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| Status |
Public on Jun 08, 2022 |
| Title |
Non_targeting_1 |
| Sample type |
SRA |
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| Source name |
DNA
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| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
tissue: bacterial culture
sample: Sample without nuclease
biological replicate: 1
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library was transformed in cells with or without Cas13a and backdiluted 1:100 in LB with antibiotics to reach OD 0.06 and let grow for 12 hours shaking at 37°C. Finally, the library was midi-prepped with ZymoPure II Plasmid Midiprep Kit (Zymo Research, D4200).
The library prep was amplified with Kapa Hifi polymerase (Kapa Biosystems- Roche, 7958889001) according to the provider protocol. The reactions were purified using Ampure beads and further amplified to add the appropriate indexes and illumina adaptors. The resulting product was again purified with Ampure beads and run on a gel to verify the presence of the correct amplicon. The samples were sent for Sanger sequencing to make sure to get the expected sequence and then their quality was checked at the Bioanalyzer. Finally, they were sent for sequencing at the Next Seq sequencer (Illumina) with a 150 bp paired-ends kit (130 million reads) to get 1000x coverage. To increase the library diversity, 20% of phiX phage was spiked-in.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Library strategy: DNA-seq
Paired-end reads were merged using BBMerge (version 38.69) with parameters “qtrim2=t, ecco, trimq=20, -Xmx1g, mix=f”
reads with perfect matches were mapped to reference genome with In-house python script
Genome_build: NC_000913.3
Supplementary_files_format_and_content: CSV, raw counts of gRNAs in each sample
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| Submission date |
Jul 12, 2021 |
| Last update date |
Jun 08, 2022 |
| Contact name |
Chase Beisel |
| E-mail(s) |
rsyn.hiri@gmail.com
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| Organization name |
HIRI
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| Street address |
Josef Schneider Strasse , D15
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| City |
Wuerzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
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| Platform ID |
GPL21117 |
| Series (2) |
| GSE179913 |
A target expression threshold dictates invader defense and autoimmunity by CRISPR-Cas13 [Genome wide screen] |
| GSE179915 |
A target expression threshold dictates invader defense and autoimmunity by CRISPR-Cas13 |
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| Relations |
| BioSample |
SAMN20169763 |
| SRA |
SRX11410625 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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