|
| Status |
Public on Sep 29, 2016 |
| Title |
cMoP mouse 3 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
cell type: monocyte
monocyte subset: cMoP
mouse number: 3
strain: C57BL/6
age: 7 weeks old
|
| Growth protocol |
Following cell sorting, cells were incubated in RPMI + 10%FCS for 3hours and were then subjected to RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Arcturus PicoPure RNA Isolation kit according to manufacturer's protocol.
cDNA libraries were prepared using 2ng of total RNA using SMARTSeq v2 protocol (Picelli et al., 2014) except for the following modifications: 1. Use of 20µM TSO, 2. Use of 250pg of cDNA with 1/5 reaction of Illumina Nextera XT kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample name: RMB3427
|
| Data processing |
50bp paired end reads from Illumina HiSeq 2500 were obtained and mapped to the mouse genome build mm10 using the STAR alignment software.
The mapped reads were counted using featureCounts (part of the Subread package) using mouse GENCODE version M9 with exons as the feature summarized to the gene level.
edgeR running in R version 3.1.2 was used to normalize the raw gene counts to normalized RPKM values.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files containing raw gene counts as well as normalized log2 RPKM values
|
| |
|
| Submission date |
Aug 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Bernett Lee |
| E-mail(s) |
bernett.lee@ntu.edu.sg
|
| Organization name |
Singapore Immunology Network
|
| Street address |
8A Biomedical Grove #03-06 Immunos
|
| City |
NA |
| ZIP/Postal code |
138648 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE86079 |
RNAseq transcriptome analysis reveals developmental heterogeneity among mouse bone marrow monocyte subsets |
|
| Relations |
| BioSample |
SAMN05687103 |
| SRA |
SRX2054490 |
