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Status |
Public on Sep 06, 2023 |
Title |
atdgcr14l-1, 200 mM NaCl, 24h, Rep 2 |
Sample type |
SRA |
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Source name |
seedling
|
Organism |
Arabidopsis thaliana |
Characteristics |
tissue: seedling genotype: atdgcr14l-1 treatment: 24h 200 mM NaCl
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Treatment protocol |
200 mM NaCl treatment
|
Growth protocol |
14-day-old plants growing hydroponically
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNAs were extracted using Spectrum Plant Total RNA kit (Sigma) following manufacturer's protocols. mRNAs with poly A tail were enriched from total RNAs using oligo dT beads. mRNA molecules were fragmented into samll pieces. The fragmented mRNA was synthesized into first strand cDNA using random primers. The second strand cDNA was synthesized with dUTP instead of dTTP. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments. Digest the U-labeled second-strand template with Uracil-DNA-Glycosylase (UDG) and perform PCR amplification. After quality control and circularization, libraries were amplified to make DNA nanoball for sequencing on DNBSEQ platform.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
DNBSEQ-T7 |
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Data processing |
Raw data with adapter sequences or low-quality sequences was filtered using SOAPnuke (v 2.1.7) with parameters: "-n 0.001 -l 20 -q 0.4 --adaMR 0.25 --ada_trim --minReadLen 150" Clean reads were mapped to TAIR11 using Bowtie2 (v 2.4.5) with default parameters Transcripts were assembled and quantified using StringTie (v 2.1.7) with default parameters DEGs were detected using DESeq2 (v 2.11.40.7) with default parameters Assembly: TAIR11 Supplementary files format and content: tab-delimited tabular.txt files include raw counts for each sample
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Submission date |
Jan 10, 2023 |
Last update date |
Sep 06, 2023 |
Contact name |
Meng Xie |
E-mail(s) |
mxie@bnl.gov
|
Organization name |
Brookhaven National Laboratory
|
Street address |
50 Bell Ave
|
City |
Upton |
State/province |
NY |
ZIP/Postal code |
11973 |
Country |
USA |
|
|
Platform ID |
GPL31102 |
Series (1) |
GSE222547 |
AtDGCR14L contributes to salt-stress tolerance via regulating pre-mRNA splicing in Arabidopsis |
|
Relations |
BioSample |
SAMN32661723 |
SRA |
SRX18990957 |