FF:11948-126B4

Name:	Pre-hematopoietic stem cell, aorta-gonad-mesonephros (AGM) region derived, embryo E9.5
Species:	Mouse (Mus musculus)
Library ID:	CNhs14149
Sample type:	time courses
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information
Sample information strain NA tissue ANATOMICAL SYSTEM dev stage NA sex NA age NA cell type NA cell line NA company NA collaboration Daisuke Sugiyama External link for information [{{{sample_info_link}}} {{{sample_info_link}}}] RNA information lot number NA catalog number NA sample type total RNA extraction protocol (Details) OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
Method Sample accession id CAGE  SAMD00021214 Library accession numbers Library id Method Exp. accession id Run accession id CNhs14149 CAGE DRX024031 DRR026436 Accession ID Mm9 Library id BAM CTSS CNhs14149 DRZ005688 DRZ006468 Accession ID Mm10 Library id BAM CTSS CNhs14149

Download raw sequence, BAM & CTSS
Mm9 Fasta BAM CTSS download download donwload Mm10 BAM CTSS download donwload

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

CNhs14149

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: CNhs14149This 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: CNhs14149This 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: CNhs14149

FANTOM5 (FF) ontology

---

Direct parent terms

is_a relathionship
FF:0200027 mouse (pre) hematopoietic stem cell,aorta-gonad-mesonephros (AGM) region derived 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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000988 (hematopoietic cell)
0000548 (animal cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0000034 (stem cell)
0000037 (hematopoietic stem cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002113 (kidney)
0002100 (trunk)
0000080 (mesonephros)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0006554 (urinary system structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0009569 (subdivision of trunk)
0000489 (cavitated compound organ)
0005177 (trunk region element)
0005172 (abdomen element)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0011143 (upper urinary tract)
0001008 (renal system)
0002417 (abdominal segment of trunk)
0000916 (abdomen)

FF: FANTOM5
0200027 (mouse (pre) hematopoietic stem cell,aorta-gonad-mesonephros (AGM) region derived 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:0000134 (mesenchymal cell)
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0003104 (mesenchyme)
UBERON:0003918 (kidney mesenchyme)
UBERON:0005754 (rostral part of nephrogenic cord)
UBERON:0007687 (kidney field)
UBERON:0007297 (presumptive pronephric mesoderm)
UBERON:0010316 (germ layer / neural crest)