|
| Status |
Public on May 03, 2024 |
| Title |
D+R, +ORF1, +ORF2, +Cas9 |
| Sample type |
SRA |
| |
|
| Source name |
10 day old whole seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: 10 day old whole seedlings
genotype: Wild type + corresponding transgenes
ecotype: Columbia
|
| Treatment protocol |
Various binary vectors were introduced into Agrobacterium tumefaciens GV3101. All transgenic lines were transformed using the Agrobacterium-mediated floral dip method and subsequent selection for Hygromycin-resistant plants.
|
| Growth protocol |
All plants were grown at 22℃ under 16-hour day conditions in a MTPS-120 growth chamber with 200 µmol m−2 s−1 light intensity.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from frozen Arabidopsis seedlings.
PCR amplicons were generated using the primers shown in the manuscript. Sequencing libraries were constructed from the PCR amplicons using the Nextera DNA Flex kit (Illumina) and Hackflex protocol (PMID: 35014949), as described in PMID: 34750500.
After quality control, the library with pooled amplicons was sequenced SE300 on an Illumina MiSeq.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
3’ adapter sequences were removed using cutadapt (parameters: -a CTGTCTCTTATACACATCT -m 10). These data were used for three different purposes: 1) Determining the insertion site precision, 2) Determining the intactness of the cargo and 3) Determining the junctions of the transposon for investigating seamless insertion. The detailed processing steps for these three investigations is provided in the manuscript.
Assembly: Custom sequences based on targeted insertion locus were used to map the reads. These sequences are provided in the manuscript.
Supplementary files format and content: A tab-delimited file with the read count of each read is provided as a processed file for each sample. These reads can be used to replicate any of the downstream analyses mentioned in the manuscript.
Library strategy: Amplicon-seq
|
| |
|
| Submission date |
Mar 10, 2023 |
| Last update date |
May 03, 2024 |
| Contact name |
R. Keith Slotkin |
| E-mail(s) |
[email protected]
|
| Organization name |
Donald Danforth Plant Science Center
|
| Street address |
975 North Warson Road
|
| City |
St. Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63132 |
| Country |
USA |
| |
|
| Platform ID |
GPL17970 |
| Series (2) |
| GSE227103 |
Targeted site integration in plants using a transposon system [Amplicon] |
| GSE227105 |
Targeted site integration in plants using a transposon system |
|
| Relations |
| BioSample |
SAMN33715447 |
| SRA |
SRX19635246 |
