SGC-1 and SGC-2 Sequencing Gel Casters User Manual
Contents
1. D Dissolved in seven days or less 5 2 Sequencing Gel Caster Thermo Scientific Section 5 Care and Cleaning Table 5 1 Chemical Compatibility for Acrylic Based Products Sei Te eege EF P CES Fa Va FE zeg Hesse Fee E es beier DI LEE fu e DIN CECI DN CE je Se bes DN CI E ae Ehe O CEI je Sep E 0 CE E CEC CIN CN O CE ESCOCIA Can EEC O CI E CEET DU ECT Eeam je ageet DU E O EE u CA IE CU fm je pea DU EEES Ve E CEI UU EEC O CN See Hee CU am E me pP o This list does not include all possible chemical incompatibilities and safe compounds Acrylic products should be cleaned with warm water a mild detergent such as Alconox and can also be exposed to a mild bleach solution 10 1 In addition RNAse removal products are also safe for acrylic Contact Technical Services with any questions Thermo Scientific Sequencing Gel Caster 5 3 Section 6 Optional Equipment Contact Technical Services to order replacement parts Stainless Steel Clamps pkg of 12 Notched Glass S1S Banks Offset Glass Thermo Scientific Sequencing Gel Caster 6 1 Section 7 Warranty Information EE REDE L006 OSI cL 6 0 AY UOHEUOJU AJUCIIEM JO JOJNQIIISIP 890 INO DEIUOO YSN 24 SPISINO suoHNeosi dde elo ads pue sonas aoueusjulew uonejado AjueJem juaudinba uo suonsanb noA Jamsue 0 Apea 919M 9 7 EZE 0PZ 1 Jo epeueo pue YSN 138py 2 y 008 1 Je Juauuedea2. Making sure that the casting area is level place the blank longer glass plate into the caster pushing it to the end with the stops The rail it is sitting on is slightly lower than the rail on the other end of the unit Moisten spacers with drops of water and place them flush to the edge of the glass against the side of the rail Moistening helps to keep the spacers from moving while sliding the notched plate over them during casting Place the notched top plate on top of the blank plate so that the two overlap by about one inch The side rail will hold the top plate above the bottom blank plate This plate should slide freely up to the top of the blank plate Have your gel solution ready at this point Slowly pour gel solution onto the bottom plate at the point where the two plates overlap The acrylamide will flow into the space between the two plates by E capillary action Gently slide the top plate across the bottom plate while pouring gel solution along the leading edge of the glass If a bubble forms simply move the Figure 2 2 Pour Gel Solution top plate backwards until you have passed the point where the bubble formed and then proceed forward again until the gel is completely cast Thermo Scientific Section 2 Using the System Operating continued 6 Clamp along the spacers in the spaces provided by the caster Clamp in the middle of the spacer and not in the gel area 7 Insert comb see page 9 for
3. plate procedure capillary action draws the gel between plates Surface tension not tape keeps the gel from leaking No taping or special assembly is required The sliding casting method has been shown to require significantly less time to cast and the clean process decreases exposure to acrylamide and reduces clean up time Gels can be cast in less than one minute Any standard size sequencing gel can be cast using either the SGC 1 or SGC 2 SGC 1 Gel Size 20 42cm W x 48cm L Footprint 21 6cm W x 71cm D fully closed x 12 2cm H SGC 2 Gel Size 20 42cm W x 65 5cm L Footprint 21 2cm W x 102cm D fully closed x 12 2cm H Before starting unpack the unit and inventory your order If any parts are missing contact Technical Services immediately Reference the order or catalog number on your invoice and check the corresponding parts list Sequencing Gel Caster 1 1 Section 1 General Information 1 2 Sequencing Gel Caster Casting Platform Binder Clamps 12 SCH Adjustable Knob 2 Figure 1 1 Parts Diagram SGC 1 SGC 2 Adjustable casting platform 2 1 Knobs for width adjustment attached 2 Binder clamps 0 2 nada ds d Ee d 12 Thermo Scientific Section 2 Using the System The following additional equipment may be required for casting e One or more pairs of glass plates to fit any standard manual or automatic sequencing electrophoresis system e Matching spacer set
