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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008761
|DRA_sample_Accession=CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761!CAGE@DRS008761
|accession_numbers=CAGE;DRX008871;DRR009743;DRZ001168;DRZ002553!CAGE;DRX008872;DRR009744;DRZ001169;DRZ002554!CAGE;DRX008873;DRR009745;DRZ001170;DRZ002555!CAGE;DRX008874;DRR009746;DRZ001171;DRZ002556!CAGE;DRX008875;DRR009747;DRZ001172;DRZ002557!CAGE;DRX008876;DRR009748;DRZ001173;DRZ002558!CAGE;DRX008877;DRR009749;DRZ001174;DRZ002559!CAGE;DRX008878;DRR009750;DRZ001175;DRZ002560!CAGE;DRX008879;DRR009751;DRZ001176;DRZ002561!CAGE;DRX008880;DRR009752;DRZ001177;DRZ002562!CAGE;DRX008881;DRR009753;DRZ001178;DRZ002563!CAGE;DRX008882;DRR009754;DRZ001179;DRZ002564!CAGE;DRX008883;DRR009755;DRZ001180;DRZ002565!CAGE;DRX008884;DRR009756;DRZ001181;DRZ002566!CAGE;DRX008885;DRR009757;DRZ001182;DRZ002567!CAGE;DRX008886;DRR009758;DRZ001183;DRZ002568!CAGE;DRX008887;DRR009759;DRZ001184;DRZ002569!CAGE;DRX008888;DRR009760;DRZ001185;DRZ002570!CAGE;DRX008889;DRR009761;DRZ001186;DRZ002571!CAGE;DRX008890;DRR009762;DRZ001187;DRZ002572!CAGE;DRX008891;DRR009763;DRZ001188;DRZ002573!CAGE;DRX008892;DRR009764;DRZ001189;DRZ002574!CAGE;DRX008893;DRR009765;DRZ001190;DRZ002575!CAGE;DRX008894;DRR009766;DRZ001191;DRZ002576!CAGE;DRX008895;DRR009767;DRZ001192;DRZ002577!CAGE;DRX008896;DRR009768;DRZ001193;DRZ002578!CAGE;DRX008897;DRR009769;DRZ001194;DRZ002579!CAGE;DRX008898;DRR009770;DRZ001195;DRZ002580
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|is_a=EFO:0001461;;FF:0011374
|is_a=EFO:0001461;;FF:0011374
|is_obsolete=
|is_obsolete=
|library_id=CNhs10479!CNhs10495!CNhs10511!CNhs10527!CNhs10591!CNhs10607!CNhs10623!CNhs10639!CNhs10655!CNhs10725!CNhs10749!CNhs10840!CNhs10856!CNhs10880!CNhs11000!CNhs11024!CNhs11032!CNhs11048!CNhs11072!CNhs11080!CNhs11096!CNhs11120!CNhs11128!CNhs11184!CNhs11208!CNhs11216!CNhs11246!CNhs11278
|library_ids=CNhs10479!CNhs10495!CNhs10511!CNhs10527!CNhs10591!CNhs10607!CNhs10623!CNhs10639!CNhs10655!CNhs10725!CNhs10749!CNhs10840!CNhs10856!CNhs10880!CNhs11000!CNhs11024!CNhs11032!CNhs11048!CNhs11072!CNhs11080!CNhs11096!CNhs11120!CNhs11128!CNhs11184!CNhs11208!CNhs11216!CNhs11246!CNhs11278
|library_ids=CNhs10479!CNhs10495!CNhs10511!CNhs10527!CNhs10591!CNhs10607!CNhs10623!CNhs10639!CNhs10655!CNhs10725!CNhs10749!CNhs10840!CNhs10856!CNhs10880!CNhs11000!CNhs11024!CNhs11032!CNhs11048!CNhs11072!CNhs11080!CNhs11096!CNhs11120!CNhs11128!CNhs11184!CNhs11208!CNhs11216!CNhs11246!CNhs11278
|name=whole body, embryo E17.5, pool1 (internal control)
|name=whole body, embryo E17.5, pool1 (internal control)
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|top_motifs=
|top_motifs=
|xref=
|xref=
}} {{DRAAccessionNumbers
|DRA_sample_Accession=CAGE@DRS008761
|accession_numbers=DRX008871;DRR009743;DRZ001168;DRZ002553;CAGE!DRX008872;DRR009744;DRZ001169;DRZ002554;CAGE!DRX008873;DRR009745;DRZ001170;DRZ002555;CAGE!DRX008874;DRR009746;DRZ001171;DRZ002556;CAGE!DRX008875;DRR009747;DRZ001172;DRZ002557;CAGE!DRX008876;DRR009748;DRZ001173;DRZ002558;CAGE!DRX008877;DRR009749;DRZ001174;DRZ002559;CAGE!DRX008878;DRR009750;DRZ001175;DRZ002560;CAGE!DRX008879;DRR009751;DRZ001176;DRZ002561;CAGE!DRX008880;DRR009752;DRZ001177;DRZ002562;CAGE!DRX008881;DRR009753;DRZ001178;DRZ002563;CAGE!DRX008882;DRR009754;DRZ001179;DRZ002564;CAGE!DRX008883;DRR009755;DRZ001180;DRZ002565;CAGE!DRX008884;DRR009756;DRZ001181;DRZ002566;CAGE!DRX008885;DRR009757;DRZ001182;DRZ002567;CAGE!DRX008886;DRR009758;DRZ001183;DRZ002568;CAGE!DRX008887;DRR009759;DRZ001184;DRZ002569;CAGE!DRX008888;DRR009760;DRZ001185;DRZ002570;CAGE!DRX008889;DRR009761;DRZ001186;DRZ002571;CAGE!DRX008890;DRR009762;DRZ001187;DRZ002572;CAGE!DRX008891;DRR009763;DRZ001188;DRZ002573;CAGE!DRX008892;DRR009764;DRZ001189;DRZ002574;CAGE!DRX008893;DRR009765;DRZ001190;DRZ002575;CAGE!DRX008894;DRR009766;DRZ001191;DRZ002576;CAGE!DRX008895;DRR009767;DRZ001192;DRZ002577;CAGE!DRX008896;DRR009768;DRZ001193;DRZ002578;CAGE!DRX008897;DRR009769;DRZ001194;DRZ002579;CAGE!DRX008898;DRR009770;DRZ001195;DRZ002580;CAGE
|library_id=CNhs10479!CNhs10495!CNhs10511!CNhs10527!CNhs10591!CNhs10607!CNhs10623!CNhs10639!CNhs10655!CNhs10725!CNhs10749!CNhs10840!CNhs10856!CNhs10880!CNhs11000!CNhs11024!CNhs11032!CNhs11048!CNhs11072!CNhs11080!CNhs11096!CNhs11120!CNhs11128!CNhs11184!CNhs11208!CNhs11216!CNhs11246!CNhs11278
}}
}}

