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Sample GSM3738436 Query DataSets for GSM3738436
Status Public on Jul 01, 2019
Title PcDC1
Sample type SRA
 
Source name Peritoneal myeloid mononuclear cell
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Peritoneal cavity
cell type: myeloid mononuclear cell
cell subtype: peritoneal type 1 dendritic cells
cell markers: mouse MHCII+ CD11c+ CD115-
age: post natal week 8
Extracted molecule total RNA
Extraction protocol Peritoneal cells were isolated by flushing peritoneal cavity with PBS containing 3% FBS. 5ml of ice-cold isolation buffer were injected into peritoneal cavity. Then peritoneal cavity was gently massaged to dislodge the attached immune cells. Suspended peritoneal cells were harvested.
Reverse transcription of mRNA and generation of cDNA libraries were carried out with SMARTer Ultra low input RNA library kit and sequencing with Illumina NovaSeq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Normalized_FPKM.txt
sample name in processed data file:
51
Data processing bcl2fastq v1.8.4 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Mus musculus using HISAT2 2.1.0, which is capable of reporting split-read alignments across splice junctions and determined using StringTie 1.3.4d software in default options.
The reference genome sequence of Mus musculus (mm10) and annotation data were downloaded from UCSC. The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values for each Sample
 
Submission date Apr 29, 2019
Last update date Jul 01, 2019
Contact name Chae Gyu Park
E-mail(s) chaegyu@gmail.com
Organization name Yonsei University College of Medicine
Department Severance Biomedical Science Institute
Lab Laboratory of Immunology
Street address 50-1 Yonsei-ro
City Seoul
State/province Seoul
ZIP/Postal code 03722
Country South Korea
 
Platform ID GPL24247
Series (1)
GSE130424 Two distinct subsets are identified from the peritoneal myeloid mononuclear cells expressing both CD11c and CD115
Relations
BioSample SAMN11526007
SRA SRX5763450

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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