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Sample GSM7829449

Query DataSets for GSM7829449

Status

Public on Oct 10, 2023

Title

DJ,Control,240m, NH4+

Sample type

SRA

Source name

Bacterial cells

Organism

Azotobacter vinelandii DJ

Characteristics

tissue: Bacterial cells
cell line: Bacterial cells
cell type: Bacterial cells
genotype: WT
treatment: 240m MH4+ control

Extracted molecule

total RNA

Extraction protocol

Total RNA was isolated using a RiboPure-Bacteria kit (Ambion, Life Technologies) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using Illumina protocol

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Sample files (FASTQ) were quality-checked with FASTQC.Adapter sequences were removed with trim-galore (2) (--length 75).
Processed reads were aligned against azotobacter genome sequence (GCA_000021045.1_ASM2104v1_genomic.fna) with RNA-STAR
Duplicated alignments (PCR or Optical) were detected and labelled using function MarkDuplicates of picard tools
Alignment files, in SAM format, were compressed, sorted and indexed with the corresponding commands of samtools.
The Azotobacter genes included in annotation file provided (GCA_000021045.1_ASM2104v1_genomic.gtf) were quantified with the function featureCounts (ignoreDup=TRUE, primaryOnly=TRUE, requireBothEndsMapped=TRUE) of Bioconductor package Rsubread.
Assembly: EnsemblBacteria Azotobacter vinelandii DJ (GCA_000021045)
Supplementary files format and content: tab-delimited text file includes RPKM normalized counts for each Sample

Submission date

Oct 05, 2023

Last update date

Oct 10, 2023

Contact name

Luis M. Rubio

E-mail(s)

[email protected]

Organization name

Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC)

Street address

Campus de Montegancedo UPM. Crta. M-40 km 38