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Genome Data
Primary Details
| Genome ID | GEN4 | ||||
| Plant Name | Ocimum tenuiflorum | ||||
| Description | Title: De-novo Ocimum sanctum Genome sequencing. Abstract: De-novo sequencing and characterization of Ocimum sanctum L. for better understanding of secondary metabolism pathways in the plants. | ||||
About Genome
| Field | Data | Plant Image |
|---|---|---|
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| Platform | LS454 GS FLX | |
| Strategy | RNA-Seq | |
| Source | Genomic | |
| Library Name | CIMAP_454_GS_FLX_SIngle_ended | |
| Layout | SIngle-end | |
| Spot Value | 643,134 | |
| Bases | 731.7 M | |
| Size | 530 Mb | |
| GC Content Percentage | 39.3% | |
| Publish Data | 2015-06-24 | |
| External Database ID | SRA Experiment ID: SRX760132 | |
| DNA C-Value | 0.36 | |
| Submitted By | Dr. Ajit Kumar Shasany, CSIR-CIMAP, Lucknow, India | |
Images
Description Details
Materials & Method
Design: Library for sequencing was constructed according to the Roche Rapid Library Preparation Method Manual (GS FLX+ Series – XL+, May 2011). Briefly, ~1 microgram of genomic DNA was made up to 100 ul with TE buffer and fragmented using a nebulizer. The resulting fragmented DNA was cleaned up using QIAGEN Minelute PCR purification kit. Subsequently, DNA was subjected to a series of enzymatic reactions that repair frayed ends, and ligates adaptors. After ligation, small fragments were removed using Agencourt Ampure SPRI beads. The prepared library was validated for quality by running an aliquot on High Sensitivity Bioanalyzer Chip (Agilent). (Refer Figure 3 for Bioanalyzer profiles of amplified product ePCR1)The library shows a peak at the range of 1.4 – 1.8 kb. The library is suitable for sequencing on 454 platform.
NCBI SRA database IDs
SRA database Experiment ID: SRX760132, Run ID: SRR1653610, Biosample ID: SAMN03196331 (SRS744768), Bioproject ID: PRJNA267195 (For more details visit SRA, NCBI website: https://www.ncbi.nlm.nih.gov/sra/SRX760132[accn] )
Sample Details
O. tenuiflorum (Syn. Krishna Tulsi, O. sanctum) (CIM Ayu) 4 months old leaf
Genomic Data
Pathway Analysis Report Data
| Transcript id | KO id | Description | Pathway | Pathway function | Organism |
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Predicted SSR Report Data
| Scaffold id | Type of ssr | Pattern of ssr | Size | ssr start position | ssr end position |
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Functional Annotation Report Data
| query_id | query_length | subject_id | subject_length | percentage_identity | alignment_length | query_coverage | subject_coverage | noof_mismatches | noof_gaps | query_start | query_end | subject_start | subject_end | e_value | score_entry | entry_name | protein_description | gene_names | ec_number | organism_name | pathway_name | protein_existence | protein_family | go_bp | go_mf | go_cc |
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