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Sample GSM3240853

Query DataSets for GSM3240853

Status

Public on Jul 02, 2018

Title

PW2-A7

Sample type

SRA

Source name

peripheral blood plasmablast

Organism

Homo sapiens

Characteristics

donor id: 240-15-051
donor gender: male
isotype: IgG
specificity: vaccine
experimental batch: PW2

Extracted molecule

polyA RNA

Extraction protocol

The Smart-seq2 protocol published in Nature Protocols by Picelli et al., 2014, was used to isolate cellular mRNA and generate single-cell libraries for RNA-sequencing.
The Smart-seq2 protocol published in Nature Protocols by Picelli et al., 2014, was used to isolate cellular mRNA and generate single-cell libraries for RNA-sequencing.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

Kallisto was used for alignment against the human transcriptome
Log2(TPM+1)
Applied threshold of detection, set all Log2(TPM+1) values below threshold to 0.
Applied cell filter, removed all cells with less than 40% of transcripts mapping to the human transcriptome.
Applied gene expression filter, removed all genes expressed in less than 5% of the cells
Performed Quantile normalization with the Preprocesscore package within each experimental plate
Performed Limma batch correction to remove variability associated with experimental plate and donor ID, while protecting BCR isotype and specificity.
Genome_build: HG19
Supplementary_files_format_and_content: normalized abundance measurement

Submission date

Jul 02, 2018

Last update date

Jul 05, 2018

Contact name

Aly Azeem Khan

Organization name

University of Chicago

Street address

6045 S. Kenwood Ave.

City

Chicago