|
Status |
Public on Feb 04, 2022 |
Title |
FLAMs_Input_Rep1 |
Sample type |
SRA |
|
|
Source name |
Macrophage Fetal Liver Cells
|
Organism |
Mus musculus |
Characteristics |
tissue: Fetal Liver derivation: cultured primary fetal liver cells strain: C57BL/6J Cas9+ surface expression: Input
|
Treatment protocol |
Transduced library was cultuted for two weeks then gDNA was isolated or cells were sorted for SiglecF expression
|
Growth protocol |
Macrophages were grown in DMEM with 10% FBS 30ng/ml GM-CSF 15 ng/ml TGFB for the duration of the experiment
|
Extracted molecule |
total RNA |
Extraction protocol |
Cells were lysed and total genomic DNA was isolated using aluminum acetate purification Libraries were constructed using the targeted PCR-mediated amplification of sgRNAs from purified gDNA. This amplification for each sample incorporated adaptors and sample indexes.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
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 Genome_build: 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 |
Feb 01, 2022 |
Last update date |
Feb 04, 2022 |
Contact name |
Andrew Olive |
E-mail(s) |
oliveand@msu.edu
|
Phone |
5178845367
|
Organization name |
Michigan State University
|
Department |
Microbiology and Molecular Genetics
|
Lab |
Olive Lab
|
Street address |
567 Wilson Rd, BPS 5100
|
City |
East Lansing |
State/province |
MI |
ZIP/Postal code |
48824-6405 |
Country |
USA |
|
|
Platform ID |
GPL24247 |
Series (1) |
GSE195868 |
A genetic screen in fetal liver-derived alveolar-like macrophages (FLAMs) identifies new regulators of Siglec-F surface expression |
|
Relations |
BioSample |
SAMN25553563 |
SRA |
SRX14004598 |