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| Status |
Public on Jul 12, 2018 |
| Title |
PB1438Pop3 |
| Sample type |
SRA |
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| Source name |
ASC, Pop3
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| Organism |
Homo sapiens |
| Characteristics |
samplenum: SL14383
samplename: PB1438Pop3
individual: 1438
cellpopulation: Pop3
cell type: Antibody Secreting Cell
tissue: Peripheral Blood
batch: B2
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| Growth protocol |
FACS-based purified ASCs
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
957983D71438Pop3S54
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| 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).
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| Submission date |
Jul 11, 2018 |
| Last update date |
Jul 16, 2018 |
| Contact name |
Greg Gibson |
| Organization name |
Georgia Institute of Technology
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| Department |
Biological Sciences
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| Lab |
Gibson Lab
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| Street address |
950 Atlantic Dr. NW
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| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30332 |
| Country |
USA |
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| Platform ID |
GPL21290 |
| Series (1) |
| GSE116971 |
Whole Transcriptome RNASeq Data for Cell-Sorted Antibody Secreting Cells (ASC) |
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| Relations |
| BioSample |
SAMN09643902 |
| SRA |
SRX4382121 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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