Transcriptomics

Dataset Information

769

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: Yi Jia   Patrick S. Schnable  Kazuhiro Ohtsu  Patrick S Schnable 

PROVIDER: E-GEOD-16868 | ArrayExpress | 2013-01-28

SECONDARY ACCESSION(S): GSE16868SRP001844PRJNA117571

REPOSITORIES: GEO, ArrayExpress, ENA

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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]

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