|
| Status |
Public on Jan 13, 2023 |
| Title |
iBMDM_Mab_Hi_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
immortalized bone marrow-derived Macrophages
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Bone marrow
derivation: J2 immortalized and Cas9 Transduced
strain: C57BL/6J
m_abscessus_intracellularlevels: Mab_High
|
| Treatment protocol |
Transduced library was infected with mEmerald M. abscessus for four hours then cells were sorted into infected and uninfected populations
|
| Growth protocol |
Macrophages were grown in DMEM with 10% FBS for the duration of the experiment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed and total genomic DNA was isolated using aluminum acetate purification
Libraries were constructed using Truseq primers and indexes
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina software was used for Basecalls
FastQC (v0.11.5) was used to assess the quality of raw data.
Cutadapt (v2.9) was used to removeadapter sequences
Assembly: sgRNA counts were determined using MAGeCK "count" function with trimmed FASTq files as input
significant changes in gene representation were quantified using MAGeCK "test" using the robust rank algorithm
Supplementary files format and content: Normalized Count table was generated using MAGeCK
|
| |
|
| Submission date |
Dec 20, 2022 |
| Last update date |
Jan 13, 2023 |
| Contact name |
Andrew Olive |
| E-mail(s) |
oliveand@msu.edu
|
| Organization name |
Michigan State University
|
| Department |
Microbiology and Molecular Genetics
|
| Street address |
567 Wilson Rd
|
| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48824 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE221413 |
A genome-wide screen in macrophages defines host genes regulating the uptake of Mycobacterium abscessus |
|
| Relations |
| BioSample |
SAMN32330285 |
| SRA |
SRX18787441 |