4. Sharktooth and Well Comb instructions at the top of the gel and clamp with two or three Figure 2 3 Clamp clamps as space allows Clamp in the middle of the comb and not on the teeth or beyond the comb into the gel area 8 After gel has polymerized for 20 30 minutes the cassette can be removed from the caster and allowed to complete polymerization on the benchtop Do not move the gel during the first minutes of polymerization Thermo Scientific Sequencing Gel Caster 2 3 Thermo Scientific Section 3 Technical Tips The difference between a standard well comb and a sharktooth comb A well comb has rectangular teeth and is similar to combs oo used for protein gels After polymerization these combs must be removed carefully to Sharktooth avoid destroying the acrylamide walls that create the wells A sharktooth comb has pointed teeth It is placed with standard the flat side down during gel casting to create a flat surface on the top of the gel and reinserted with the teeth down towards the gel for loading Samples are loaded in the space between the teeth Figure 3 1 Combs Sharktooth comb Carefully insert the flat edge of the sharktooth comb between the plates to a depth of 2 to 3mm below the shorter plate If the flat edge of the comb is inserted too deeply more than 4 or 5mm during gel casting the resulting trough will be too deep to load samples easily with a pipet It is wise to make marks on the comb t
5. UE uodo s oWJay yy jueudinba Jo juauoduo9 Aue jo uanza JO eAOUdde sod 3516 Jsnw juauuedag SE8dIAJES jeoiuyos ay poled jueJem jeuiBuo ay PuoAag ped juauoduo9 y 0 Jo juawdinba y JOY o jueJem ay PUS X9 JOU IEUS jueJem siy apun Juswd nba Jo syed Jusuodwos jo Jeda Jo juauaJe day QUeJem siy WO papnjoxa ale sjayseb pue sia ssej6 sway ajgepuadxy sedas Aue jo soueWO Jod 0 JOUd UO 93 1p pue UONEUIWIEJSP JUeJJem JO pajoe uos aq 3snu juewiedag seoinlas esluyos y yuewsalBe Aueulem siy Aq pajaros jou SI uoe pue uo je4qies uoejjejsuj oqe Bundaoxa esuadxa sowsayL Je pasejda ag Wi dIYSUBLUYJOM JO jenayew Ul HUILWOJUOD UOU eq 0 UBAOId syed Jusuodwos syJuow 9 xis Apy 1844 ayy Buung Jaumo juanbasqns Aue o spuajxe uol 2998 01d JUeJJem ay Pa1an lop si juaudinba noA au wes ay jejeuixoldde Je Pays ou OB im jueJem y os au Buiddiys smojje s y Aloe uno wo paddiys si juaudinba JnoA ayep ay OU SUJUOW OM SUEIS pollag Alueuemn ey TWNOLLVNYSLNI ALNVYUVM SLINAOAd IMO OISILNSIOS Y43HSI4 OINYSHL Thermo Scientific Sequencing Gel Caster 7 2 Thermo Fisher Scientific 401 Millcreek Road Marietta Ohio 45750 United States www thermofisher com ThermoFisher SCIENTIFIC
6. glass Notched or eared glass plates face in towards the upper buffer chamber during a gel run The ears are glass tabs on each side of the plate which prevent buffer from running out of the upper buffer chamber Offset glass plates serve the same purpose as notched plates Offset glass is usually about 2 cm shorter than the front or blank glass plate Instead of glass ears pieces of adhesive sponge are adhered either to the top of the spacers or to the apparatus itself These sponge tips wear out and may leak Notched glass plates are more fragile and expensive than offset glass and sponge tips but many researchers prefer notched glass because it is easier to use The third spacer This is a bottom spacer and u BLANK F NOTCHED OFFSET Figure 3 2 Glass SPONGE TIP can be cut to the desired length It is optional SPACER If you use a bottom spacer when casting remember to remove it before running the gel Sa Figure 3 3 Spacer Thermo Scientific Section 4 Troubleshooting Problem Bubbles continually form between glass plates while casting Solution Be sure plates are clean of any acrylamide debris and are dust free If bubbles do occur even after cleaning plates simply move the top plate backwards until the bubble is cleared and then proceed forward From time to time a more thorough cleaning of plates is required 5 minutes in IN HCI rinse in hot water then rinse in deionized water Repe
7. 114 ayy Bung Jaumo juanbasqns Aue o spuajxe uonoajold AUELIEM y palanijap s juaudinba noA au swes y jajeuwixoldde Je Pays out OB WA jueJem ay os aul Burddiys smojje s y Aloe sno Woy paddiys si juauwdinba noA ep ay WOJ Saa OM SUB S polla g AIUEUEM SUL VSN ALNVYYVM SLONGOYd IMO OISILNAIDS 43HSIA OWYSHL 7 1 Sequencing Gel Caster Thermo Scientific Section 7 Warranty Information lEXNENODEL 1006 OSI cL 6 0 ASN UONEUUOJU AJUCIIEM JO JOINLISIP 290 INO JOeIUOD YSN 24 SPISIMO suO eo dde jeloeds pue aolalas aoueusjUlewW UuoNeJedo AjUeWeM Juswd nba uo suonsanb noA Jamsue 0 Apea 919M EILFEIE OVI L Jo epeued JO YSN 1S8y 2 y 008 1 Je jJueuuedag SEdIAIaS jes1uyoa INOA jeo se jd p nb s sones Juswd nbe y a9ueua julew anuansld pue uoljejado uorejjejsul juaudinba jezap Anjale sjenuew UONONI SU paud Sane juauwdinba noA aojaq uoewoyzu uonesedasd ous SAISUBYSJGLUOD yym djay 0 Apes s 0YO sejes OWS 890 INOA SIONPOId JO SSO JO syyoJd eo 0 sobewep uoyeyu moyym Buipnjou sebewep jenuenbasuos Jo jossipul Aue 104 ap eq jou eys oway AlddV TIVHS 3ISOdYINdA YVWINOLLAVA Y YOW SSANLIS YO ALITISVLNVHOUFN JO SSILNVYYVM ON Cal Idi YO WHO NFLLIUM YSHLSHM SSILNVYYVM Y3H LO TIY 40 N4 NI GNV 3A180719X3 SI ALNVYYVM SIHL uoneunsep go peddiys ale syed juawsaoe dal pue pied aBejsod ouuaut o pauunjas aq Jsnw syed Bulwyojuod uou
