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Sample GSM5849631 Query DataSets for GSM5849631
Status Public on Nov 01, 2022
Title JY_14_IM_Control_PBS_2
Sample type SRA
 
Source name IM Control PBS
Organism Mus musculus
Characteristics cell type: Interstitial macrophage
treatment: PBS
strain: C57Bl/6
Treatment protocol 6-8 weeks old C57Bl/6 mice maintained under Specific Pathogen Free (SPF) conditions were injected intra-peritoneally with 1mg of WGP or PBS for 6 days.
Growth protocol 6-8 weeks old C57Bl/6 mice maintained under Specific Pathogen Free (SPF) conditions with 12 hrs light/dark cycle and 55% humidity.
Extracted molecule polyA RNA
Extraction protocol PBS vs WGP-trained mice were euthanized on Day 7 following treatment to harvest the lungs. Lungs were digested and processed to obtain single cell suspensions. The Lung single cell suspensions were stained with fluorochrome-labelled antibodies to obtain the Lung Interstitial macrophages. Cells were then washed with Ice-cold PBS, stored in TRIzol followed by RNA extraction (QIAGEN RNAeasy Kit), quantification IQubit fluorometric assay) and sequencing.
Libraries were prepared using the Universal Plus mRNA-Seq with NuQuant (NuGEN Cat# 0520-24) and PolyA selection.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Illumina BaseSpace FastQ v1.0.0 used for basecalling
Raw sequences were checked for quality values using fastQC v0.10.1. Quality trimming was not deemed necessary.
The sequences were directly aligned to the Mus musculus reference genome assembly (mm10) using Star version 2.6.
Read counts for gene regions were obtained with HTSeq v.0.10.0 using Ensembl annotations (GRCm38.93).
The annotation file was parsed to exclude mitochondria and ribosomal protein genes in an effort to reduce non-relevant variation in subsequent steps of the analysis. The resulting annotation file tested 21,965 gene locations.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts
 
Submission date Jan 30, 2022
Last update date Nov 01, 2022
Contact name Eric Christian Rouchka
E-mail(s) eric.rouchka@louisville.edu
Organization name University of Louisville
Department Biochemistry and Molecular Genetics
Lab KY INBRE Bioinformatics Core
Street address 522 East Gray Street
City Louisville
State/province Kentucky
ZIP/Postal code 40292
Country USA
 
Platform ID GPL19057
Series (1)
GSE195750 Harnessing the Pre-metastatic Niche Macrophages through the Induction of Trained Immunity to control Metastasis.
Relations
BioSample SAMN25509399
SRA SRX13991859

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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