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| Status |
Public on Dec 26, 2018 |
| Title |
Col-0 WT TRAP 2 |
| Sample type |
SRA |
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| Source name |
Columbia-0
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| Organism |
Arabidopsis thaliana |
| Characteristics |
replicate: biological rep 2
tissue: floral stem
genotype/variation: wild type TRAP
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| Treatment protocol |
Two samples from each Col-0 wild type TRAP, msh1 TRAP, Col-0 Total, and msh1 Total. Floral stem tissue was used.
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| Growth protocol |
Seeds were sown on peat mix in square pots in reach-in chambers at 16hrs daylenght (22 °C, 120-150 μmol/(m^2*s) light)
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| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA from each sample was extracted by NucleoSpin RNA Plant kit (Macherey-Nagel, Germany) following manufacturer’s protocol, including genomic DNA removal.
RNA libraries were constructed as described in the TruSeq RNA Sample Preparation v2 Guide.
These libraries were sequenced with the 100-bp paired-end reads option, in Hi-Seq 4000 analyzer (Illumina, USA) at BGI-Tech (Shenzhen, China).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Illumina for basecalling
Alignments were performed using RUM 2.0.4 (--min-length 70) (Grant et al., 2011) keeping only uniquely mapped reads
The read count data were generated from the SAM files by using QoRTs software package (Hartley and Mullikin, 2015) --stranded --minMAPQ 25 --dropChrom Pt,Mt
DESeq2 (Love, M.I., Huber, W., Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Genome Biology 15(12):550 2014) was used for gene count normalization and to identify differentially expressed genes (FDR < 0.05, |log2FC| > 0.5. GTF file TAIR10.31
Genome_build: TAIR 10
Supplementary_files_format_and_content: Text file with GENEID and COUNTS to be used with DESeq2
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| Submission date |
May 08, 2018 |
| Last update date |
Dec 26, 2018 |
| Contact name |
Hardik Kundariya |
| E-mail(s) |
hsk13@psu.edu
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| Organization name |
The Pennsylvania State University
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| Street address |
361 N. Frear
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| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16801 |
| Country |
USA |
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| Platform ID |
GPL21785 |
| Series (1) |
| GSE114199 |
mRNA sequencing of samples coming from Translating Ribosome Affinity Purification (TRAP) using MSH1P::FLAG::RPL18 |
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| Relations |
| BioSample |
SAMN09094587 |
| SRA |
SRX4055990 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3137769_210.geneCounts.formatted.for.DESeq.txt.gz |
121.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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