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Sample GSM7884190 Query DataSets for GSM7884190
Status Public on Feb 22, 2024
Title whole lung_stress_bio rep2
Sample type SRA
Source name lung
Organism Mus musculus
Characteristics tissue: lung
cell type: whole lung
genotype: WT
treatment: stress
Growth protocol Mouse neutrophils were isolated from the bone marrow of 8-week-old female BL/6 mice. Briefly, bone marrow was flushed from both femurs and tibias with 1x Hanks’ Balanced Salt Solution (HBSS) using a syringe with a 26G needle. After washing the bone marrow cells once with 1x HBSS, the cells were resuspended in ammonium-chloride-potassium (ACK) lysis buffer for 3 minutes on ice. The cells were then washed twice with 1x HBSS, resuspended in 2 ml of HBSS. Neutrophils were isolated by density gradient separation. The density gradient was made by layering 2 mL of bone marrow cells on top of 3 mL of 62% Percoll (#17-0891-02, GE Healthcare) on top of 3 mL of 81% Percoll in a 15 ml falcon tube, followed by centrifugation at 2,500 x g for 20 minutes at 4°C. Neutrophils were then taken from the middle interface, washed in HBSS, and resuspended in serum-free DMEM before use.
Extracted molecule total RNA
Extraction protocol For RNA-seq experiments, total RNA was isolated using TRIzol (Thermo Fisher, 15596026) according to the manufacturer’s instructions. For ChIP_seq experiments, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
was constructed using the Illumina TruSeq RNA library prep kit v2 (Illumina, RS-122-2001) or Illumina TruSeq ChIP library prep kit (Illumina, IP-202-1012) based on the manufacturer’s instructions.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Raw reads from RNA-seq were mapped to reference genome mm10 using RNA STAR with default parameters. Read count tables were created using FeatureCounts with a custom GTF file containing protein coding genes only. Differentially expressed genes were analyzed using DESeq2 with two independent replicates using default parameters.
Raw reads from ChIP-seq were aligned to the reference genome hg38 using Bowtie2 with sensitive end-to-end setting. After removal of PCR duplication reads by SAMtools, peaks were identified using MACS2, with narrow peak option for TFs and broad peak option for H3K27Ac. Genome-wide read coverage was calculated by deepTools with a bin size of 50 bp.
Assembly: mm10
Supplementary files format and content: bigwig
Submission date Nov 06, 2023
Last update date Feb 22, 2024
Contact name Yuan Gao
Phone 5075130882
Organization name CSHL
Street address One Bungtown Rd
City Cold Spring Harbor
State/province NY
ZIP/Postal code 11724
Country USA
Platform ID GPL19057
Series (1)
GSE247144 Chronic stress causes metastasis via neutrophil-mediated changes to the microenvironment.
BioSample SAMN38123396
SRA SRX22385981

Supplementary file Size Download File type/resource
GSM7884190_S2_tpm.tsv.gz 1.4 Mb (ftp)(http) TSV
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Raw data are available in SRA

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