|
| Status |
Public on Aug 25, 2010 |
| Title |
New ZFNs DD/RR 20pg normal stage_1_off_target_seq_barcode_GT |
| Sample type |
SRA |
| |
|
| Source name |
New ZFNs DD/RR 20pg Normals
|
| Organism |
Danio rerio |
| Characteristics |
developmental stage: 24 h old embryos
genotype: Wild Type
treatment: New ZFNs DD/RR 20 pg
phenotype: normal
|
| Treatment protocol |
zebrafish embryos at single cell stage were injected with ZFN mRNAs at different doses
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The off-target sites were amplified from genomic DNA from ZFNs treated embryos and pooled together. PCR products from different treatments of ZFNs were barcoed and the pools were amplified using Illumina 1.1 and 2.1 geomic primers.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
48 off-target sites and the target site were PCR amplified using the genomic DNA from the ZFN treated embryos. The different ZFN treatments were barcoded and sequences belonging to different sites can be binned using 9 bp unique prefix
raw reads, no quality score
|
| Data processing |
Sequences were categorized into different treatments using the 2bp barcode. Sequences belonging to different off-target sites and the target site were binned using a unique 9 bp nonamer
|
| |
|
| Submission date |
Aug 23, 2010 |
| Last update date |
May 27, 2014 |
| Contact name |
Scot Wolfe |
| E-mail(s) |
scot.wolfe@umassmed.edu
|
| Organization name |
UMass Medical School
|
| Department |
MCCB
|
| Street address |
364 Plantation Street, LRB 619
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL10164 |
| Series (1) |
| GSE23762 |
Off-Target Analysis of Zinc Finger Nucleases |
|
| Relations |
| BioSample |
SAMN02195993 |
