Sequencing and Bioinformatics Module

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Sequencing and Bioinformatics Module

Overview

Lab Preparation Checklist
Lab Preparation Checklist
Kit contains sufficient materials for 12 student workstations, or 96 sequencing reactions.
pJETF primer 1
pJETR primer 1
GAPSEQF primer 1
GAPSEQR primer 1
Control plasmid 1
Barcoded 96-well plate 1
Sealing film 1
Colored micro test tubes, 2 ml 60
Curriculum, including Teacher's Guide, Student Manual, and graphic Quick Guide 1
Required Accessories Not Included in Kit:
Adjustable micropipets  
2–20 µl  
Pipet tips  
Computers and internet access  
Sequencing and Bioinformatics Module
Sequencing and Bioinformatics

Sequencing and Bioinformatics Overview

Sequencing and Bioinformatics: part of the Cloning and Sequencing Explorer Series

Sequence and analyze your cloned DNA. Students combine plasmid DNA containing PCR products with sequencing primers in a 96-well plate and send them to a sequencing service.

The portion of the GAPDH gene to be cloned using the Cloning and Sequencing Explorer Series can vary from 0.6 to over 2 kb in length depending on the plant source. To ensure complete coverage of the gene, four sequencing primers are provided: one forward and one reverse primer specific to either side of the pJET1.2 cloning site, and one forward and one reverse primer homologous to different regions in the middle of the GAPDH gene. Thus, four independent sequences will be generated for each plasmid — these sequences can be assembled into a contig using the bioinformatics module. We recommend each student team submit two plasmids for sequencing with all four primers. The ultimate goal of the Cloning and Sequencing Explorer Series is to generate sequence data that can be uploaded into NCBI's GenBank database to be used by other scientists. It is important to generate many sequence-reads to guard against sequencing errors and ensure data accuracy. If multiple groups within a class independently clone the same GAPDH gene, the repetition will be sufficient to confirm the sequence. Additionally, sequencing primers are provided to allow for sequence reads in both forward and reverse directions, providing another method of sequence confirmation.

Once the plasmid has been cloned and sequenced, the real work begins — interpreting the sequence data. This module teaches students the essential bioinformatics skills needed to study biology with the power of computer analysis. The Sequencing and Bioinformatics Module includes a 3-month subscription to the Geneious software, a program that provides students with access to the latest tools in bioinformatics data analysis. After downloading Geneious, raw sequence files are imported and are immediately ready for exploration. Students will view and edit the original chromatograms of their sequences, screen out vector sequences, confirm their sequences are GAPDH, perform NCBI BLAST searches on their data to identify and find related sequences, assemble their forward and reverse sequences into contigs, predict intron and exon structure, transcribe and translate the GAPDH sequence, and compare it to known gene, mRNA, and protein sequences. Finally, confirmed sequences can be added to NCBI’s GenBank database where scientists around the world will be able to use that data for their research.

The sequencing and bioinformatics module is used to analyze a portion of the GAPC gene isolated from a plant. Students are guided through a sequence analysis that allows them to make a real contribution to science!


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Description

The Sequencing and Bioinformatics Module is an integral component of the Cloning and Sequencing Explorer Series. This module is used to sequence and analyze a portion of the GAPC gene, a housekeeping gene in the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) family, from a plant of each student's choice. Once sequence data are generated* and verified, they can be uploaded into NCBI's GenBank database and used by other scientists.

This module combines the power of computer analysis with student-generated cloning data to teach students essential bioinformatics skills. The Sequencing and Bioinformatics Module includes a 3-month subscription for unrestricted access to Geneious Prime, a software program that provides students with the latest tools in bioinformatics data analysis.

The Sequencing and Bioinformatics Module can also be purchased separately and used to sequence any PCR product that is cloned into the pJET1.2 plasmid. Four sequencing primers are provided to sequence PCR fragments up to 1 kb in length. Once the sequence of the cloned gene has been obtained, use Geneious to assemble the sequences into a contig and analyze the data.

*Sequencing service is not included.

