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Sample GSM7804791 Query DataSets for GSM7804791
Status Public on Sep 11, 2024
Title Col-0_T10_ inflorescence_sRNA-seq_Rep2
Sample type SRA
 
Source name inflorescence
Organism Arabidopsis thaliana
Characteristics tissue: inflorescence
genotype: Col-0
ecotype: Col-0
library type: conventional sRNA-seq
Treatment protocol None
Growth protocol The seeds were grown in soil. After cultivated in 4 ℃ for three days, the seeds were transferred to 16/8 h (light/dark) greenhouse.
Extracted molecule total RNA
Extraction protocol Total RNAs were extracted from inflorescence tissues using TRIzol reagent (Invitrogen, USA) following standard protocols. For "conventional sRNA-seq" library, total RNA was separated in 16% denaturing PAGE gel to excise 18-30 nt, and gel purified RNA was treated by NaCl solution. For "NaIO4 treatment" library, total RNA was separated in 16% denaturing PAGE gel to excise 18-30 nt, and gel purified RNA was treated by NaIO4 solution. For "PBA-PAGE" library, total RNA was separated in 16% denaturing PAGE gel supplemented with 2% PBA to excise 18-30 nt, and gel purified RNA was treated by NaCl solution. For "TRM-sRNA-seq" library, total RNA was separated in 16% denaturing PAGE gel supplemented with 2% PBA to excise 18-30 nt, and gel purified RNA was treated by NaIO4 solution. For AGO1-RIP samples, protein was extracted from Col-0 inflorescence. After immunoprecipitation, AGO1-bound RNAs were isolated by phenol-chloroform extraction and ethanol precipitation.
All types of small RNA libraries were constructed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, USA) following manufacturer's instructions and purified using Monarch PCR & DNA kit (NEB, USA).
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NovaSeq 6000
 
Description T10 CK R2
Data processing Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore (version 0.6.6).
Trimmed sequence reads were mapped to TAIR10 using ShortStack (version- 3.8.5 parameters- --align_only –nohp --mmap u --bowtie_m 1000 --ranmax 50 --mismatches 0).
Reads count extraction was performed using featureCounts (version- v2.0.1 parameters- -O --largestOverlap -fraction).
Reads count normalization was performed using DESeq2 and custom R scripts.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text files include sequence counts for each Sample.
 
Submission date Sep 25, 2023
Last update date Sep 11, 2024
Contact name Susu Chen
E-mail(s) 18110700075@fudan.edu.cn
Organization name Fudan university
Street address 2005 Songhu Rd. Yangpu District
City Shanghai
ZIP/Postal code 200438
Country China
 
Platform ID GPL26208
Series (1)
GSE244009 An improved terminal ribose-modified small RNA sequencing (TRM-sRNA-seq) reveals novel features of miRNA modification and identifies HEN1-independent 2’-O-modified sRNAs derived from tRNAs
Relations
BioSample SAMN37537709
SRA SRX21882965

Supplementary file Size Download File type/resource
GSM7804791_CK_10_2.txt.gz 3.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA

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