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Sample GSM4100357 Query DataSets for GSM4100357
Status Public on Dec 20, 2019
Title EXP3-EBM2_longRNA
Sample type SRA
 
Source name BiologicalReplicate3.EBM_only_longRNA
Organism Homo sapiens
Characteristics tissue: Brain Microvascular Endothelial Cell
commercial source: HBMVEC Cell Systems (Catalogue #ACBRI-376, Kirkland, WA, USA)
Treatment protocol EBM_only
Growth protocol HBMVECs (500,000/well) were cultured on Matrigelâ„¢-coated (BD Matrigelâ„¢ 10mg/mL, BD Biosciences, Franklin Lakes, NJ, USA) wells in a 6-well plate in endothelial basal medium (EBM-2)
Extracted molecule total RNA
Extraction protocol Total RNA for this study was isolated from samples using the Qiagen (Exiqon) miRCURY RNA isolation kit.
RNA-sequencing was performed using the Clontech/Takara SMARTer Stranded Total RNA-seq PICO v2 kit (Clontech/Takara 634414) for long RNA expression profiling.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing base-calling: All libraries then had 75 bp paired end sequencing on the NextSeq500 with default parameters using a 150 cycle high output kit. Raw Illumina reads were quality filtered as follows. First, ends of the reads were trimmed to remove N's and bases with quality less than 20. After that the quality scores of the remaining bases were sorted and the quality at the 20th percentile was computed. If the quality at the 20th percentile was less than 15, the whole read was discarded. Also, reads shorter than 40 bases after trimming were discarded. If at least one of the reads in the pair failed the quality check and had to be discarded, we discarded the mate as well.
sample quality assessment: Prior to mapping for transcript-level quantification, to assess sample integrity all fastq files from long-RNA sequencing runs were uploaded to the Genboree workbench and mapped to hg19 and all exogenous genomes using the exceRpt [v4.6.3] small RNA-seq pipeline (Kaczor-Urbanowicz et. al., 2017). Biological Replicate 2 was excluded due to low sample quality.
read quality filtering: Data quality assessment and read clipping was performed using TrimGalore [v0.4.1] with CutAdapt [v1.15] and FastQC[v0.11.6] (Martin 2011).
alignment: Paired-reads were mapped simultaneously to the GRCh37.83 cDNA and ncRNA transcriptomes (Kinsella et.al., 2011) using Kallisto[v0.44.0] (Bray et. al., 2016). Kallistos were imported to R with tximport. All reads mapping to ncRNA were excluded from the analysis, then transcript abundances were aggregated by Ensembl Gene ID. Genes with less than 10 reads across all samples were excluded from further analysis.
Differential transcript abundance was characterized by DeSeq2 with EBM as the baseline for all treatments, and samples treated as paired within replicates. Threshold values for differential expression were set at 2 and 0.05, respectively, for fold change and adjusted p-value.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab delimited, transcript abundance fold change, p-value
 
Submission date Sep 27, 2019
Last update date Dec 20, 2019
Contact name Aleksandar Milosavljevic
E-mail(s) amilosav@bcm.edu
Organization name Baylor College of Medicine
Department Genetics and Genomics
Lab Bioinformatics Research Laboratory
Street address 1 Baylor Plaza
City Houston
State/province Texas
ZIP/Postal code 77030
Country USA
 
Platform ID GPL18573
Series (2)
GSE138113 Glioma-derived miRNA-containing extracellular vesicles induce angiogenesis by reprogramming brain endothelial cells (longRNA-seq)
GSE138115 Glioma-derived miRNA-containing extracellular vesicles induce angiogenesis by reprogramming brain endothelial cells
Relations
BioSample SAMN12863626
SRA SRX6917323

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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