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Sample GSM756822 Query DataSets for GSM756822
Status Public on Jul 18, 2011
Title Col x Ler endosperm RNA-seq
Sample type SRA
 
Source name endosperm 6-7 days after pollination
Organism Arabidopsis thaliana
Characteristics genetic background: Col-0 female X Ler male
tissue: endosperm
age: 6-7 days after pollination
Growth protocol Plants were grown on soil in 16h days at 22 C.
Extracted molecule polyA RNA
Extraction protocol Seeds (600-1000) from crosses between multiple individuals were hand-dissected and total embryo or endosperm RNA isolated using the Ambion RNaqueous Kit with Plant RNA Isolation Aid. LIbraries were constructed using the Illumina mRNA-seq kit and protocol. 1 microgram of total RNA was poly-A selected twice, fragmented, and converted into double-stranded cDNA. The cDNA was end-repaired, adenylated, and adapters ligated. Adapter-ligated DNA approximately 200 bp in length was gel purified and amplified using Illumina PCR primers PE1.0 and PE2.0 with 15 amplification cycles.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Description mRNA-seq
Data processing Sequencing reads were aligned to the TAIR 9.0 version of the Arabidopsis reference genome (www.arabidopsis.org) using the TopHat read aligner (http://tophat.cbcb.umd.edu/). Low quality reads and reads that mapped to more than one position in the genome with the same alignment score were discarded. Reads that mapped to more than one gene due to overlapping exons were not considered in further analyses. SAM files for each sequencing run of the same library are deposited separately.
 
Submission date Jul 08, 2011
Last update date May 15, 2019
Contact name Mary Gehring
Organization name Whitehead Institute for Biomedical Research
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL9302
Series (1)
GSE30511 Allele specific mRNA-seq expression profiling in Arabidopsis thaliana Col and Ler reciprocal F1 hybrid embryo and endosperm
Relations
SRA SRX082187
BioSample SAMN00632350

Supplementary file Size Download File type/resource
GSM756822_CLN_run1_accepted_reads.sam.gz 186.3 Mb (ftp)(http) SAM
GSM756822_CLN_run2_accepted_reads.sam.gz 451.6 Mb (ftp)(http) SAM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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