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Sample GSM1131343 Query DataSets for GSM1131343
Status Public on Jan 01, 2014
Title PR+LPS+P_8h
Sample type SRA
 
Source name primary HUVECs
Organism Homo sapiens
Characteristics cell type: primary human umbilical vein endothelial cells
passage: 4-6
infected with: a lentivirus containing human PR
treated with: LPS (1μM) + progesterone (100nM) for 8 hrs
Treatment protocol Primary HUVECS were infected at passage 4 with a lentivirus containing human PR, then split onto 10cm dishes and grown to confluence. Three days after they reached confluence they were treated with LPS (1μM) and/or progesterone (100nM) for 4 or 8 hours, then harvested for the experiment.
Growth protocol HUVECs (VEC Technologies, Rensselaer, NY), passages 4-6, were cultured in MCDB-131 (VEC Technologies, Rensselaer, NY) with the addition of 10% fetal bovine serum (Omega Scientific, Tarzana, CA) that was stripped using 0.25% dextran coated charcoal (Sigma, St. Louis, MO).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using RNeasy Kit (Qiagen, Valencia, CA) according to manufacturer instructions.
The library for sequencing was constructed using an Illumina Multiplex System according to manufacturer's instructions (Illumina, San Diego, CA). Libraries were sequenced using HIseq-2000 (Illumina, San Diego, CA) to obtain 50 bp long reads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Sample 6
Data processing Debarcoding of the multiplex runs was performed using in house shell script
Reads were then processed and aligned to the human genome (hg19) using TopHat v2.0.4 (Trapnell et al., 2009) with default parameters.
The aligned read files were further processed with Cufflinks v2.0.1 (Trapnell et al., 2010) to calculate RPKP values. Assemblies for all samples were merged using CuffMerge and differential expression was determined using Cuffdiff. Genes with a p-value smaller than 0.01 where considered as differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample and Excel table final lists of differentially expressed genes
 
Submission date Apr 30, 2013
Last update date May 15, 2019
Contact name Lauren Goddard
Organization name University of California-Los Angeles
Department Molecular, Cell, and Developmental Biology
Lab Dr. Luisa Iruela-Arispe
Street address 621 Charles E. Young Dr. S.
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL11154
Series (2)
GSE46502 Selective suppression of endothelial cytokine production by progesterone receptor [RNA-seq]
GSE46503 Selective suppression of endothelial cytokine production by progesterone receptor
Relations
BioSample SAMN02087538
SRA SRX272854

Supplementary file Size Download File type/resource
GSM1131343_PR+LPS_8h+P_transcripts.gtf.gz 4.2 Mb (ftp)(http) GTF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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