|
| Status |
Public on Dec 01, 2019 |
| Title |
DNP-BSA (50 ng/ml) treated BMMC [Ag1] |
| Sample type |
SRA |
| |
|
| Source name |
BMMCs_DNP-BSA
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: wild type
cell type: Bone marrow derived mast cells (BMMCs)
passages: >95% FcER1+ CD117+
treatment group: treated with DNP-BSA (50 ng/ml) for 2h
molecule subtype: mRNA and lncRNA
|
| Treatment protocol |
IgE (0.5 ug/ml) treatment for 18 h, Ag (50 ng/ml) treatment for 2h after IgE treatment
|
| Growth protocol |
10 ng/ml IL-3 and 10 ng/ml SCF for 4-6 weeks after bone marrow isolation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The sequenced reads were mapped tomm9 build of the human genome using TopHat version 2.0.12 with the aligner Bowtie 0.12.7 with their default parameters except –m 1 and –segment-mismatches 2.
FPKMs were calculated by Cufflink (2.2.1)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.
|
| |
|
| Submission date |
Nov 30, 2015 |
| Last update date |
Dec 01, 2019 |
| Contact name |
Jingxian Zhang |
| E-mail(s) |
zhangjingxian.nus@gmail.com
|
| Organization name |
Institute of Molecular and Cell Biology (IMCB), A-Star, Singapore
|
| Department |
IMCB
|
| Street address |
61 Biopolis Drive Proteos
|
| City |
Singapore |
| State/province |
Singpaore |
| ZIP/Postal code |
138673 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE75526 |
Transcriptomic profiling of bone marrow derived mast cells (BMMCs) [RNA-seq] |
| GSE111547 |
Landscape of mouse mast cell chromatin: a rich resource for identification of novel mediators and genetic drivers of allergic and inflammatory diseases |
|
| Relations |
| BioSample |
SAMN04302840 |
| SRA |
SRX1456408 |
