Team:Vanderbilt/NotebookSubPageBuilder

From 2014.igem.org

(Difference between revisions)
Line 174: Line 174:
     subPage.createSpring2014Right = function() {
     subPage.createSpring2014Right = function() {
-
         var img1 = subPage.createPhoto("http://parts.igem.org/wiki/images/0/00/VU_Genomic_DNA_bands_check_LNS.JPG", "Genomic DNA bonds check", 395.2, 516.8,
+
         var img1 = subPage.createPhoto("http://parts.igem.org/wiki/images/0/00/VU_Genomic_DNA_bands_check_LNS.JPG", "Genomic DNA bonds check", 380, 508,
         "An example of a gel showing high molecular weight (>10 kb) bands corresponding to successfully " +
         "An example of a gel showing high molecular weight (>10 kb) bands corresponding to successfully " +
         "extracted plant genomic DNA (in this case, samples LNS1 and LNS2 from Arabidopsis DNA");
         "extracted plant genomic DNA (in this case, samples LNS1 and LNS2 from Arabidopsis DNA");

Revision as of 00:01, 26 January 2015

function NotebookSubPageBuilder() {

   var subPage = new SubPageBuilder();
   subPage.maxSubPage = 3;
   subPage.getMaxSubPage = function() {
       return subPage.maxSubPage;
   };
   subPage.createSubPage = function(subPageNum) {
       switch(subPageNum) {
           case 1:
               subPage.createSpring2014Left();
               subPage.createSpring2014Right();
               break;
           case 2:
               subPage.createSummer2014Left();
               subPage.createSummer2014Right();
               break;
           case 3:
               subPage.createFall2014Left();
               subPage.createFall2014Right();
               break;
       }
   };
   subPage.createSpring2014Left = function() {
       var header = document.createElement("header");
       header.appendChild(document.createTextNode("Spring 2014"));
       var p_m27 = subPage.createP("March 27th");
       var p_m30 = subPage.createP("March 30th");
       var p_m31 = subPage.createP("March 31st");
       var p_a1 = subPage.createP("April 1st");
       var p_a2 = subPage.createP("April 2nd");
       var p_a3 = subPage.createP("April 3rd");
       var p_a4 = subPage.createP("April 4th");
       var p_a5 = subPage.createP("April 5th");
       var p_a7 = subPage.createP("April 7th");
       var p_a24 = subPage.createP("April 24th");
       var p_a25 = subPage.createP("April 25th");
       var p_a27 = subPage.createP("April 27th");
       var p_a29 = subPage.createP("April 29th");
       var m27 = document.createElement("ul");
       var m30 = document.createElement("ul");
       var m31 = document.createElement("ul");
       var a1 = document.createElement("ul");
       var a2 = document.createElement("ul");
       var a3 = document.createElement("ul");
       var a4 = document.createElement("ul");
       var a5 = document.createElement("ul");
       var a7 = document.createElement("ul");
       var a24 = document.createElement("ul");
       var a25 = document.createElement("ul");
       var a27 = document.createElement("ul");
       var a29 = document.createElement("ul");
       var text = [["Extracted genomic DNA from 100 mg of Arabidopsis thaliana leaves using a Viogene DNA extraction kit. Samples were " +
       "labeled ZIN for zingiberene."],
           ["Two samples were prepared and nanodropped. The concentration of the first w" +
           "as 2.6 ng/ul, and the second was 3.5 ng/ul of DNA, indicating a minimal yield of DNA."]];
       subPage.addMultLI(m27, text);
       text = [["Extracted genomic DNA from 100 mg of Picea abies needles using the same extr" +
       "action kit and protocol. Samples were labeled CAR for carene."],
           ["Two samples were prepared and nanodropped. The concentration of the first w" +
           "as 2.6 ng/ul, and the second was 3.5 ng/ul of DNA, indicating a minimal yield of DNA."]];
       subPage.addMultLI(m30, text);
       text = [["Ran a 0.6 % argarose gel on the DNA extracted from ZIN and CAR, as well as the column flow-throu" +
