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Sample GSM4104216 Query DataSets for GSM4104216
Status Public on Dec 15, 2019
Title CD4_siNS_rep1
Sample type SRA
 
Source name CD4 T cells
Organism Homo sapiens
Characteristics sirna: siNS
t cell subtype: CD4
antibody blockade: n/a
Treatment protocol T cells were electroporated with siRNAs against FOXP3 (FOXP3HSS121456) using the Amaxa Nucleofection 4D system and the P3 Primary Cell kit (Lonza). Stealth RNAi negative control medium GC duplex siRNA (ThermoFisher) was used as a non-specific (NS) control, and all assays were conducted 4 days post electroporation for peak knockdown efficiency.
Growth protocol T cells were purified from PBMC by immunomagnetic negative selection using the specific EasySep Human T cell isolation kit
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from primary T cells using the Qiagen RNeasy Plus Mini Kit with on-column DNase digestion. Total RNA integrity was assessed using automated capillary electrophoresis on a AATI Fragment Analyzer. The integrity of all samples are RQI > 8.0
A minimum starting amount of 75 ng was used as input for library preparation using the Illumina TruSeq Stranded mRNA Library Preparation Kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Raw paired-end sequencing reads were aligned to the human reference genome (hg19) using STAR (version 2.4.2a).
Gene quantification was performed with RSEM (version 1.2.22)
Genome_build: hg19
Supplementary_files_format_and_content: FOXP3_sample_gene_expected_counts.txt – Expected gene counts for samples produced by RSEM
Supplementary_files_format_and_content: FOXP3_sample_gene_FPKMs.txt - Gene FPKM values for samples produced by RSEM
 
Submission date Oct 01, 2019
Last update date Dec 15, 2019
Contact name Clifton Lee Dalgard
E-mail(s) cdalgard@usuhs.edu
Organization name Uniformed Services University
Department Anatomy Physiology & Genetics
Lab Dalgard
Street address 4301 Jones Bridge Road B2038
City Bethesda
State/province Maryland
ZIP/Postal code 20814
Country USA
 
Platform ID GPL21290
Series (1)
GSE138272 FOXP3 protects conventional human T cells from premature restimulation-induced cell death
Relations
BioSample SAMN12881568
SRA SRX6931793

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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