title: DNA pooling using Affymetrix HindIII and Ilummina HumanHap arrays

status: Public on Nov 06 2007

city: Brisbane

first: Stuart

last: Macgregor

state: Queensland

address: 300 Herston Road

department: Genetic Epidemiology

institute: Queensland Institute of Medical Research

summary:
The experiment was based on 3 arrays (3 Illumina HumanHap300 and 3 Affymetrix Genechip HindIII arrays) of each  type being hybridized to a single pool which contained equal amounts of DNA from each of 384 individuals. The goal is to  estimate a pooling allele frequency, the average frequency of allele 1, say, in the set of 384 individuals. After processing, the raw data are summarized to give pooling allele frequency estimates for each array.
Abstract from paper comparing two arrays (one affy, one illumina) is as follows; Genome wide association (GWA) studies to map genes for complex traits are powerful yet costly. DNA pooling strategies have the potential to dramatically reduce the cost of GWA studies. Pooling using Affymetrix arrays has been proposed and used but the efficiency of these arrays has not been quantified. We compared and contrasted Affymetrix Genechip HindIII and Illumina HumanHap300 arrays on the same DNA pools and show that the HumanHap300 arrays are substantially more efficient. In terms of effective sample size, HumanHap300 based pooling extracts >80% of the information available with individual genotyping (IG). In contrast, Genechip HindIII based pooling only extracts ~30% of the available information. With HumanHap300 arrays concordance with IG data is excellent. Guidance is given on best study design and it is shown that even after taking into account pooling error, one stage scans can be performed for >100 fold reduced cost compared with IG. With appropriately designed two stage studies, IG can provide confirmation of pooling results whilst still providing ~20 fold reduction in total cost compared with IG based alternatives. The large cost savings with Illumina HumanHap300 based pooling imply that future studies need only be limited by the availability of samples and not cost.
Keywords: DNA pooling experiment

overall_design:
A pool was typed using 3 Affymetrix HindIII arrays. Estimates of pooling allele frequency were obtained.
Pool of 384 individuals - data in matrix is for 3 replicate arrays on this pool. Information on each array individually is in the uploaded files with raw match and mismatch scores
Further details on the raw probe score data also included with this submission are below
For Affymetrix arrays, there is information on Perfect Match (PM) and Mis-Match (MM) intensities for each allele. Essentially the estimate of pooling allele frequency (PAF) comes from A/(A+B) where A is PM-MM, similarly for B. From the header line of the affy file  "0586-EN Control Pool Repl 1 50KHind 09-03-05_Quartet1 - PA(Sense)","0586-EN Control Pool Repl 1 50KHind 09-03-05_Quartet1 - PB(Sense)","0586-EN Control Pool  Repl 1 50KHind 09-03-05_Quartet1 - MA(Sense)","0586-EN Control Pool Repl 1 50KHind 09-03-05_Quartet1 -  MB(Sense)"  so the order of the information is  PM-(allele A) PM-(allele B) MM-(allele A) MM-(allele B)  This same information is also available on the anti-sense strand of the array. Further, the sense and antisense strands have data at up to 7 locations on the array. That is, the 4 columns of PM/MM data are repeated (2*7) 14 times - so there are 56 columns of data plus the column with the snp name. In practice only 10 of the possible 14 sets of 4 columns give valid data so there are 10 sets of 4 columns that yield estimates of A/(A+B) (i.e. pooling allele frequency estimates or PAFs). These 10 PAFs are accumulated over mutiple arrays and finally used to get an overall estimate (using a statistical model described in Macgregor et al, Nucleic Acids Research,  34(7):e55, 2006) of the frequency of a particular allele in the set of pooled individuals. In our case, 3 affymetrix arrays for each pool are used so there are up to 30 PAF values used in the final calculation. In practice some of the individual PAFs don't get included as they fail on the array. Since the array data are fairly noisy, we use the ~30 PAF values to bring down the array error - essentially it is the fact that there is up to 30 fold redundancy of the array that enables the pooling to work satisfactorily.
The raw probe score data for the 3 arrays is in the text files conrep1.csv, conrep2.csv and conrep3.csv

