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Digital Northern

Digital Northern

Digital Northern heat map representing the library distribution of ESTs representing gene models within PopulusDB as described in this paper(http://www.biomedcentral.com/1471-2164/9/589/).Which is based on EST frequencies in different libraries (Sterky et al. 2004) – of the OPLS-generated leaf gene list and shows that the greatest prevalence of genes was found in the shoot meristem, young leaf and apical shoot libraries. New RIA(Rich Internet Application) based Digital Northern tool  developed using Adobe Flash technology.Main goal is to enhance simplicity,efficiency and  real time interaction to user.
How to use?
Type in some Poplar gene ids inside the right side text input box by separating comma, newline or tab .Then change the variable drop down lists(Plot gene names?, Plot dendrogram?, Clustering method ...) ,Color picker(Background colour) or slider values(Max genes for colour, Min gene frequency) according to your requirement and it will simultaneously update the Heatmap otherwise click Submit button.Finally you can download the PDF file by clicking Download PDF link.


cDNA librarys
Cambial zone (A + B)   Populus tremula x tremuloides T89. Bark was peeled, and tissue scraped from both exposed surfaces with a scalpel. Sample includes developing xylem, cambial zone and mature phloem.
 
Active cambium (UB)   Populus tremula. Stem samples were collected from 3 different trees growing south of UmeŒ on July 10th 2001. 30-micrometer section were obtained by cryosectioning and used for RNA preparation.
 
Dormant cambium (UA)   Populus tremula. Stem samples were collected from 3 different trees growing south of UmeŒ on October 5th 2001. 30-micrometer section were obtained by cryosectioning and used for RNA preparation.
 
Tension wood (G)   Populus tremula x tremuloides T89. Wood scrapings of a tree inclined for 3 weeks in the greenhouse. Tissues should mainly contain wood cells that are actively forming secondary cell wall and a G-layer
 
Wood cell death (X)   Populus tremula x tremuloides T89. Sample was taken from stem and included xylem cells that started secondary cell wall formation but mainly those where cell wall was fully developed. The sample also included cells that had died.
 
Young leaves (C)   Populus tremula x tremuloides T89. Library described in Larsson S, Bjorkbacka H, Forsman C, Samuelsson G, Olsson O. (1997). Molecular cloning and biochemical characterization of carbonic anhydrase from Populus tremula x tremuloides. Plant Molecular Biology 34: 583-592. Trees cultured in greenhouse in fertilized peat under natural light supplemented with metal l halogen lamps at a PPF of 150 microE. Photoperiod 18 hrs, 20/15 C. watered daily and fertilized once a week.
 
Senescing leaves (I)   Populus tremula, Library described in Bhalerao et al. (2003) Gene expression in autumn leaves. Plant Physiol. 131: 430Ð442. Sample collected from one wild tree on the UmeŒ University campus. Sampled September 14th 1999 (few days before visible leaf senescence was observed) at 11.00. Mid-rib were removed.
 
Cold stressed leaves (L)   Populus tremula x tremuloides T89. Greenhouse plants were transferred to 5¡C. Fully developed leaves were sampled 3 and 4 days after transfer and pooled.
 
Dormant buds (Q)   Populus tremula. The same tree as in the senescing leaves library. Dormant buds were collected in February.
 
Petioles (P)   Populus tremula. Petioles was collected from several individuals, growing in long days conditions and stressed in different ways were pooled. Stress treatments were 1) Mechanical stress: A tree was hit every second for 20 hours, resulting in trembling of the whole tree 2) Nutrient stress: A tree was planted in perlit and grown without nutrients for two weeks 3) Biotic stress: A tree infested with (ticks) 4) Cold stress: A tree was exposed to 5¡C(under short day conditions and sampled after 15, 10, 20 and 37 days.
 
Virus/fugus-infected leaves (Y)   Populus tremula. Leaves from different stages infected either with 1) Poplar Mosaic Virus or 2) Venturia tremulae were sampled and pooled. Healthy non-infected leaves were sampled and used as driver pool in a partial subtraction step of the cDNA synthesis. Sequences Y001-Y004 are from the Virus infected and Y005-Y024 from the fungi infected partial subtractive library.
 
Flower buds (F)   Populus trichocarpa. Library described in Rottmann, W.H. et al. (2000). Diverse effects of overexpression of AFY and PTLF, a poplar (Populus) homolog of LEAFY/FLORICAULA, in transgenic poplar and Arabidopsis. Plant J. 22: 235-246. Immature female inflorescence tissue was collected in mid to late May from wild trees growing in the vicinity of Corvallis, Oregon. Reproductive buds were dissected to remove the young bud scales and the entire inflorescences were collected.
 
Female catkins (M)   Populus trichocarpa. Flushing catkins were collected in early spring (around March 1) from wild trees growing in the vicinity of Corvallis, Oregon.
 
Male catkins (V)   Populus trichocarpa. Flushing catkins were collected in early spring (around March 1) wild trees growing in the vicinity of Corvallis, Oregon
 
Apical shoot (K)   Populus tremula x tremuloides T89. 150 apical shoots (top 3 mm, biggest leaf ca. 5 mm, weight ca 4 mg) from 3-month-old greenhouse-grown plants were collected and pooled.
 
Shoot meristem (T)   Populus tremula x tremuloides T89. Shoot apexes were dissected under microscope .
 
Bark (N)   Populus tremula x tremuloides T89. Long-day treated plants (about 3 m). Bark was sampled from under the "crown" and 75 cm downwards. The sample was peeled off with a "potato peeler", buds were avoided and the cells were inspected in the microscope.
 
Roots (R)   Populus tremula x tremuloides T89. Plants grown in agar under sterile conditions. The whole root system (primary roots) up to 0.5-1 cm from the stem was used. Roots were still white.
 
Imbibed seeds (S)   Populus tremula. Seeds from a seed lot were imbibed and samples were taken 1) right after imbibition and 2) after 24 hours and pooled.
 
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