 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 13, 2019 |
| Title |
IFN-alpha-pMC_left_03 |
| Sample type |
SRA |
| |
|
| Source name |
IFN-alpha-pMC_left
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: melanoma
treatment: IFN-α-iPSC-pMCs
tissue type: distant tumor (left)
|
| 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 |
SAMN10888864 |
| SRA |
SRX5352170 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3595680_IFN-alpha-pMC_left_03.txt.gz |
140.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
