|
| Status |
Public on May 11, 2020 |
| Title |
DASH_100_1000 |
| Sample type |
SRA |
| |
|
| Source name |
whole cells
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Characteristics |
strain: SL1344
growth phase: Exponential
agent: DASH
library prep kit: NEB NEBNext Multiplex Small RNA Library Prep Kit for Illumina #E7560S
rna template in rt (ng): 180
sgrna pool size: 113
pre-incubation: no
cdna: cas9:sgrna: 1:100:1,000
cdna removal: Column purification
|
| Treatment protocol |
-
|
| Growth protocol |
Salmonella was grown until OD 2.0; Bacteroides until OD 0.5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures were pelleted by centrifugation and RNA was extracted with Trizol. To remove contaminating genomic DNA, samples were further treated with 0.25 U of DNase I (Fermentas) per 1 µg of RNA for 45 min at 37°C, followed by phenol-chloroform extraction and ethanol precipitation of RNA.
Libraries were generated with NEBNext Magnesium RNA Fragmentation Module (# E6150S) in combination with NEB NEBNext Multiplex Small RNA Library Prep Kit for Illumina (#E7560S) or Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (#634411). Where indicated, ribosomal cDNA was depleted by the DASH procedure: Depletion of Abundant Sequences by Hybridization using target specific sgRNAs and Cas9 to remove unwanted high-abundance species in sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
salmonella_read_count.csv
|
| Data processing |
FastQ reads trimmed for the adapter sequences using Cutadapt version 2.5 with the –nextseq-trim=20
Mapping with segemehl via READemption with the argument –a 80 (NEB samples) or –a 80 –R (Takara samples)
Gene quantification via READemption subcommand gene_quanti with arguments –a –o 10
wig files for coverage plots were generated via READemption subcommand coverage
Genome_build: Salmonella (NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1); Bacteroides (NC_004663.1, NC_004703.1)
Supplementary_files_format_and_content: Tab-delimited text files include read count values for each sample
Supplementary_files_format_and_content: wig files
|
| |
|
| Submission date |
Mar 18, 2020 |
| Last update date |
May 11, 2020 |
| Contact name |
Tom Gräfenhan |
| E-mail(s) |
[email protected]
|
| Phone |
+49 - 931 - 31 - 80814
|
| Organization name |
University of Wuerzburg
|
| Department |
Core Unit SysMed
|
| Lab |
Raum D15.02.045
|
| Street address |
Josef-Schneider-Str. 2, Bau D15
|
| City |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
| |
|
| Platform ID |
GPL20056 |
| Series (1) |
| GSE147155 |
Improved bacterial RNA-seq by Cas9-based depletion of ribosomal RNA reads |
|
| Relations |
| BioSample |
SAMN14396771 |
| SRA |
SRX7945525 |