Revision as of 18:18, 17 October 2013


Name:whole body, embryo E17.5, pool1 (internal control)
Species:Mouse (Mus musculus)
Library ID:CNhs10479,CNhs10495,CNhs10511,CNhs10527,CNhs10591,CNhs10607,CNhs10623,CNhs10639,CNhs10655,CNhs10725,CNhs10749,CNhs10840,CNhs10856,CNhs10880,CNhs11000,CNhs11024,CNhs11032,CNhs11048,CNhs11072,CNhs11080,CNhs11096,CNhs11120,CNhs11128,CNhs11184,CNhs11208,CNhs11216,CNhs11246,CNhs11278
Sample type:developmental
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

CAGE Accession numbers
MethodSample accession id
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
CAGE  DRS008761
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10479 CAGE DRX008871 DRR009743
CNhs10495 CAGE DRX008872 DRR009744
CNhs10511 CAGE DRX008873 DRR009745
CNhs10527 CAGE DRX008874 DRR009746
CNhs10591 CAGE DRX008875 DRR009747
CNhs10607 CAGE DRX008876 DRR009748
CNhs10623 CAGE DRX008877 DRR009749
CNhs10639 CAGE DRX008878 DRR009750
CNhs10655 CAGE DRX008879 DRR009751
CNhs10725 CAGE DRX008880 DRR009752
CNhs10749 CAGE DRX008881 DRR009753
CNhs10840 CAGE DRX008882 DRR009754
CNhs10856 CAGE DRX008883 DRR009755
CNhs10880 CAGE DRX008884 DRR009756
CNhs11000 CAGE DRX008885 DRR009757
CNhs11024 CAGE DRX008886 DRR009758
CNhs11032 CAGE DRX008887 DRR009759
CNhs11048 CAGE DRX008888 DRR009760
CNhs11072 CAGE DRX008889 DRR009761
CNhs11080 CAGE DRX008890 DRR009762
CNhs11096 CAGE DRX008891 DRR009763
CNhs11120 CAGE DRX008892 DRR009764
CNhs11128 CAGE DRX008893 DRR009765
CNhs11184 CAGE DRX008894 DRR009766
CNhs11208 CAGE DRX008895 DRR009767
CNhs11216 CAGE DRX008896 DRR009768
CNhs11246 CAGE DRX008897 DRR009769
CNhs11278 CAGE DRX008898 DRR009770
Accession ID Mm9

Library idBAMCTSS
CNhs10479 DRZ001168 DRZ002553
CNhs10495 DRZ001169 DRZ002554
CNhs10511 DRZ001170 DRZ002555
CNhs10527 DRZ001171 DRZ002556
CNhs10591 DRZ001172 DRZ002557
CNhs10607 DRZ001173 DRZ002558
CNhs10623 DRZ001174 DRZ002559
CNhs10639 DRZ001175 DRZ002560
CNhs10655 DRZ001176 DRZ002561
CNhs10725 DRZ001177 DRZ002562
CNhs10749 DRZ001178 DRZ002563
CNhs10840 DRZ001179 DRZ002564
CNhs10856 DRZ001180 DRZ002565
CNhs10880 DRZ001181 DRZ002566
CNhs11000 DRZ001182 DRZ002567
CNhs11024 DRZ001183 DRZ002568
CNhs11032 DRZ001184 DRZ002569
CNhs11048 DRZ001185 DRZ002570
CNhs11072 DRZ001186 DRZ002571
CNhs11080 DRZ001187 DRZ002572
CNhs11096 DRZ001188 DRZ002573
CNhs11120 DRZ001189 DRZ002574
CNhs11128 DRZ001190 DRZ002575
CNhs11184 DRZ001191 DRZ002576
CNhs11208 DRZ001192 DRZ002577
CNhs11216 DRZ001193 DRZ002578
CNhs11246 DRZ001194 DRZ002579
CNhs11278 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. <br>Analyst:NA <br><br>link to dataset.<br>data

multiple



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

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: multipleThis 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: multipleThis 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: multiple


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

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)<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
FF:0000294 (mouse embryonic day 11 sample)

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