|
Status |
Public on Dec 05, 2011 |
Title |
Total nuclei RNA 3 (20110624_gDNA_vs_nuc_4_453614-3) |
Sample type |
mixed |
|
|
Channel 1 |
Source name |
total nuclei
|
Organism |
Caenorhabditis elegans |
Characteristics |
age: adult strain: JJ2289 tissue: 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 |
age: adult strain: N2 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_3.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 |
Aug 12, 2011 |
Last update date |
Apr 11, 2012 |
Contact name |
Jorja Henikoff |
E-mail(s) |
jorja@fhcrc.org
|
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. |
|