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Sample GSM6176454 Query DataSets for GSM6176454
Status Public on May 19, 2024
Title MCA fibrosarcoma (9609 MEK1-low) tumor derived macrophages 1
Sample type SRA
 
Source name 9609 MEK1-low
Organism Mus musculus
Characteristics cell line: 9609 MEK1-low
cell type: Tumor macrophage
genotype: MEK1-low
treatment: MEK1-low (GFP) exosomes
Extracted molecule total RNA
Extraction protocol RNA was harvested using TRIzol reagent
Total RNA was assessed for quality using an Agilent Tapestation 4200, and samples with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Kit with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer's instructoins, starting with 750 ng of RNA and modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) paired end reads (PE100) to a depth of approximately 25 million reads per sample on an Illumina NovaSeq 6000. Samples were demultiplexed using bcl2fastq v2.2.0 Conversion Software (Illumina, San Diego, CA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing usegalaxy.org. Galaxy is an open source, web-based platform for bioinformatic analyses. All data processing was performed with Galaxy tools.
All read files were assesed for quality control using FastQC (Galaxy Version 0.73+galaxy0).
Quality checked paired-end reads were aligned with Tophat (Galaxy v 2.1.1) against mm10 reference genome.
Transcript assemblies from aligned reads were created using Cufflinks (Galaxy v 2.2.1.3) using mm10 reference annotation (UCSC genome browser)
All assemblies were merged into a singluar file using Cuffmerge (Galaxy v 0.0.6) and analyzed with Cuffdiff (Galaxy v 2.2.1.6)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each gene for both "MEK1_exo" and "GFP_exo"
 
Submission date May 23, 2022
Last update date May 19, 2024
Contact name Jack Bui
E-mail(s) jbui@health.ucsd.edu
Organization name UC San Diego
Lab Bui lab
Street address 9500 Gilman Dr
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platform ID GPL24247
Series (1)
GSE203576 Tumor macrophages from rejecting and growing tumors
Relations
BioSample SAMN28596951
SRA SRX15413925

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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