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| Status |
Public on Jan 01, 2014 |
| Title |
PR_PR_infected [RNA-Seq] |
| Sample type |
SRA |
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| Source name |
primary HUVECs
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| Organism |
Homo sapiens |
| Characteristics |
cell type: endothelial cells
passage nr.: 4-5
treatment: PR infected
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| 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 progesterone (100nM) for 4 hours, then harvested for the experiment.
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| Growth protocol |
HUVECs, 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).
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
RNA-seq
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| 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 PR and PR+P endothelial cells 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
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| Submission date |
Jan 27, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Lauren Goddard |
| Organization name |
University of California-Los Angeles
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| Department |
Molecular, Cell, and Developmental Biology
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| Lab |
Dr. Luisa Iruela-Arispe
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| Street address |
621 Charles E. Young Dr. S.
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE43788 |
Physiological Vascular Permeability Requires Induction of Endothelial NR4A1 by Progesterone Receptor [RNA-Seq] |
| GSE43789 |
Physiological Vascular Permeability Requires Induction of Endothelial NR4A1 by Progesterone Receptor |
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| Relations |
| SRA |
SRX220059 |
| BioSample |
SAMN01906474 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1071304_PR_transcripts.gtf.gz |
4.0 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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