|
| Status |
Public on Dec 05, 2011 |
| Title |
Total nuclei RNA 5 (20111110_gDNA_vs_nuc120_1_507461-2) |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
total nuclei
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: JJ2371
background: unc-120(st364)
age: adult
cell type: whole organism
sample type: total nuclei
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
RNA isolation was done with Qiagen RNeasy micro kit. cDNA preparation and amplification were done with the Sigma WTA2 kit. Detailed protocol in supplementary file INTACT_ChIP_protocol.rtf .
|
| Label |
Cy5
|
| Label protocol |
Standard NimbleGen protocol using 6 hour labeling reaction rather than 2 hour reaction.
|
| |
|
| Channel 2 |
| Source name |
Fragmented genomic DNA
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
age: adult
tissue: whole organism
sample type: fragmented genomic DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was fragmented by sonication to
about 400bp.
|
| Label |
Cy3
|
| Label protocol |
Standard NimbleGen protocol using 6 hour labeling reaction rather than 2 hour reaction.
|
| |
|
| |
| Hybridization protocol |
Standard NimbleGen protocol.
|
| Scan protocol |
Standard NimbleGen protocol.
|
| Description |
Expression profiling of nuclear RNA from total nuclei.
|
| Data processing |
Standard NimbleGen bi-weight mean adjusted log base 2 ratios (Cy5/Cy3) were converted to standard deviates by subtracting their mean and dividing by their standard deviation. Per-gene expression values in supplementary file Total_nuclei_RNA_5.txt were computed as described in http://nettie.fhcrc.org/labuser/protocols/expression.html: The standardized log ratios for all exonic probes starting with the 20th probe from the 3' ends of WS220 genes were averaged to give a single expression value for each gene.
|
| |
|
| Submission date |
Nov 18, 2011 |
| Last update date |
Apr 11, 2012 |
| 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 |
| |
|
| Platform ID |
GPL7098 |
| Series (1) |
| GSE31602 |
Tissue-specific nuclei purification from animal models for genome-wide expression and chromatin profiling. |
|
