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Sample GSM5741797

Query DataSets for GSM5741797

Status

Public on Jan 10, 2022

Title

Salt_24h_3

Sample type

SRA

Source name

alga cells

Organism

Chlamydomonas reinhardtii

Characteristics

strain: GY-D55
treatment: 200mM NaCl 24h

Treatment protocol

Briefly, 50 mL medium containing 800 mM NaCl was added to a 150-mL culture medium, the final NaCl concentration was 200 mM, and the pH of the medium was adjusted to 7.0. Cells cultured in the absence of NaCl were used as the control group. Each experiment was conducted in triplicate. The cells of C. reinhardtii were collected at eight pre-set time points after exposure to 200 mM NaCl: 2, 4, 8,12, 24, 48, 72, and 96 h.

Growth protocol

The wild-type C. reinhardtii strain GY-D55 was obtained from LeadingTec Co., Ltd. (http://www.leadingtec.cn/) and maintained in 150 mL of BG-11 medium on a shaking table at 120 rpm under the following conditions: photoperiod 16-8 h/light-dark, temperature 23℃, and light intensity 100 μmol m-2 s-1. Under the above-mentioned conditions, C. reinhardtii cells were cultured in BG11 medium for approximately 14 days until the cell density reached 2 × 106 cells/mL. The cells of the mid-logarithmic phase were used for salt stress treatment.

Extracted molecule

total RNA

Extraction protocol

Briefly, 100 mL cell cultures from different groups were subjected to centrifugation at 3,000 g for 5 min, and the cell pellet was re-suspended in 25 mL RNAlater solution (Ambion). Total RNA was isolated using the TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions. The integrity of RNA was evaluated using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA) and the NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

The RNA sample of every accession was sequenced by the Illumina NovaSeq 6000. cDNA library was constructed, and Illumina pair-end 150 bp sequencing (PE150)
Raw reads of fastq format were firstly processed through in-house perl scripts. In this step, adapt-er-containing reads, ploy-N-containing reads, and low-quality reads were removed from raw data, yielding clean reads. Meanwhile, Q20, Q30, GC-content, and sequence duplication levels of the clean data were determined.
Reference genome (ftp://ftp.ensemblgenomes.org/pub/release39/plants/fasta/chlamydomonas_reinhardtii/dna/) and gene model annotation files (ftp://ftp.ensemblgenomes.org/pub/release39/plants/gtf/chlamydomonas_reinhardtii/Chlamydomonas_reinhardtii.v3.1.39.gtf.gz) were downloaded from the genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5), which was adopted to align paired-end clean reads to the reference genome.
For the prediction of novel transcripts, StringTie (v1.3.3b) was adopted to assemble the mapped reads of each sample as previously described (Pertea et al., 2015).
Genome_build: ftp://ftp.ensemblgenomes.org/pub/release39/plants/fasta/chlamydomonas_reinhardtii/dna/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

Submission date

Dec 19, 2021

Last update date

Jan 10, 2022

Contact name

Luoyan Zhang

E-mail(s)

zhangluoyan@sdnu.edu.cn

Organization name

shandong normal university

Street address

wenhuadong 88