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| Status |
Public on Jan 21, 2014 |
| Title |
Tissue-specific pioneer factors associate with androgen receptor cistromes and transcription programs. [ChIP-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We report the in vivo androgen receptor (AR) binding sites in murine prostate, epididymis and kidney in response to physiological androgen testosterone using ChIP-sequencing and gene expression profiling by microarray. From AR cistrome analysis, we identified tissue-specific collaborating factors i.e. FoxA1 in prostate, Hnf4a in kidney and AP2a in epididymis and validated by ChIP-seq. The ChIP experiments have been performed using antibodies specific to AR, FoxA1, Hnf4a, AP-2a and IgG non-specific antibody as a negative control.
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| Overall design |
Examination of AR binding sites in murine androgen-responsive tissues prostate, epididymis and kidney using ChIP-seq. Further analysis of AR cistromes led to identification of tissue-specific collaborating factors and these collaborating factors are validated by ChIP-seq from the same tissues. Two parallel IgG samples were sequenced, merged together and used as a control data set. Parallel ChIP-seq samples were sequenced and merged for each replicate wherever required to contain approximately the same amount of reads across all tissues and conditions. All ChIP-seq experiments are performed in biological duplicates except for the castrated conditions.
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| Contributor(s) |
Pihlajamaa P, Sahu B, Lyly L, Aittomäki V, Hautaniemi S, Jänne OA |
| Citation(s) |
24451200 |
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| Submission date |
May 22, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Olli A. Jänne |
| E-mail(s) |
olli.janne@helsinki.fi
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| Phone |
+358919125040
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| Organization name |
University of Helsinki
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| Department |
Inst. of Biomedicine/Physiology
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| Lab |
Androgen Receptor Laboratory
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| Street address |
Haartmaninkatu-8
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| City |
Helsinki |
| ZIP/Postal code |
FI-00014 |
| Country |
Finland |
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| Platforms (1) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
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| Samples (41)
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| GSM1146459 |
AR_Cast1a [prostate, castrated+vehicle] |
| GSM1146460 |
AR_Cast1b [prostate, castrated+vehicle] |
| GSM1146461 |
AR_Cast+T_rep1a [prostate, castrated+testosterone] |
| GSM1146462 |
AR_Cast+T_rep1b [prostate, castrated+testosterone] |
| GSM1146463 |
AR_Cast+T_rep2a [prostate, castrated+testosterone] |
| GSM1146464 |
AR_Cast+T_rep2b [prostate, castrated+testosterone] |
| GSM1146465 |
FoxA1_Cast [prostate, castrated+vehicle] |
| GSM1146466 |
FoxA1_Cast+T_rep1 [prostate, castrated+testosterone] |
| GSM1146467 |
FoxA1_Cast+T_rep2 [prostate, castrated+testosterone] |
| GSM1146468 |
Hnf4a_Cast+T [prostate, castrated+testosterone] |
| GSM1146469 |
AP2a_Cast+T [prostate, castrated+testosterone] |
| GSM1146470 |
rIgG1a [prostate, castrated+vehicle] |
| GSM1146471 |
rIgG1b [prostate, castrated+testosterone] |
| GSM1146472 |
mIgG1 [prostate, castrated+testosterone] |
| GSM1146473 |
AR_Cast1 [kidney, castrated+vehicle] |
| GSM1146474 |
AR_Cast+T_rep1 [kidney, castrated+testosterone] |
| GSM1146475 |
AR_Cast+T_rep2 [kidney, castrated+testosterone] |
| GSM1146476 |
Hnf4a_Cast1a [kidney, castrated+vehicle] |
| GSM1146477 |
Hnf4a_Cast1b [kidney, castrated+vehicle] |
| GSM1146478 |
Hnf4a_Cast+T [kidney, castrated+testosterone] |
| GSM1146479 |
FoxA1_Cast+T [kidney, castrated+testosterone] |
| GSM1146480 |
AP2a_Cast+T [kidney, castrated+testosterone] |
| GSM1146481 |
rIgG1 [kidney, castrated+testosterone] |
| GSM1146482 |
mIgG1 [kidney, castrated+testosterone] |
| GSM1146483 |
AR_Cast1 [caput epididymis, castrated+vehicle] |
| GSM1146484 |
AR_Intact_rep1 [caput epididymis, intact] |
| GSM1146485 |
AR_Intact_rep2 [caput epididymis, intact] |
| GSM1146486 |
AP2a_Cast1a [caput epididymis, castrated+vehicle] |
| GSM1146487 |
AP2a_Cast1b [caput epididymis, castrated+vehicle] |
| GSM1146488 |
AP2a_Intact_rep1 [caput epididymis, intact] |
| GSM1146489 |
AP2a_Intact_rep2 [caput epididymis, intact] |
| GSM1146490 |
FoxA1_Intact [caput epididymis, intact] |
| GSM1146491 |
Hnf4a_Intact [caput epididymis, intact] |
| GSM1146492 |
rIgG1 [caput epididymis, intact] |
| GSM1146493 |
mIgG1 [caput epididymis, intact] |
| GSM1259356 |
H3K4me1_Pro |
| GSM1259357 |
H3K27ac_Pro |
| GSM1259358 |
H3K4me1_Kid |
| GSM1259359 |
H3K27ac_Kid |
| GSM1259360 |
H3K4me1_Epi |
| GSM1259361 |
H3K27ac_Epi |
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| This SubSeries is part of SuperSeries: |
| GSE47194 |
Tissue-specific pioneer factors associate with androgen receptor cistromes and transcription programs |
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| Relations |
| BioProject |
PRJNA205243 |
| SRA |
SRP023135 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE47192_AR_Pro_Cast+T_rep1_peaks.txt.gz |
683.4 Kb |
(ftp)(http) |
TXT |
| GSE47192_AR_Pro_Cast+T_rep2_peaks.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
| GSE47192_AR_Pro_Cast1_peaks.txt.gz |
1.0 Kb |
(ftp)(http) |
TXT |
| GSE47192_Hnf4a_Kid_Cast1_peaks.txt.gz |
171.6 Kb |
(ftp)(http) |
TXT |
| GSE47192_RAW.tar |
1.8 Gb |
(http)(custom) |
TAR (of TXT, WIG) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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