|
| Status |
Public on Aug 01, 2019 |
| Title |
WT_CD103+CD11b-_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Intestinal Dendritic Cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: wild type
strain: mixed background
tissue: gut
cell types: Dendritic cell
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single cell suspensions from mouse intestine were prepared using EDTA and collagenase IV with agitations. Dendritic cells were flow-sorted into buffer TCL (QIAGEN) by FACS Aria and RNA were isolated using Agencourt RNAClean XP beads (Beckman Coulter).
RNA libraries were prepared for sequencing applying scRNA-seq procedure with modofications
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Sequenced reads were quality and adapter trimmed by trim_galore, then mapped to mm10 whole genome using STAR v2.7 with a gtf file from EMBL-EBI (GRCm38.92)
Reads on each gene were counted using htseq-count with -s no option and a GTF file from EMBL-EBI (GRCm38.92)
Genome_build: mm10
|
| |
|
| Submission date |
Apr 26, 2019 |
| Last update date |
Aug 01, 2019 |
| Contact name |
Hideyuki Yoshida |
| E-mail(s) |
hideyuki.yoshida@riken.jp
|
| Organization name |
RIKEN IMS
|
| Street address |
1-7-22 Suehiro-cho
|
| City |
Tsurumi-ku, Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE130380 |
RNA-seq analyses of two intestinal dendritic cell subsets, CD103+CD11b- and CD103-CD11b+, from wild type and CbfbF/F:CD11c-Cre mice. |
|
| Relations |
| BioSample |
SAMN11515809 |
| SRA |
SRX5758599 |