Specifications

Kit contains reagents sufficient materials for 12 student workstations or 96 sequencing reactions  
pJETF primer 1
pJETR primer 1
GAPSEQF primer 1
GAPSEQR primer 1
Control plasmid 1
Barcoded 96-well plate 1
Sealing film 1
Colored microcentrifuge tubes, 2 ml 60
Curriculum, including instruction manual 1

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Sequencing and Bioinformatics Module

1665025EDU
Eighth module in Cloning and Sequencing Explorer Series classroom study kit, includes primers, plasmid, barcoded 96-well plate, test tubes, curriculum, and more, for 12 workstations; education use only (Sequencing service not included)

0 1665025EDU /templatedata/internet/product_SKU/data/LSE/Cloning-and-Sequencing-Explore/Cloning-and-Sequencing-Explore/166-5025EDU_0921121012411.xml 1665025EDU /default/main/bio-rad/WORKAREA/default 09/21/09 12:10 PM en_US jc99dspn 2017-11-14 07:07:14 true true internet/product_SKU jc99dspn templatedata/internet/product_SKU/data/LSE/Cloning-and-Sequencing-Explore/Cloning-and-Sequencing-Explore/166-5025EDU_0921121012411.xml LSE 2019-05-04 11:13:58 /default/main/bio-rad/STAGING N /default/main/bio-rad en 12/31/37 11:59 PM 1555972631895 AE,AI,AL,AM,AR,AT,AU,AZ,BA,BD,BE,BF,BG,BH,BN,BO,BR,BW,CA,CH,CL,CM,CN,CO,CR,CY,CZ,DE,DK,DO,DZ,EC,EE,EG,EH,ER,ES,ET,FI,FM,FO,FR,GA,GE,GF,GH,GP,GR,GT,GU,HK,HN,HR,HT,HU,ID,IE,IL,IN,IS,IT,JM,JO,JP,KE,KH,KR,KW,KZ,LB,LI,LK,LT,LU,LV,MA,MD,MG,MK,ML,MO,MQ,MS,MT,MU,MX,MY,NG,NI,NL,NO,NP,NZ,OM,PA,PE,PF,PG,PH,PK,PL,PR,PS,PT,PW,PY,QA,RO,RS,RU,SA,SB,SE,SG,SI,SK,SN,ST,SV,TG,TH,TN,TO,TR,TT,TW,TZ,UA,UG,UK,US,UY,UZ,VA,VE,VU,XK,YE,ZA,VN 2019-05-04 11:13:58 /default/main/bio-rad/WORKAREA/default/templatedata/internet/product_SKU/data/LSE/Cloning-and-Sequencing-Explore/Cloning-and-Sequencing-Explore/166-5025EDU_0921121012411.xml templatedata/internet/product_SKU/data/LSE/Cloning-and-Sequencing-Explore/Cloning-and-Sequencing-Explore/166-5025EDU_0921121012411.xml 1665025edu-sequencing-bioinformatics-module 1665025EDU Sequencing And Bioinformatics Module Sequencing and Bioinformatics Module Eighth module in Cloning and Sequencing Explorer Series classroom study kit, includes primers, plasmid, barcoded 96-well plate, test tubes, curriculum, and more, for 12 workstations; education use only (Sequencing service not included) Eighth module in Cloning and Sequencing Explorer Series classroom study kit, includes primers, plasmid, barcoded 96-well plate, test tubes, curriculum, and more, for 12 workstations; education use only Eighth module in Cloning and Sequencing Explorer Series classroom study kit, includes primers, plasmid, barcoded 96-well plate, test tubes, curriculum, and more, for 12 workstations; education use only (Sequencing service not included) /webroot/web/images/lse/products/cloning_sequ_explorer_series/sku_thumb/global/166-5025EDU_tn.jpg /webroot/web/images/lse/products/cloning_sequ_explorer_series/sku_view/global/166-5025EDU_view.jpg /webroot/web/images/lse/products/cloning_sequ_explorer_series/sku_feature/global/166-5025EDU_feature.jpg Sequencing and Bioinformatics Module #166-5025EDU ,VN RepEx Sequencing and Bioinformatics Module #166-5025EDU Eighth module in Cloning and Sequencing Explorer Series classroom study kit, includes primers, plasmid, barcoded 96-well plate, test tubes, curriculum, and more, for 12 workstations; education use only (Sequencing service not included) 1665025EDU, 1665025, cloning, sequencing, dna sequencing, gene sequencing, explorer, gapc, bioinformatics, lab, education, classroom 09/21/09 12:10 PM 12/31/37 11:59 PM AE,AI,AL,AM,AR,AT,AU,AZ,BA,BD,BE,BF,BG,BH,BN,BO,BR,BW,CA,CH,CL,CM,CN,CO,CR,CY,CZ,DE,DK,DO,DZ,EC,EE,EG,EH,ER,ES,ET,FI,FM,FO,FR,GA,GE,GF,GH,GP,GR,GT,GU,HK,HN,HR,HT,HU,ID,IE,IL,IN,IS,IT,JM,JO,JP,KE,KH,KR,KW,KZ,LB,LI,LK,LT,LU,LV,MA,MD,MG,MK,ML,MO,MQ,MS,MT,MU,MX,MY,NG,NI,NL,NO,NP,NZ,OM,PA,PE,PF,PG,PH,PK,PL,PR,PS,PT,PW,PY,QA,RO,RS,RU,SA,SB,SE,SG,SI,SK,SN,ST,SV,TG,TH,TN,TO,TR,TT,TW,TZ,UA,UG,UK,US,UY,UZ,VA,VE,VU,XK,YE,ZA,VN en LSE /LSE/Cloning-and-Sequencing-Explore/Cloning-and-Sequencing-Explore N 0 <p>The eighth module in Cloning and Sequencing Explorer Series, the Sequencing and Bioinformatics Module is used to sequence and analyze a portion of the <em>GAPC</em> gene. Materials include primers, plasmid, barcoded 96-well plate and sealing film, test tubes, and curriculum. Materials are sufficient for 12 workstations. This product is for education use only. Sequencing service is not included.</p> <p><strong>Notification:</strong> <a href="/webroot/web/pdf/lse/literature/Bulletin_6858.pdf" target="_blank">Download a revised workflow for mapping the intron-exon boundaries when using Geneious&trade;</a>.</p> /webroot/web/html/lse/products/SKUs/autopopulated/ 166-5025EDU_0921121012411_en.html /webroot/web/html/lse/products/SKUs/autopopulated//166-5025EDU_0921121012411_en.html <b>Kit contains sufficient materials for 12 student workstations (2&ndash;4 students per workstation) or 96 sequencing reactions</b> 1138 &nbsp; 1 0 pJETF primer 2408 1 1 0 pJETR primer 2409 1 1 0 GAPSEQF primer 1676 1 1 0 GAPSEQR primer 1677 1 1 0 Control plasmid 2410 1 1 0 Barcoded 96-well plate 1368 1 1 0 Sealing film 2411 1 1 0 Colored microcentrifuge tubes, 2.0 ml 2421 60 1 0 Curriculum, including teacher's guide, student manual, and graphic quick guide 2398 1 1 0 false $327.50 true $ %24262.00 true false true true false USD true true true /prd/en/US/adirect/biorad?cmd=ajaxAddToCart&AddToCartProductID=1665025EDU&quantity= false false /prd/en/US/adirect/biorad?cmd=ajaxAddToCart&AddToCartProductID=1665025EDU&CartQuote=QT&quantity= 1711 false true false /prd/en/US/adirect/biorad?cmd=ajaxAddToCart&AddToCartProductID=1665025EDU&AddToDefaultWishList=true&quantity= 41105600 327.50 Product detail page 1665025EDU
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Sequencing Kit Refill Pack

