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Finish the paper with no plagiarism, and active all requirements on the rubric.Poor (1)

Fair (2)

Good (3)

Excellent (4)

Points Earned

Weighting

Title

Either missing or fails to describe the topic

Identifies a broad topic but fails to convey the more narrowly defined focus of the paper

Identifies the topic but is excessively wordy

Identifies the narrowly defined topic and avoids unnecessary words and phrases

5%

Introduction and Discussion

The research focus is unclear. The concepts in the discussion are not tied back to the information presented in the background. Future work is missing.

An attempt was made to state the topic and to review key knowledge in the field but the arguments are not well-supported by references to the published literature. Future work is missing.

The topic is stated and information presented gives the reader a general idea of the state of knowledge in the field. Key points made in the discussion tie back to points introduced in the background section. An attempt was made to suggest useful next steps or future works.

The topic is clearly stated and information presented clearly supports the topic. The discussion ties back to key points made in the background section. Logical experiments are proposed for future work.

30%

Content

-# of up-/down-regulated genes

-GO Biological processes pie chart

-gene locus, other names, biological processes, cellular component, growth and development stages when expressed, plant structures where protein is expressed, protein length, molecular weight, isoelectric point, interpro domains

Multiple required elements are missing (see list under content) and/or figure legends are missing and/or text other than the figure legends is lacking to support the figures.

A few elements are missing (see list under content) and/or figure legends lack clarity and/or text does not adequately inform the reader what data has been compiled.

All elements are present, figure legends are present, and text is included to inform the reader what data has been compiled.

All elements are present. Figure legends are clear. The text adequately informs the reader what data has been compiled and refers the reader to the appropriate figures.

50%

Organization

Writing does not logically flow from one concept to the next. Paragraphs lack topic sentences. The writer’s meaning or intent is often unclear.

In general, the writing is logically organized. Occasionally paragraphs contain more than one main idea or concepts unrelated to the main idea of the paragraph or lack a topic sentence. The writer’s meaning or intent is occassionally unclear.

The writing is logically organized. Paragraphs contain one topic sentence and supporting sentences clearly flow from one to the other. Paragraphs are clearly linked to each other. The reader has a fairly clear idea of what the writer intends.

The writing is logically organized to support the central purpose. Paragraphs contain a topic sentence, only one mainSheet1

AGI # Affy Probe Index # WT min germ 1_Signal WT min germ 1_Detection converted detection value WT min germ 1_Detection p-value WT min germ 64_Signal WT min germ 64_Detection converted detection value WT min germ 64_Detection p-value WT min germ 246_Signal WT min germ 246_Detection converted detection value WT min germ 246_Detection p-value WT min germ 251_Signal WT min germ 251_Detection converted detection value WT min germ 251_Detection p-value Descriptions

AFFX-BioB-5_at 1115.7 P 2 0.000297 312.7 P 2 0.004998 466.3 P 2 0.005565 290.2 P 2 0.036569 J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)

AFFX-BioB-M_at 1851.8 P 2 0.000052 540.4 P 2 0.00007 519.7 P 2 0.000081 398.6 P 2 0.000081 J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)

AFFX-BioB-3_at 1537.2 P 2 0.00006 294.5 P 2 0.000857 416 P 2 0.000581 221.1 P 2 0.001102 J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)

AFFX-BioC-5_at 3684.2 P 2 0.000044 819.9 P 2 0.000095 1092.7 P 2 0.00007 815.2 P 2 0.000044 J04423 E coli bioC protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)

AFFX-BioC-3_at 2222.2 P 2 0.000052 487.3 P 2 0.000297 852.4 P 2 0.000081 500.8 P 2 0.00007 J04423 E coli bioC protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)

AFFX-BioDn-5_at 2238.5 P 2 0.000044 629.8 P 2 0.000044 1404 P 2 0.000044 818.2 P 2 0.000052 J04423 E coli bioD gene dethiobiotin synthetase (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)

