NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3595677 Query DataSets for GSM3595677
Status Public on Feb 13, 2019
Title IFN-alpha-pMC_right_02
Sample type SRA
 
Source name IFN-alpha-pMC_right
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: melanoma
treatment: IFN-α-iPSC-pMCs
tissue type: treated tumor (right)
Treatment protocol C57BL/6 mice were inoculated subcutaneously with tumor cells (MO4; an ovalbumin (OVA)-expressing B16F10 melanoma cell line of C57BL/6 origin) into the right and left hindlimb simultaneously (1 × 10^5) on day 0. On day 5, when tumors were palpable, mice were treated peritumorally with iPSC-pMCs or IFN-α-iPSC-pMCs (1 × 10^6) into the right hindlimb on days 5, 6, and 7. Total RNA from tumor tissue was extracted on day 11. Tumor tissue samples with no treatment were served as references.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with the RNeasy Mini Kit Plus (Qiagen, Valencia, CA, USA).
Libraries were prepared for sequencing using library creation kits (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 Illlumina 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 Hisat2 version 2.1.0
Raw read counts were determined using HT-Seq Count version 0.10.0 with -m union -r pos -t exon --stranded=no as options
Differentially expressed genes were identified using DESeq2 version 1.20.0 (log fold change x>1, x<-1)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including read counts from HTSeq-count
 
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)
GSE126279 Local administration of IFN-α-iPSC-pMCs alters gene expression profiles in tumor microenvironment.
GSE126281 Type I Interferon Delivery by iPSC-Derived Myeloid Cells Elicits Antitumor Immunity via XCR1+ Dendritic Cells
Relations
BioSample SAMN10888867
SRA SRX5352167

Supplementary file Size Download File type/resource
GSM3595677_IFN-alpha-pMC_right_02.txt.gz 140.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap