|
| Status |
Public on Sep 21, 2024 |
| Title |
Neu_Ctrl_s.n._3 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Bone marrow
cell line: primary immune cell
cell type: Neutrophil
genotype: WT
strain: C57/B6
treatment: in vitro stimulated with control supernatant
|
| Treatment protocol |
Il5cre/+Hilpda+/+ and Il5cre/+Hilpdaflox/flox mice were intranasally challenged with IL-33 for three days.
|
| Growth protocol |
Flow-sorted Bone marrow neutrophils were stimulated in vitro with control supernatant (s.n.) or ILC2 s.n for 1 hour. Flow-sorted lung ILC2s were cultured with IL-2 and IL-7, plus vehicle, NmU23, IL-25 or IL-33 for 72 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
DNA and RNA were extracted from cells using AMPure XP beads (Backman)
Bulk RNAseq: Full-length Smart-seq2; scRNAseq: 10x Genomics Chromium Next GEM Single Cell 3’ v3.1
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Bulk RNA-seq: raw fastq files were trimmed with cutadapt v2.10. Alignment to mm10 genome/transcriptome and quantification of gene expression were done using STAR v2.7.5c and RSEM v1.3.3. Differential gene expression was analyzed using edgeR.
scRNA-seq: 10x Genomics Cellranger v7.0.0 was used to process fastq files and generate matrix files. Downstream normalization, filtering and clustering were done using Seurat v4.1.1 in R v4.1.3/ Rstudio.
Assembly: mm10
Supplementary files format and content: Bulk RNAseq: TPM expression matrix files were extracted from RSEM gene-results and initially filtered for expressed protein-coding genes.
Supplementary files format and content: scRNAseq: Cellranger output expression matrix files and feature barcode setting file packaged in tar.gz; analyzed LUNG only seurat object in rds file.
|
| |
|
| Submission date |
Oct 21, 2023 |
| Last update date |
Sep 21, 2024 |
| Contact name |
Heping Xu |
| E-mail(s) |
xuheping@westlake.edu.cn
|
| Organization name |
Westlake University
|
| Street address |
18 Shilongshan Road
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310024 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE245964 |
Alarmin-loaded extracellular lipid droplets induce airway neutrophil infiltration during type 2 inflammation |
|
| Relations |
| BioSample |
SAMN37915350 |
| SRA |
SRX22161941 |