       "gh from the kit."],
           ["ZIN1, ZIN2, CAR1, and CAR2 all show a faint but distinct DNA band above the highest rung on the DNA l" +
           "adder (>10kb), showing the presence of DNA. No bands were seen on the kit flow-through. Indicates successful g" +
           "enomic extraction."],
           ["Preformed a second genomic extraction on Picea abies to improve yield. Nanodrop shows CAR3 to be " +
           "at 6.2 ng/ul and CAR4 to be 11.5 ng/ul."],
           ["Extracted genomic DNA from Gossypium hirsutum. Samples nanodroppped: CAD1 1.8 ng/ul and CAD2 7.8 ng/ul."]];
       subPage.addMultLI(m31, text);
       text = [["Ran a gel on CAR3, CAR4, CAD1, and CAD2. Brighter genomic DNA bands were seen on the cadinene camples" +
       " than before, but cadinene samples showed significant smearing near the top of the gel."]];
       subPage.addMultLI(a1, text);
       text = [["Extracted genomic DNA from Salvia officinalis . Samples nanodropped: SAB1 7.5 ng/ul, and SAB 11.4 ng/ul."],
           ["Extracted genomic DNA from Mentha citrata . Samples nanodropped: LNR1 3.4 ng/ul, LNR2 6.2 ng/ul, LNR3 7.3 ng/ul"],
           ["E. coli containing p404GALS and pDZ207 from Addgene were grown on LB plates with ampicilin. These were min" +
           "iprepped using a Viogen kit. Samples nanodropped: p404GALS (A) 130.2 ng/ul, p404GALS (B) 112.3 ng/ul, pDZ2" +
           "07 (A) 145.3 ng/ul, pDZ207 (B) 84.1 ng/ul."]];
       subPage.addMultLI(a2, text);
       text = [["Extracted genomic DNA again from Arabidopsis thaliana . Sample nanodropped: LNS1 53.4 ng/ul, LNS2 585.2 ng/ul"],
           ["Ran gel on LNR1, LNR2, LNR3, LNS1, LNS2, SAB1, and SAB2. All show high weight DNA bands, with Linalool (S) sampl" +
           "es having the brightest."]];
       subPage.addMultLI(a3, text);
       text = [["Extracted genomic DNA from Zingiber zermbet . Sample nanodropped: HUM1 31.9 ng/ul and HUM2 18.6 ng/ul"],
           ["Extracted genomic DNA from Ocimum basilicum . Sample nanodropped: GER1 2.3 ng/ul"]];
       subPage.addMultLI(a4, text);
       text = [["Extracted genomic DNA from Santalum album seeds since the sapling was still not fully grown. Sample nan" +
       "odropped: SAN1 53.8 ng/ul and SAN2 28.4 ng/ul"]];
       subPage.addMultLI(a5, text);
       text = [["Extracted genomic DNA from Perilla frutescens . Sample nanodropped: MYR1 632.8 ng/ul and MYR2 958.6 ng/ul"],
           ["Extracted genomic DNA from Perilla frutescens . Sample nanodropped: MYR1 632.8 ng/ul and MYR2 958.6 ng/ul"]];
       subPage.addMultLI(a7, text);
       text = [["Preformed PCR using zingiberene synthase primers on LNS2 genomic DNA and using linalool (S) synthase p" +
       "rimers on the sample template."],
           ["Ran gel on PCR product. Resulted in no visible bands formed."]];
       subPage.addMultLI(a24, text);
       text = [["Took 1.8 ul of HUM1 genomic DNA and preformed a PCR with humelene synthase primers."],
           ["Ran gel on PCR product. Resulted in three total bands, one faint around 1.2 kb, and two bands very close " +
           "in size just under 3.0 kb."],
           ["Both ~3 kb bands were gel extracted, combining across all four lanes. Samples nanodropped: HUM-top 8.5 ng/u" +
           "l, HUM-bottom 10.6 ng/ul."]];
       subPage.addMultLI(a25, text);
       text = [["Preformed PCR using linalool (R) synthase primers on LNR3 genomic DNA."],
           ["Ran gel on PCR product. Resulted in no visible bands formed."]];
       subPage.addMultLI(a27, text);
       text = [["Preformed PCR using myrcene synthase primers on MYR2 genomic DNA."],
           ["Ran gel on PCR product. Smeared bands on gel but no distinct bands."],
           ["Preformed overlap-extension PCR on the gel extracted humelene samples (both HUM-top and HUM-bottom) to add " +
           "epitope tag sequence."],
           ["Ran gel on OE-PCR product. Only extremely faint bands were visible."]];
       subPage.addMultLI(a29, text);
