This is an old revision of the document!
=====Banana Slug RNA===== =====RNA isolates===== In Feburary 2015 the [[http://omegabiotek.com/store/product/e-z-n-a-mollusc-rna-kit/|Omega Bio Tek E.Z.N.A.® Mollusc RNA kit]] was used to prepare 28 isolations of RNA from 16 tissue samples. Note that this kit is not recommended for RNA <200nt In April 2015 the [[http://www.lifetechnologies.com/order/catalog/product/AM1561|mirVana™ miRNA Isolation Kit, without phenol]] was used to create a size selected sample of one of the RNA isolates (dg2). Later that month 9 RNA samples (V2, K, SMT, DA2, PA1, DG3, DG1, DG2-S, DG2-L) were run on a 1.5% CE Agarose gel compared to a 100nt RNA ladder. Unfortunately there was a miss-communication between Jared and his supervisor it is mostly unknown which sample made it to what well. Note that there is still a presence of small RNA (<200 nt) but no distinct rRNA, tRNA, or miRNA bands. {{ :rnagel.png?nolink |}} =====RNA samples===== Abbreviations for tissues cuts: | Tissue cut | Abbreviation ID | number of cuts from tissue | | Albumen gland (proximal) | pa | 2 | | Albumen gland (distal) | da | 2 | | Penis | p | 3 | | Digestive Gland | dg | 3 | | Vagina | v | 2 | | Penis Muscle | pm | 2 | | Foot | f | 2 | | Salivary Gland | sg | 2 | | Ovotestis | ot | 2 | | Body Wall | bw | 2 | | Shell | sh | 1 | | Vas Deferons | vd | 1 | | Ovoduct | od | 1 | | Connective tissue | ct | 1 | | spermathecca | smt | 1 | | Kidney | k | 1 | The following table of data was generated with a [[http://www.nanodrop.com/Productnd8000overview.aspx?gclid=CJaNntn0sMUCFU6VfgodXI4AlQ|nanodrop]] | Sample ID | Conc. (ng/ul)| 260/280 | 260/230 | Vol. (ul)| Total (ug)| notes | | pa1 | 180.9 | 2 | 1.87 | 64.4 | 11.65 | | | pa2 | 279.3 | 1.99 | 2.32 | 70 | 19.55 | | | da1 | 150.2 | 2.04 | 1.36 | 70 | 10.51 | | | da2 | 113.4 | 2.09 | 0.23 | 61 | 6.93 | contaminated? | | v1 | 112 | 2.02 | 0.97 | 70 | 7.84 | tougher, lighter, bulbous | | v2 | 78.42 | 2.03 | 0.83 | 56 | 4.39 | flimsy, darker, sleeve-like | | pm1 | 3.207 | 1.91 | 0.41 | 70 | 0.22 | | | pm2 | 25.79 | 1.95 | 0.31 | 70 | 2.86 | | | f1 | 40.84 | 1.88 | 0.89 | 70 | 2.86 | | | f2 | 47.03 | 1.84 | 1.77 | 69 | 3.25 | | | sg1 | 338 | 1.9 | 1.62 | 70 | 23.66 | dense with dark veins | | sg2 | 64.12 | 1.9 | 0.54 | 70 | 4.49 | absent of dark veins | | ot1 | 39.95 | 1.82 | 1.2 | 70 | 2.80 | | | ot2 | 32.53 | 1.79 | 1.46 | 70 | 2.28 | | | bw1 | 7.527 | 1.65 | 0.69 | 70 | 0.53 | | | bw2 | 15.21 | 1.84 | 0.29 | 70 | 1.06 | | | sh | 3.768 | 1.23 | 0.39 | 70 | 0.26 | | | vd | 7.468 | 1.67 | 0.36 | 70 | 0.52 | | | od | 26.13 | 1.99 | 1.56 | 70 | 1.83 | | | ct | 40.43 | 1.92 | 1.82 | 70 | 2.83 | | | smt | 93.26 | 1.95 | 1.86 | 59 | 5.50 | Steven spilled some | | k | 160 | 1.98 | 2.11 | 63.5 | 10.16 | | | p1 | 53.08 | 1.89 | 1.59 | 70 | 3.72 | only epiphallus | | p2 | 16.91 | 1.75 | 1.06 | 70 | 1.18 | | | p3 | 9.761 | 1.55 | 0.48 | 70 | 0.68 | no epiphallus | | dg1 | 439.6 | 1.95 | 2.1 | 67 | 29.45 | iron? | | dg2 | 253.6 | 1.98 | 2.16 | 0 | 0.00 | size selected | | dg3 | 429.4 | 1.99 | 2.12 | 67 | 28.77 | iron? | | dg2-S | 91.24 | 2.07 | 1.83 | 98.5 | 8.99 | <200nt | | dg2-L | 225.3 | 2.09 | 1.74 | 55.5 | 12.50 | >200nt |
Discussion
I would like to flag this page for removal (or burial somewhere deep in the wiki), I don't see any use for the page when we don't have labeled lanes.
just bury this page as old_RNA or something as you add new data here.
How are we going to use these data when we don't know which lanes are which? Maybe I am misunderstanding this… “Unfortunately there was a miss-communication between Jared and his supervisor it is mostly unknown which sample made it to what well.”