8. Sequencing Gel Casters Models SGC 1 and SGC 2 Operating and Maintenance Manual 7218313 Visit us online to register your warranty w www thermoscientific com warranty Owl Ki A eparation Preface MANUAL NUMBER 7218313 0 4 25 12 Transfer to Marietta was 3 2003 CCS REV ECR ECN DATE DESCRIPTION By Thermo Scientific Sequencing Gel Caster i Preface CAUTION Contains Parts and Assemblies Susceptible to Damage by Electrostatic Discharge ESD Important Read this instruction manual Failure to read understand and follow the instructions in this manual may result in damage to the unit injury to operating personnel and poor equipment performance A Caution All internal adjustments and maintenance must be performed by qualified service personnel A Statement of Proper Use Use this product only for its intended purpose as described in this manual Do not use this product if the power leads are damaged or if any of its surfaces are cracked Material in this manual is for information purposes only The contents and the product it describes are subject to change without notice Thermo Fisher Scientific makes no representations or warranties with respect to this manual In no event shall Thermo be held liable for any damages direct or incidental arising out of or related to the use of this manual 2012 Thermo Fisher Scientific All rights reserved Sequencing Gel Caster Thermo Scientific Preface I
9. afety Thermo Scientific Sequencing Gel Caster iil Preface Do You Need Information or Assistance on Thermo Scientific Products If you do please contact us 8 00 a m to 6 00 p m Eastern Time at 1 740 373 4763 Direct 1 800 438 4851 Toll Free U S and Canada 1 877 213 8051 FAX http www thermoscientific com Internet Worldwide Web Home Page service led marietta thermofisher com Tech Support Email Address www unitylabservices com Certified Service Web Page Our Sales Support staff can provide information on pricing and give you quotations We can take your order and provide delivery information on major equipment items or make arrangements to have your local sales representative contact you Our products are listed on the Internet and we can be contacted through our Internet home page Our Service Support staff can supply technical information about proper setup operation or troubleshooting of your equipment We can fill your needs for spare or replacement parts or provide you with on site service We can also provide you with a quotation on our Extended Warranty for your Thermo Scientific products Whatever Thermo Scientific products you need or use we will be happy to discuss your applications If you are experiencing technical problems working together we will help you locate the problem and chances are correct it yourself over the telephone without a service call When more extensive service is necessary we will assis
10. and comb for each gel to be cast e Binder clamps 9 per gel cassette Owl catalog CL 12 e Rain X or Sigmacote Sigma Chemical St Louis MO e Ethanol for washing plates combs and spacers Gel Casting Basic laboratory safety procedures should be followed when preparing sequencing gels When working with acrylamide solutions always wear proper protective clothing gloves and eye protection Careful attention must be given during each step of sequencing gel preparation for consistent results Begin by cleaning plates thoroughly 1 To completely clean glass plates of any acrylamide residue leftover detergents and dust wash plates with warm water and detergent 2 Rinse plates completely with deionized water then wipe with 95 ethanol to eliminate any traces of detergent and water marks A final wipe should be done using a dust free cloth such as Kimwipes Thermo Scientific Sequencing Gel Caster 2 1 Section 2 Using the System 2 2 Operating Sequencing Gel Caster l The caster consists of two adjustable ends and two side pieces with a cut out railing The railing is open at one end so that long glass can slide past the length of the caster The opposite end has a stop cut into the sides so that the bottom plate is held in position Loosen knobs on the ends of the caster and place glass into unit Slide the sides of the caster together to tightly fit the glass plate Figure 2 1 Knob Location Tighten knobs
