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Sample GSM4543953 Query DataSets for GSM4543953
Status Public on Aug 01, 2020
Title 70_VijaySeq1_2_SoZa06_04MAY17_N727S520
Sample type SRA
 
Source name Ltbrfl/fl x Mrp8-Cre (LTβRΔN) unstim
Organism Mus musculus
Characteristics genotype: Ltbrfl/fl x Mrp8-Cre (LT{beta}R{delta}N)
treatment: unstimulated
tissue: Blood
strain: C57/Bl6
cell type: Neutrophil
Treatment protocol Following isolation, cells were stimulated for 2 hours with recombinant, colitis associated, cytokines (TNF [100ng/ml], IL-6 [50ng/ml] and GM-CSF [100ng/ml]) in the presence or absence of soluble LIGHT stimulation [500ng/ml].
Growth protocol Neutrophils were isolated from the blood of 8 week old LTβRΔN, and littermate controls, using a magnetic bead negative selection kit (Stem Cell Technologies).
Extracted molecule total RNA
Extraction protocol Cells were lysed in Trizol LS (Thermo Fisher). RNA extraction, reverse transcription, cDNA amplification, fragmentation, additional PCR amplification, final library purification, and quality control were performed as described (methodology section).
Sequencing was performed according to a single-end strategy using the HiSeq2500 sequencer (Illumina). Samples that failed quality control standards were eliminated from further analysis21.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the mm10 reference using Tophat v1.4.1 (--library-type fr-firststrand)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: mm10
Supplementary_files_format_and_content: read count matrix with rows as genes and columns as cells
 
Submission date May 11, 2020
Last update date Aug 01, 2020
Contact name Thomas Riffelmacher
E-mail(s) [email protected]
Organization name La Jolla Institute for Immunology
Lab Kronenberg
Street address 9420 Athena Circle
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL17021
Series (1)
GSE150243 Differential gene expression of neutrophils that lack lymphotoxin beta receptor identifies a metabolic gene signature
Relations
BioSample SAMN14885072
SRA SRX8321017

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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