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|is_a=EFO:0001461;;FF:0011374
 
|is_a=EFO:0001461;;FF:0011374
 
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|is_obsolete=
|library_id=CNhs12585
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|library_id=
|library_id_phase_based=2:CNhs12585
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|library_id_phase_based=
 
|name=whole body, embryo E17.5, pool1 (internal control)
 
|name=whole body, embryo E17.5, pool1 (internal control)
 
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Revision as of 05:11, 1 December 2014


Name:whole body, embryo E17.5, pool1 (internal control)
Species:Mouse (Mus musculus)
Library ID:
Sample type:control
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuewhole body
dev stage17.5 days embryo
sexunknown_sex_type
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00005832
Library accession numbers

Library idMethodExp. accession idRun accession id
CAGE DRX008871 DRR009743
CAGE DRX008872 DRR009744
CAGE DRX008873 DRR009745
CAGE DRX008874 DRR009746
CAGE DRX008875 DRR009747
CAGE DRX008876 DRR009748
CAGE DRX008877 DRR009749
CAGE DRX008878 DRR009750
CAGE DRX008879 DRR009751
CAGE DRX008880 DRR009752
CAGE DRX008881 DRR009753
CAGE DRX008882 DRR009754
CAGE DRX008883 DRR009755
CAGE DRX008884 DRR009756
CAGE DRX008885 DRR009757
CAGE DRX008886 DRR009758
CAGE DRX008887 DRR009759
CAGE DRX008888 DRR009760
CAGE DRX008889 DRR009761
CAGE DRX008890 DRR009762
CAGE DRX008891 DRR009763
CAGE DRX008892 DRR009764
CAGE DRX008893 DRR009765
CAGE DRX008894 DRR009766
CAGE DRX008895 DRR009767
CAGE DRX008896 DRR009768
CAGE DRX008897 DRR009769
CAGE DRX008898 DRR009770
Accession ID Mm9

Library idBAMCTSS
DRZ001168 DRZ002553
DRZ001169 DRZ002554
DRZ001170 DRZ002555
DRZ001171 DRZ002556
DRZ001172 DRZ002557
DRZ001173 DRZ002558
DRZ001174 DRZ002559
DRZ001175 DRZ002560
DRZ001176 DRZ002561
DRZ001177 DRZ002562
DRZ001178 DRZ002563
DRZ001179 DRZ002564
DRZ001180 DRZ002565
DRZ001181 DRZ002566
DRZ001182 DRZ002567
DRZ001183 DRZ002568
DRZ001184 DRZ002569
DRZ001185 DRZ002570
DRZ001186 DRZ002571
DRZ001187 DRZ002572
DRZ001188 DRZ002573
DRZ001189 DRZ002574
DRZ001190 DRZ002575
DRZ001191 DRZ002576
DRZ001192 DRZ002577
DRZ001193 DRZ002578
DRZ001194 DRZ002579
DRZ001195 DRZ002580
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


Relative expression to median (log10)


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.
Analyst:NA

link to dataset.
data


Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data



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


JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data



FANTOM5 phase1 novel unique motifsSummary: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 in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data



de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
data

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000301 (mouse embryonic day 17.5 sample)
0011374 (mouse whole body- embryo E17.5 sample)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

FF:0000294 (mouse embryonic day 11 sample)