11. at if necessary Problem Gel solution appears to be leaking while pouring Solution Be sure the caster is set up on a level surface Leveling platforms are avail able from Owl catalog B LP If gel will not stay between the plates at the bottom of the cassette this may be caused by bowed plates Try another set of glass or flip the top piece so that the other side is facing the gel solution Dirty glass can also cause slight leaking See cleaning instructions above and in the Gel Casting section of this manual Problem When loading samples the samples seem to be running into other well Solution This may be due to a slight thickness variation between the comb and the spacers used to pour the gel Clamping the plates over the comb as well as over the spacers will allow the gel to polymerize evenly and should alleviate this problem Using glass plates that are not completely flat may also cause this problem try flipping the plate over and using the other side for casting or try a new plate Thermo Scientific Sequencing Gel Caster 4 1 Section 5 Care and Cleaning Caution Organic solvents cause acrylic to craze or crack Clean all acrylic systems with warm water and a mild detergent Do not use ethanol or other organic solvents to clean these products Do not autoclave bake or microwave your unit Temperatures over 50 C can damage the acrylic A Note If an RNase free electrophoresis system is desired there are various m
12. ethods to rid the system of RNA contamination For fast and easy decontamination use RNase AWAY Spray wipe or soak labware with RNase Away then wipe or rinse the surface clean it instantly eliminates RNase RNase Away eliminates the old methods that include treatment with 0 1 Diethyl Pyrocarbonate DEPC treated water and soaking in dilute bleach DEPC is suspected to be a carcinogen and should be handled with care This electrophoresis system should never be autoclaved baked or placed in a microwave To order RNase AWAY contact Technical Services Part Number er 1 0 054208 Description LODO are ka de 250ml bottle TOOLS ASAS 475ml spray bottle LOS ae nee 1 liter bottle KL GE 4 liter bottle Rnase AWAY is a registered trademark of Molecular BioProducts Thermo Scientific Sequencing Gel Caster 5 1 Section 5 Care and Cleaning Care of Acrylic The following chemical compatibility chart is supplied for the convenience of our customers Although acrylic is compatible with most solvents and solutions found in the biochemical laboratory some solvents can cause substantial damage Keep this chart handy to avoid harm to your apparatus by the use of an inappropriate solvent Codes S Safe no effect except possibly some staining A Attacked slight attack by or absorption of the liquid slight crazing or swelling but acrylic has retained most of its strength U Unsatisfactory softened swollen slowly dissolved
13. g sanas esluyoa INOA eo aseajd paunba s sonas Juawd nbo y s9ueuajulieW anpuensld pue UOHeJEdO uorrejje sum Juswd nba j e op Ajjnjoueo sjenuew UONONIJSU paud SSALJJe juauwdinba noA aJojaq uoneuwJojul uoneJedald ous aassusyalduloo YIM djay 0 Apes s au Sajes ovuJay 890 INOA SIONPOIA Jo sso JO SHO Iso 0 sobewep uonenuwij ynoyyim Hulpnjoul sebewep jeyuenbesuod Jo apu Aue 104 jqe aq jou eys oway L AlddV TIVHS 3ISOdYINdA YVINOILYVd Y YOW SSANLIS YO ALMIIVINVHOYIN JO SSILNVYYVM ON Cal dWI YO WHO NFLLIUM YSHLSHM SSILNVYYVM YSHLO TIV 40 N4 NI ANY 3AISNT19X3 SI ALNVYYVM SIHL uoneulnsep gO4 peddiys aie sped juawsaoejdaj pue pied aBejsod oway L 0 pau nja aq 3snu sped Hulwsojuod uoU UE uoNdo Soe jw JUeWdINbs Jo yUsUOdWOD Aue jo uanza Joy enoJdde Jod 216 Jsnw zu wyed q S391A19S jeoluyos SUL pouad jueJem jeuiBuo ay puoAaq ped juauodulo9 y 0 Jo juawdinba ay JOYS 0 jueJem ay PUS X9 JOU Jeys jueJem siy Japun juauwdinba Jo syed Jusuodwos jo Jeda JO juauaJe day AUeJJem SIU wo papnjoxe ase sjayseb pue sa ssej6 sway ajqepuedxy sed Aue jo aoue Wuojad 0 JOUd U0n9aJIp pue UOINEUNWS SP jueJem JO pajoejuos aq jsnu Juswpedag SEDIAJES jesiuyoa ay juawsalbBe AyueJem siy Aq palanos jou SI uoge pue uolje4q es uoejjejsuj oqe Bulpnjoul aesuadxa s owuey Je paveda aq Uu diysuewyom Jo IEUSIEU Ul HulWJOJUOD UOU aq 0 UBAOJd syed jueuodulo9 syzuow oe Xis Auiy 18
