GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM7988375 Query DataSets for GSM7988375
Status Public on Jan 25, 2024
Title Untreated biol rep 6 [TCR-3]
Sample type SRA
Source name brain tumor
Organism Mus musculus
Characteristics tissue: brain tumor
time: Day 21 post implantation
cell type: immune cells
genotype: WT
treatment: none
Extracted molecule other
Extraction protocol RNA was extracted using Zymo mini/midi RNA extraction kit.
Celero™ EZ DNA-Seq, 24 reactions kit (Tecan Genomics) was utilized to generate sequencing libraries following the manufacturer’s instructions. RNA-sequencing was performed using Illumina NovaSeq 6000, SP 2 x 50.
Library strategy OTHER
Library source other
Library selection other
Instrument model Illumina MiSeq
Description CD45+ immune cell were selected from GBM tumor microenvironment following tissue dissociation and positive cell selection. SMARTer Mouse TCR a/b Profiling Kit (Takara Bio) was utilized to amplify TCR beta chains using PCR and sequencing libraries were generated following the manufacturers instructions. RNA-sequencing was performed using Illumina MiSeq x 300.
Data processing *library strategy: RNA seq of TCR
TCR vb data alignment and analysis were performed using MixCR 4.0
Assembly: mm10
Supplementary files format and content: Processed text files contains count values for each sample
Submission date Dec 21, 2023
Last update date Jan 25, 2024
Contact name Duane Mitchell
Organization name University of Florida
Street address 1333 Center Drive, BSB B1-150
City Gainesville
State/province Florida
ZIP/Postal code 32610
Country USA
Platform ID GPL16417
Series (1)
GSE251800 mRNA-based precision targeting of neoantigens and tumor-associated antigens in malignant brain tumors [KR158 RNA-TCR]
BioSample SAMN38931896
SRA SRX22969579

Supplementary file Size Download File type/resource
GSM7988375_vdjformat.TCR-3_S3_L001_clones_sed.txt.gz 250.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA

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