|
| Status |
Public on Jun 18, 2021 |
| Title |
Replicate C PprS (Dsr2) knockdown strain, unirradiated |
| Sample type |
SRA |
| |
|
| Source name |
PprS (Dsr2) knockdown_unirradiated
|
| Organism |
Deinococcus radiodurans |
| Characteristics |
strain: R1
genotype: PprSKD
plasmid: none
treatment: unirradiated
|
| Treatment protocol |
D. radiodurans R1 and PprSKD cultures were irradiated with 10 kGy acute ionizing radiation by a 10-MeV, 18-kW linear accelerator (LINAC) β-ray source (250 Gy/s) at the National Center for Electron Beam Research, Texas A&M University. Samples were kept static on dry ice during transport to and from the irradiator (~2 hr each way). Samples were recovered for 2hrs after IR exposure before RNA processing
|
| Growth protocol |
D. radiodurans R1 (WT) or PprSKD,or WT cells expressing pRADgro-MS2-PprS or pRADgro-MS2only plasmids were grown to late exponential phase cultures (OD600 0.8) in TGY media at 32˚C before IR treatment with 2hr recovery (for WT and KD samples) and collection for RNAseq library preparation (or MS2 co-immunoprecipitation for the MS2 strains).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol reagent and bead beating. The cDNA libraries were prepared from total RNAs using NEBNext RNA First Strand Synthesis Module (NEB E7525L) and NEBNext DNA Library Prep Master Mix Set for Illumina (NEB E6040L)
cDNA libraries were prepared using NEBNext RNA First Strand Synthesis Module (NEB E7525L) according to standard protocols without any modification. Single-end reads were analyzed with Illumina NextSeq 500 single-end platform
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
KO2C0_S33
|
| Data processing |
Trimming adaptors with cutadapt (1.14, -q 30 - m 22)
Alignment to reference D. radiodurans genome (GenBank accession numbers NC_001263.1 and NC_001264.1) with Bowtie2 aligner (2.3.2, -local-very-sensitive)
Convert from sam to bam files (samtools (1.10) view) and sort (samtools sort -n)
Read counts obtained using htseq-count (0.9.1) union settings (-m union -s no -a 10) using gff file that had D. radiodurans sRNAs manually added
Differential gene expression determined using DESeq2 (1.30.1) in R (4.0.2)
Genome_build: GenBank accession numbers NC_001263.1 and NC_001264.1
Supplementary_files_format_and_content: Processed data is tab-deliminated text file from Htseq-count that lists the gene number in one column and the count in the other column
|
| |
|
| Submission date |
Jun 05, 2021 |
| Last update date |
Jun 18, 2021 |
| Contact name |
Lydia Contreras |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Texas at Austin
|
| Street address |
200 E Dean Keeton St
|
| City |
Austin |
| State/province |
Texas |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL30231 |
| Series (1) |
| GSE176207 |
A small RNA regulates pprM, a modulator of pleiotropic proteins promoting DNA repair, in Deinococcus radiodurans under ionizing radiation |
|
| Relations |
| BioSample |
SAMN19580030 |
| SRA |
SRX11074699 |
