Download Microarray Analysis

Sher-e-Kashmir
University of Agricultural Sciences and Technology of Kashmir
Centre of Animal Biotechnology
NAIP on Bioprospecting of Genes and Allele Mining
Shuhama , Srinagar –190006
Tel. : 0194 – 2262612, Fax 0194-2262207
email [email protected] web. skuastkashmir.org.in
No/AU/CAB/NAIP-Allele Mining/
Dated: 30-01-2009
To
(Microarray Analysis Service Provider)
Dear Sir,
Sub :
INVITATION FOR QUOTATIONS FOR OUTSOURCING OF THE EXPERIMENTAL
WORK ON MICROARRAY ANALYSIS
1.
You are invited to submit your most competitive quotation for the following services:-
Brief Description
of the Goods /
Services
Specifications
Quantity
Delivery
Period
Place of Delivery
Outsourcing for
Microarray Analysis
for Gene Expression
profiling in goats
under cold stress
conditions
Annexure -I
as mentioned in
the annexure
Winter
samples by
March 31,
2010
Centre of Animal
Biotechnology,
Faculty of Veterinary
Sciences (SKUAST-K)
Shuhama 19006 Srinagar
Summer
samples in
July 2010
2.
Government of India has received a credit from the International Development Association
(IDA) in various currencies equivalent to US$ 200 million towards the cost of the National
Innovation Project and intends to apply part of the proceeds of this credit to eligible payments
under the contract for which this invitation for quotations is issued.
3.
Bid Price
a) The quotation(s) should reach undersigned on or before 17-01-2010.
b) Quotations can be as send as hard copy (post) and soft copy through email.
c) The rates quoted should be CIP.
d) All duties, taxes and other levies payable shall be included in the total price.
e) Bill / Invoice to be submitted in triplicate along with advance stamped receipt
for arranging payment, after placing of the work order.
f) Payment will be made after satisfactory completion of work.
g) Validity of the quotations should be mentioned.
h) The Prices shall be quoted in Indian Rupees only.
i)
4.
5.
6.
7.
8.
The rates quoted by the bidder shall be fixed for the duration of the contract
and shall not be subject to adjustment on any account.
Each bidder shall submit only one quotation.
Validity of Quotation:
Quotation shall remain valid for a period not less than 180
days after the deadline date specified for submission.
Evaluation of Quotations
The Purchaser will evaluate and compare the quotations determined to be substantially
responsive i.e. which
(a)
are properly signed ; and
(b)
conform to the terms and conditions, and specifications.
Award of contract: The Purchaser will award the contract to the bidder whose quotation
has been determined to be substantially responsive and who has offered the lowest evaluated
quotation price.
7.1
Notwithstanding the above, the CCPI, NAIP Allele Mining SKUAST-K reserves the
right to accept or reject any quotations and to cancel the bidding process and reject all
quotations at any time prior to the award of contract.
7.2
The bidder whose bid is accepted will be notified of the award of contract. The terms
of the accepted offer shall be incorporated in the purchase order.
Payment shall be made immediately after completion of the job.
You are requested to provide your offer latest by 14:00 hours on 17-01-2010.
We look forward to receiving your quotations and thank you for your interest in this project.
Name:
Dr Nazir A Ganai
Designation: CCPI, NAIP on Bioprospecting of genes and allele mining
Address:
Centre of Animal Biotechnology
Faculty of Veterinary Sciences and Animal Husbandry
SKUAST-K
Shuhama 190006 Srinagar (Kashmir)
Tel. No. 0194-2262642
Mobile: 09419018745
Fax No .0194-2262207
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NSP/GOODS
FORMAT OF QUOTATION *
Sl.
No.
Description of
Services
Specifications
Samples
Quoted per
sample Rate
(in Rs.)
Total Amount
In
Figures
In
Words
Sales / Service Tax if any
TOTAL
We agree to supply the above goods/ services in accordance with the technical specifications
on per sample basis for a contract price of Rs. ...........(amount in figures ) (Rs. ........... amount
in words) within the period specified in the Invitation for Quotations.
We hereby certify that we have taken steps to ensure that no person acting for us or on our
behalf will engage in bribery.
Signature of Service Provider
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ANNEXURE - I
SPECIFICATIONS FOR EXPERIMENTAL WORK

Providing service in the area of Gene Expression through microarray analysis.

