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Sample GSM7567376 Query DataSets for GSM7567376
Status Public on Nov 02, 2023
Title C_1 (biol rep 1)
Sample type SRA
 
Source name spleen of C57BL/6 mice
Organism Mus musculus
Characteristics tissue: spleen of C57BL/6 mice
cell line: primary T cell
cell type: CD8+T cells
genotype: WT
treatment: Control
Treatment protocol 72 hr after anti-CD3/28 stimulation, activated CD8+ T cells were further treated by 200 ng/ml recombinant murine NGF for another 24 hr. Cells were then collected for bulk RNA-seq.
Growth protocol CD8+ T cells were isolated by MACS from 6-8 week old C57BL/6 mice, and activated by plate-bound anti-CD3/28 antibodies. T cells were culutred in T cell specific media.
Extracted molecule total RNA
Extraction protocol Total RNA was extrated using a kit from ZYMO RESEARCH (Direct-zol RNA miniprep, cat. No. R2052) according to the manufacturer’s instructions and dissolved in RNase-free water.
Sequencing libraries were prepared using the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s protocol. Libraries were sequenced using an Illumina HiSeq machine and paired-end reads were generated.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing RNA-seq data were processed using the fastp toolkit to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads with default parameter. Only bases with quality ≥20 and only reads that were ≥20nt after trimming were kept for further analysis.
Reads were mapped to mouse genome reference combining the GRCm38. STAR software was used to align reads to reference genome. Reads were kept for subsequent analysis if they mapped to a single genomic location. Reads with mappiing quality <20 were excluded. Gene counts were measured using the featureCounts.
Assembly: GRCm38
Supplementary files format and content: Tao_NGF_featurecount_matrix.txt: Reads mapped to human GRCm38, featurecount was used to count reads per gene per sample, tab-delimited txt file
 
Submission date Jul 06, 2023
Last update date Nov 02, 2023
Contact name Liuyang Wang
Organization name Duke University
Street address 213 Research Drive
City Durham
State/province NC
ZIP/Postal code 27710
Country USA
 
Platform ID GPL21103
Series (2)
GSE236674 Breaking through NGF-TrkA immunosuppression in melanoma sensitizes immunotherapy for durable memory T cell protection [RNA-Seq 2]
GSE236682 Breaking through NGF-TrkA immunosuppression in melanoma sensitizes immunotherapy for durable memory T cell protection
Relations
BioSample SAMN36345315
SRA SRX20928435

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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