Nucleic Acid Sequencing And Genotyping Service - DNA Sequencing, RNA Sequencing / Transcriptome Sequencing, Epigenome Analysis; Animal; Human / Animal Tissue, Blood; To Be Collected By The Service Pr…

OPTION CLAUSE 25% : The buyer can increase or decrease the contract quantity or contract duration up to 25 percent at the time of issue of the contract. However, once the contract is issued, the contract quantity or contract duration can only be increased up to 25 percent. Bidders are bound to accept the revised quantity or duration. For lumpsum-based service contracts, the buyer may increase the scope of work and contract value up to 25 percent with the consent of the service provider

Buyer Added text based ATC clauses BIDDER MUST READ THE HIGHLIGHTED POINT NO. A1, A2, A3 & A4 FOR NO. OF SAMPLES BEFORE PARTICIPATING IN THE BID Sequencing services Specifications: Development of a T2T assembl y for Murrah buffalo A1: Service De-Novo Genome Sequencing

• 1.No. of samples-1, Sample Type- Whole Blood
• 2.DNA Isolation & Quality Control: Ultra-High Molecular Weight DNA extraction is mandatory.
• 3.A comprehensive DNA QC report must be provided. Supported by QC in Agarose Gel, Nanodrop, Q ubit, Fragment Analyser and Pulsed-field capillary electrophoresis system. DNA quality parameter should be passed with respect to DNA integrity: DIN ≥ 8.0 or better, A260/A280 ratio between 1.8 to 2.0; A260/A230 ratio (~2.0 to 2.2) and total DNA quantity: ≥ 20 µg or better
• 4.Pac-Bio Hifi reads should be generated on a sequencing platform such as the PacBio Revio or an e quivalent or higher version, maintaining a minimum per-read accuracy of ≥ Q25 (99.68%) and a M ean HiFi read length N50 ≥ 15kb, generating a minimum of ≥80X coverage or better.
• 5.Library preparation should be carried out using SMRT bell Express Template Prep Kit 3.0 or higher version, with minimum library size varying between 15-20 kb
• 6.Sequencing should be carried out in Circular Consensus Sequencing HiFi
• 7.Methylation profiling should be generated natively from the same HiFi kinetics data with per-CpG- site methylation calling performed with ≥15X effective per-site read depth, methylation probabilit y/confidence score ≥ 0.95 per called site. A2: Service ONT Ultra Long Sequencing
• 1.No. of samples-1, Sample Type- whole Blood
• 2.DNA Isolation & Quality Control: Ultra-High Molecular Weight DNA extraction is mandatory. QC by Agarose Gel, Nanodrop, Qubit, Fragment Analyser and Pulsed-field capillary electrophoresis syste

