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Sample GSM6064620 Query DataSets for GSM6064620
Status Public on Feb 15, 2023
Title Th17 cells, ILA, biological replicate 2
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics tissue: Spleen
strain: C57BL/6J
cell type: Navie CD4+ T cells
genotype: WT
treatment: Th17 differentiation+ILA
Treatment protocol Cells were treated with vehivle control or ILA (200 uM) or GSK805 (0.5 uM) or combined
Growth protocol Naïve CD4+ mouse T cells were magnetically isolated, cultured in RPMI 1640 medium supplemented with CytoBox Th17, and activated with CD3/CD28 activation cocktail
Extracted molecule total RNA
Extraction protocol Total RNA was extracted by RNAiso Plus according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing The raw data was handled by Perl and data quality was checked by FastQC v0.11.2
Clean reads were aligned to the mouse genome from NCBI using Bowtie
The expression of the transcript was calculated by FPKM using Perl
Differentially expression transcripts were determined using the MA-plot-based method with Random Sampling (MARS) model in the DEGseq package
Function and signaling pathway enrichment analysis using GO and KEGG database
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample
 
Submission date Apr 25, 2022
Last update date Feb 18, 2023
Contact name Ji-Xuan Han
E-mail(s) jixuanhan@gmail.com
Phone 02163882212
Organization name Renji Hospital, Shanghai Jiao-Tong University School of Medicine
Street address 145 Middle Shandong Road
City Shanghai
ZIP/Postal code 200011
Country China
 
Platform ID GPL24247
Series (2)
GSE201448 Microbiota-derived tryptophan catabolites mediate the chemopreventive effects of statins on colorectal cancer I
GSE201453 Microbiota-derived tryptophan catabolites mediate the chemopreventive effects of statins on colorectal cancer
Relations
BioSample SAMN27763646
SRA SRX14990361

Supplementary file Size Download File type/resource
GSM6064620_ILA_rep2.txt.gz 214.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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