|
| Status |
Public on Dec 29, 2021 |
| Title |
pSRKa |
| Sample type |
SRA |
| |
|
| Source name |
Vector Control
|
| Organism |
Agrobacterium fabrum str. C58 |
| Characteristics |
genotype: pSRKGM vector control
|
| Treatment protocol |
Cells were collected by centrifugation
|
| Growth protocol |
Cultures of the strains for comparison were grown in ATGN minimal medium at 30 C with agitation to an OD600 of ~0.6.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using Qiagen RNEasy kit, and contaminating DNA was removed with the Turbo RNAse-free DNAse kit for 1 hr at 37 ⁰C
Integrity of the RNA was checked with Agilent Tapestation, samples with RIN >7 were processed using the following steps. 1ug of total RNA was used for ribosomal RNA depletion with the Illumina Ribo-Zero kit bacteria. After rRNA depletion, the libraries were prepared following the Illumina TruSeq Stranded mRNA library preparation kit protocol. The cleaned adapter ligated libraries were pooled and loaded on the NextSeq 500 with a 75 cycle sequencing module to generate paired-end reads. Finally, the demultiplexing of the reads was performed with bcl2fastq version 2.20.0 pipeline.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Illumina sequenced using adaptor-specific primers
|
| Data processing |
The raw RNA-seq reads were cleaned using Trimmomatic version 0.33 (Bolger et al. 2014) setting the cutoff threshold for average base quality score at 20 over a window of 3 bases. Reads shorter than 20 bases post-trimming were excluded. (parameters: LEADING:20 TRAILING:20 SLIDINGWINDOW:3:20 MINLEN:20)
The cleaned reads were aligned to the Agrobacterium tumefaciens C58 genome reference, AE007869.2, AE007870.2, AE007871.2 and AE007872.2 using bowtie2 (version 2.3.2) (Langmead et al. 2012).
Individual gene expression was quantified by counting the number reads mapping to each of the annotated genes using htseq-count tool (version 0.11.1) . Those reads that mapped to antisense strand, or mapped to multiple regions on the genome or those reads that overlapped with multiple genes were excluded. (parameters: -s reverse -m union)
Genome_build: Agrobacterium tumefaciens C58 genome reference, AE007869.2, AE007870.2, AE007871.2 and AE007872.2
Supplementary_files_format_and_content: Text files with counts of reads aligned to each annotated gene
|
| |
|
| Submission date |
May 14, 2021 |
| Last update date |
Dec 29, 2021 |
| Contact name |
Clay Fuqua |
| E-mail(s) |
cfuqua@indiana.edu
|
| Organization name |
Indiana University
|
| Department |
Biology
|
| Lab |
425E
|
| Street address |
1001 E. Third Street
|
| City |
Bloomington |
| State/province |
IN |
| ZIP/Postal code |
47405 |
| Country |
USA |
| |
|
| Platform ID |
GPL30075 |
| Series (1) |
| GSE174467 |
RNASeq Analysis of MirA Regulator in Agrobacterium tumefaciens C58 |
|
| Relations |
| BioSample |
SAMN19193645 |
| SRA |
SRX10889829 |
