NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM8092422 Query DataSets for GSM8092422
Status Public on Dec 20, 2024
Title p35S:MIR396, 5DAC, Replicate 3
Sample type SRA
 
Source name Root tips
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
tissue: Root tips
age: 8 days old (cut at 3 days old)
genotype: p35S:MIR396
treatment: 5 days after cut
Treatment protocol Control samples were collected ad 3 days old without treatment. For 5DAC samples, 3-day-old seedlings were cut with surgical microblades under a stereoscopic microscope, on agar plates with a nylon mesh of 100µm pore and 70µm fiber. Pores and fibers were used as reference for cut positions. Te samples were collected 5 days after cutting (8 days old).
Growth protocol Sterilized seeds were sown in Petri dishes containing solid medium (Murashige and Skoog salts, 1% sucrose, 0.5g/L MES, 0.8% w/v agar, pH = 5,7) and stratified at 4°C in the dark for at least one day. The plates were placed vertically under continuous light at 22°C.
Extracted molecule total RNA
Extraction protocol Approximately 1000 roots per sample (wild type and p35S:MIR396, uncut controls and 5 days after cut) were collected per quadruplicate for protoplasting. The seeds were sown on nylon mesh, roots were cut at approximately 1cm from the tip, and placed in digesting solution (20mM MES, 400mM mannitol, 20mM KCl, 1.5% cellulase, 0.4% macerozyme, 10mM CaCl2) covered from the light. To enrich the samples with meristematic tissue, the roots were incubated for 20 minutes until the transition zone (between the proliferation and elongation zones) was digested and the tips were released, which was confirmed under microscope. Then, the excess tissue was filtered out using a 1 mm-pore mesh. Digestion continued for 90 minutes and, after filtering the solution twice with a 40µm pore cell strainer, cells were centrifuged down for two minutes at 300rcf and 4°C, washed with washing buffer (enzyme-free digestion solution) and centrifuged again with the same conditions. Buffer was discarded, leaving a small amount at the bottom to resuspend protoplasts, which were then counted in a Neubauer chamber under a light field microscope, and diluted to a concentration of 1000cells/µl.
12000 cells per replicate were sorted on a 10x Chromium platform and libraries were prepared using a 3’ Gene Expression v3.1 kit, following the provider’s instructions.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model NextSeq 550
 
Description JB12
10x Genomics
Data processing Yielded reads were pseudo-aligned to the Arabidopsis genome (TAIR10) using the kallisto bustools software.
Seurat matrices were constructed with the Seurat R package.
Assembly: TAIR10
Supplementary files format and content: Seurat object
 
Submission date Feb 21, 2024
Last update date Dec 20, 2024
Contact name Julia Lidia Baulies
E-mail(s) baulies@ibr-conicet.gov.ar
Organization name Instituto de Biología Molecular y Celular de Rosario
Lab RNA Biology
Street address Ocampo y Esmeralda s/n
City Rosario
State/province Santa Fe
ZIP/Postal code 2000
Country Argentina
 
Platform ID GPL24270
Series (1)
GSE256274 microRNA control of stem cell reconstitution and growth in root regeneration
Relations
BioSample SAMN40022759
SRA SRX23687212

Supplementary file Size Download File type/resource
GSM8092422_JB12.seu.RData.gz 235.0 Mb (ftp)(http) RDATA
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap