|
| Status |
Public on Nov 09, 2019 |
| Title |
Col-0_stranded-RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Arabidopsis seedlings
genotype: Col-0
|
| Growth protocol |
The Arabidopsis materials were all in the Columbia (Col-0) background and grown on Murashige and Skoog (MS) medium at 22°C with 16-h light/8-h dark (long-day conditions).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 14-day-old seedlings and subjected to the Vazyme VAHTS Total RNA-seq Library Prep Kit for deep sequencing (Vazyme, NR603)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using STAR-2.5.2b with parameters --runThreadN 30 --quantMode TranscriptomeSAM --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --chimSegmentMin 20 --readFilesCommand zcat --outSAMattrIHstart 0 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --alignSoftClipAtReferenceEnds No
bedgraph file were generated from High-throughput sequencing reads of bam format
Genome_build: TAIR10
Supplementary_files_format_and_content: bw files were generated using bedGraphToBigWig with default parameters.
|
| |
|
| Submission date |
Nov 08, 2019 |
| Last update date |
Nov 11, 2019 |
| Contact name |
xinjian He |
| E-mail(s) |
[email protected]
|
| Organization name |
National Institute of Biological Sciences
|
| Lab |
hexinjian
|
| Street address |
No. 7, zhongguancun life science park road, changping district
|
| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
|
| Platform ID |
GPL17639 |
| Series (2) |
| GSE140139 |
Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis (stranded-RNA-seq) |
| GSE140140 |
Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis |
|
| Relations |
| BioSample |
SAMN13243074 |
| SRA |
SRX7119180 |
