Bids Are Invited For Custom Bid For Services -Bids Are Invited For Custom Bid For Services -Whole Genome Sequencing Specification Whole Genome Sequencing Of Japanese Quail Using Pacbio Sequel Ii; Instrument: Pacbiosequel Ii; Species: Quail; Sample Type:, Bareilly-Uttar Pradesh

Bids Are Invited For Custom Bid For Services -Whole Genome Sequencing SPECIFICATION Whole Genome sequencing of Japanese quail using PacBio Sequel II; Instrument: PacBioSequel II; Species: Quail; Sample type: High molecular weight DNA This is a sequencing service for the samples provided, bidding may please be done by GEM. It is to certify that, specifications mentioned in the SRS are of generic in nature according to the research requirement and does not target any single company. Whole Genome sequencing of Japanese quail using PacBio Sequel II Requirements 1) Instrument: PacBio Sequel II; Species: Quail; Sample type: High molecular weight Genomic DNA 2) Sample Specification: Qty: ≥ 6 μg, Conc: ≥ 80 ng/μL, Vol: ≥ 100 μl; No of samples: 1; 3) Sample Quality Control: Gel, Femtopulse, Nanodrop, Qubit; Library Type: SMRT bell Express Template Prep Kit 2.0; Shearing, Size Selection and Library QC: Megaruptor 3 -DNA shearing image; Blue Pippin/ AMPure PB bead Size selection; Femtopulse; Qubit; Library Size: 15 - 20 Kb 4) SMRT: 2 SMRT 5) Data output: Total 400-500 GB Raw data and Total 50-60 GB HiFi data Additional specifications along with terms and conditions 1) 5 ml blood samples in EDTA Tube stored in -800C will be provided. A minimum of 10 μg Ultra High molecular gDNA of more than 100Kb should be isolated from Blood Sample. The isolated HMW DNA QC using Qubit, Nanodrop, Femtopulse and DNA QC report should be provided. 2) DNA Shearing should be done on the Megaruptor-3 platform and the quality control check shearing should be done on Femtopulse. 3) Sheared DNA should be purified using AMPure PB beads and analyzed through FEMTO before preparing SMRTbell library. 4) Multiple QCs at each step should be done by FEMTO (Sample QC pre shearing, post shearing and post library preparation) 5) Two SMRT Libraries of 10-15Kb and 15-20 Kb size SMRTbell Library should be prepared using SMRTbell Express Template Prep Kit 2.0/3.0. 6) Size selection should be using Bluepippin/ PacBio AMPure PB bead size selection. 7) The size selected and purified samples were further confirmed using Femtopulse and bound complex will be prepared using Binding kit. Multiplexing of libraries should not be done. Individual library should be sequenced in one SMRT Cell. 8) A total of 50 GB of Hifi data along with subreads file. 9) SMRT Libraries should be sequenced on PacBio Sequel II (30hr movie) 10) Scientists should be allowed to participate during the PacBio Sequel II run. 11) Wet lab workflow and Analysis Pipeline should be discussed and executed as per the Indenters project requirement. Any deviation from the specification will not be allowed without prior approval from the PI. 12) Raw data should be trimmed and a contamination check should be done to remove adapter sequences and errors. 13) Data access and submission: The raw data and analyzed data if any must be provided in a dedicated HDD along with online access at least for two years. Company must provide complete data access stored in the data base at-least for 2 years from submission of final result upon request without any extra charge. No data should be deleted without prior written permission from PI. 14) The biological samples should not be sent outside of India and Sequencer and technology should not be changed. 15) It is the responsible of the sequencing company to collect samples from designated laboratory of the institute with proper shipping containers and temperature (preferably dry ice) at no additional or extra cost as and when required (multiple shipments at no extra cost). 16) Service provider should submit the detailed Methodology, Deliverables, Time frames, and Milestones in the Bid. 17) Service provider will take concurrence of the client before proceeding to each step i.e. from DNA QC to data generation. 18) Data submission in the NCBI database should be included in the cost. 19) Billing should be done after the completion and submission of data from each batch. 20) Any deviation from this strategy is not acceptable and the indenter will not pay if specifications will be changed without permission. Mandatory certifications, publications and users list to be provided 1) A written certificate stating no samples will be sent outside India should be provided by the participating firm. 2) In-house PacBio Sequel II facility and provide an OEM certificate and Installation certificate in India as per ISO standards. 3) At least 20 purchase orders as proof of working with PacBio /Hi-C in the last 5 years. 4) Prior experience on working with PacBio, Hi-C and ISO Sequencing as evident by publications and work orders from national laboratories.on working with PacBio, Hi-C and ISO Sequencing as evident by publications and work orders from national laboratories. 5) The Service provider should have an experience of completing a minimum 2000 genome Sequencing Sample. 6) Service provider should have minimum 5 publications on De novo Genome Annotation and Assembly. 7) Minimum 100 publications in last 5 years should be provided from Indian academia clients. 8) Valid DSIR certified Indian laboratory with more than 51% ownership with the Indian citizen. Minimum 5 years revenue, Income tax return, P&L should be submitted. 9) Service providers should provide certificates that all technical points mentioned in technical specification will be followed and no change will be done from the technical Specification. ---- Total Quantity :

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