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Sample GSM7157446

Query DataSets for GSM7157446

Status

Public on Dec 04, 2023

Title

col-NAA-3

Sample type

SRA

Source name

root

Organism

Arabidopsis

Characteristics

tissue: root
genotype: col
treatment: NAA

Extracted molecule

total RNA

Extraction protocol

Total RNA was isolated using a RNeasy Mini Kit (Qiagen).
First strand cDNA was generated using reverse transcriptase and random primers. The constructed cDNA libraries was qualified and quantified with Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System, and then sequenced via Illumina HiSeqTM 2000 or other sequencer when necessary at the Beijing Genomics Institute, Shenzhen, China.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

The RNA was purified by electrophoresis through a TBE-urea polyacrylamide gel. The gel regions harboring 18-30 nt fragments were excised and the RNA recovered. The resulting population of sRNAs was 5' and 3' RNA adapter-ligated using T4 RNA ligase, and amplified for 18 PCR cycles
The amplicons were purified and sequenced using an Illumina/Solexa Genome Analyzer (Beijing Genomics Institute, Shenzhen, China).
Raw reads were trimmed by removing low-quality and adaptor sequences, then aligned to the A. thaliana genome using SOAP2 software.
Transcript frequency was calculated using the reads per kilobase per million reads method. Differentially transcribed genes were identified using a method modified from Audic and Claverie (1997). Significance was based on the P value and the false discovery rate (FDR) (Audic and Claverie, 1997).

Submission date

Apr 08, 2023

Last update date

Dec 04, 2023

Contact name

jia jia liu

E-mail(s)

liujiajia106@126.com

Organization name

shandong university

Street address

qingdaojimoaoshanwei