 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 02, 2014 |
| Title |
A_blood_postLPS |
| Sample type |
SRA |
| |
|
| Source name |
blood, post-LPS
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: healthy
tissue: blood
treatment: LPS
time point: 2 hr post-LPS
subject: individual A
|
| Treatment protocol |
Each clinical study was performed with approval of the University of Pennsylvania (U.Penn) Institutional Review Board after written informed consent was obtained from all research participants. The Genetics of Evoked-responses to Niacin and Endotoxemia (GENE) study is a single-center U.Penn-based National Institute of Health-sponsored experimental endotoxemia protocol (NIH.gov clinical trial NCT00953667). Briefly, the GENE study recruited healthy African-American or Caucasian individuals (N = 284, 33% African Americans, age 18-45) to an inpatient protocol that included a pre-LPS acclimatization phase, administration of intravenous LPS bolus (1ng/kg U.S. standard reference endotoxin), and a 30 hour post-LPS phase. Multiple clinical and biochemical variables were recorded. Whole blood RNA samples were collected in Qiagen PAX gene tubes at baseline, 1, 2, 4, 6, 12, and 24 hours post-LPS. Samples of gluteal subcutaneous fat tissue were obtained at baseline, 4, 12 and 24 hours following LPS as previously described and snap-frozen for subsequent RNA extraction. In this report, we focus initially on a self-reported European Ancestry (EA) individual (subject A) for deep RNA-seq. To enrich discovery of evoked transcriptome responses, subject A was chosen from those with above median inflammatory response to LPS. Selective findings in subject A were assessed for replication in additional GENE study participants (n=6) chosen also from those with above average inflammatory response. Based on previous mRNA profiling, we selected baseline and 2-hr blood samples, and baseline and 4-hr adipose samples for RNA-seq.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA samples were extracted using the RNeasy Lipid Tissue total RNA mini kit (Qiagen, Valencia, CA). 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, with a minimum of 1µg input RNA. Poly-A library preparation and sequencing were performed at the Penn Genome Frontiers Institute's High-Throughput Sequencing Facility per standard protocols. Briefly, we generated first-strand cDNA using random hexamer-primed reverse transcription, followed by second-strand cDNA synthesis using RNase H and DNA polymerase, and ligation of sequencing adapters using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA). Fragments of ~350 bp were selected by gel electrophoresis, followed by 15 cycles of PCR amplification. The prepared libraries were then sequenced using Illumina's HiSeq 2000 with four lanes per sample which generated 2×101 bp paired-end reads generating ~1,000 million reads for adipose and blood samples. We also performed RNA-seq of replicate samples from subject A at lower sequencing depth (~50 million reads/sample) for comparison of findings at different RNA-seq depths.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
polyA RNA
Processed data file: lincRNA_A_blood_gene_exp.diff
|
| Data processing |
Generate lincRNA expression by Cufflinks v1.3.0. For linc-RNAs, we obtained the locations of 4,662 pre-defined linc-RNAs based on RNA-seq data from 24 different human tissues and that also met the following criteria: at least one isoform of the linc-RNA was reconstructed in at least two different tissues or by two assemblers in the same tissue. For consistency across tissues, we included linc-RNAs that were expressed at either time point at FPKM >0. For each linc-RNA, we compared the estimated expression level pre- and post-LPS within the same tissue for a given individual using the cuffdiff option in Cufflinks version 1.3.0. Our analysis of differential expression (DE) involves only one sample in each group.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Standard Cufflink outputs, tab-delimited text files including FPKM values and FDR adjusted p-values.
Supplementary_files_format_and_content: lincRNA_A_adipose_exp.diff contains the expressed lincRNA for adipose tissue of subject A (900M reads). sample_1 = pre-LPS, sample_2 = post-LPS.
Supplementary_files_format_and_content: lincRNA_A_blood_exp.diff contains the expressed lincRNA for blood tissue of subject A (900M reads). sample_1 = pre-LPS, sample_2 = post-LPS.
Supplementary_files_format_and_content: lincRNA_A_adipose_replicate_exp.diff contains the expressed lincRNA for adipose tissue of technical replicate of subject A in much lower depth (67M reads). sample_1 = pre-LPS, sample_2 = post-LPS.
Supplementary_files_format_and_content: lincRNA_A_blood_replicate_exp.diff contains the expressed lincRNA for blood tissue of technical replicate of subject A in much lower depth (67M reads). sample_1 = pre-LPS, sample_2 = post-LPS.
|
| |
|
| Submission date |
Sep 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Chenyi Xue |
| Organization name |
Columbia University
|
| Street address |
630 W 168th St.
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE39118 |
RNA-Seq and expression data from human adipose tissue |
| GSE50792 |
Tissue-specific RNA-seq in human evoked inflammation identifies novel blood and adipose lincRNA signatures of cardio-metabolic diseases |
|
| Relations |
| BioSample |
SAMN02354072 |
| SRA |
SRX348813 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
