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| Status |
Public on Oct 01, 2015 |
| Title |
sub081 |
| Sample type |
SRA |
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| Source name |
PBMC
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| Organism |
Homo sapiens |
| Characteristics |
collectiondate: 2013-10-01
rin: 8.8
tissue: Peripheral blood mononuclear cells (PBMCs)
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| Treatment protocol |
na
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| Growth protocol |
n/a
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| Extracted molecule |
total RNA |
| Extraction protocol |
Peripheral blood mononuclear cells (PBMCs) were harvested by Ficoll gradient from whole blood, and immediately placed in lysis solution to eliminate nuclease activity for RNA isolation. RNA was extracted using the Qiagen RNeasy Mini Kit.
RNA libraries were prepared for sequencing according to "Next-Generation Sequencing RNA-Seq Library Construction", Podnar et. al. Curr Protoc Mol Bio 106:4.21, 2014.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Illumina RTA version 1.17 used for base calling, and Casava version 1.8 used for extraction from BCL to fastq format
Paired-end reads aligned to hg19 reference assembly using bowtie 2.2.2 via tophat 2.0.11: tophat --rg-id Paired --rg-library RNAseq --rg-platform ILLUMINA --mate-inner-dist 100 --b2-very-sensitive -p 15 -r 250
Per-gene read counts were obtained using htseq-count [HTSeq package, version 0.5.4p5]
Read counts were normalized for library size using the estimateSizeFactors function [DeSeq package, version 1.14.0], and genes were then filtered for a mean read count across sessions of at least 4 and no more than 10,000,
Variance-stabilized read counts were obtained using the varianceStabilizingTransformation in DeSeq (version 1.14.0).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files including gene names and variance-stabilized per-gene read counts
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| Submission date |
May 30, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Russell Poldrack |
| E-mail(s) |
poldrack@gmail.com
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| Phone |
15122329504
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| Organization name |
University of Texas at Austin
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| Street address |
100 East 24th Street, R9975
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| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE58122 |
Serial RNA-seq of a single human |
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| Relations |
| BioSample |
SAMN02808342 |
| SRA |
SRX556238 |
| 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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