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Sample GSM7884208 Query DataSets for GSM7884208
Status Public on Feb 22, 2024
Title primary tumor_stress_d35_bio rep3
Sample type SRA
 
Source name tumor
Organism Mus musculus
Characteristics tissue: tumor
cell type: primary tumor
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
E-mail(s) yuangao.ustc@gmail.com
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.
Relations
BioSample SAMN38123378
SRA SRX22385999

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

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