NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6925803 Query DataSets for GSM6925803
Status Public on Sep 06, 2023
Title atdgcr14l-1, 200 mM NaCl, 24h, Rep 2
Sample type SRA
 
Source name seedling
Organism Arabidopsis thaliana
Characteristics tissue: seedling
genotype: atdgcr14l-1
treatment: 24h 200 mM NaCl
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-T7
 
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
 
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

Supplementary file Size Download File type/resource
GSM6925803_AtDG8-2.tabular.txt.gz 198.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.