin, 04hr, biol_rep1 |sample_id=13090 |rna_tube_id=140C3 |rna_box=140 |rna_position=C3 |...")
 
No edit summary
 
(18 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|id=FF:13090-140C3
|DRA_sample_Accession=CAGE@SAMD00021729
|name=K562 erythroblastic leukemia response to hemin, 04hr, biol_rep1
|accession_numbers=CAGE;DRX022916;DRR025255;DRZ003680;DRZ004563;DRZ008421;DRZ009304
|sample_id=13090
|ancestors_in_anatomy_facet=
|rna_tube_id=140C3
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000764,CL:0000548,CL:0000763,CL:0002371,CL:0002242,CL:0000255,CL:0000765
|rna_box=140
|ancestors_in_disease_facet=DOID:4,DOID:0050686,DOID:162,DOID:2531,DOID:14566,DOID:0060083,DOID:1240
|rna_position=C3
|ancestors_in_ff_facet=FF:0000102,FF:0000003,FF:0000210,FF:0000101,FF:0000001,FF:0100737,FF:0000401,FF:0000350,FF:0000361,FF:0000338,FF:0000402,FF:0101035,FF:0000525
|sample_cell_lot=
|comment=
|sample_cell_catalog=
|created_by=
|sample_company=
|creation_date=
|rna_lot_number=
|data_phase=2
|rna_catalog_number=
|datafreeze_phase=2
|sample_species=Human (Homo sapiens)
|def=
|sample_strain=
|ffid_belonging_in_development=CL:0000049,CL:0000134
|sample_dev_stage=
|sample_tissue=blood
|sample_donor(cell lot)=rep1
|sample_sex=female
|sample_age=
|sample_ethnicity=
|rna_rin=
|rna_od260/230=2.01000
|rna_od260/280=2.01000
|sample_cell_type=erythroblast
|sample_cell_line=K562
|sample_collaboration=Peter Klinken (Western Australian Institute of Medical Research)
|sample_experimental_condition=K562 erythroblastic leukemia response to hemin
|sample_disease=
|rna_sample_type=
|rna_extraction_protocol=Repurified by minelute
|rna_weight_ug=8.77660
|rna_concentration=0.87766
|sample_note=
|profile_hcage=CNhs12468,LSID916,release011,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000038,CL:0000048,CL:0000049,CL:0000050,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000547,CL:0000548,CL:0000566,CL:0000723,CL:0000763,CL:0000764,CL:0000765,CL:0000837,CL:0000839,CL:0000988,CL:0002031,CL:0002032,CL:0002320,CL:0002371
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_disease_facet=DOID:0050686,DOID:0060083,DOID:1240,DOID:14566,DOID:162,DOID:2531,DOID:4
|sample_description=
 
|fonse_cell_line=FF:0101035
|fonse_cell_line=FF:0101035
|fonse_cell_line_closure=FF:0101035
|fonse_cell_line_closure=FF:0101035
Line 67: Line 39:
|fonse_treatment=EFO:0000369,FF:0000338,FF:0000525,FF:13090-140C3
|fonse_treatment=EFO:0000369,FF:0000338,FF:0000525,FF:13090-140C3
|fonse_treatment_closure=EFO:0000369,FF:0000338,FF:0000525,FF:13090-140C3
|fonse_treatment_closure=EFO:0000369,FF:0000338,FF:0000525,FF:13090-140C3
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/K562%2520erythroblastic%2520leukemia%2520response%2520to%2520hemin%252c%252004hr%252c%2520biol_rep1.CNhs12468.13090-140C3.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/K562%2520erythroblastic%2520leukemia%2520response%2520to%2520hemin%252c%252004hr%252c%2520biol_rep1.CNhs12468.13090-140C3.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/K562%2520erythroblastic%2520leukemia%2520response%2520to%2520hemin%252c%252004hr%252c%2520biol_rep1.CNhs12468.13090-140C3.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/K562%2520erythroblastic%2520leukemia%2520response%2520to%2520hemin%252c%252004hr%252c%2520biol_rep1.CNhs12468.13090-140C3.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/K562%2520erythroblastic%2520leukemia%2520response%2520to%2520hemin%252c%252004hr%252c%2520biol_rep1.CNhs12468.13090-140C3.hg38.nobarcode.ctss.bed.gz
|id=FF:13090-140C3
|is_a=EFO:0002091;;FF:0000525
|is_obsolete=
|library_id=CNhs12468
|library_id_phase_based=2:CNhs12468
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;13090
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;13090
|name=K562 erythroblastic leukemia response to hemin, 04hr, biol_rep1
|namespace=FANTOM5
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12468,LSID916,release011,COMPLETED
|profile_rnaseq=
|profile_srnaseq=,,,
|rna_box=140
|rna_catalog_number=
|rna_concentration=0.88
|rna_extraction_protocol=Repurified by minelute
|rna_lot_number=
|rna_od260/230=2.01
|rna_od260/280=2.01
|rna_position=C3
|rna_rin=
|rna_sample_type=
|rna_tube_id=140C3
|rna_weight_ug=8.78
|sample_age=
|sample_category=time courses
|sample_cell_catalog=
|sample_cell_line=K562
|sample_cell_lot=
|sample_cell_type=erythroblast
|sample_collaboration=Peter Klinken (Western Australian Institute of Medical Research)
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=rep1
|sample_ethnicity=
|sample_experimental_condition=K562 erythroblastic leukemia response to hemin
|sample_id=13090
|sample_note=
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=blood
|timecourse=Erythropoiesis_K562
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:13090-140C3;search_select_hide=table117:FF:13090-140C3
}}
}}

Latest revision as of 18:50, 4 June 2020


Name:K562 erythroblastic leukemia response to hemin, 04hr, biol_rep1
Species:Human (Homo sapiens)
Library ID:CNhs12468
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexfemale
ageNA
cell typeerythroblast
cell lineK562
companyNA
collaborationPeter Klinken (Western Australian Institute of Medical Research)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)Repurified by minelute

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00021729
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12468 CAGE DRX022916 DRR025255
Accession ID Hg19

Library idBAMCTSS
CNhs12468 DRZ003680 DRZ004563
Accession ID Hg38

Library idBAMCTSS
CNhs12468 DRZ008421 DRZ009304
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: CNhs12468This 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: CNhs12468This 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: CNhs12468


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)
0000003 (native cell)
0000988 (hematopoietic cell)
0000764 (erythroid lineage cell)
0000548 (animal cell)
0000763 (myeloid cell)
0002371 (somatic cell)
0002242 (nucleate cell)
0000255 (eukaryotic cell)
0000765 (erythroblast)

DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
2531 (hematologic cancer)
14566 (disease of cellular proliferation)
0060083 (immune system cancer)
1240 (leukemia)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100737 (leukemia cell line sample)
0000401 (erythroblastic leukemia cell line sample)
0000350 (experimentally modified sample)
0000361 (4 hr sample)
0000338 (hemin treatment sample)
0000402 (human K562 erythroblastic leukemia cell line sample)
0101035 (hematopoietic cell line sample)
0000525 (human K562 erythroblastic leukemia line 4hr after treatment with hemin 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:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:13090-140C3&oldid=4577513"