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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 01, 2024 |
| Title |
KOOTI-WT6_replicate 2 |
| Sample type |
SRA |
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| Source name |
tumor
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| Organism |
Mus musculus |
| Characteristics |
tissue: tumor
cell line: primary cells
cell type: Tumor-infiltrating CD8 T cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
To analyze the function of CD8+ T cells in the TME, we sorted tumor-infiltrating CD8+ T cells from tumor-bearing mice.
TruSeq Stranded Total RNA Reference Guide(1000000040499 v00)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Before proceeding with the analysis of the raw sequence, a quality check is performed using the FASTQC program v.0.11.7 to ensure that there are no problems with the data.
Trimming for illumina paired-end was performed using the Trimmomatic 0.38 program.
Mapping to a known reference genome using the HISAT2 program version 2.1.0
After read mapping, transcript assembly was performed using the StringTie version 2.1.3b
Assembly: Mus musculus mm10
Supplementary files format and content: 1. raw data --> fastq (fastq.gz) file, read sequence and quality information 2. mapping --> bam, bam.bai file, mapping information of mapped reads 3. trasncript assembly --> txt or excel file, expression profiling result after trasncript assembly based on mm10 reference gtf annotation
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| Submission date |
Apr 18, 2023 |
| Last update date |
Apr 01, 2024 |
| Contact name |
YUNA JO |
| E-mail(s) |
yoona8987@gmail.com
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| Phone |
+821080048987
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| Organization name |
Pusan National University
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| Street address |
49, Busandaehak-ro
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| City |
Yangsan |
| ZIP/Postal code |
50612 |
| Country |
South Korea |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE229992 |
Effect of anti-tumor efficacy of depletion of Nrf2 in effector T cells |
| GSE229994 |
tumor-infiltrating CD8+ T cells from tumor-bearing mice transferred Nrf2-deficient CD8+ T cells. |
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| Relations |
| BioSample |
SAMN34238053 |
| SRA |
SRX20002990 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7182534_KOOTI-WT_6.gtf.gz |
16.3 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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