|
| Status |
Public on Dec 05, 2011 |
| Title |
Tissue-specific nuclei purification from animal models for genome-wide expression and chromatin profiling. |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Expression profiling by genome tiling array
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Here we describe a method for purifying nuclei from specific tissues of animal models that allows simultaneous analysis of both expression and chromatin profiles. The method is based on in vivo labeling of the nuclear envelope and subsequent affinity purification. We describe the use of the method to isolate nuclei from muscle.
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| |
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| Overall design |
We determined genes preferentially expressed in muscle cells of adult C. elegans by analyzing RNA from total and affinity-puridied muscle nuclei using microarrays. We also determined the nucleosome occupancy in these nuclei by micrococcal nuclease mapping and paired-end sequencing.
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| |
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| Contributor(s) |
Steiner FA, Henikoff S, Talbert PB, Kasinathan S, Deal RB, Priess JR |
| Citation(s) |
22219512 |
| |
| Submission date |
Aug 23, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
[email protected]
|
| Phone |
206-667-4850
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
Basic Sciences
|
| Lab |
Henikoff
|
| Street address |
1100 Fairview AV N, A1-162
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL7098 |
NimbleGen C_elegans_WS170_Tiling_Iso_HX1 tiling design |
| GPL13657 |
Illumina HiSeq 2000 (Caenorhabditis elegans) |
|
| Samples (18)
|
| GSM777718 |
Muscle nuclei DNA 1 (IP20_20110313_7) |
| GSM777719 |
Total nuclei DNA 1 (Nuc10_20110313_3) |
| GSM777720 |
Muscle nuclei RNA 1 (20110323_gDNA_vs_PmyoL1_453631) |
| GSM777721 |
Muscle nuclei RNA 2 (20110527_gDNA_vs_myoL1_3_453614-2) |
| GSM777722 |
Muscle nuclei RNA 3 (20110624_gDNA_vs_myoL_4_454304-2) |
| GSM777723 |
Muscle nuclei RNA 4 (20110624_gDNA_vs_LmyoA_1_454479) |
| GSM777724 |
Total nuclei RNA 1 (20110323_gDNA_vs_nuc_453625) |
| GSM777725 |
Total nuclei RNA 2 (20110527_gDNA_vs_nuc_2_453529-2) |
| GSM777726 |
Total nuclei RNA 3 (20110624_gDNA_vs_nuc_4_453614-3) |
| GSM777727 |
Total nuclei RNA 4 (20110624_gDNA_vs_nucA_1_453625-3) |
| GSM807108 |
Muscle nuclei DNA 2 (nuc5_20110622_7) |
| GSM807109 |
Total nuclei DNA 2 (PD5_rep2_20110622_3) |
| GSM836187 |
Muscle nuclei RNA 5 (20111012_gDNA_vs_unc120_1_507460) |
| GSM836188 |
Muscle nuclei RNA 6 (20111012_gDNA_vs_unc120_2_507461) |
| GSM836189 |
Total nuclei RNA 5 (20111110_gDNA_vs_nuc120_1_507461-2) |
| GSM836190 |
Total nuclei RNA 6 (20111110_gDNA_vs_nuc120_2_507524-2) |
| GSM836191 |
Total RNA 1 (20111110_gDNA_vs_total_3_507526-2) |
| GSM836192 |
Total RNA 2 (20111110_gDNA_vs_total_4_507308-2) |
|
| Relations |
| SRA |
SRP007948 |
| BioProject |
PRJNA145583 |
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