The summary file, forgeoconpoolfreq.txt, contains the rs and Illumina names (Code), along with the physical position, chromosome and estimate of allele frequency for the pool based on the raw data from all 3 arrays used.  The estimate of pooling allele frequency (PAF) comes from PAF=R/(R+G) where R and G are the red and green intensities respectively. The PAFs were normalized to ensure that the mean allele frequency was 0.5 over each strand of the array (i.e. over each of the 10 sets of ~30k SNPs on the array).

first: Zhen-Zhen

last: Zhao

first: Anjali

last: Henders

middle: G

last: Martin

first: Grant

middle: W

last: Montgomery

last: Visscher


title: SNPchip analysis of single cell products

status: Public on Dec 20 2007

city: Wako

first: Kazuya

last: Iwamoto

address: 2-1 Hirosawa

department: Brain Science Institute

country: Japan

institute: RIKEN

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary:
Single-cell human genome analysis using whole-genome amplified product is hampered by allele bias during amplification. Using an oligonucleotide SNP array, we examined the nature of the allele bias and its effect on the chromosomal copy number analysis.
Keywords: single cell, copy number analysis, whole genome amplification, brain

overall_design: TB106, lymphoblastoid cell line; CMK11-5 and CMK86, cell line; WGA, whole-genome amplified from bulk DNA; SC, whole-genome amplified product from single cell. Genotype and copy number status were compared between non-amplified products and their single cell products.

first: Miki

last: Bundo

first: Junko

last: Ueda

first: Yoko

last: Nakano

first: Wataru

last: Ukai

first: Eri

last: Hashimoto

first: Toshikazu

last: Saito

first: Tadafumi

last: Kato


title: SCLC cell line profiling on 100K arrays

status: Public on Apr 15 2007

city: Abbott Park

first: Dimitri

last: Semizarov

state: IL

address: 100 Abbott Park Rd, bld AP10, dept R4CD

country: USA

institute: Abbott Laboratories

summary:
Twenty three small-cell lung carcinoma (SCLC) cell lines from ATCC profiled on 100K genotyping arrays
Keywords: comparative genomic hybridization

overall_design: The cell lines were run on 100K SNP genotyping arrays to obtain copy number information


title: A comparison of DNA copy number profiling platforms using a panel of melanoma cell lines

status: Public on Nov 02 2007

city: King of Prussia

first: Joel

last: Greshock

state: PA

address: 2301 Renaissance Blvd.

department: Translational Medicine, Oncology

institute: GlaxoSmithKline

type: Genome variation profiling by genome tiling array

summary:
The accurate mapping of recurring DNA copy number aberrations (CNAs), a hallmark feature of the cancer genome, has facilitated the discovery of tumor suppressor genes and oncogenes.  Microarray-based assays designed to detect these chromosomal copy number alterations on a genome-wide and high-resolution scale have emerged as a cornerstone technology in the genomic era.   The diversity of commercially-available platforms prompted a systematic comparison of five copy number profiling assays for their ability to detect 2-fold copy number gain and loss (4n or 1n, respectively) as well as focal high-amplitude CNAs.   Here, using a collection of established human melanoma cell lines, we defined the reproducibility, absolute signals, signal:noise, false-positive and false-negative rates for each of the five assays against ground-truth defined by Spectral Karyotyping (SKY), in addition to comparing the concordance of CNAs detection by two high-resolution Agilent and Affymetrix microarray platforms.  Our analyses concluded that the Agilent’s 60mer oligo-microarray with probe design optimized for genomic hybridization offers the highest sensitivity and specificity [area under Receiver Operator Characteristic (ROC) curve >0.99] while Affymetrix’s SNP microarray appears to offer better detection of CNAs in gene-poor region.  Availability of these comparison results should guide study design decisions and facilitate further computational development.
Keywords: comparative genomic hybridization

overall_design: We generated copy number profiles of a defined set of tumor cell lines on five oligo-microarray-based assays of three platforms (Agilent, Affymetrix and NimbleGen) and determined the reproducibility, signal and noise as well as sensitivity and specificity of each in detecting two-fold signals based on SKY-defined aberrations as ground-truth for comparison.  In addition, high-density microarray assays from Agilent and Affymetrix platforms were further compared for definition of CNAs in an independent dataset using published analytical approaches.  All arrays were run from the same DNA harvest from respective cell lines.  Each array was run according to the protocol of the manufacturer.