14. mportant operating and or maintenance instructions Read the accompanying text carefully gt gt gt Potential electrical hazards Only qualified persons should perform procedures associated with this symbol re gt Equipment being maintained or serviced must be turned off and locked off to prevent possible injury Hot surface s present which may cause burns to unprotected skin or to materials which may be damaged by elevated temperatures Marking of electrical and electronic equipment which applies to electrical and electronic equipment falling under the Directive 2002 96 EC WEEE and the equipment that has been put on the market after 13 August 2005 Lars This product is required to comply with the European Union s Waste Electrical amp Electronic Equipment WEEE Directive 2002 96 EC It is marked with the WEEE symbol Thermo Fisher Scientific has contracted with one or more recycling disposal companies in each EU Member State European Country and this product should be disposed of or recycled through them Further information on Thermo s compliance with this directive the recyclers in your country and information on Thermo products will be available at www thermofisher com Y Always use the proper protective equipment clothing gloves goggles etc Y Always dissipate extreme cold or heat and wear protective clothing Y Always follow good hygiene practices Y Each individual is responsible for his or her own s
15. o distinguish the right left sides so the comb can be put back in the same orientation for sample loading later in the event that the material has any slight variation in thickness Place binder clamps over the comb and glass plates along the upper edge to force the glass plates against the comb This will ensure a tight fit of the comb during and after polymerization If top binder clamps are not used the comb may not be tight enough to prevent sample leaks between wells following gel polymerization Do not clamp the outer edges over the side spacers Allow the gel to completely polymerize After polymerization wash out the trough with buffer gently in order to remove any unpolymerized acrylamide and excess urea Place the comb between the glass plates in the correct left to right orientation the same orientation the trough was cast in with the comb teeth pointing down toward the gel Slowly and carefully slide the comb until it just makes contact with the gel surface without piercing it Sequencing Gel Caster 3 1 Section 3 Technical Tips 3 2 Sequencing Gel Caster Well comb Carefully insert the comb Place binder clamps over the comb and glass plates along the upper edge to force the glass plates against the comb After polymerization flood the comb with 1X TBE and remove gently Rinse the wells out with deionized water or TBE in order to remove excess urea or unpolymerized acrylamide The difference between notched and offset
16. t you with direct factory trained technicians or a qualified service organization for on the spot repair If your service need is covered by the warranty we will arrange for the unit to be repaired at our expense and to your satisfaction Regardless of your needs our professional telephone technicians are available to assist you Monday through Friday from 8 00 a m to 6 00 p m Eastern Time Please contact us by telephone or fax If you wish to write our mailing address is Thermo Fisher Scientific 401 Millcreek Road Box 649 Marietta OH 45750 International customers please contact your local Thermo Scientific distributor iv Sequencing Gel Caster Thermo Scientific Thermo Scientific Section 1 Section 2 Section 3 Section 4 Section 5 Section 6 Table of Contents General Information Unpack and Check Your Order Using the System 2000e Gel Castine reo ho Were eae ees Operating east Technical Tips oo o Troubleshooting Care and Cleaning Chemical Compatibility for Acrylic Based Products Optional Equipment Sequencing Gel Caster V Unpack and Check Thermo Scientific Your Order Section 1 General Information The Otter Sequencing Gel Caster provides the user with a simple and easy to use method for casting sequencing gels Relying on a horizontal sliding
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