Resequencing

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Overview

Resequencing analysis is used to reveal genome-wide variations of sequenced data through comparison to a known reference genome. The variants are genotyped, annotated, and compared between the samples. 

Library preparation

To prepare for sequencing, our lab provides library preparation on an initial sample of DNA.

 

Sample requirements (for all libraries)
DNA and RNA samples:

 

     Library Preparation Type Input Material Min. Amount Volume Dilution Buffer
  • TruSeq Nano DNA (standard DNA sample prep) 
 gDNA    500 ng  < 50 ul        H2O, or 10 mM Tris-Cl, pH 8.5
  • Nextera XT (small genomes and amplicons*)
 gDNA     10 ng   < 10 ul H2O, or 10 mM Tris-Cl, pH 8.5
  • Exome Sequencing
 gDNA    100 ng   < 10 ul H2O, or 10 mM Tris-Cl, pH 8.5
  • ChIP-Seq
 ChIP DNA    20 ng   < 50 ul H2O, or 10 mM Tris-Cl, pH 8.5
  • TruSeq RNA
 Total RNA    1 ug   < 50 ul H2O
  • Small RNA
 Total RNA    1 ug   < 5 ul H2O

 

*Amplicons will be accepted only following DNA purification.

 

  • Sample quality requirements:

Please note that the user is responsible for the quality of each sample. Genomic DNA should be intact. Please contact the Lab to coordinate suitable sample prep if your DNA sample is degraded. RNA integrity must be confirmed using the Agilent Bioanalyzer, TapeStation, or a similar instrument, or by running the sample on an agarose gel.

  • Sample purity:

OD260/280 = 1.8-2.2
OD260/230 ≥ 2.0

 

Sequencing
At this time, TAU's Genomics Analysis Lab does not perform sequencing in-house. We prepare and submit libraries to outisde laboratories, such as the Technion Genome Center and G-INCPM, where the sequencing is performed.

 

Costs

Please contact Dr. Orly Yaron in the Functional Genomics Lab at  03 640 5251 or orlyyaron@post.tau.ac.il for pricing information.

Analysis options

The preliminary analysis from raw datafiles is performed on various platforms such as the Partek Genomics Suite. Further analysis of differentially expressed gene-lists function and pathways is performed using various updated web-based tools. The analysis is generally done on a collaborative basis. For more details, please contact Dr. Metsada Pasmanik-Chor: metsada@post.tau.ac.il , 03 640 6992.

 

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