Genetics August 2004

genetics@lists.oulu.fi

3 participants
6 discussions

ABI3730-info
by Helmi Kuittinen 24 Nov '04

24 Nov '04

Hello DNA analyzers, Great that so many attended the 3730 meeting on Tuesday. Those that did not participate in the practical demonstrations, please do not hesitate to ask Johanna Leppälä, Laura Kvist, Sami Sivula or Marjut Kreivi to help you in starting to work with the new machine. You can always also contact Jussi Vanhatalo from Applied Biosystems (09-69379427). There are printed guides for the software available in room PT331. Tutorials for GeneMapper and SeqScape and a guide for sequencing chemistry are available only as CDs. I have downloaded these CDs on the server BIOL4 and you can copy them onto your PC. The two training CDs are quite big and you can also run them directly on CD (CDs are in PT331). When you have samples run in the 3730, the idea is that the machine is told to send your data to the server (BIOL4) into your personal folder. You can then transfer or copy the data from the server to your own computer, where you analyze it with the appropriate software. You will also be able put the sample information in a file to a shared folder (shared/future_runs/36cm_aray or /50cm_array) in the server. Hannele will use that file for the run and then she will move it to the "processed runs" folder. There will be template excell files and instructions available under the "Shared" folder for making these sample informations files. In this way the one PC in PT331 can only be used for running the machine. I have also put guides and training programs (3730 DNA Analyzeres User Guide, 3730 Sequencing chemistry guide, GeneMapper 3.5 training Seqscape 1.1.1 training) under a folder called "Shared/guides/". To get an access to the server BIOL4, you need to write an e-mail to Kai Niemelä, and tell him your name, domain name and whether you are a student or a researcher (graduate students are reseachers). If you want to keep a copy of your data in that server it is possible for some time, we will just need to follow how fast the hard disc will get filled. The software that is used for analyzing the data (SeqA, GeneMapper, and Seqscape) can be donwloaded to your own PC. Seqscape and GeneMapper work only in quite efficient PCs, so pay attention to the requirements. Seqscape and SeqA work with Windows 2000 and XP. The current version of Genemapper only works with Windows 2000, the new (will be available in December) works with XP too. There are three registration codes for the programs and thee simultaneous users are allowed. If you want to download a program, please contact me or Johanna Leppälä. I have attached the special offer for the first order ("kertatilaus laitehankinnan yhteydessä") that I got from Applied Biosystems. I will receive prices for the reagent agreement for new consumables later, maybe not before next Tuesday. I will forward them as soon as I get them. The preliminary information was that in the reagent agreement we will have 35% reduction for plasticware and at least 10% for other things (buffer, polymer, size standards, capillaries); for oligos there was no info. The existing reagent agreement is of course valid and it already includes e.g. the Big Dye kits. The reference price lists of Genomic assays and custom oligos, and Genetic analysis reagents and application kits are available in PT331 and if needed I can send them electronically. I suggest that you compare the regular agreement and the special offer prices, and of course prices from other suppliers, and let me know if you want to order something with the special offer prices. We hope that we will be able to send the order soon, lets aim for Thursday next week. We make a joint order and Sisko will divide the bill for each group accordingly. There are some consumable that need not to be ordered from Applied, e.g. plates (check!). Of the dye set G5, PET, NED, VIC and the size standard LIZ are only produced by them, and with a licence by some other company. At least TAG Copenhagen has a cheaper dye that can be used instead of VIC. We think that it is best that every user/group buys their formamide, because for sequencing there is also the option to put the samples in water, and the sample volume is now much higher (10-20ul). The costs of polymer, buffer, septas etc. will be shared as before, based on the number of samples run by each group. Last, I have booked a computer class (TH118) for the next training session, for 27.-29.9. 8-16. There will be more information in September. I hope these days suit many of you. With regards, Helmi Helmi Kuittinen Oulun yliopisto University of Oulu Biologian laitos Department of Biology PL 3000 P.O.Box 3000, 90014 University of Oulu 90014 Oulun yliopisto Finland email: Helmi.Kuittinen(a)oulu.fi tel. 358-(0)8-553 1803 fax 358-(0)8-553 1061

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about the melted deep freezer
by Liisa Raisanen 27 Aug '04

27 Aug '04

I would be happy about any information which would help to estimate how long our deep freezer has been melted. According to Jaana the deep freezer worked properly at least on Wednesday (last week!). Liisa Räisänen University of Oulu Department of Biology/Genetics PO.Box 3000 FIN-90014 Oulu Finland Liisa.Raisanen(a)oulu.fi fax 358 8 553 1061 tel 358 8 553 1792

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abi3730
by Helmi Kuittinen 18 Aug '04

