|
Status |
Public on Dec 09, 2013 |
Title |
Untreated 6hpf embryo replicate 2 |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
pooled whole zebrafish embryo 6hpf_untreated
|
Organism |
Danio rerio |
Characteristics |
tissue: whole embryo developmental stage: 6 hr post fertilization treated with: none (untreated) 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 2 of 2 WT6h-2
|
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 |
|