       leftPageBuilder.appendChild(header);
       leftPageBuilder.appendChild(p_m27);
       leftPageBuilder.appendChild(m27);
       leftPageBuilder.appendChild(p_m30);
       leftPageBuilder.appendChild(m30);
       leftPageBuilder.appendChild(p_m31);
       leftPageBuilder.appendChild(m31);
       leftPageBuilder.appendChild(p_a1);
       leftPageBuilder.appendChild(a1);
       leftPageBuilder.appendChild(p_a2);
       leftPageBuilder.appendChild(a2);
       leftPageBuilder.appendChild(p_a3);
       leftPageBuilder.appendChild(a3);
       leftPageBuilder.appendChild(p_a4);
       leftPageBuilder.appendChild(a4);
       leftPageBuilder.appendChild(p_a5);
       leftPageBuilder.appendChild(a5);
       leftPageBuilder.appendChild(p_a7);
       leftPageBuilder.appendChild(a7);
       leftPageBuilder.appendChild(p_a24);
       leftPageBuilder.appendChild(a24);
       leftPageBuilder.appendChild(p_a25);
       leftPageBuilder.appendChild(a25);
       leftPageBuilder.appendChild(p_a27);
       leftPageBuilder.appendChild(a27);
       leftPageBuilder.appendChild(p_a29);
       leftPageBuilder.appendChild(a29);
   };
   subPage.createSpring2014Right = function() {
       var img1 = subPage.createPhoto("VU_Genomic_DNA_bands_check_LNS.JPG", "Genomic DNA bonds check", 380, 508,
       "An example of a gel showing high molecular weight (>10 kb) bands corresponding to successfully " +
       "extracted plant genomic DNA (in this case, samples LNS1 and LNS2 from Arabidopsis DNA");
       var img2 = subPage.createPhoto("VU_humelene_genomic_dna_pcr.JPG", "Humelene Genomic DNA PCR", 374, 348.5,
           "PCR products resulting from primers targeted to hmelene synthase using Zingiber genomic" +
           "DNA as a template. The sixth ladder band down corresponds to 3000 bp.");
       var img3 = subPage.createPhoto("VU_labeled_PCON_Gel.jpg", "Labeled PCON Gel", 374, 348.5, "Labeled PCON Gel");
       rightPageBuilder.appendChild(img1);
       rightPageBuilder.appendChild(img2);
       rightPageBuilder.appendChild(img3);
   };
   subPage.createSummer2014Left = function() {
       var header = document.createElement("header");
       header.appendChild(document.createTextNode("Summer 2014"));
       var p_may = subPage.createP("May");
       var p_june = subPage.createP("June");
       var p_july = subPage.createP("July");
       var may = document.createElement("ul");
       var june = document.createElement("ul");
       var july = document.createElement("ul");
       var text = [["Continued troubleshooting PCR reaction conditions for all of the terpenes that failed " +
                   "to amplify. Tried adjusting template concentration, adding DMSO, changing thermocycler program, hot " +
                   "start PCR, new polymerase and dNTPs."],
                   ["Re-did genomic extractions for those that produced less than 50 ng/ul of genomic DNA. " +
                   "Used this new template in further PCRs."],
                   ["Extracted the Gal10 gene from our template plasmid and a kanomycin resistance gene borde" +
                   "red by LoxP sites."]];
       subPage.addMultLI(may, text);
       text = [["All of the gene cassettes for plasmid construction that were successfully extracted so far" +
       " were ligated together and inserted into the MCS of pUC19. This formed our first intermediate plasmid."]];
       subPage.addMultLI(june, text);
       text = [["Finally reached the point that all terpene genes were consistently amplifying with the " +
       "synthase gene primers. The genomic DNA sample for sabinene was completely used before this point, " +
       "although all other of the 8 terpenes showed clear bands.."]];
       subPage.addMultLI(july, text);
       leftPageBuilder.appendChild(header);
       leftPageBuilder.appendChild(p_may);
       leftPageBuilder.appendChild(may);
       leftPageBuilder.appendChild(p_june);
       leftPageBuilder.appendChild(june);
