Dataset

GSM1979148: WT(Col0) seedlings

The University of Western Australia
ARC Centre of Excellence in Plant Energy Biology (Is associated with , Managed by)
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ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=https://research-repository.uwa.edu.au/en/datasets/f235185e-9f0f-4221-8c45-23adee69f24e&rft.title=GSM1979148: WT(Col0) seedlings&rft.identifier=f235185e-9f0f-4221-8c45-23adee69f24e&rft.publisher=Gene Expression Omnibus (NCBI)&rft.description= 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. seedling_col0vdko_tair.txt 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 &rft.creator=Narsai, Reena &rft.date=2015&rft.relation=https://research-repository.uwa.edu.au/en/publications/b35f65f8-34ec-43a7-9317-3154a8300a72&rft.type=dataset&rft.language=English Access the data

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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.
seedling_col0vdko_tair.txt

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

Notes

Associated Persons
Reena Narsai ( Creator )

Issued: 2015-12-23

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  • global : f235185e-9f0f-4221-8c45-23adee69f24e