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Sample GSM7445241 Query DataSets for GSM7445241
Status Public on Jun 07, 2023
Title WT Rep 3
Sample type SRA
 
Source name bacteria
Organism Azotobacter vinelandii DJ
Characteristics cell type: bacteria
genotype: WT
treatment: Diazotrophic growth
Growth protocol Cells were grown to an OD600 of ~0.7 in Burke's nitrogen free media.
Extracted molecule total RNA
Extraction protocol RNA was harvested using Rneasy mini plus kit (Qiagen). RNA extracts were assessed on a Nanodrop 2000c (Thermofisher Scientific) and confirmed to contain >2.5 µg of RNA with a purity of A260/280 = 1.8-2.2; A260/230 > 1.8. RNA extracts were stored at -80 °C.
RNA-seq library preparation and sequencing was performed by Novogene. \
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Wildtype
Data processing Raw FASTQ reads were trimmed using Trimmomatic version 0.3 (49) (default settings except for HEADCROP = 5, LEADING = 3, TRAILING = 3, SLIDINGWINDOW = 3:30, MINLEN = 36).
Trimmed reads were aligned to the A. vinelandii DJ genome sequence (GenBank accession CP001157.1) using bwa-mem v0.7.17 (version 0.7.17-h5bf99c6_8) (50) with default parameters. Alignment files were further processed with Picard-tools v2.26.10 (https://broadinstitute.github.io/picard/) (CleanSAM and AddOrRepleaceReadGroups commands) and samtools v1.2 (51) (sort and index commands).
Paired aligned reads were mapped to gene locations using HTSeq v0.6.0 (52) with default parameters.
The R package edgeR v3.30.3 (53) was used to identify significantly differentially expressed genes from pairwise analyses, using Benjamini and Hochberg (54) false discovery rate (FDR) adjusted p-value < 0.05 as a significance threshold.
Raw sequencing reads were normalized using the fragments per kilobase per million mapped reads method (FPKM).
Assembly: CP001157.1
Supplementary files format and content: FPKM-data.txt
Supplementary files format and content: Htseq-counts.txt
 
Submission date Jun 05, 2023
Last update date Jun 07, 2023
Contact name Betül Kaçar
E-mail(s) kacarlab@gmail.com
Organization name University of Wisconsin-Madison
Department Department of Bacteriology
Lab Kaçar Lab
Street address 1550 Linden Dr.
City Madison
State/province WI
ZIP/Postal code 53706
Country USA
 
Platform ID GPL33461
Series (1)
GSE234075 A hybrid nitrogenase with regulatory elasticity in Azotobacter vinelandii
Relations
BioSample SAMN35619597
SRA SRX20591096

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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