TestSample

Name:	Clontech Human Universal Reference Total RNA, pool1
Species:	Human (Homo sapiens)
Library ID:	CNhs10608
Sample type:	tissues
Genomic View:	UCSC
RefEX:	Specific genes
CAGEd-oPOSSUM:	link

Additional information

Sample information strain NA tissue unclassifiable dev stage UNDEFINED sex mixed age NA cell type CELL MIXTURE - tissue sample cell line NA company Clontech collaboration FANTOM5 OSC CORE (contact: Al Forrest) External link for information [{{{sample_info_link}}} {{{sample_info_link}}}] RNA information lot number 9052727A catalog number Cat:636538 sample type total RNA extraction protocol (Details) OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
Method Sample accession id CAGE  SAMD00005752 Library accession numbers Library id Method Exp. accession id Run accession id CNhs10608 CAGE DRX008608 DRR009480 Accession ID Hg19 Library id BAM CTSS CNhs10608 DRZ000905 DRZ002290 Accession ID Hg38 Library id BAM CTSS CNhs10608 DRZ012255 DRZ013640

Download raw sequence, BAM & CTSS
Hg19 Fasta BAM CTSS download download donwload Hg38 BAM CTSS download donwload

RNA-Seq Accession numbers

Method Sample accession id sRNA-Seq  SAMD00005752 Library accession numbers Library id Method Exp. accession id Run accession id SRhi10002.CGTACG sRNA-Seq DRX037336 DRR041702 SRhi10008.CGATGT sRNA-Seq DRX037337 DRR041703 SRhi10012.GGCTAC sRNA-Seq DRX037338 DRR041704 Accession ID Hg19 Library id BAM CTSS SRhi10002.CGTACG DRZ007344 SRhi10008.CGATGT DRZ007345 SRhi10012.GGCTAC DRZ007346 Accession ID Hg38 Library id BAM CTSS SRhi10002.CGTACG SRhi10008.CGATGT SRhi10012.GGCTAC

Relative expression to median (log10)

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Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.

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

TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

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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: CNhs10608This 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: CNhs10608This 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: CNhs10608

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
FF:0000004 tissue sample
FF:0000210 human sample

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
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000004 (tissue 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
NA