Personal tools

Difference between revisions of "FF:13077-140A8"

From FANTOM5_SSTAR

Jump to: navigation, search
 
(One intermediate revision by the same user not shown)
Line 1: Line 1:
 
{{f5samples
 
{{f5samples
 
|DRA_sample_Accession=CAGE@SAMD00021716
 
|DRA_sample_Accession=CAGE@SAMD00021716
 +
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00021716
 
|accession_numbers=CAGE;DRX023811;DRR026210;DRZ005462;DRZ006248;DRZ010077;DRZ010741
 
|accession_numbers=CAGE;DRX023811;DRR026210;DRZ005462;DRZ006248;DRZ010077;DRZ010741
 +
|accession_numbers_RNASeq=sRNA-Seq;DRX037396;DRR041762;DRZ007371
 
|ancestors_in_anatomy_facet=
 
|ancestors_in_anatomy_facet=
 
|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
 
|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
Line 76: Line 78:
 
|rna_tube_id=140A8
 
|rna_tube_id=140A8
 
|rna_weight_ug=43.83
 
|rna_weight_ug=43.83
 +
|rnaseq_library_id=SRhi10062.CAGATC
 
|sample_age=
 
|sample_age=
 
|sample_category=time courses
 
|sample_category=time courses
Line 100: Line 103:
 
|top_motifs=
 
|top_motifs=
 
|xref=
 
|xref=
 +
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:13077-140A8;search_select_hide=table117:13077-140A8
 
}}
 
}}

Latest revision as of 09:50, 4 June 2020


Name:J2E erythroblastic leukemia response to erythropoietin
Species:Mouse (Mus musculus)
Library ID:CNhs12455
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexNA
ageNA
cell typeerythroblast
cell lineJ2E
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  SAMD00021716
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12455 CAGE DRX023811 DRR026210
Accession ID Mm9

Library idBAMCTSS
CNhs12455 DRZ005462 DRZ006248
Accession ID Mm10

Library idBAMCTSS
CNhs12455 DRZ010077 DRZ010741
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00021716
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10062.CAGATC sRNA-Seq DRX037396 DRR041762
Accession ID Mm9

Library idBAMCTSS
SRhi10062.CAGATC DRZ007371





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

CNhs12455



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: CNhs12455This 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: CNhs12455This 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: CNhs12455


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)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0100737 (leukemia cell line sample)
0000401 (erythroblastic leukemia cell line sample)
0000350 (experimentally modified sample)
0000373 (24 hr sample)
0000337 (erythropoietin treatment sample)
0000403 (mouse J2E erythroblastic leukemia cell line sample)
0101035 (hematopoietic cell line sample)
0000512 (mouse J2E erythroblastic leukemia line 24hr after treatment with erythropoietin 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)