GSM1979148: WT(Col0) seedlings

  • Reena Narsai (Creator)



3 replicates
Seeds were sown on MS media, statified at 4 C for 2-d before being transferred to growth chambers at 22C, following a 16 h photoperiod. Tissue was collected at 2 weeks.

Sequenced reads were trimmed for adaptor sequence, and filtered for low-quality sequence, then mapped to the tair10 whole genome using bowtie v2.2.0-beta7 and tophat v2.2.0 with the parameters:–b2-sensitive –r 0 –mate-std-dev 100 –g 1 –G .
Transcript abundance was estimated by FPKM (fragment per Kilobase of exon per million fragments mapped) using Cufflinks pipeline (version 2.2.0) and RNAseq data was analysed using Cuffdiff 2.2.0 under default parameters.
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample, as part of Cuffdiff output
Date made available23 Dec 2015
PublisherGene Expression Omnibus (NCBI)

Cite this

Narsai, R. (Creator)(23 Dec 2015). GSM1979148: WT(Col0) seedlings. Gene Expression Omnibus (NCBI).