middle: D

first: Bin

last: Feng

first: Barbara

middle: L

last: Weber

first: Lynda

last: Chin


title: Global gene expression profiles of Oryza sativa wild type Zhonghua11 and mutant gif1 in filling stage

city: Shanghai

first: Li

last: Qun

state: Shanghai

address: 300 Fenglin Road

department: National Key Laboratory of Plant Molecular Genetics

country: China

institute: Institute of plant physiology & ecology, SIBS, CAS

summary:
To reveal the underlying molecular mechanism of Gif1 action in the control of grain filling and yield improvement, we performed transcriptional profiling of wild type Zhonghua11 and mutant gif1 plants in early filling stage on a global scale using the Affymetrix GeneChip Rice Genome Array
Keywords: Filling stage

overall_design: Rice caryopsis were harvested in 7 days after flowering and three biological repeats were performed on Zhonghua11 (wild-type) and gif1 (mutant), respectively.

first: Qun

last: Li

first: Ertao

last: Wang

first: Zuhua

last: He


title: The evolution of β-thalassemia major from minor is associated with paternal uniparental isodisomy of chromosome 11p15

status: Public on May 22 2007

city: Kaohsiung

first: Ta-Chih

last: Liu

address: 100, Shih-Chuan 1st Rd.

department: Department of Internal Medicine

country: Taiwan

institute: Kaohsiung Medical University Hospital

summary:
β-thalassemia major can be caused by homozygous mutations of the HBB gene, most of the cases are inherited from parents who both have β-thalassemia minor. Herein, we show that a mosaic paternal uniparental isodisomy of chromosome 11p14.3-15.5 is associated with β-thalassemia major in a patient with β-thalassemia minor-that evolved to β-thalassemia major. From this case, we suggest that analysis of HBB gene for non-hematopoietic tissues should be performed in late-onset β-thalassemia major patients.
Keywords: genomic

overall_design: This study is to evaluate the cause of delay-onset β-thalassemia major in our patient. Patients peripheral blood, hair follicle, and oral mucosa, and her parents pripheral blood samples were analyzed.


title: Gene expression in OsRR6-overexpression line

status: Public on Feb 15 2007

city: Yokohama

first: Hitoshi

last: Sakakibara

address: 1-7-22 Suehiro, Tsurumi

department: Plant Science Center

summary:
Cytokinins (CKs) are a class of plant hormones that regulate many aspects of growth and development, including cell division, apical dominance, leaf senescence, nutrient signaling, and shoot differentiation. In the past decade, substantial progress has been made in understanding CK biosynthesis, metabolism and signal transduction. Much of this knowledge is based on research in Arabidopsis, a dicotyledonous model plant. The current model of the CK signaling pathway is a multi-step His-Asp phosphorelay system. Some of the cytokinin-inducible response regulators are thought to act as negative regulators of CK signaling. We tried to identify rice genes regulated by CK-inducible response regulator using an Affymetrix rice genome array and transgenic rice that over-express OsRR6.
Keywords: genetic modification

overall_design: 4 samples were used in this experiment

first: Naoya

last: Hirose


title: Expression data from rice under salinity stress

status: Public on Sep 15 2006

city: Riverside

first: HARKAMAL

last: WALIA

state: CA

address: Department of Botany & Plant Sciecnes

institute: University of California

summary:
Expression Data of Rice Crown and Growing Point Tissue Under Salt Stress imposed during the Panicle Initiation Stage

Keywords: genotypes and growth conditions (control and salt stressed)

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: Rice Genotypes a sensitive japonica, m103, tolerant japonica agami, sensitive indica ir29 and tolerant indica ir63731 were used for expression anlaysis using the tissue from crown and growing point under control and salt stressed conditions at the sensitive early reproductive stage (panicel initiation).

