|
| Status |
Public on Feb 13, 2024 |
| Title |
ProQ CLIP_SPI2_minusCL_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
SL1344
|
| Organism |
Salmonella enterica |
| Characteristics |
strain: SL1344
|
| Treatment protocol |
none
|
| Growth protocol |
SPI2-medium to OD600 of 0.3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CLIP
NEBNext Small RNA Prep Kit
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Adapter removal and read pair merging performed with SeqPrep (https://github.com/jstjohn/SeqPrep)
Read mapping performed with bowtie 1.2.2 allowing for 1 mismatch and one match per read
Mapped reads were converted to strand separated bedgraph files with samtools and bedtools genomecov.
Bedgraph files converted to Wig file format (www.encodeproject.org/software/bedgraphtobigwig/)
Assembly: NC_016810.1
Supplementary files format and content: Strand separated bigWig files for viewing mapping coverage in genome browsers.
|
| |
|
| Submission date |
Dec 12, 2023 |
| Last update date |
Feb 13, 2024 |
| Contact name |
Erik Holmqvist |
| E-mail(s) |
erik.holmqvist@icm.uu.se
|
| Organization name |
Uppsala University
|
| Street address |
Husargatan 3, Box 596, Uppsala University, Dept. of Cell and Molecular Biology
|
| City |
Uppsala |
| State/province |
Uppland |
| ZIP/Postal code |
75124 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL27048 |
| Series (1) |
| GSE250014 |
CLIP-seq of Salmonella ProQ in intracellular-like conditions |
|
| Relations |
| BioSample |
SAMN38797745 |
| SRA |
SRX22874359 |
