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Sample GSM2326902

Query DataSets for GSM2326902

Status

Public on Sep 27, 2016

Title

PBMC_replicate_1 intravenous LPS high inflammation

Sample type

SRA

Source name

PBMC

Organism

Homo sapiens

Characteristics

tissue: PBMC
Sex: Female
race: African American
treatment: intravenous LPS
inflammatory response: high

Treatment protocol

N/A

Growth protocol

N/A

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.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

PBMC_high_pre_vs_post_gene_exp.diff.gz

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

Submission date

Sep 22, 2016

Last update date

May 15, 2019

Contact name

Chenyi Xue

Organization name

Columbia University

Street address

630 W 168th St.

City

New York