first: Timothy

last: Close

first: Harkamal

last: Walia


title: Renal Cell Carcinoma Differential Expression

status: Public on Jul 19 2001

city: Heidelberg

first: Wolfgang

last: Huber

address: Im Neuenheimer Feld 280

department: Molecular Genome Analysis

country: Germany

institute: German Cancer Research Center

summary:
We investigated the changes in gene expression accompanying the development and progression of kidney cancer using 31,500 element complementary DNA arrays. We measured expression profiles for paired neoplastic and non-cancerous renal epithelium samples from 37 individuals. Using an experimental design optimized for factoring out technological and biological noise, and an adapted statistical test, we find 1738 differentially expressed cDNAs with an expected number of 6 false positives. Functional annotation of these genes provided views of the changes in the activities of specific biological pathways in renal cancer. Cell adhesion, signal transduction, and nucleotide metabolism were among the biological processes with a large proportion of genes overexpressed in renal cell carcinoma. Downregulated pathways in the kidney tumor cells included small molecule transport, ion homeostasis, and oxygen and radical metabolism. Our expression profiling data uncover gene expression changes shared with other epithelial tumors, as well as a unique signature for renal cell carcinoma. Expression data for the differentially expressed cDNAs are available in the web supplement (http://www.dkfz-heidelberg.de/abt0840/whuber/rcc).
Keywords = renal clear cell carcinoma, kidney
Keywords: other

first: Judith

middle: M

last: Boer

first: Holger

last: Sueltmann

first: Friederike

last: Wilmer

first: Anja

last: von Heydebreck

first: Stefan

last: Haas

first: Bernhard

last: Korn

first: Andreas

last: Vente

first: Laszlo

last: Fuzesi

first: Martin

last: Vingron

first: Annemarie

last: Poustka


title: Cytokinin responsive genes in rice

summary:
Cytokinins (CKs) are a class of plant hormones that regulate many aspects of growth and development, including cell division, apical dominance, leaf senescence, nutrient signaling, and shoot differentiation. In the past decade, substantial progress has been made in understanding CK biosynthesis, metabolism and signal transduction. Much of this knowledge is based on research in Arabidopsis, a dicotyledonous model plant. Although cytokinin plays an important role for growth and development in the Gramineae, our knowledge of cytokinin responsive genes in monocotyledonous species is very limited compared to Arabidopsis. The search for genes whose expression is modified by CK has yielded a number of valuable tools that have been used to understand CK signaling and the complex developmental processes under control of this hormone. We tried to identify rice genes regulated by CK using an Affymetrix rice genome array.
Keywords: time_course; hormone_response; organ_specific_response

overall_design: 24 samples were used in this experiment


title: Down-regulation of  OsSRT1 induces DNA fragmentation and cell death in rice

status: Public on Apr 04 2007

city: Wuhan

first: Qianwen

last: Sun

state: Hubei

address: Luoshi Road

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agriculture University

summary:
In order to study the physiological function of OsSRT1, a 412 bp segment of the 3’-untranslated region of OsSRT1, which was not conserved with OsSRT2, was inserted in inverted repeats to build a construct for RNA interference (RNAi). The construct was used to transform an indica rice variety (Minghui63).To study whether the down-regulation of OsSRT1 affected gene expression, we compared the transcripts of the RNAi to the wild type plants by microarray analysis (Affymetrix). RNAs were isolated from young leaves of 11 day-old plants (before appearance of lesions in the RNAi plants). Affymetrix GeneChip® Rice Genome Array were performed. Data was analyzed with SAM excel add-in and in-house perl scripts.Analysis of data from three biological repeats revealed that 521 genes are up-regulated, and 213 genes are down-regulated (with q – value at 5%).
Keywords: expression analysis

first: Limin

last: Huang

first: Fujun

last: Qin

first: Chen

last: Li

first: Yu

last: Zhao

first: Dao-Xiu

last: Zhou


title: Over-expression of a Type-A Response Regulator Alters Rice Morphology and Cytokinin Metabolism

first: Hitoshi

last: Sakakibara

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: SNP expression data from breast cancer

