|
| Status |
Public on Oct 02, 2023 |
| Title |
Day3-YPPP, CD11c+I-AI-Ehigh cells day3_YPPP |
| Sample type |
SRA |
| |
|
| Source name |
GM-CSF Bone marrow culture
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Bone marrrow derived dendritic cells
cell subset: CD11c+I-AI-Ehigh
treatment: YPPP for 3 days
library type: NEB Next Ultra II Directional RNA Library Prep Kit
|
| Treatment protocol |
DMSO or YPPP added to the dish of bone marrow culture at day 0.
|
| Growth protocol |
Bone marrow cells from femur of C57BL/6 mice were cultured with 25 ng/ml GM-CSF and DMSO or YPPP.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of the dendritic cells were extracted with AllPrep DNA/RNA kit (QIAGEN) according to manufacturer instructions.
The libraries were constructed using NEB Next Ultra II Directional RNA Library Prep Kit according to manufacturer instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Day3-YPPP, CD11c+I-AI-Ehigh cells
day3_YPPP
|
| Data processing |
The fastq fieles were generated using bcl2fastq software.
Sequenced reads were mapped to hg38 using HISAT2 (v2.1.0) with default parameter.
Reads Per Kilobase of exon per Megabase of library size (RPKM) and Transcripts per Million (TPM) were calcurated by StringTie (v1.3.4d) with default parameter.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM and TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jul 26, 2023 |
| Last update date |
Oct 02, 2023 |
| Contact name |
Hiroki Ura |
| E-mail(s) |
h-ura@kanazawa-med.ac.jp
|
| Organization name |
Kanazawa Medical University Hospital
|
| Lab |
Center for Clinical Genomics
|
| Street address |
1-1 Daigaku
|
| City |
Uchinada |
| State/province |
Ishikawa |
| ZIP/Postal code |
920-0293 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE239334 |
Transcriptome analysis of high potent DCs using small molecule compounds |
|
| Relations |
| BioSample |
SAMN36716253 |
| SRA |
SRX21164659 |
