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Status |
Public on Dec 20, 2019 |
Title |
EXP3-EGM_longRNA |
Sample type |
SRA |
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Source name |
BiologicalReplicate3.GrowthFactors_longRNA
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Organism |
Homo sapiens |
Characteristics |
tissue: Brain Microvascular Endothelial Cell commercial source: HBMVEC Cell Systems (Catalogue #ACBRI-376, Kirkland, WA, USA)
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Treatment protocol |
angiogenic growth factors; EGM-2 SingleQuot Kit Suppl. & Growth Factors (Lonza, Basel, Switzerland) supplemented with 5% EV-depleted FBS according to manufacturer protocol.
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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)
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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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
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Submission date |
Sep 27, 2019 |
Last update date |
Dec 20, 2019 |
Contact name |
Aleksandar Milosavljevic |
E-mail(s) |
amilosav@bcm.edu
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Organization name |
Baylor College of Medicine
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Department |
Genetics and Genomics
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Lab |
Bioinformatics Research Laboratory
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Street address |
1 Baylor Plaza
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City |
Houston |
State/province |
Texas |
ZIP/Postal code |
77030 |
Country |
USA |
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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 |
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Relations |
BioSample |
SAMN12863625 |
SRA |
SRX6917324 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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