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| Status |
Public on Mar 01, 2024 |
| Title |
Root total RNA isolate from six Months old Dendrobium Sonia under white light root total RNA |
| Sample type |
SRA |
| |
|
| Source name |
Root
|
| Organism |
Dendrobium hybrid cultivar |
| Characteristics |
tissue: Root
genotype: WT
treatment: White light
|
| Treatment protocol |
Plants were grown in gowth chambers with 16-hour light and 8-hour dark cycle in fluorescence cool white light (WL). The white light was obtained from Philips 17-watt F17T8/TL741 USA Alto II technology tubes with 100% light intensity, which is equivalent to ~100 μmols/min chambers under white light.
|
| Growth protocol |
Plants of Dendrobium Sonia in juvenile stage (6 months) with ~4’ in height were grown in plant growth chambers (Percival Scientific, USA). All plants growtt was maintained at 25 °C temperature and with 70 % relative humidity.The plants were sprayed with water regularly and with standard N, P, K nutrient solution once every week.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Plant root was cut out and immediately frozen in liquid nitrogen. The frozen roots were ground into powder form using RNAase treated mortar and pestle. The powder was then used for RNA extraction using Qiagen Plant RNeasy mini kit (Cat #74104). 1.26 μg RNA was used for preparation of Library.
SMARTer RNA-seq kit was used for preparation of the library using manufacturer's protocol
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| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Fastq quality check: checking of quality parameters for the sequences obtained from sequencer. The following checks are performed for an input fastq file • base quality score distributions • average base content per read • GC distribution in the reads
Preprocessing step : From the raw reads, the adaptor sequences and low quality bases are trimmed using AdapterRemoval-v2 (version 2.2.0). From the preprocessed reads, ribosomal rna sequences are removed by aligning the reads with silva database using bowtie2 (version 2.2.9) and subsequent workflow using sam-tools (version 0.1.19), sambamba (version 0.6.5), BamUtil (version 1.0.13) tools and in-house scripts. T
De novo transcriptome assembly :The high quality reads were then assembled using Trinity with default options
The trimmed reads were aligned to the assembled transcriptome (length >= 200bp) using Bowtie2 program. We allowed up to 1-mismatches in the seed region (length = 31bp) and all multiple mapped position were reported. Of all filtered reads about ~ 93.29% of reads from sample were properly aligned back to the assembled transcriptome.
Annotation: The assembled transcript is annotated using our in-house pipeline for de novo transcriptome assembly. Briefly, we perform the following steps for annotation of assembled transcripts. Comparison with TAIR Araport protein database using BLASTX program Gene and protein annotation to the matched transcript Gene ontology annotation Pathway annotation
Assembly: Araport11
Supplementary files format and content: Fasta file containing the sequence of respective assembeled transcripts
Supplementary files format and content: Tab delimited text file containing annotation for all the Transcripts along with their ReadCounts and FPKM
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| |
|
| Submission date |
Dec 27, 2023 |
| Last update date |
Mar 01, 2024 |
| Contact name |
Kishore Cs Panigrahi |
| E-mail(s) |
panigrahi@niser.ac.in
|
| Organization name |
National Institute of Science Education and Research
|
| Department |
School of Biological Sciences
|
| Lab |
Kish Lab
|
| Street address |
NISER, P.O Jatni
|
| City |
Khurda |
| State/province |
Odisha |
| ZIP/Postal code |
752050 |
| Country |
India |
| |
|
| Platform ID |
GPL34042 |
| Series (1) |
| GSE252123 |
Root growth in Orchid Dendrobium cv. Sonia requires shade avoidance response of PHYB along with regulation of auxin pathway genes |
|
| Relations |
| BioSample |
SAMN39153144 |
| SRA |
SRX23045363 |
