|
| Status |
Public on Feb 13, 2019 |
| Title |
IFN-alpha-pMC_01 |
| Sample type |
SRA |
| |
|
| Source name |
IFN-α-transuduced iPSC-pMCs
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: iPSC-derived myeloid cells
treatment: IFN-alpha-pMC
|
| Growth protocol |
iPSC-pMCs or IFN-α- iPSC-pMCs (2 × 10^6 cells/well/6 well plate) were cultured for 24 h in RPMI1640 supplemented with 10%FBS. iPSC-pMCs stimulated with recombinant IFN-α (10^4 U/mL) were served as a reference.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the RNeasy Mini Kit Plus (Qiagen, Valencia, CA, USA).
Libraries were prepared using (TruSeq Stranded mRNA sample prep kit, Illumina, San Diego, CA, USA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Samples were sequenced using Illumina HiSeq2500 instrument with paired-end 2 x 100-bp cycle
Base calls were performed on CASAVA 1.8.2. pipeline
Quality check for sequence reads using FastQC
Pre-processing of sequence reads using Trimmomatic version 0.36 with LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 as command option. Fastq reads were generated using BCL2FASTQ Conversion Software1.8.4; First line begins with a '@' character and is followed by a sequence identifier. Second line represent raw nucleotide sequence letters. The last line encodes the quality values for the sequence.
Mapping of sequence reads using TopHat version 2.1.1
Raw read counts were determined using Cufflinks version 2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurements
|
| |
|
| Submission date |
Feb 08, 2019 |
| Last update date |
Feb 14, 2019 |
| Contact name |
Ranmaru Shimoda |
| E-mail(s) |
shimoda@rhelixa.com
|
| Phone |
+818043368250
|
| Organization name |
Rhelixa, Inc.
|
| Street address |
3F Yayoi Bldg., 3-7-4 Iwamotocho
|
| City |
Chiyoda |
| State/province |
Tokyo |
| ZIP/Postal code |
101-0032 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE126277 |
IFN-α-producing proliferating myeloid cells reveal type I IFN-stimulating gene signature |
| GSE126281 |
Type I Interferon Delivery by iPSC-Derived Myeloid Cells Elicits Antitumor Immunity via XCR1+ Dendritic Cells |
|
| Relations |
| BioSample |
SAMN10888860 |
| SRA |
SRX5352143 |