status: Public on Feb 20 2007

city: Singapore

first: wei

last: chen

address: 11 Hospital Drive

country: Singapore

institute: Agenica Research Pte Ltd

summary:
SNP Expression profiling of human breast cancer: 29 tumor samples, 4 pure normal breat samples and 8 lymphocytes samples
Keywords: Human Cancer

overall_design: In the operating theater, morphologically visible tumors were removed by surgery and examined by a surgical pathologist to confirm the presence of cancer cells by cryosections. The tissue samples were divided into discrete aliquots, flash frozen and subsequently stored in liquid nitrogen. Pure normal breast tissues are got from costmetic surgery and pure lymphocytes samples are from donators.

first: Wei

last: Chen

first: Patrick

last: Tan


title: Transcript Profiling of the Aerobic and Anoxic Rice Coleoptile

status: Public on Mar 19 2007

city: San Giuliano Terme

first: Pierdomenico

last: Perata

state: Pisa

address: Via Guidiccioni 8-10

department: Institute of Life Sciences

country: Italy

institute: Sant'Anna School of Advanced Studies

summary:
Rice (Oryza sativa L.) seeds can germinate in complete absence of oxygen. Under anoxia, the rice coleoptile elongates, reaching a length greater than that of the aerobic one. In this series, we compare the transcriptome of rice coleoptiles grown under aerobic and anaerobic conditions.
Lasanthi-Kudahettige, R, et. al. Plant Physiology (2007). Transcript Profiling of the Anoxic Rice Coleoptile.
Keywords: stress response

overall_design: Rice seeds were germinated in the dark, at 28°C for four days. The coleoptiles were surgically dissected, the primary leaf was removed from the aerobic coleoptiles (anoxic coleoptiles do not contain the primary leaf), RNA was extracted and used for the microarray experiment. An enclosed anaerobic work station (Anaerobic System model 1025; Forma Scientific, Marietta, OH) was used to provide an oxygen-free (anoxia)environment for seed germination. This chamber uses palladium catalyst wafers and desiccant wafers to maintain strict anaerobiosis to less than 10 µg mL–1 O2 (according to the specifications provided by the manufacturer). High-purity N2 was used for purging the chamber initially and the working anaerobic gas mixture was N2:H2 proportioned at 90:10.

first: Rasika

last: Lasanthi-Kudahettige

first: Leonardo

last: Magneschi

first: Elena

last: Loreti

first: Silvia

last: Gonzali

first: Francesco

last: Licausi

first: Giacomo

last: Novi

first: Amedeo

last: Alpi


title: Expression data from rice varieties Azucena and Bala grown in 0 and 1ppm arsenate

status: Public on Mar 16 2006

city: Aberdeen

first: Gareth

last: Norton

address: St Machar drive

department: Plant and Soil Science

country: United Kingdom

institute: University of Aberdeen

summary:
We advance a three gene model of arsenate tolerance in rice based on testing root growth of 108 recombinant inbred lines (RILs) of the Bala x Azucena population. Marker genotype at 3 loci determined arsenate tolerance in 99% of RILs tested. Interestingly, plants must inherit 2, but any two alleles from the tolerant parent (Bala) to have the tolerant phenotype. Challenging the Affymetrix GeneChip Rice Genome array with Azucena and Bala RNA isolated from control and arsenate treated plants revealed 592 genes 2 fold-upregulated by arsenate and 696 downregulated. The array data was also used to identify which genes are expressed within the three target loci.
We used microarrays to detail the gene expression at three locations in the rice genome termed AsTol6.1, AsTol6.2 and AsTol10 in response to 1ppm arsenate. The data was also used to study the global gene expression of the two varieties of rice, Azucena and Bala, in the presence of 1ppm arsenate.
Keywords: Hydroponics, 0 and 1ppm sodium arsenate, Rice varieties Azucena and Bala

overall_design: Rice varieties Bala and Azucena were grown for 7 days in hydroponics either with or without 1ppm (13.3 uM) arsenate. RNA was harvested from four plants all growing in the same pot for each replicate after measuring the roots lengths to confirm the predicted effect of 1ppm arsenate. The four conditions for each replication were harvested at the same time. Different replicates were grown at different times in independent experiments. A total RNA extraction was performed using the TRIzol method followed by RNA clean up and DNase treatment using the RNeasy clean up method. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5ug of total RNA followed by hybridization on Affymetrix microarrays.