       leftPageBuilder.appendChild(p_july);
       leftPageBuilder.appendChild(july);
   };
   subPage.createSummer2014Right = function() {
       var img = subPage.createPhoto("VU_genomic_DNA_PCR.jpg",
           "The results of the genomic DNA PCR on all of the plant species.",
           554, 735,
           "The results of the genomic DNA PCR indicated each gene had a large fraction of introns. " +
           "None of the genes had a distinct band at exactly the right weight corresponding with what " +
           "the intron-less cDNA size would be.");
       rightPageBuilder.appendChild(img);
   };
   subPage.createFall2014Left = function() {
       var header = document.createElement("header");
       header.appendChild(document.createTextNode("Spring 2014"));
       var p_aug = subPage.createP("August");
       var p_sept = subPage.createP("September");
       var p_s17 = subPage.createP("September 17th");
       var p_s18 = subPage.createP("September 18th");
       var p_s19 = subPage.createP("September 19th");
       var p_s20 = subPage.createP("September 20th");
       var p_s26 = subPage.createP("September 26th");
       var p_o5 = subPage.createP("October 5th");
       var p_o7 = subPage.createP("October 7th");
       var p_o9 = subPage.createP("October 9th");
       var p_o10 = subPage.createP("October 10th");
       var p_o11 = subPage.createP("October 11th");
       var p_o12 = subPage.createP("October 12th");
       var p_o13 = subPage.createP("October 13th");
       var p_o14 = subPage.createP("October 14th");
       var p_o15 = subPage.createP("October 15th");
       var p_o16 = subPage.createP("October 16th");
       var aug = document.createElement("ul");
       var sept = document.createElement("ul");
       var s17 = document.createElement("ul");
       var s18 = document.createElement("ul");
       var s19 = document.createElement("ul");
       var s20 = document.createElement("ul");
       var s26 = document.createElement("ul");
       var o5 = document.createElement("ul");
       var o7 = document.createElement("ul");
       var o9 = document.createElement("ul");
       var o10 = document.createElement("ul");
       var o11 = document.createElement("ul");
       var o12 = document.createElement("ul");
       var o13 = document.createElement("ul");
       var o14 = document.createElement("ul");
       var o15 = document.createElement("ul");
       var o16 = document.createElement("ul");
       var text = [["Moved the lab into its new space before the start of the semester."],
           ["Created the plasmid intermediate pVU1400A, which is missing only a single insert to become pVU14004."]];
       subPage.addMultLI(p_aug, text);
       text = [["Ran RNA extraction on all the plants that were still available. This excluded Myrcene and " +
       "Linalool (R) since both Perilla frutescens and Mentha aquatica had withered over the summered."],
           ["Repeated RNA extractions on those which showed appreciable concentration on the nanodrop. Event" +
           "ually all 7 remanining terpenes had plant RNA in appreciable quantities (most between 20-50 " +
           "ng/ul, with a few less than 10 and a few more than 100 ng/ul)."]];
       subPage.addMultLI(p_sept, text);
       text = [["Digested plasmid intermediate grown in demethylated bacteria with ClaI. Ligated final " +
           "insert into vector. No transfomants grow after 24 hours."],
           ["Diagnostic digest shows the ClaI enzyme is cutting properly. pUC19 positive control for transforma" +
           "tions show that the competent cells are working."]];
       subPage.addMultLI(p_s17, text);
       text = [["Ran reverse transcription PCR on extracted RNA to isolate synthase cDNA. Humelene and sabinene " +
       "show clear positive results, santalene shows amplification at smaller region, and cadinene shows no" +
       " cDNA bands."]];
       subPage.addMultLI(p_s18, text);
