Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene Expression between two cell layers in maize shoot apical meristem

ABSTRACT: All above ground organs of higher plants are ultimately derived from shoot apical meristems (SAMs). The SAM exhibits distinctive structural organization, and monocot SAMs such as maize are comprised of two cell layers, a single cell layered tunica (L1) and a corpus (L2). Although recent research has revealed roles of these cell layers in the SAM, intra- and inter-cell-layer signaling networks involved in organ development remain largely unknown except for a few differentially expressed genes. Here, we used Illumnia technology to conduct RNA-seq of L1 and L2 cell layers in maize B73 maize shoot apical meristem. Single sequencing library was constructed for L1 and L2 cell layer. Each library was sequenced using 2 lanes on a Solexa flow cell. Processed data file 'ZmB73_4a.53_filtered_genes.fasta' and its README file are linked below as supplementary files. The fasta file contains the gene model ID and corresponding sequence generated from maize genome project. This fasta file was used for the following samples: GSM418173, GSM418174, GSM420173, GSM420174, GSM422828, GSM422829.

ORGANISM(S): Zea mays

SUBMITTER: Patrick Schnable

PROVIDER: E-GEOD-16868 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The B73 maize genome: complexity, diversity, and dynamics.

Schnable Patrick S PS Ware Doreen D Fulton Robert S RS Stein Joshua C JC Wei Fusheng F Pasternak Shiran S Liang Chengzhi C Zhang Jianwei J Fulton Lucinda L Graves Tina A TA Minx Patrick P Reily Amy Denise AD Courtney Laura L Kruchowski Scott S SS Tomlinson Chad C Strong Cindy C Delehaunty Kim K Fronick Catrina C Courtney Bill B Rock Susan M SM Belter Eddie E Du Feiyu F Kim Kyung K Abbott Rachel M RM Cotton Marc M Levy Andy A Marchetto Pamela P Ochoa Kerri K Jackson Stephanie M SM Gillam Barbara B Chen Weizu W Yan Le L Higginbotham Jamey J Cardenas Marco M Waligorski Jason J Applebaum Elizabeth E Phelps Lindsey L Falcone Jason J Kanchi Krishna K Thane Thynn T Scimone Adam A Thane Nay N Henke Jessica J Wang Tom T Ruppert Jessica J Shah Neha N Rotter Kelsi K Hodges Jennifer J Ingenthron Elizabeth E Cordes Matt M Kohlberg Sara S Sgro Jennifer J Delgado Brandon B Mead Kelly K Chinwalla Asif A Leonard Shawn S Crouse Kevin K Collura Kristi K Kudrna Dave D Currie Jennifer J He Ruifeng R Angelova Angelina A Rajasekar Shanmugam S Mueller Teri T Lomeli Rene R Scara Gabriel G Ko Ara A Delaney Krista K Wissotski Marina M Lopez Georgina G Campos David D Braidotti Michele M Ashley Elizabeth E Golser Wolfgang W Kim HyeRan H Lee Seunghee S Lin Jinke J Dujmic Zeljko Z Kim Woojin W Talag Jayson J Zuccolo Andrea A Fan Chuanzhu C Sebastian Aswathy A Kramer Melissa M Spiegel Lori L Nascimento Lidia L Zutavern Theresa T Miller Beth B Ambroise Claude C Muller Stephanie S Spooner Will W Narechania Apurva A Ren Liya L Wei Sharon S Kumari Sunita S Faga Ben B Levy Michael J MJ McMahan Linda L Van Buren Peter P Vaughn Matthew W MW Ying Kai K Yeh Cheng-Ting CT Emrich Scott J SJ Jia Yi Y Kalyanaraman Ananth A Hsia An-Ping AP Barbazuk W Brad WB Baucom Regina S RS Brutnell Thomas P TP Carpita Nicholas C NC Chaparro Cristian C Chia Jer-Ming JM Deragon Jean-Marc JM Estill James C JC Fu Yan Y Jeddeloh Jeffrey A JA Han Yujun Y Lee Hyeran H Li Pinghua P Lisch Damon R DR Liu Sanzhen S Liu Zhijie Z Nagel Dawn Holligan DH McCann Maureen C MC SanMiguel Phillip P Myers Alan M AM Nettleton Dan D Nguyen John J Penning Bryan W BW Ponnala Lalit L Schneider Kevin L KL Schwartz David C DC Sharma Anupma A Soderlund Carol C Springer Nathan M NM Sun Qi Q Wang Hao H Waterman Michael M Westerman Richard R Wolfgruber Thomas K TK Yang Lixing L Yu Yeisoo Y Zhang Lifang L Zhou Shiguo S Zhu Qihui Q Bennetzen Jeffrey L JL Dawe R Kelly RK Jiang Jiming J Jiang Ning N Presting Gernot G GG Wessler Susan R SR Aluru Srinivas S Martienssen Robert A RA Clifton Sandra W SW McCombie W Richard WR Wing Rod A RA Wilson Richard K RK

