|
| Status |
Public on Jun 07, 2023 |
| Title |
ancNif Mutant Rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Azotobacter vinelandii DJ |
| Characteristics |
cell type: bacteria
genotype: ancNif
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 |
Alternative nifD subunit derived by ancestral sequence reconstruction
|
| 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 |
SAMN35619596 |
| SRA |
SRX20591097 |
