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| Status |
Public on Jul 08, 2014 |
| Title |
top1a-2 smallRNAseq |
| Sample type |
SRA |
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| Source name |
top1a-2 smallRNAseq
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Landsberg erecta
tissue: ten-day-old seedlings
genotype: top1a-2
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| Growth protocol |
Arabidopsis thaliana seeds were surface sterilized by either 30% bleach or fumigated in an airtight container with a solution containing 50 mL of 100% bleach and 8% HCl for six hours. After, the seeds were planted on half-strength MS-agar plates containing 1% sucrose (no sucrose was added in plates used for chemical screening to minimize fungal growth), stratified at 4°C for two days and moved into a growth chamber. Plants were grown under continuous light at 23°C. All experiments were performed with ten-day-old seedlings.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Fifty μg total RNA was resolved on a 15% denaturing polyacrylamide gel and a gel slice containing RNAs of 15 to 40 nucleotides (based on the O’ Range Ruler 10 bp RNA ladder (Thermo Scientific)) was extracted and transferred to a 1.5 ml tube. The gel piece was ground, 500μl of 0.4N NaCl (DEPC) was added to the ground mixture, and the tube containing the gel slice was shaken overnight at 4°C. Eluted RNAs were precipitated using ethanol, re-suspended in DEPC water
Library was constructed with the Illumina TruSeq-small RNA sample preparation kit per manufacturer’s instructions (Illumina). In brief, gel-purified small RNAs were ligated sequentially to 3’ and 5’ adaptors. Following reverse transcription, PCR amplification of the cDNA resulted in the small RNA library, which was gel-purified and subjected to high throughput sequencing
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina Casava software used for basecalling.
The raw reads of small RNAs were processed by PERL scripts built in house. Briefly, the raw reads were screened with Illumina’s quality control filter. The reads that passed the filter were separated into different bins according to their barcodes (indexes). The adaptor was trimmed for each read. Reads that match known rRNAs, tRNAs, snRNAs, and snoRNAs were removed. Reads of 20–24 nt were selected as the raw small RNA sequences. For Col-0, sde4-3, and nrpe1-11, which are in the Columbia ecotype, the small RNA reads were mapped to the Tair10 Arabidopsis genome with SOAP2. For Ler and top1a, which are in the Landsberg ecotype, the small RNA reads were mapped to a pseudo-Ler genome generated by incorporating the Ler polymorphisms into the Tair10 Columbia genome (ftp://ftp.arabidopsis.org/Polymorphisms/Ecker_ler.homozygous_snp.txt).
Every chromosome of Arabidopsis was divided into continuous 500 bp windows. Small RNAs whose 5’ nucleotide falls into a 500 bp window were counted as those belonging to this window. The number of reads in every window was recorded and served as the abundance of small RNAs in this window. The reads were normalized to RPM (reads per million)
Genome_build: TAIR10, and pseudo-Ler genome generated by incorporating the Ler polymorphisms into the Tair10 Columbia genome (ftp://ftp.arabidopsis.org/Polymorphisms/Ecker_ler.homozygous_snp.txt)
Supplementary_files_format_and_content: txt file, which has two columns chr_postion, RPM (reads per million)
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| Submission date |
Sep 10, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Lei Gao |
| E-mail(s) |
[email protected]
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| Organization name |
shenzhen university
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| Department |
College of Life Sciences
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| Street address |
Nanhai Ave 3688
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| City |
shenzhen |
| State/province |
guangdong |
| ZIP/Postal code |
518060 |
| Country |
China |
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| Platform ID |
GPL13222 |
| Series (2) |
| GSE50719 |
DNA Topoisomerase 1a Promotes RNA-directed DNA Methylation and Histone Lysine 9 Dimethylation at Transposable Elements in Arabidopsis [RNA-Seq] |
| GSE50720 |
DNA Topoisomerase 1α Promotes RNA-directed DNA Methylation and Histone Lysine 9 Dimethylation at Transposable Elements in Arabidopsis |
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| Relations |
| BioSample |
SAMN02351666 |
| SRA |
SRX347407 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1227192_top1a-2_sRNAseq.txt.gz |
718.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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