|
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 |