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Sample GSM1577172 Query DataSets for GSM1577172
Status Public on May 12, 2015
Title Naive T cells NLRP3KO
Sample type SRA
Source name Naive T cells from spleen and nodes
Organism Mus musculus
Characteristics strain: C57/Bl6j
age: 7 weeks
genotype/variation: NLRP3 KO
cell type: CD4 T cells
Treatment protocol Differentiation was induced with 10 ng/ml IL-4 in presence of IFNgamma blocking antibody for 3 or 6 days,
Growth protocol CD4 T naive cells were isolated from C57/Bl6 Wt and NLRP3-/- mice. Differentiation was induced in RPMI culture medium complemented with 10% FBS,1% antibiotics in CD3/CD28 coating plates
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from 300,000 Th2 cells with Trireagent by following manufacturer protocol. Then, 1µg of total RNA was rRNA depleted thanks to Ribominus Eukaryote kit for RNAseq or mRNA purified thanks to NEB kit
Libraries were prepared according to Bioo Scientific's instructions accompanying the Nextflex RNA Seq-Kit for Illumina. Briefly, RNA was heat fragmented and double strand cDNA synthesis was performed in 2 steps. After purification, the double strand cDNA was end repaired and then adenylated. After adapter ligation, DNA was PCR amplified for 12 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were obtained. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the MiSeq device following the manufacturer's protocols.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
Description mRNA purified
Data processing Data were processed thanks to galaxy website
Fastq groomer tool was applied
Alignment was performed with TopHat on mm9 reference genome
Cufflink was applied
Genome_build: mm9
Supplementary_files_format_and_content: txt files with Cufflinks output
Submission date Jan 06, 2015
Last update date May 15, 2019
Contact name Romain Boidot
Organization name CGFL
Lab Molecular Biology Unit
Street address 1, rue Pr Marion
City Dijon
ZIP/Postal code 21079
Country France
Platform ID GPL16417
Series (1)
GSE54561 Transcriptome analysis of Th2 CD4+ T cells differentiated from wild-type and NLRP3KO mice
BioSample SAMN03276159
SRA SRX831393

Supplementary file Size Download File type/resource
GSM1577172_Naive_T_cells_NLRP3KO.txt.gz 722.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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