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Sample GSM5074122 Query DataSets for GSM5074122
Status Public on Feb 10, 2024
Title CGD_Ly6C+_MHC2-_6h_rep1_L002
Sample type SRA
 
Source name CGD 6h LyC6+ MHC2– rep1
Organism Mus musculus
Characteristics strain: C57Bl/6
tissue: Peritoneal Lavage
genotype: gp91phox/y
Sex: Male
age: 8-12 weeks
treatment: i.p. Zymosan
time point: 6 hours
cell type: MoMac Ly6C+ MHCII-
Treatment protocol Mice were treated with intraperitoneal injection of 200ug Zymosan A (Sigma)
Growth protocol Parent animals were obtained from Jackson laboratories. Experimental mice were bred and housed in a specific pathogen free facility at National Jewish Health, Denver, CO, USA.
Extracted molecule total RNA
Extraction protocol Peritoneal lavage was collected using 8mL buffer (HBSS w/o Ca2+ Mg2+, 20mM HEPES, 1mM EDTA). Total lavage cells were stained with antibodies for FACS and sorted to purify monocytes/macrophages of the indicated phenotype. Total RNA was extracted using the Qiagen RNeasy micro kit according to manufacturer's instructions.
A Clontech SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Mountain View, CA, USA) and Nextera XT (San Diego, CA, USA) kit were used. Briefly, library construction started from isolation of total RNA species, followed by SMARTer 1st strand cDNA synthesis, full length dscDNA amplification by LD-PCR, followed by purification and validation. After that, the samples were taken to the Nextera XT protocol where the sample is simultaneously fragmented and tagged with adapters followed by a limited-cycle PCR that adds indexes. Once validated, the barcoded-pooled libraries were sequenced using 1×50bp chemistry on the HiSeq 2500 as routinely performed by the NJH Genomics Facility.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description CGD_Ly6C+_MHC2-_6h_rep1_L002
Data processing FASTQ files were generated using the Illumina bcl2fastq converter (version 2.17).
Nextera TruSight adapters were trimmed with skewer (version 0.2.2), which by default removes reads with a remaining length of less than 18 nt.
Trimmed reads were mapped with the STAR aligner (version 2.4.1d) to the GRCm38 assembly of the mouse genome using gene using gene annotations from Ensembl version 84.
Reads mapping to each gene of the Ensembl 84 annotation were counted with the featureCounts program from the Subread software package (v1.5.1).
Transcripts per million aligned fragments (TPM) were calculated from the gene counts using the sum of all bases covered by any transcript of a gene as its transcript length.
Genome_build: GRCm38
Supplementary_files_format_and_content: read counts and transcripts per million (TPM) assigned to each gene of the mouse Ensembl 84 annotation and sample, as tab-separated text tables: 1) output from subread featureCounts (2 subread_genecounts.txt* files), separated by sequencing run, 2) aggregated by adding different sequencing runs for each sample (counts and TPM)
 
Submission date Feb 10, 2021
Last update date Feb 10, 2024
Contact name Donna Leslie Bratton
E-mail(s) brattond@njhealth.org
Organization name National Jewish Health
Department Pediatrics
Lab Bratton
Street address 1400 Jackson St. Rm A540
City Denver
State/province CO
ZIP/Postal code 80206
Country USA
 
Platform ID GPL17021
Series (1)
GSE166542 Heightened turnover and failed maturation of monocyte-derived macrophages in Chronic Granulomatous Disease
Relations
BioSample SAMN17854559
SRA SRX10066111

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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