AFFX-BioDn-3_at 13292.8 P 2 0.000044 3855.1 P 2 0.000052 7058.9 P 2 0.000044 4392 P 2 0.000052 J04423 E coli bioD gene dethiobiotin synthetase (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)

AFFX-CreX-5_at 25577.6 P 2 0.000044 7119.8 P 2 0.000044 13472.7 P 2 0.000044 7634.8 P 2 0.000044 X03453 Bacteriophage P1 cre recombinase protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)

AFFX-CreX-3_at 39488.5 P 2 0.000044 10425.6 P 2 0.000044 20126.7 P 2 0.000044 11296.8 P 2 0.000044 X03453 Bacteriophage P1 cre recombinase protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)

AFFX-DapX-5_at 40.7 A 0 0.382599 46.3 A 0 0.095667 81.5 P 2 0.046482 67.6 P 2 0.005565 L38424 B subtilis dapB, jojF, jojG genes corresponding to nucleotides 1358-3197 of L38424 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)

AFFX-DapX-M_at 12.8 A 0 0.834139 23.6 A 0 0.737173 118.9 P 2 0.039661 87.5 P 2 0.042962 L38424 B subtilis dapB, jojF, jojG genes corresponding to nucleotides 1358-3197 of L38424 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)

AFFX-DapX-3_at 4.2 A 0 0.993813 4.5 A 0 0.987453 146.7 P 2 0.00BCHS3201: Microarray Paper

Background

You will be working with data generated using Affymetrix Arabidopsis thaliana (ATH1) full genome chips. Please watch the microarray lecture posted in Blackboard for information on how the chips are constructed and how they are used. Step-by-step instructions are provided here for managing the data. While I have provided details here, keep in mind that in a real research lab, you would have to decide for yourself how to organize the data and make sense of it.

Arabidopsis thaliana

Arabidopsis thaliana is a small, flowering plant found all over the world. It is commonly considered a weed in the United States and can be found in the Midwest (Texas is too hot; the plant likes temperatures around 68°F). Arabidopsis serves as a model plant because it has a number of characteristics that make it amenable to study. The plant is small, reaching only 30 cm in height when full grown. It grows well grows well in both soil and nutrient media making it easier to develop carefully controlled studies (Meyerowitz, 1989). It is easily grown indoors in a laboratory. Crop plants require much larger facilities and land to study. The life cycle of Arabidoposis is only 6 weeks from seed to seed-producing. This allows a much faster pace for experiments than most crop plants where only one generation of plants can be grown in a calendar year (unless your university is fortunate enough to have land on two hemispheres so you can get two growing seasons in). Arabidopsis plants produce thousands of seeds per plant and these seeds are tiny making them easy to store in microcentrifuge tubes in the freezer (Meyerowitz, 1989).

Arabidopsis has a haploid genome of 5 chromosomes consisting of approximately 125 megabases (The Arabidopsis Genome Initiative, 2000). This is a very small genome compared to that of crop species. Maize, for example, is around 2,500 megabases in size (Adam, 2000). Most genes in Arabidopsis exist at a single locus in the genome. Crop plant genomes are large in part because their genomes contain large sections that are duplicated. This makes creating complete knock-outs of a particular gene difficult. Arabidopsis is amenable to genetic manipulations either through traditional cross-breeding techniques or more modern genetic modification techniques (mutation through T-DNA inserts, chemical agents, or CRISPR-CAS9). Studies conducted in Arabidopsis are often directly transferable to crop species as many of the genes have homologues in crop plants. Studying them first in Arabidopsis is easier, cheaper, and faster.

Sugar and Phytohormone Signaling Pathways

Sugars have a role in basic plant metabolism as a carbon source and also play a role as signaling molecules, contributing to the regulation of a number of pathways in plants. The expression of genes involved in mobilization of starch and lipid reserves is usually repressed by the presence of high sugar levels in the plant while genes inv

  
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