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Sample GSM5852392 Query DataSets for GSM5852392
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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