GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM5820975

Query DataSets for GSM5820975

Status

Public on Nov 22, 2022

Title

lysR_A

Sample type

SRA

Source name

cell

Organism

Burkholderia sp. JP2-270

Characteristics

strain: JP2-270
genotype: bysR deletion
growth: 24 hour after inoculation

Extracted molecule

total RNA

Extraction protocol

Briefly, a total of 3 µg RNA per sample was obtained and rRNA were depleted using Ribo-Zero rRNA removal kit (G- bacteria). The mRNA were fragmented using diavalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5 X). Then, the cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacture’s instructions. The cDNA fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA), and then 3µl USER Enzyme (NEB，USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion HighFidelity DNA polymerase, Universal PCR primers and Index Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The resultant samples were sequenced on an Illumina Hiseq 2000 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

Illumina Casava1.8 software used for basecalling.
Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. Clean reads were mapped to the Burkholderia sp. JP2-270 reference genome (CP029824-CP029828) using Bowtie 2-2.2.3.
Then Htseq v0.6.1 was used to count the reads numbers mapped to each gene. FPKM (Fragment Per Kilobase of transcript sequence per Millions base pairs sequenced) was used to estimate gene expression levels.
Genome_build: NCBI accession number: CP029824-CP029828
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

Submission date

Jan 16, 2022

Last update date

Nov 22, 2022

Contact name

Lijuan Wu

E-mail(s)

[email protected]

Organization name

China national rice research institute

Street address

28 Shui Dao Suo Road, Fuyang District