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Sample GSM3595652 Query DataSets for GSM3595652
Status Public on Feb 13, 2019
Title pMC_02
Sample type SRA
 
Source name iPSC-pMCs
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: iPSC-derived myeloid cells
treatment: 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 SAMN10888861
SRA SRX5352142

Supplementary file Size Download File type/resource
GSM3595652_pMC_2_FPKM.txt.gz 668.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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