|
| Status |
Public on Dec 31, 2022 |
| Title |
βC1OE_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Transgenic plant leaves (2nd leaf from top)
|
| Organism |
Nicotiana tabacum |
| Characteristics |
genotype: Tobacco, Wisconsin 38
|
| Treatment protocol |
Samples were collected equally at 6 week post transfer to Green house.
|
| Growth protocol |
Rooted βC1 O.E lines were transferred to soil and kept for acclimatization for 3 days in plant growth chamber (12 hr light /Dark cycle, 70% RH, 24°C Temperature). The plants were then transferred to bigger pots in transgenic green house with the same condition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from seedlings were extracted using Trizol (Invitrogen) reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Adapter was removed and low quality bases were trimmed from sequenced reads using cutadapt.
The processed reads were aligned to the tobacco (TN90) genome, GCF_000715135_TN90, using Hisat2.
Gene expressions were calculated using CuffLinks (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Supplementary_files_format_and_content: FPKM values of the genes obtained using Cuffdiff are provided as xlsx format
|
| |
|
| Submission date |
Nov 24, 2021 |
| Last update date |
Dec 31, 2022 |
| Contact name |
Shivaprasad Padubidri V. |
| E-mail(s) |
shivaprasad@ncbs.res.in
|
| Phone |
+918023666511
|
| Organization name |
National Centre for Biological Sciences, TIFR
|
| Street address |
GKVK Campus, Bellary Road
|
| City |
Bengaluru |
| State/province |
Karnataka |
| ZIP/Postal code |
560065 |
| Country |
India |
| |
|
| Platform ID |
GPL22345 |
| Series (1) |
| GSE189526 |
Understanding biochemical properties and functions of SyYVCV βC1 |
|
| Relations |
| BioSample |
SAMN23427938 |
| SRA |
SRX13220367 |
