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Sample GSM6946014 Query DataSets for GSM6946014
Status Public on Jan 14, 2025
Title Resting_Lung 5
Sample type SRA
 
Source name lung
Organism Mus musculus
Characteristics tissue: lung
strain: C57BL/6
cell type: Eosinophil
treatment: none
Growth protocol C57BL/6 mice were either untreated or transplanted with Balb/c lungs with costimulatory blockade. Infiltrating lung eosinophils are recipient origin in this lung transplant model. Eosinophils were isolated by flow cytometry sorting on resting, day 7 or day 30 post-transplant lungs.
Extracted molecule total RNA
Extraction protocol Trizol Extraction
NEBNext Ultra II RNA Library Prep Kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Samples were sequenced using a 2x150bp Paired End (PE) configuration with Illumina HiSeq instrument (4000)
Image analysis and base calling were conducted by the HiSeq Control Software (HCS)
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Sequence read was trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fall within exon regions were counted.
Assembly: mm10
Supplementary files format and content: raw count
 
Submission date Jan 20, 2023
Last update date Jan 14, 2025
Contact name Elizabeth A. Jacobsen
E-mail(s) jacobsen.elizabeth@mayo.edu
Phone 4803014091
Organization name Mayo Clinic
Street address 13400 E. Shea Blvd.
City Scottsdale
State/province AZ
ZIP/Postal code 85259
Country USA
 
Platform ID GPL21103
Series (2)
GSE223352 Eosinophils in Lung Allograft
GSE223907 Eosinophils Restrain Humoral Alloimmunity after Lung Transplantation
Relations
BioSample SAMN32812578
SRA SRX19103703

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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