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Sample GSM3319748 Query DataSets for GSM3319748
Status Public on Sep 05, 2018
Title 1001-Naive_B-S
Sample type SRA
Source name primary blood
Organism Homo sapiens
Characteristics donor: 1001
cell type: Naive_B
lineage: B
treatment: treatment1
Treatment protocol Treatment 1: T lymphocytes were activated for 24 hours with dynabead conjugated CD3/CD28 antibodies at 1:1 ratio, supplemented with 50 unit/ml of human IL-2 or 300 unit/ml for regulatory T cells. B lymphocytes were activated for 24 hours with 10µg/ml anti-IgG/IgM antibodies and 20ng/ml of human IL-4. Monocytes were activated with 1µg/ml of LPS for 24 hours. NK cells were activated with 200 unit/ml of human IL2 for 24 hours.
Treatment 2: Monocytes were activated with 100ng/ml of LPS for 6 hours. NK cells were activated with CD2 and CD355 coated beads at 1:2 cell to bead ratio supplemented with 500 unit/ml IL-2 for 48 hours.
Extracted molecule polyA RNA
Extraction protocol RNA sequencing libraries were prepared according to the Smart-seq2 protocol (Picelli et al. ,2014). Custom Nextera barcoded PCR primers (Buenrostro et al., 2015) were used for dual indexing. Amplified libraries were purified using AMPure XP beads (Beckman Coulter) using a 1:1 ratio.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description RNA_gene_abundance.txt.gz
Data processing Tn5 transposase adapters were trimmed with cutadapt version 1.13 with a minimum length of 20 and an overlap of 5 in paired-end mode.
RNA-seq reads were pseudoaligned using Kallisto version 0.43.0 (Bray et al., 2016). The Kallisto index was made with default parameters and the gencode v25lift37 fasta file (Harrow et al., 2012) and was run in quant mode with default parameters.
Gene abundances were computed using tximport version 1.2.0 (Soneson et al., 2015).
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file including gene abundance estimate for protein coding genes
Submission date Aug 06, 2018
Last update date Sep 05, 2018
Contact name Diego Calderon
Organization name University of Washington
Street address 3720 15th Ave NE
City Seattle
ZIP/Postal code 98105
Country USA
Platform ID GPL24676
Series (1)
GSE118165 RNA-seq data
BioSample SAMN09768436
SRA SRX4510599

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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