       text = [["Made liquid cultures of K546546 in preparation for mutagenesis. Also made glycerol stock to store at -80."],
           ["Diagnostic digest of ligation of pVU1400A intermediate and the final insert needed to make " +
           "finished plasmid. Gel clearly shows bands in exactly the correct positions for each of three " +
           "comparison conditions, proving that the creation of pVU14004 was finally successful.."]];
       subPage.addMultLI(p_s19, text);
       text = [["Miniprep of K546546 liquid cultures (1 ml ). First culture tube concentration of 85.7 ng/ul " +
               "DNA, second 105.1 ng/ul."],
               ["RNA extracted arabadopsis and Picea abies to improve yield and quality. Carene still failed to " +
               "get an RNA concentration greater than 10 ng/ul, while Arabidopsis produced 107 ng/ul with a go" +
               "od A260/A280 ratio."],
               ["Miniprep of K546546 liquid cultures (1 ml ). First culture tube concentration of 85.7 ng/ul " +
               "DNA, second 105.1 ng/ul"]];
       subPage.addMultLI(p_s20, text);
       text = [["RT-PCR done on humelene, linalool (S), sabinene, and zingiberene. Sabinene produces clear " +
       "bands, while zingiberene shows one faint band at roughly the correct size. Positive controls are also " +
       "run to confirm that the reverse transcription step is not the cause of any failures to amplify."]];
       subPage.addMultLI(p_s26, text);
       text = [["RT-PCR done on humelene, sabinene, and santalene. Sabinene again produces clear bands,and " +
       "santalene does as well although much fainter. Both bands were gel extracted to yield a small " +
       "(<10 ng/ul) amount of DNA."],
       ["Extracted DNA was ligated into pUC19 and transformed into E. coli."]];
       subPage.addMultLI(p_o5, text);
       text = [["Site direction mutagenesis kit and specially designed primers were used to mutagenize K546546 " +
       "at its BglI site, sabinene cDNA at its XbaI and EcoRI sites, and pVU14004 at its EcoRI and XbaI sites."],
           ["Mutagenesis product was transformed into E. coli."]];
       subPage.addMultLI(p_o7, text);
       text = [["Minipreps were done on 5 ml liquid cultures of mutagenized pVU14004, sabinene, and K546546. " +
       "Four liquid cultures were made for each, and both sabinene and pVU14004 were done in duplicate."],
           ["Diagnostic digests were done on miniprepped plasmid to check if the restriction sites were " +
           "mutagenized. pVU14004 appeared to have lost its XbaI site but not its EcoRI site, sabinene shows " +
           "a size that suggests it failed to ligate as an insert into pUC19, and K546 shows only a single " +
           "band at around its starting weight."]];
       subPage.addMultLI(p_o9, text);
       text = [["All 8 minipreps of sabinene ligated into pUC19 were digested with SpeI and ApaI to check for " +
       "the synthase insert. Only one, Sab B2, shows a second band at the right size."]];
       subPage.addMultLI(p_o10, text);
       text = [["Santalene synthase was ligated into pVU14004 and pSB1C3. E. coli was transformed and incubated."],
           ["The sites that failed to show mutagenesis were mutagenized again using and transformed into E. " +
           "coli. K546546 had its AgeI site mutagenized."]];
       subPage.addMultLI(p_o11, text);
       text = [["All liquid cultures were miniprepped, producing 8 samples of pVU14004 with confirmed XbaI " +
       "mutagenesis, 4 pVU14004 with no sites confirmed, 4 sabinene, and 6 samples produced from santalene in " +
       "pVU14004. None of the plates with santalene in pSB1C3 produced colonies."],
           ["Diagnostic digests were run on all miniprepped plasmid (K546- AgeI, BglI, SphI. Sabinene- EcoRI, " +
           "BamH1. Santalene in pVU- ApaI, XbaI. pVU- EcoRI, XbaI, BamHI, KpnI). Santalene appeared not to have " +
           "ligated into pVU14004. Sabinene did not have its EcoRI site removed by mutagenesis. K546546 had at least" +
