|
| Status |
Public on Aug 01, 2020 |
| Title |
77_VijaySeq1_2_SoZa06_04MAY17_N721S521 |
| Sample type |
SRA |
| |
|
| Source name |
Ltbrfl/fl x Mrp8-Cre (LTβRΔN) stim
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Ltbrfl/fl x Mrp8-Cre (LT{beta}R{delta}N)
treatment: stimulated
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 |
SAMN14885065 |
| SRA |
SRX8321023 |
