|
| Status |
Public on May 28, 2024 |
| Title |
ss_Cold_3h_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Shoot
|
| Organism |
Manihot esculenta |
| Characteristics |
cultivar: TM12
genotype: WT
tissue: Shoot
treatment: cold (4 C)
time: 3 hours
protocol: stranded RNA-Seq
|
| Treatment protocol |
For cold treatment, seedlings were grown in control conditions for two weeks and subsequently transferred to a cold room (4°C) with light for 3 h before harvesting.
|
| Growth protocol |
Seedlings were grown in climate chambers with a long day photoperiod (16h light/8h dark cycle) at 20°C/18°C. Light intensity and humidity during control growth conditions was ~100 μE m−2 s−1 and 60% respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen) and treated with Turbo DNase (ThermoFisher Scientific) according to manufacturers’ instructions. DNase-treated RNA was recovered by acid–phenol extraction and ethanol precipitation.
Strand specific RNA-Seq libraries were prepared using TruSeq stranded total RNA preparation kit from Illumina following manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Cold3h_Rep1
|
| Data processing |
The reads were aligned using STAR v2.7.10a with parameters --outSAMmultNmax 1, --alignEndsType Local, --clip3pAdapterSeq AGATCGGAAGAGC AGATCGGAAGAGC, --clip3pAdapterMMp 0.1 0.1
The reads that aligned below mapping quality of 10 were filtered out using samtools v1.6.
The duplicate reads are removed after fixing the mate pairs using samtools v1.6.
The strand specific coverage was calculated using bedtools (v2.30) genomecov
Assembly: EnsemblePlants v6.54
Supplementary files format and content: Normalised read counts in bedgraph format
|
| |
|
| Submission date |
Feb 15, 2023 |
| Last update date |
May 28, 2024 |
| Contact name |
Swetha Chenna |
| E-mail(s) |
chennaswetha890@gmail.com
|
| Phone |
+4571521934
|
| Organization name |
University of Copenhagen
|
| Street address |
Bülowsvej
|
| City |
Frederiksberg |
| State/province |
Choose State |
| ZIP/Postal code |
1870 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL28909 |
| Series (2) |
| GSE225365 |
Strand specific RNA-Seq of transcripts from cassava, Maihot esculenta variety TM12 |
| GSE225366 |
Transcriptome analysis of cassava, Manihot esculenta variety TM12 |
|
| Relations |
| BioSample |
SAMN33315615 |
| SRA |
SRX19382873 |
