|
| Status |
Public on Feb 28, 2017 |
| Title |
P-MEM49_02 |
| Sample type |
SRA |
| |
|
| Source name |
ileum of small intestine
|
| Organism |
Mus musculus |
| Characteristics |
stain: BALB/c
tissue: ileum of small intestine
sample group: MEM49-encoding DNA vaccine pre-vaccinated
|
| Treatment protocol |
BALB/c mice were intradermally injected with 100 ug MEM49-encoding DNA vaccine prior to or after shrimp tropomyosin sensitization
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ileum sections were isolated within 24h after intragastric challenge and stored in RNAlater RNA stabilization reagent. Total RNA was extracted using the Rneasy Mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard ion proton protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
MEM49-encoding DNA vaccine pre-vaccinated mice
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for short reads and low-quality sequences, then mapped to the mouse reference genome mm10 using TMAP.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Sailfish.
Genome_build: mm10
Supplementary_files_format_and_content: excel file containing the gene id, transcript id, length of the transcript, expected read count and RPKM value
|
| |
|
| Submission date |
Sep 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Christine Yee Yan Wai |
| E-mail(s) |
christinewai0816@gmail.com
|
| Phone |
+852 39436018
|
| Organization name |
The Chinese University of Hong Kong
|
| Department |
School of Life Sciences
|
| Lab |
Simon F.S. Li Marine Science Laboratory
|
| Street address |
Shatin, N.T.
|
| City |
HKSAR |
| ZIP/Postal code |
852 |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE86840 |
Transcriptomic profiling of mice receiving immunoprophylactic and immunotherapeutic hypoallergen-encoding DNA vaccine |
|
| Relations |
| BioSample |
SAMN05763228 |
| SRA |
SRX2160540 |