first: Meher

last: Nigar

first: Paul

last: Williams

first: Tapash

last: Dasgupta

first: Andy

last: Meharg

first: Adam

middle: H

last: Price


title: Rice salt expression

status: Public on Aug 04 2005

first: HARKAMAL

last: WALIA

summary:
Crown and growing point tissue was used for expression analysis in control and salt stressed samples.  Targets from biological replicates of both genotypes were generated and the expression profiles were determined using Affymetrix Rice Genome arrays.
Keywords: repeat

overall_design: FL478 and IR29 control and stressed biological replicates were analyzed

first: Timothy

last: Close

first: Harkamal

last: Walia


title: High-resolution Global Genomic Survey of 178 Gliomas

status: Public on Oct 24 2006

city: Bethesda

first: Howard

last: Fine

state: MD

address: 9030 Old Georgetown Rd

department: Neurological Disorders and Stroke

institute: National Cancer Institute

summary:
Primary brain tumors are the fourth leading cause of cancer mortality in adults under the age of 54 years and the leading cause of cancer mortality in children in the United States. Therapy for the most common type of primary brain tumors, gliomas, remains suboptimal. The development of new and more effective treatments will likely require a better understanding of the biology of these tumors. Here, we show that use of the high-density 100K single-nucleotide polymorphism arrays in a large number of primary tumor samples allows for a much higher resolution survey of the glioma genome than has been previously reported in any tumor type. We not only confirmed alterations in genomic areas previously reported to be affected in gliomas, but we also refined the location of those sites and uncovered multiple, previously unknown regions that are affected by copy number alterations (amplifications, homozygous and heterozygous deletions) as well as allelic imbalances (loss of heterozygosity/gene conversions). The wealth of genomic data produced may allow for the development of a more rational molecular classification of gliomas and serve as an important starting point in the search for new molecular therapeutic targets. (Cancer Res 2006; 66(19): 9428-36)
Keywords: survey

overall_design: 178 glioma samples including 82 glioblastomas, 33 astrocytomas, 52 oligodendrogliomas and 11 mixed gliomas were hybridized to 100K mapping arrays (Hind and Xba) to detect and summarize chromosomal aberations in those samples.

first: Yuri

last: Kotliarov

first: Mary

middle: E

last: Steed

first: Neil

last: Christopher

first: Jennifer

last: Walling

first: Qin

last: Su

first: Angela

last: Center

first: John

last: Heiss

first: Mark

last: Rosenblum

first: Tom

last: Mikkelsen

first: Jean-Claude

last: Zenklusen

middle: A


title: Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation.

status: Public on Mar 12 2007

city: Vancouver

first: BCGSC

last: BC Cancer Agency

state: BC

address: 675 West 10th Avenue

department: Gene Expression

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

summary:
The cause of mental retardation in one-third to one-half of all affected individuals is unknown. Microscopically-detectable chromosomal abnormalities are the most frequent recognized cause, but gain or loss of chromosomal segments that are too small to be seen by conventional cytogenetic analysis has been found to be another important cause. Array-based methods offer a practical means of performing a high-resolution survey of the entire genome for submicroscopic copy number variants. We studied 100 children with idiopathic mental retardation and their parents using the Affymetrix GeneChip® Mapping 100K Assay and found de novo duplications as small as 1.1 Mb in three cases, de novo deletions as small as 178 kb in eight cases, and unsuspected mosaic trisomy 9 in another case. This technology can detect at least twice as many potentially pathogenic de novo copy number variants as conventional cytogenetic analysis in people with mental retardation.
Keywords: mental retardation, trio analysis, copy number variant, CNV, chromosome aberration, array CGH

overall_design:
Using the Affymetrix GeneChip® Mapping 100K Assay we studied 100 trios that each included one child with idiopathic mental retardation (MR) and both of his/her unaffected biological parents. We also tested 10 unaffected siblings of the MR children from 10 of the above families. In addition, we analyzed 7 trios (child and both unaffected biological parents) as positive controls with previously identified chromosomal aberrations.
Within each sample ID the four digit number refers to a family. Following this four digit family number, 'c' indicates child with MR, 'm' means unaffected mother, 'f' means unaffected father and 's' means unaffected sibling.