1665026EDU
Consumables refill kit for use with Sequencing and Bioinformatics module (#166-5025EDU), contains pJETF, pJETR, GAPSEQF, and GAPSEQR primers, and control plasmid; education use only (Sequencing service not included)

1665026EDU /templatedata/internet/product_SKU/data/LSE/Cloning-and-Sequencing-Explore/Sequencing-and-Bioinformatics-/166-5026EDU_0921121013003.xml 2 1665026EDU /default/main/bio-rad/WORKAREA/default 09/21/09 12:10 PM en_US jcv374xa 2017-11-14 07:07:15 true true internet/product_SKU jcv374xa templatedata/internet/product_SKU/data/LSE/Cloning-and-Sequencing-Explore/Sequencing-and-Bioinformatics-/166-5026EDU_0921121013003.xml LSE 2019-05-04 11:13:45 /default/main/bio-rad/STAGING N /default/main/bio-rad en 12/31/37 11:59 PM 1555972632820 AE,AI,AL,AM,AR,AT,AU,AZ,BA,BD,BE,BF,BG,BH,BN,BO,BR,BW,CA,CH,CL,CM,CN,CO,CR,CY,CZ,DE,DK,DO,DZ,EC,EE,EG,EH,ER,ES,ET,FI,FM,FO,FR,GA,GE,GF,GH,GP,GR,GT,GU,HK,HN,HR,HT,HU,ID,IE,IL,IN,IS,IT,JM,JO,JP,KE,KH,KR,KW,KZ,LB,LI,LK,LT,LU,LV,MA,MD,MG,MK,ML,MO,MQ,MS,MT,MU,MX,MY,NG,NI,NL,NO,NP,NZ,OM,PA,PE,PF,PG,PH,PK,PL,PR,PS,PT,PW,PY,QA,RO,RS,RU,SA,SB,SE,SG,SI,SK,SN,ST,SV,TG,TH,TN,TO,TR,TT,TW,TZ,UA,UG,UK,US,UY,UZ,VA,VE,VU,XK,YE,ZA,VN 2019-05-04 11:13:45 /default/main/bio-rad/WORKAREA/default/templatedata/internet/product_SKU/data/LSE/Cloning-and-Sequencing-Explore/Sequencing-and-Bioinformatics-/166-5026EDU_0921121013003.xml templatedata/internet/product_SKU/data/LSE/Cloning-and-Sequencing-Explore/Sequencing-and-Bioinformatics-/166-5026EDU_0921121013003.xml 1665026edu-sequencing-kit-refill-pack 1665026EDU Sequencing Kit Refill Pack Sequencing Kit Refill Pack Consumables refill kit for use with Sequencing and Bioinformatics module (#166-5025EDU), contains pJETF, pJETR, GAPSEQF, and GAPSEQR primers, and control plasmid; education use only (Sequencing service not included) Consumables refill kit for use with Sequencing and Bioinformatics module (#166-5025EDU), contains pJETF, pJETR, GAPSEQF, and GAPSEQR primers, and control plasmid; education use only Consumables refill kit for use with Sequencing and Bioinformatics module (#166-5025EDU), contains pJETF, pJETR, GAPSEQF, and GAPSEQR primers, and control plasmid; education use only (Sequencing service not included) /webroot/web/images/lse/products/cloning_sequ_explorer_series/sku_thumb/global/166-5026EDU_tn.jpg /webroot/web/images/lse/products/cloning_sequ_explorer_series/sku_view/global/166-5026EDU_view.jpg /webroot/web/images/lse/products/cloning_sequ_explorer_series/sku_feature/global/166-5026EDU_feature.jpg preview ,VN RepEx 166-5026EDU Consumables refill kit for use with Sequencing and Bioinformatics module (#166-5025EDU), contains pJETF, pJETR, GAPSEQF, and GAPSEQR primers, and control plasmid; education use only (sequencing service not included) 09/21/09 12:10 PM 12/31/37 11:59 PM AE,AI,AL,AM,AR,AT,AU,AZ,BA,BD,BE,BF,BG,BH,BN,BO,BR,BW,CA,CH,CL,CM,CN,CO,CR,CY,CZ,DE,DK,DO,DZ,EC,EE,EG,EH,ER,ES,ET,FI,FM,FO,FR,GA,GE,GF,GH,GP,GR,GT,GU,HK,HN,HR,HT,HU,ID,IE,IL,IN,IS,IT,JM,JO,JP,KE,KH,KR,KW,KZ,LB,LI,LK,LT,LU,LV,MA,MD,MG,MK,ML,MO,MQ,MS,MT,MU,MX,MY,NG,NI,NL,NO,NP,NZ,OM,PA,PE,PF,PG,PH,PK,PL,PR,PS,PT,PW,PY,QA,RO,RS,RU,SA,SB,SE,SG,SI,SK,SN,ST,SV,TG,TH,TN,TO,TR,TT,TW,TZ,UA,UG,UK,US,UY,UZ,VA,VE,VU,XK,YE,ZA,VN en LSE /LSE/Cloning-and-Sequencing-Explore/Sequencing-and-Bioinformatics- N 0 false $195.00 true $ %24156.00 true false true true false USD true true true /prd/en/US/adirect/biorad?cmd=ajaxAddToCart&AddToCartProductID=1665026EDU&quantity= false false /prd/en/US/adirect/biorad?cmd=ajaxAddToCart&AddToCartProductID=1665026EDU&CartQuote=QT&quantity= 1711 false true false /prd/en/US/adirect/biorad?cmd=ajaxAddToCart&AddToCartProductID=1665026EDU&AddToDefaultWishList=true&quantity= 41105600 195.00 Product detail page 1665026EDU
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10000069189 Instruction Manual, Sequencing and Bioinformatics Module, Bio-Rad Explorer, Ver E Click to download

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