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Sample GSM1070413 Query DataSets for GSM1070413
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

Data table header descriptions
ID_REF
VALUE log2 ratio (Cy3/Cy5) representing test/reference

Data table
ID_REF VALUE
1CUST_4744_PI413487499 0.026967048
1CUST_400_PI413487504 0.484825829
1CUST_3960_PI413487499 0.026752728
1CUST_1557_PI413487506 0.246706236
1CUST_1094_PI413487496 0.038994132
1CUST_2878_PI413487499 0.038819249
1CUST_564_PI413487497 0.788138246
1CUST_2586_PI413487504 1.211121309
1CUST_739_PI412252212 0.068610612
1CUST_1577_PI413487494 0.057947349
1CUST_594_PI412252212 0.59946207
1CUST_1867_PI413487484 0.535037275
1CUST_2191_PI413487512 0.190942783
1CUST_3814_PI413487497 0.142019005
1CUST_1522_PI413487512 0.067114196
1CUST_396_PI413487494 0.12588444
1CUST_985_PI413487494 -0.420662048
1CUST_3248_PI413487497 0.116324118
1CUST_2537_PI413487499 -0.612810486
1CUST_849_PI413487506 0.692050307

Total number of rows: 43993

Table truncated, full table size 1500 Kbytes.




Supplementary file Size Download File type/resource
GSM1070413_WT6h_2.txt.gz 12.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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