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Status |
Public on Sep 27, 2016 |
Title |
PBMC_replicate_13 baseline low inflammation |
Sample type |
SRA |
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Source name |
PBMC
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Organism |
Homo sapiens |
Characteristics |
tissue: PBMC Sex: Male race: African American treatment: baseline inflammatory response: low
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Treatment protocol |
N/A
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Growth protocol |
N/A
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Extracted molecule |
polyA RNA |
Extraction protocol |
PBMCs were isolated from whole blood using magnetic bead selection (Dynabeads® CD14, ThermoFisher, Waltham MA), and frozen in TRIzol reagent (ThermoFisher, Waltham MA) for subsequent RNA extraction via standard protocol. Extracted RNA samples underwent quality control (QC) assessment using the Agilent Bioanalyzer (Agilent, Santa Clara, CA) and all RNA samples submitted for sequencing had an RNA Integrity Number (RIN) >6. Using a minimum of 300ng input RNA, Poly-A libraries were prepared using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) per standard protocols. The prepared libraries were sequenced on an Illumina HiSeq 2000 at the UPenn Next Generation Sequencing Core (NGSC). We sequenced samples at a depth of 1-2 samples per lane, which generated ~150-200 million 2×101 bp paired-end reads per sample.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
PBMC_low_pre_vs_post_gene_exp.diff.gz
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Data processing |
Base calling was done by RTA v1.13.48.0 Sequence reads were aligned to hg19 genome using STAR with default options. Alignment was filtered using the following specifications: 1) read was uniquely mapped, 2) reads from the same pair were mapped to the same chromosome with expected orientations and mapping distance between the read pair was < 500,000 bp Fragments Per Kilobase of exon per Million reads mapped (FPKM) was estimated by Cufflinks 2.1.1. Differential expression was tested by Cuffdiff with options "-u --max-bundle-frags 50000000". Annotation included mRNAs from RefSeq, stringent set of lincRNAs from Cabili et al. 2011 and lincRNAs from GENCODE v19. Genome_build: hg19 Supplementary_files_format_and_content: DIFF files were obtained from Cuffdiff output. Supplementary_files_format_and_content: PBMC_high_pre_vs_post_gene_exp.diff contains differential expression result from PBMC high responders. Annotation included mRNAs from GENCODE, lincRNAs from GENCODE and stringent set of lincRNAs form Cabili et al. sample_1 = baseline, sample_2 = post-LPS Supplementary_files_format_and_content: PBMC_low_pre_vs_post_gene_exp.diff contains differential expression result from PBMC low responders. Annotation included mRNAs from GENCODE, lincRNAs from GENCODE and stringent set of lincRNAs form Cabili et al. sample_1 = baseline, sample_2 = post-LPS
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Submission date |
Sep 22, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Chenyi Xue |
Organization name |
Columbia University
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Street address |
630 W 168th St.
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City |
New York |
State/province |
NY |
ZIP/Postal code |
10032 |
Country |
USA |
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Platform ID |
GPL11154 |
Series (1) |
GSE87290 |
RNA-seq of human peripheral blood mononuclear cells |
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Relations |
BioSample |
SAMN05806829 |
SRA |
SRX2187588 |
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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