           " one cut, but the second sample may have had one site mutagenized."],
           ["Santalene was re-ligated into pSB1C3 and transformed."]];
       subPage.addMultLI(p_o12, text);
       text = [["Santalene in pSB1C3 was miniprepped to good yield. Each of 4 replicates was digested with " +
       "SpeI and ApaI to test for ligation. The ApaI enzyme appears not have cut, but the fourth sample showed an " +
       "uncut plasmid size which corresponded to that of pSB1C with santalene successfully inserted."]];
       subPage.addMultLI(p_o13, text);
       text = "Ligated santalene synthase again into pVU14004 and transformed into E. coli.";
       subPage.addMultLI(p_o14, text);
       text = [["One colony grew and was put in liquid culture."],
           ["Culture miniprepped and digested. Again no gene insertion was detectable."]];
       subPage.addMultLI(p_o15, text);
       text = [["Transformed pVU14004 into a dam- strain of E. coli to address the methylation sensitivity of ApaI."],
           ["Finished planning and acquiring materials for GC-MS confirmation of terpene presence."]];
       subPage.addMultLI(p_o16, text);
       leftPageBuilder.appendChild(header);
       leftPageBuilder.appendChild(p_aug);
       leftPageBuilder.appendChild(aug);
       leftPageBuilder.appendChild(p_sept);
       leftPageBuilder.appendChild(sept);
       leftPageBuilder.appendChild(p_s17);
       leftPageBuilder.appendChild(s17);
       leftPageBuilder.appendChild(p_s18);
       leftPageBuilder.appendChild(s18);
       leftPageBuilder.appendChild(p_s19);
       leftPageBuilder.appendChild(s19);
       leftPageBuilder.appendChild(p_s20);
       leftPageBuilder.appendChild(s20);
       leftPageBuilder.appendChild(p_s26);
       leftPageBuilder.appendChild(s26);
       leftPageBuilder.appendChild(p_o5);
       leftPageBuilder.appendChild(o5);
       leftPageBuilder.appendChild(p_o7);
       leftPageBuilder.appendChild(o7);
       leftPageBuilder.appendChild(p_o9);
       leftPageBuilder.appendChild(o9);
       leftPageBuilder.appendChild(p_o10);
       leftPageBuilder.appendChild(o10);
       leftPageBuilder.appendChild(p_o11);
       leftPageBuilder.appendChild(o11);
       leftPageBuilder.appendChild(p_o12);
       leftPageBuilder.appendChild(o12);
       leftPageBuilder.appendChild(p_o13);
       leftPageBuilder.appendChild(o13);
       leftPageBuilder.appendChild(p_o14);
       leftPageBuilder.appendChild(o14);
       leftPageBuilder.appendChild(p_o15);
       leftPageBuilder.appendChild(o15);
       leftPageBuilder.appendChild(p_o16);
       leftPageBuilder.appendChild(o16);
   };
   subPage.createFall2014Right = function() {
       var img1 = subPage.createPhoto("VU_First_RT_PCR_results.JPG",
           "Results of a reverse transcription PCR, showing the cDNA amplified from plant RNA template.",
           346, 417,
       "Results of a reverse transcription PCR, showing the cDNA amplified from plant RNA template.");
       var img2 = subPage.createPhoto("VU_DD.png",
           "Diagnostic digest produces bands of exactly the correct size (from left to right, 2700, 2700," +
           "and 950, 2700, and 1700, confirming that pVU14004 was successfully constructed.",
           303, 314,
           "Diagnostic digest produces bands of exactly the correct size (from left to right, 2700, 2700," +
           "and 950, 2700, and 1700, confirming that pVU14004 was successfully constructed.");
       var img3 = subPage.createPhoto("VU_PVU14004.png",
           "10-9 Diagnostic digest",
           340, 286.375,
           "10-9 Diagnostic digest");
       var img4 = subPage.createPhoto("VU_10-11_diagnostic_digest.JPG",
           "10-11 Diagnostic digest",
           331.5, 381.8,
           "10-11 Diagnostic digest");
       rightPageBuilder.appendChild(img1);
       rightPageBuilder.appendChild(img2);
       rightPageBuilder.appendChild(img3);
       rightPageBuilder.appendChild(img4);
   };
   return subPage;

}