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Sample GSM3265759 Query DataSets for GSM3265759
Status Public on Jul 12, 2018
Title PB103Pop3
Sample type SRA
 
Source name ASC, Pop3
Organism Homo sapiens
Characteristics samplenum: SL1033
samplename: PB103Pop3
individual: 103
cellpopulation: Pop3
cell type: Antibody Secreting Cell
tissue: Peripheral Blood
batch: B2
Growth protocol FACS-based purified ASCs
Extracted molecule total RNA
Extraction protocol RNA was purified using QIAGEN Micro RNEasy columns, and RNA quality assessed using Agilent Bioanalyzer
2 ng of total RNA was used as input for mRNA amplification using 5’ template-switch PCR with the Clontech SMART-Seq v4 Ultra Low Input RNA kit, according to manufacturer’s instructions. Amplified mRNA was fragmented and appended with dual indexed bar codes using Illumina NexteraXT DNA Library Prep kits
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description 1357983D7103Pop3S58
Data processing Paired end 100bp reads were mapped to hg38, using Tophat2 to generate bam files
HTseq (version) was then used to assess read counts at the gene level in each gene
The mapped libraries were then normalized accounting for differences in size and dispersion using the default parameters of EdgeR for gene abundance levels)
Read counts were converted to the log base 2 scale and principal component variance analysis (PCVA) in JMP-Genomics (version 8.0) was used to assess the contributions of Individual, Batch, Cell Population, and Tissue to the weighted average variance explained by the first 3 PCs
Since Batch explained 53% of the variance, in order to maximize the contrasts across the populations, we elected to use remove the batch effect using the SNM (supervised normalization of microarray) method 54 with Cell Population as the Biological variable and Batch as the adjustment variable with the Rm=True option
Genome_build: hg38
Supplementary_files_format_and_content: CSV file containing log2 of normalized read counts (expression values).
 
Submission date Jul 11, 2018
Last update date Jul 16, 2018
Contact name Greg Gibson
Organization name Georgia Institute of Technology
Department Biological Sciences
Lab Gibson Lab
Street address 950 Atlantic Dr. NW
City Atlanta
State/province GA
ZIP/Postal code 30332
Country USA
 
Platform ID GPL21290
Series (1)
GSE116971 Whole Transcriptome RNASeq Data for Cell-Sorted Antibody Secreting Cells (ASC)
Relations
BioSample SAMN09643910
SRA SRX4382113

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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