Companies should clearly mention the platform (Agilent / Affymetrix Gene Chip) for microarray analysis,
with the total number of the gene sequences spotted on bovine gene chip.

Companies can provide alternate approaches for the same experimental output (details given below), and
quote for the same.

In case, there are technical doubts, the companies can ask for clarifications before tendering the quotes.

There must be scope for constant and close interaction between the company and University during the
course of the out-sourced experimentation so that any minor changes deemed essential during
experimentation could be entertained.

List of clientele to whom similar services have been provided may be attached.
Description of the work:
Identification and characterization of differentially expressed genes imparting cold stress tolerance in pashmina
goat. Thus basically it involves comparison of the expression profile of Pashmina goat in Leh under stressed (25OC) and unstressed (thermo-neutral) conditions to identify and catalogue the genes that are differentially
expressed under stress conditions. Regarding the experimental set up, 4 to 5 tissues / biopsies (Skin,
hypothalamus, liver, thyroid gland, adrenal gland, blood) shall be collected from 3-4 pashmina goats exposed to
cold stress (-25OC) conditions at Leh. The tissue sampling would be repeated from 3-4 goats under thermoneutral conditions (+ 20OC) during summer in Leh. Thus a total of ~ 30 tissue samples (3-4 goats X 4-5 tissues X
2 time points) will be used for the analyses. It is preferred to have a biological and a technical control in the
analysis.
Services to be included:




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Your technical person to be present during collection of biopsies or tissues (skin, hypothalamus, liver,
thyroid gland, adrenal gland, blood, any other tissue) at Leh Ladakh for precision sampling, and
transportation to your laboratory.
RNA Extraction from biopsies or tissues. RNA Quality and Quantity check.
Labelling and Cross Hybridisation for Gene Expression using the Agilent / Affymetrix Gene Chip
platform, with Bovine Genome Microarrays
Data Extraction and Analysis:
o Extraction of Expression data and its assessment for quality metrics- including mean signals of
spikeins, mean signals of the positive and negative controls.
o Graphical representation of data using Scatter Plot(s), Pair-wise volcano plot(s), Box plot(s).
o Fold Changes and other relevant statistical analyses to identify differentially expressed genes.
o Clustering (hierarchical and non-hierarchical) of the gene expression data to group together
genes with similar profiles and to discover gene relationships
o Gene Ontology and pathway analysis on differentially expressed genes
o Annotation of the differentially expressed gene lists with gene identifiers and functional
information.
o Inference of biological networks from gene expression microarray data.
o Gene set enrichment analysis (GSEA) to evaluate expression microarray data at the level of
gene sets (pathways). Discovery of pathway network relationships within the data in the context
of known pathways. Extraction of network relationships within PubMed for the data.
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Deliverables




Publication Quality RNA gel photographs, Data on RNA yield and quality from different tissues,
Raw Microarray analysis data
Final Bioinformatics analysis report:
o No. of bovine gene sequences conserved in goat
o Functional Gene Annotations: Known gene, ontology, pathway
o Unigene annotations provided with expression data and results
o Summary statistics for each treatment group.
o Multiple pair-wise comparisons of principle interest using fold change and t-test derived pvalues
o Biological Network pathways (within the data) regulating cold stress tolerance.
o Tissue specificity of the differentially expressed genes
DNA sequences of the differentially expressed genes in pashmiona goat with annotations
Pricing:
Pricing be quoted separately as:
 per sample basis for the expression profiling detailed under services and deliverables.
 DNA sequencing per gene of the differentially expressed genes.
 Pricing be quoted in rupees.
Other terms and conditions:
Terms and conditions, if any, with respect to collection of the samples may be mentioned.
The work should be completed in two months after receiving of the samples.
There should be scope for participatory approach during the experimentation.
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