|
| Status |
Public on Jul 01, 2019 |
| Title |
SPM rep2 |
| 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: small peritoneal macrophages
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:
55
|
| 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 |
SAMN11526014 |
| SRA |
SRX5763443 |
