|
| Status |
Public on Apr 01, 2023 |
| Title |
LOCALS2 |
| Sample type |
SRA |
| |
|
| Source name |
Leaf
|
| Organism |
Solanum lycopersicum |
| Characteristics |
domestication: Cultivated
tissue: Leaf
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was isolated from leaf samples by using Xcelgen Plant gDNA Isolation Kit (XG2611-01) as per the protocol described. The DNA was eluted in 50µl Nuclease-Free Water. The samples were quantified using Qubit Fluorometer. For determining A260/280 ratio, 1µl of sample was loaded in Nanodrop8000 spectrophotometer. The quality of samples was checked in 0.8% Agarose gel electrophoresis along with Hind III marker for the presence of intact bands.
To 100ng of gDNA, barcoded adapters (~0.1pM) were added and digested with Apek1 enzyme for 12h at 75oC. The barcoded and common adapters were ligated to the sticky ends of the digested DNA with T4 DNA Ligase enzyme at 22oC for 180 mins, followed by heat inactivation. The ligated products were pooled into 12 groups of 12 samples each group. The pool was PCR amplified to generate the final library pool.
High Sensitivity (HS) DNA chip and library pool was sequenced on Illumina platform to generate ~ 3 million reads/sample.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
KM_TMRL_39
|
| Data processing |
Illumina platform used for base calling
TASSEL5 GBSv2 pipeline was used for identification of tags at cut sites and SNPs located across reference genome.
The fastq files were aligned against the tomato reference genome using the Bowtie2 tool version 2.2.9. The .sam file created from the Bowtie2 aligner program was used through SAMToGBSdbPlugin()
DiscoverySNPCallerPluginV2 took a GBSv2 database file as input and identified SNPs from the aligned tags.
Assembly: mm9
Supplementary files format and content: The VCF file generated from tassel pipeline was generated.
Supplementary files format and content: After filtration SNPs were retained provided in hapmap (hmp) format.
|
| |
|
| Submission date |
Apr 03, 2022 |
| Last update date |
Apr 01, 2023 |
| Contact name |
Basharat Ahmad Bhat |
| E-mail(s) |
bb284@snu.edu.in
|
| Phone |
9469662374
|
| Organization name |
Sher-e-Kashmir University of Agricultural Sciences and Technology
|
| Department |
Animal Biotechnology
|
| Street address |
Shuhama
|
| City |
Gandarbal |
| State/province |
Kashmir |
| ZIP/Postal code |
190006 |
| Country |
India |
| |
|
| Platform ID |
GPL19694 |
| Series (1) |
| GSE200034 |
Next Generation Sequencing of tomato germplasm for cold tolerance and yield studies |
|
| Relations |
| BioSample |
SAMN27277495 |
| SRA |
SRX14716763 |
