|
| Status |
Public on Aug 11, 2021 |
| Title |
In vitro 28.2-Y.pestis |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria grown in LB at 28°C
|
| Organism |
Yersinia pestis |
| Characteristics |
strain: Kimberley53
treatment: Grown in calture at 28degreeC
|
| Treatment protocol |
Mice (OF1) were infected intranasally with 800,000 cfu/mouse (~1500 LD50).
|
| Growth protocol |
Yersinia pestis Kimberly53 strain were used for intranasal infection. Bacterial cultures were grown at 28◦C overnight in HIB (BD, MD USA), supplemented with 0.2% (+) xylose and 2.5 mM CaCl2 (Sigma-Aldrich). The bacteria were used for intranasal infection of mice (OF1 strain).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
One, 24 and 48 hours post infection, mice were sacrificed, lungs were removed and used for RNA extraction. RNA was also extracted from bacteria grown in culture (at 28° and 37° C) and naive mice, as control. Total RNA was extracted using the RNeasy kit (Qiagen) and residual DNA was digested using RNase-free DNase (Qiagen). In order to enrich the mRNA bacteria grown in culture (In vitro) we used riboZiro rRNA removal kit for depletion of rRNA, in each sample and ribozero gold rRNA depletion for dual RNA samples (mouse and Y. pestis).
Library construction using Illumina TruSeq chemistry
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mRNA after depletion with riboZiro rRNA removal kit (Gram negative bacteria).
OA007
|
| Data processing |
RTA (Illumina) for base calling
bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming.
Reads were mapped to the reference genome Mouse: UCSC/mm10 using STAR(2.5.2b) and featureCounts(v1.5.0-p3)
Reads were mapped to the reference genome Yersinia pestis CO92 (NC_003143,NC_003131, NC_003132, NC_003134) using bowtie2 (2.2.0) and htseq-count 0.6.1
Supplementary_files_format_and_content: Matrix table with raw read counts for every gene and every sample
|
| |
|
| Submission date |
Aug 09, 2021 |
| Last update date |
Aug 11, 2021 |
| Contact name |
Inbar Cohen Gihon |
| E-mail(s) |
inbarg@iibr.gov.il
|
| Organization name |
Israel Institute For Biological Research
|
| Department |
Biochemistry
|
| Street address |
Reuven 24
|
| City |
Ness Ziona |
| ZIP/Postal code |
14100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL24209 |
| Series (1) |
| GSE181680 |
RNA-seq analysis of pathogen and host in the early stages of Plague pulmonary infection using a novel dual RNA extraction method |
|
| Relations |
| BioSample |
SAMN20669391 |
| SRA |
SRX11675340 |
