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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 13, 2019 |
| Title |
TCR_treated_tumor_01 |
| Sample type |
SRA |
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| Source name |
TCR_treated_tumor
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: melanoma
tissue: IFN-α-iPSC-pMC-treated tumor
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| 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.
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| 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)).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
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| 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
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| Submission date |
Feb 08, 2019 |
| Last update date |
Feb 14, 2019 |
| Contact name |
Ranmaru Shimoda |
| E-mail(s) |
shimoda@rhelixa.com
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| Phone |
+818043368250
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| Organization name |
Rhelixa, Inc.
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| Street address |
3F Yayoi Bldg., 3-7-4 Iwamotocho
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| City |
Chiyoda |
| State/province |
Tokyo |
| ZIP/Postal code |
101-0032 |
| Country |
Japan |
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| 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 |
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| Relations |
| BioSample |
SAMN10888856 |
| SRA |
SRX5352147 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3595657_TCR_treated_tumor_01.txt.gz |
93.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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