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Sample GSM3595662 Query DataSets for GSM3595662
Status Public on Feb 13, 2019
Title TCR_spleen_02
Sample type SRA
 
Source name TCR_spleen
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: spleen
tissue: spleen
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 IFN-α-iPSC-pMCs (1 × 10^6) into the right hindlimb on days 5, 6, 7, 12, and 13. Total RNA from tumor tissue was extracted on day 14.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with the RNeasy Mini Kit Plus (Qiagen, Valencia, CA, USA).
Total RNA was converted to complementary DNA (cDNA) with Superscript III reverse transcriptase (Invitrogen, Carlsbad, California, USA). Then, double strand (ds)-cDNA was synthesized and an adaptor was ligated to the 5′ end of the ds-cDNA and cut with SphI restriction enzyme. For TCRβ, PCR was performed with a P20EA adaptor primer and a TCRβ-chain constant region-specific primer (mCB1). The second PCR was performed with mCB2 and P20EA primers using the same PCR conditions. After Tag PCR amplification, index (barcode) sequences were added by amplification with a Nextera XT Index Kit v2 setA (Illumina, San Diego, California, USA). Sequence was done with the Illumina MiSeq paired-end platform (2 × 300 base pairs (bp)).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
 
Data processing Data processing, assignment, and data aggregation were automatically performed using repertoire analysis software originally developed by Repertoire Genesis.
Sequence reads were used for repertoire analysis of T cell receptor beta locus
Genome_build: Mouse TRB
Supplementary_files_format_and_content: tab-delimited text files including TRBV/TRBJ , amino acid sequence, read counts
 
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 GPL16417
Series (2)
GSE126278 Characterization of tumor-infiltrating T cells by TCR-β repertoire analyses
GSE126281 Type I Interferon Delivery by iPSC-Derived Myeloid Cells Elicits Antitumor Immunity via XCR1+ Dendritic Cells
Relations
BioSample SAMN10888851
SRA SRX5352152

Supplementary file Size Download File type/resource
GSM3595662_TCR_spleen_02.txt.gz 432.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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