first: J

last: Friedman

first: Agnes

last: Baross

first: Allen

last: Delaney

first: Adrian

last: Ally

first: Laura

last: Arbour

last: Asano

first: Dione

middle: K

last: Bailey

first: Sarah

last: Barber

first: Patricia

last: Birch

first: Mabel

last: Brown-John

first: Manqiu

last: Cao

first: Susanna

last: Chan

first: David

last: Charest

first: Noushin

last: Farnoud

first: Nicole

last: Fernandes

first: Stephane

last: Flibotte

first: Anne

last: Go

first: William

middle: T

last: Gibson

first: Robert

last: Holt

first: Steven

middle: J

last: Jones

first: Giulia

middle: C

last: Kennedy

first: Martin

last: Krzywinski

first: Sylvie

last: Langlois

first: Haiyan

middle: I

last: Li

first: Barbara

last: McGillivray

first: Tarun

last: Nayar

first: Trevor

last: Pugh

first: Evica

last: Rajcan-Separovic

first: Jacqueline

last: Schein

first: Angelique

last: Schnerch

first: Asim

last: Siddiqui

first: Richard

last: Varhol

first: Margot

last: Van Allen

first: Gary

last: Wilson

first: Tina

last: Wong

first: Siu-Li

last: Yong

first: Farah

last: Zahir

first: Patrice

last: Eydoux

first: Marco

last: Marra


title: Gene expression of rice root tips before, at and buckled by a hard layer in two rice varieties

status: Public on Mar 19 2008

first: Gareth

last: Norton

summary:
The aim of this study was to determine the changes in gene expression of rice root tips when they came in to contact with a hard layer (60% wax layer). Three categories of root tips were sampled; tips before the hard layer, tips that had come into contact with the hard layer and root tips which had buckled after coming into contact with the hard layer.
Two genotypes (Azucena and Bala) that vary in there ability to penetrate a hard layer were selected for a genotype comparison of gene expression at the hard layer.
Keywords: Genotype comparison, root impedance response

overall_design:
A chamber with the internal dimensions of 10 x 5 x 25cm consisting of a glass back, Perspex front and aluminium spacers with an open bottom and top was set at an angle of 15o in a large sand filled tray and filled up to 19.5 cm with dry sand. The sand was watered with nutrient solution, the sand was levelled and then a 5mm thick 60% wax layer (prepared using a ratio of 3:2 (w/w) of pastillated paraffin wax / white soft wax) was poured on the sand. Once the wax layer had set, two small holes were placed at the back of the wax layer to allow water drainage and water exchange via capillary action. The chamber was then filled up with more dry sand, and then watered using nutrient solution. Nutrient solution was then added to the large tray which the chamber had been placed; this was regularly topped up and allowed the watering of the chamber by capillary action. Light was eliminated from the chambers using white (exterior face)/black (interior face) plastic sheeting.
Azucena and Bala seeds were surface sterilized with 1% (v/w) sodium hypochlorate for 5 minutes, then rinsed thoroughly three times with water and then germinated on moist tissue paper for 48 hours at 37oC. A single germinated seed was then sown 1 cm below the surface of the sand in each chamber.
The plants were grown in a controlled environment room with a 12 hour day and night, with a day temperature of 30oC and a night temperature of 24oC with 300 µmol m-2 s-1 PAR. After 24 days the chamber was dismantled and the root tips of 5 mm length were harvested from Azucena plants for subsequent RNA extractions from the three categories as follows; a) roots which were between 5-10 mm above the wax layer; b) roots at the wax layer; c) roots which had buckled at the wax layer and grown 7-10 mm after buckling.  From Bala plants, only root tips at the layer were harvested.
Each condition was indsependently replicated 3 times.

first: Adam

last: Price