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• 3.A comprehensive DNA QC report must be provided. Supported by QC in Agarose Gel, Nanodrop, Q ubit, Fragment Analyser and Pulsed-field capillary electrophoresis system. DNA quality parameter should be passed with respect to DNA integrity: DIN ≥ 8.0 or better, A260/A280 ratio between 1.8 to 2.0; A260/A230 ratio (~2.0 to 2.2) and total DNA quantity: ≥ 20 µg or better
• 4.ONT Sequencing should be carried out in sequencing Platform such as Oxford Nanopore Technolo gies PromethION or better versions, with minimum per-read accuracy of ≥ Q25 (99.68%) and mea n read N50 ≥ 50 kb or better
• 5.It should provide Ultra long reads ≥ 50 kb and more than 100X coverage data or better
• 6.Library preparation should be carried out either using ONT Ultra Long specific or higher version, w ith minimum library size varying between 50 to 100 kb
• 7.Methylation (5mC/5hmC) profiling should be generated natively from the same ONT raw signal da ta, with base modification calling at the same ≥100X coverage, ensuring ≥15X effective per-site re ad depth and per-site modification probability/confidence score ≥ 0.95. A3: Service Hi-C Sequencing
• 1.No. of samples-1, Sample Type- whole Blood
• 2.DNA Isolation & Quality Control: Ultra-High Molecular Weight DNA extraction is mandatory. QC by Agarose Gel, Nanodrop, Qubit, Fragment Analyser and Pulsed-field capillary electrophoresis syste
• m.A comprehensive DNA QC report must be provided. DNA quality parameter should be passed w ith respect to DNA integrity: DIN ≥ 8.0 or better, A260/A280 ratio between 1.8 to 2.0; A260/A230 r atio (~2.0 to 2.2) and total DNA quantity: ≥ 20 µg, or better
• 3.Enzyme-free Hi-C library should be prepared.
• 4.Hi-C Sequencing should be carried out in sequencing Platform such as Illumina Novaseq 6000 or b etter versions without any form of multiplexing with other libraries and mean per-read accuracy of Q30 (99.9%) or higher generating
• 5.Dovetail Omni-C protocol for chromosome-level scaffolding and sequencing with more than 100x c overage or better A4: Service ISO Sequencing
• 1.No. of samples- 12; Sample Type: Tissue
• 2.RNA Isolation & Quality Control: QC of RNA should be carried out by Agarose Gel, Nanodrop, Qubit , Fragment Analyser.
• 3.Service provider should prepare full length transcriptome library by utilizing ISO seq Kinnex protoc ol with the qualified RNA as the starting material
• 4.Iso Seq libraries shall be generated using two insert size ranges, 2.5 to 3.5 Kb and 3-5 Kb resultin g in 24 libraries.
• 5.Service provider should perform sequencing exclusively on Pac Bio platform maintaining consiste ncy, with minimum per-read accuracy ≥ Q25 (99.68%) or higher generating 20 million full transcri pts per library.
• 6.Sequencing should be carried out in Circular Consensus Sequencing HiFi B1: Bio-informatics All relevant Bioinformatics should be included for the creation of T2T genome assembly and to check the a ccuracy of the T2 to T2 assembly generated with complete annotation C1: Other Specifications:
• 1.The bidder shall submit a comprehensive quotation for execution of Telomere-to-Telomere (T2T) g enome assembly of Murrah buffalo, including generation of a gap-free chromosome-level assembly , assembly polishing, scaffolding, quality assessment, genome annotation support, and submission -ready data packages for national public repositories.
• 2.The quotation shall clearly specify the scope of work, platform details, expected data yield, bioinformatics workflow, deliverables, timeline, item-wise financial breakup, and after-service tech nical support.
• 3.All services listed under A1, A2, A3, A4, and B1 shall be executed at a single facility using the sam e whole-blood sample and tissue samples derived from the same experiment, so as to maintain sa mple uniformity and analytical consistency.
• 4.Raw and assembled genome data need to be submitted to recognized repositories, including IBDC . Supported with documents proof of past experience for submission of raw and assembled genom e data to recognized international repositories, including registration and handling of BioProject, Bi oSample, SRA, and genome assembly submission to GenBank/NCBI or equivalent archives.
• 5.The bidder/service provider must possess and submit valid documentary proof of the following:
• a.Valid accreditation of the testing/sequencing laboratory under ISO and DSIR/NABL for mol ecular/genomic laboratory operations by a national accreditation body.
• b.Certification under ISO 9001 or equivalent quality-management system for service deliver y and process control.
• c.Documented standard operating procedures for high-molecular-weight DNA extraction, lo ng-read sequencing, library preparation, assembly, polishing, and quality control, or equiv alent as supported with a P.O. from an institute of repute.
• d.Compliance with applicable biosafety, biodiversity, sample traceability, confidentiality, an d data-protection requirements, or equivalent compliance.
• e.Proven prior experience in long-read genome assembly projects with documentary evide nce, preferably chromosome-level or T2T-grade assemblies or denovo genome assembly e xperience with PO and relevant publications in livestock or in other large mammalian geno mes.
• f.The bidder should provide documentary evidence regarding having the availability of ade quate computational infrastructure and validated bioinformatics pipelines for assembly of r epeat-rich, centromeric, and telomeric regions.
• g.Results must provide assembly-quality metrics and validation reports, including contiguity and completeness assessment, read-mapping statistics, and repository-ready metadata pa ckages.
• 6.The cool chain / dry-ice should be maintained while collection, samples that failed after QC check must be re-collected without additional charges.
• 7.Results must be delivered within 180 working days of sample receipt acceptance.
• 8.The service provider should have an in-house sequencing facility, supported by the Installation ce rtificate of PacBio Revio or Oxford Nanopore Promethion and Illumina Novaseq or better version of these equipments. Complete scope of work should be performed within India.
• 9.Data Delivery: Data should be provided via FTP mode, as well as in Hard Disk in compatible forma ts
• 10.Total timeline for the work is maximum 6 months from the date of issue of PO, a delay beyond the time may attract penalty as per ICAR rules.
• 11.Data Confidentiality: All generated data is strictly confidential and shall not be shared with any thir d party or other Institute. PAYMENT TERMS & CONDITIONS:- payment will be made quarterly on bill basis after satisfactorly services and completion of each activit y as specified in the bid .