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| Status |
Public on Apr 13, 2015 |
| Title |
Col-0_replicate_2 |
| Sample type |
SRA |
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| Source name |
plant
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| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: 18-day-old adult plant
tissue: aerial tissue
genotype: Col-0
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| Growth protocol |
Seeds pretreated with stratification for 2-4 days at 4°C were kept in the greenhouse for another 6 days (22°C, 16 h/8 h photoperiod) before transferring the seedlings to the soil for another 12 days.Aerial tissues were collected from the 18-day-old adult plants.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Plant tissues were flash frozen in liquid nitrogen, and RNA was harvested using the microRNA Purification Kit (Norgen). Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
small RNA ( < 200 nt)
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| Data processing |
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to tair 10.0 genomic sequence using Bowtie with parameters bowtie2 --very-sensitive-local -k 50
The 21-22 nt clean reads after adaptor-removal and filtering were mapped to the reference (main gene models, TAIR 10.0 release) using the Bowtie program. Stringent mapping of the short reads was performed with a mismatch penalty of 10000 and no gaps allowed.
Reads mapped to each gene model were counted, then followed by normalization and differential expression analysis (DESeq, es/c AND es/res, > 2 fold change,p < 0.005,q < 0.1)
Genome_build: tair 10.0
Supplementary_files_format_and_content: spreadsheets include numbers of mapped reads and normalized expression levels for each Sample
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| Submission date |
May 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Damon Lisch |
| Organization name |
Purdue University
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| Street address |
915 West State Street
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| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
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| Platform ID |
GPL17639 |
| Series (1) |
| GSE57936 |
Analysis of the RDR6-dependent small RNA profile in ein5 ski2 in Arabidopsis with biological replications and increased sequencing depth |
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| Relations |
| BioSample |
SAMN02798677 |
| SRA |
SRX551620 |
| 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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