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| Status |
Public on Jun 05, 2016 |
| Title |
G1_1 |
| Sample type |
SRA |
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| Source name |
Leaf Tissue
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| Organism |
Nicotiana tabacum |
| Characteristics |
tissue: Leaf
genotype/variation: Introduction 1068 expressing chloroplast-targeted avian farnesyl diphosphate synthase and yeast squalene synthase
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| Treatment protocol |
MS medium with 2% sucrose
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| Growth protocol |
Tissue culture with 16 h light/8 h dark
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted from the third youngest leaf of each plant using miRNeasy kit (Qiagen)
Poly(A)+ RNA was isolated using oligo dT beads (Life Technologies, Frederick, MD). RNA was fragmented for 7 minutes using Fragmentation Reagent (Life Technologies, Waltham, MA). mRNA-seq libraries were then generated using the Illumina mRNA-seq kit (illumina, San Diego, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
G1_1
normalized_counts_annotated.txt
Tobacco_G1_v_WT_DESeq_refGene.all.annotated.txt
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| Data processing |
Adapter sequences were removed from sequencing reads were with Cutadapt, and mapped to the Tobacco genome with Tophat2 (Martin, 2011; Kim et al., 2013).
Cufflinks was used to predict transcripts, and HTSeq and DESeq2 were used to quantify expression of each transcript and perform differential expression analysis (Love et al., 2014; Anders et al., 2015)
We used transdecoder from the Trinity package to identify open reading frames within predicted transcripts, and annotated them with BLASTP to TAIR10 proteins (Gish and States, 1993; Haas et al., 2013).
Genome_build: Ntab-K326
Supplementary_files_format_and_content: Normalized read counts (variance stabilizing transformation) for each sample with TAIR10 BlastP annotations: normalized_counts_annotated.txt
Supplementary_files_format_and_content: DESeq2 Output: differential expression analysis of RNA-seq data with TAIR10 BlastP annotations
Supplementary_files_format_and_content: Tobacco_G1_v_WT_DESeq_refGene.all.annotated.txt
Supplementary_files_format_and_content: Tobacco_GS_v_WT_DESeq_refGene.all.annotated.txt
Supplementary_files_format_and_content: Tobacco_FS_v_WT_DESeq_refGene.all.annotated.txt
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| Submission date |
Oct 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Henry Daniell |
| E-mail(s) |
hdaniell@upenn.edu
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| Phone |
1-215-746-2563
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| Organization name |
University of Pennsylvania
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| Department |
Biochemistry
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| Street address |
240 South 40th street
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| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104-6030 |
| Country |
USA |
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| Platform ID |
GPL13760 |
| Series (1) |
| GSE74103 |
Metabolic Engineering of Squalene Biosynthesis via Different Genomes Impacts Non-target Cellular Metabolomic and Transcriptomic Pathways |
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| Relations |
| BioSample |
SAMN04192099 |
| SRA |
SRX1342046 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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