18 Aug '04

hei, finally I got the information about the additions to the reagent agreement EW031104 (see attachment 2). In summary, we will get reductions that are almost as good as in the special offer VP040821 until the end of the year (but note that the list prices will have their yearly increment in October, see attachment 1). However, we did not get any information at all about the prices next year. Earlier Virpi Parviainen promised that we would get 35% reduction for plasticware and at least 10% for everything else, now she only says that it will depend on the negociation at the end of the year. If you want to order oligos this week, we will make a joint order under VP040821 (bring me the information indicated below e.g. by email), but you can as well do it individually referring to the reagent agreement (EW031104) because the prices are the same as in the special offer VP040821. The oligos can be ordered with the following instructions (remember to refer to EW031104). Write an email to finland.order(a)eur.appliedbiosystems.com with the following information. a) tuotteen nimi ja tuotenumero (Readypure ABI Prism Primer, P/N 450007, maksimipituus 30 bp)(name and code of the product, max length of the primer=30bp)) b) primerin nimi (Cox-2) (name of the primer) c) primerin sekvenssi (5'acgt......cgta3') (sequence) d) haluttu leima (6-FAM, TET, VIC, HEX, NED, PET) (label) A few things about consumables and reagents: We have figured out that it would be fare and simple if all groups/researcher would buy plastic plates for their sequencing and fragment analysis samples to be run in ABI3730. The machine needs a barcode on the plate. Septas will be provided by Hannele Parkkinen, she will cover the plates with septas when she prepares them for a run. If you keep your samples e.g. in a fridge or a freezer before bringing them to PT331, you should cover them with plastic or folio. Those researchers who only have a few samples to be run can share a plate in the same way as before (the first one should bring the plate). And, please remember that you should not write on top of the plate, ink may damage capillaries. You are allowed to write on sides. In summary: plates and formamide are provided by the groups; septas, polymer, buffer are ordered by Hannele and the costs are shared by the users. Capillary arrays need to be replaced once in a while and the costs will also be shared by the users. I have calculated that the cost of capillaries would be about 13 cnt/sample (including ALV), please take this into account in your budget. Please let me know if you want to order something, at last tomorrow at 4 pm. With regards, Helmi Helmi Kuittinen Oulun yliopisto University of Oulu Biologian laitos Department of Biology PL 3000 P.O.Box 3000, 90014 University of Oulu 90014 Oulun yliopisto Finland email: Helmi.Kuittinen(a)oulu.fi tel. 358-(0)8-553 1803 fax 358-(0)8-553 1061

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3730 training
by Helmi Kuittinen 13 Aug '04

13 Aug '04

Hi, to arrange for the 3730 training session at the end of September (27.-29.9.), I would like to know which programs you are interested to learn. It is recommended that you attend the course only if you are going to do actively sequencing/fragment analysis this autumn, because the number of participants will have a limit after all (appr. 14). Please answer by August 20th. Name: e-mail: tel.: I want to participate in the course and learn following programs SequencingAnalysis _________ GeneMapper _________ Seqscape _________ With regards, Helmi Kuittinen Oulun yliopisto University of Oulu Biologian laitos Department of Biology PL 3000 P.O.Box 3000, 90014 University of Oulu 90014 Oulun yliopisto Finland email: Helmi.Kuittinen(a)oulu.fi tel. 358-(0)8-553 1803 fax 358-(0)8-553 1061

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tutkijakoulun kurssi
by Pekka Pamilo 10 Aug '04

10 Aug '04

>Hei > >Populaatiogenetiikan tutkijakoulu järjestää syyskuussa kurssin aiheesta >Forensic genetics. Antti Sajantila ja Matti Karjalainen ovat valmistelleet >kurssia ja sen alustava ohjelma on tutkijakoulun verkkosivulla >http://cc.oulu.fi/%7Ebiolwww/PopGenSchool/index.html kohdassa uutisia. >Muutokset ovat mahdollisia. >Paikka: oikeuslääketieteen laitos Helsingissä ja tutustumiskäynti myös >Keskusrikospoliisiin >Aika: maanantai ja tiistai 20-21.9 (mahdollinen pidennys keskiviikkoon) >Ilmoittautumiset 20.8 mennessä ensisijaisesti Antti Sajantilalle >(antti.sajantila(a)helsinki.fi) tai Pekka Pamilolle (pekka.pamilo(a)oulu.fi) >Kurssista saa yhden opintoviikon > >Tutkijakoulu maksaa osallistujien matkat ja majoitukset matkalaskun >mukaan. Majoitusta tarvitsevien kannattaa ilmoittaa minulle, koska voimme >siten yhdessä hoitaa majoitusvaraukset. > > >terveisin, Pekka

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ABI3730
by Helmi Kuittinen 04 Aug '04

04 Aug '04

Hi all, Good news: the new 48 capillary sequence analyzer is being installed during this week! Next week on Tuesday Jussi Vanhatalo from Applied Biosystems will give an introductory course so that we can get started with running microsatellites, sequences and AFLPs. When we have some experience, there will be another course (probably mid September). On Tuesday at 9.30 there will be a gettogether in room YB211 and Jussi will give some information about major things that change (e.g. some changes in chemistry) and fitting the old and new data. Everybody can come there. Then only a couple of people are able to participate later in the day in the practical demonstrations on running the machine and using the software. These persons (Johanna Leppälä (tel. 1795), Laura Kvist (1802), Sami Sivula (tel. 044-5390979) and Hannele Parkkinen (1779) will share their knowledge with others, so you can ask one of them to show you how to do the samples and how to analyze them with the new software. If an AFLP person wants to attend next Tuesday the practical part we can try to fit one more person. Everybody is wellcome to the longer (two days?) course in September (probably weeks 37-38). If you want to attend and know some days in September when you are away, please inform me by e-mail, so we can try to avoid those days. The old sequencing machine will be in use until the end of January, then it will go back to the Applied Biosystems together with the MAC computer that has been used for running the machine. The newer MAC will stay here also after that. We will be getting a special offer from the Applied Biosystems for consumables and chemicals at the first order after purchasing the sequencing machine: some things are cheaper than normally. This offer is due only once (a single order). We could aim to do a joint order e.g. during the week 34. I will try to get an updated offer from Applied Biosystems soon. Regards, Helmi Helmi Kuittinen Oulun yliopisto University of Oulu Biologian laitos Department of Biology PL 3000 P.O.Box 3000, 90014 University of Oulu 90014 Oulun yliopisto Finland email: Helmi.Kuittinen(a)oulu.fi tel. 358-(0)8-553 1803 fax 358-(0)8-553 1061

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Genetics August 2004