Science (New York, N.Y.) 20091101 5956

We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of cent ...[more]

PMID: 19965430

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Project description:Transposable elements (TEs) comprise a substantial portion of many eukaryotic genomes and are typically transcriptionally silenced. RNA–dependent RNA polymerase 2 (RDR2) is a component of the RNA–directed DNA methylation (RdDM) silencing pathway. In maize, loss of mediator of paramutation1 (mop1) encoded RDR2 function results in reactivation of transcriptionally silenced Mu transposons and a substantial reduction in the accumulation of 24 nt short-interfering RNAs (siRNAs) that recruit RNA silencing components. An RNA–seq experiment conducted on shoot apical meristems (SAMs) revealed that, as expected based on a model in which RDR2 generates 24 nt siRNAs that suppress expression, most differentially expressed DNA TEs (78%) were up-regulated in the mop1 mutant. In contrast, most differentially expressed retrotransposons (68%) were down-regulated. This striking difference suggests that distinct silencing mechanisms are applied to different silencing templates. In addition, 6,000 genes (24% of analyzed genes), including nearly 80% (286/361) of genes in chromatin modification pathways, were differentially expressed. Overall, two-thirds of differentially regulated genes were down-regulated in the mop1 mutant. This finding suggests that RDR2 plays a significant role in regulating the expression of not only transposons, but also of genes. A re-analysis of existing small RNA data identified both RDR2–sensitive and RDR2–resistant species of 24 nt siRNAs that we hypothesize may at least partially explain the complex changes in the expression of genes and transposons observed in the mop1 mutant. Single sequencing library was constructed for mop1 mutant and non-mutant. Each library was sequenced using 2 lanes on a Solexa flow cell. Processed data file 'ZmB73_4a.53_filtered_genes.fasta' and its README file are linked below as supplementary files. The fasta file contains the gene model ID and corresponding sequence generated from maize genome project. This fasta file was used for the following samples: GSM418173, GSM418174, GSM420173, GSM420174, GSM422828, GSM422829.

Project description:Leptospirosis, an emerging zoonotic disease with worldwide distribution, is caused by spirochetes belonging to the genus Leptospira. More than 500,000 cases of severe leptospirosis are reported annually, with .10% of these being fatal. Leptospires can survive for weeks in suitably moist conditions before encountering a new host. Reservoir hosts, typically rodents, exhibit little to no signs of disease but shed large numbers of organisms in their urine. Transmission occurs when mucosal surfaces or abraded skin come into contact with infected urine or urine-contaminated water or soil. In humans, leptospires can cause a variety of clinical manifestations, ranging from asymptomatic or mild fever to severe icteric (Weil’s) disease and pulmonary haemorrhage. Currently, little is known about how Leptospira persist within a reservoir host. Prior in vitro studies have suggested that leptospires alter their transcriptomic and proteomic profiles in response to environmental signals encountered during mammalian infection. However, no study has examined gene expression by leptospires within a mammalian host-adapted state. To obtain a more faithful representation of how leptospires respond to host-derived signals, we used RNA-Seq to compare the transcriptome of L. interrogans cultivated within dialysis membrane chambers (DMCs) implanted into the peritoneal cavities of rats with that of organisms grown in vitro. In addition to determining the relative expression levels of ‘‘core’’ housekeeping genes under both growth conditions, we identified 166 genes that are differentially-expressed by L. interrogans in vivo. Our analyses highlight physiological aspects of host adaptation by leptospires relating to heme uptake and utilization. We also identified 11 novel non-coding transcripts that are candidate small regulatory RNAs. The DMC model provides a facile system for studying the transcriptional and antigenic changes associated with mammalian host-adaption, selection of targets for mutagenesis, and the identification of previously unrecognized virulence determinants. Transcriptome analysis of L. interrogans Copenhageni FIOCRUZ L1-130 using RNA from 2 different conditions using RNA-seq. Also, the reproducibility and robustness of data is ensured by three biological replicates from each condition.

Dataset Information

Gene Expression between two cell layers in maize shoot apical meristem

Publications

The B73 maize genome: complexity, diversity, and dynamics.

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