|
| Status |
Public on Dec 09, 2013 |
| Title |
RA treated 6hpf embryo replicate 1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
pooled whole zebrafish embryo 6hpf_RA treated
|
| Organism |
Danio rerio |
| Characteristics |
tissue: whole embryo
developmental stage: 6 hr post fertilization
treated with: Retinoic acid (RA)
dna fragmentation: Micrococcal Nuclease
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Adapted from Dennis et al 2007 Genome Research
|
| Label |
Cy3
|
| Label protocol |
Adapted from Yuan et al 2005 Science
|
| |
|
| Channel 2 |
| Source name |
pooled whole zebrafish embryo 6hpf
|
| Organism |
Danio rerio |
| Characteristics |
tissue: whole embryo
developmental stage: 6 hr post fertilization
treated with: none (untreated)
dna fragmentation: Sonication
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Adapted from Dennis et al 2007 Genome Research
|
| Label |
Cy5
|
| Label protocol |
Adapted from Yuan et al 2005 Science
|
| |
|
| |
| Hybridization protocol |
Adapted from Yuan et al 2005 Science
|
| Scan protocol |
Scanned on an Agilent High-Resolution C Scanner or an Axon 4000B.
Images were quantified and background subtraction was done using Agilent Feature Extraction Software.
|
| Description |
6hpf biological replicate 1 of 2
RA6h-1
|
| Data processing |
Mean singals of the background subtracted data from two replicates for each sample was assigned to each probe location. Signals were then taillied using a 30bp sliding window with a 10bp step. A Lowess fitting line (f=.05) then plotted to show the trend of the aggregated signals.
|
| |
|
| Submission date |
Jan 25, 2013 |
| Last update date |
Dec 09, 2013 |
| Contact name |
Steven Weicksel |
| E-mail(s) |
steven.weicksel@umassmed.edu
|
| Organization name |
UMass Medical School
|
| Department |
BMP
|
| Lab |
Sagerstrom
|
| Street address |
55 Lake Ave
|
| City |
Worcester |
| State/province |
Massachusetts |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL16536 |
| Series (2) |
| GSE43757 |
Identification of nucleosome positions at hox TSSs during zebrafish embryonic development |
| GSE43758 |
Identification of nucleosome positions at hox TSSs during zebrafish early embryonic development |
|
