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Sample GSM7852437 Query DataSets for GSM7852437
Status Public on Sep 21, 2024
Title Neu_ILC2_s.n._1
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 ILC2 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 SAMN37915349
SRA SRX22161942

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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