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| Status |
Public on Aug 10, 2017 |
| Title |
hPC_1.1KD HypER |
| Sample type |
SRA |
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| Source name |
human primary pericytes
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| Organism |
Homo sapiens |
| Characteristics |
cell type: human primary pericytes
passage: passage 2-9
treatment: HypERrlnc knockdown LNA GapmeR
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| Treatment protocol |
Hypoxia was induced using a hypoxic incubator (Labotect, Göttingen, Germany). Cell culture medium was pre-equilibrated overnight at 1% O2, 5% CO2 in a humidified atmosphere. Normoxic cell culture medium was carefully switched to hypoxic medium and hypoxic pO2 levels were verified by measuring VEGFA induction by qPCR and pO2 levels with a hypoxia sensing probe from Oxford Optronix (Oxford, UK) as described in detail before (Zehendner et al. Plos One 2013). Cells were transfected after reaching a confluency of 60-80% using Opti-MEM Medium, Lipofectamine RNAiMAX (both from Life technologies, Carlsbad, CA, USA) and 50 nmol/l of LNA GapmeR (Exiqon, Vedbaek, Denmark). After 4h transfection medium was exchanged to the appropriate cell culture medium. 48h upon transfection RNA was isolated and processed for RNA Sequencing.
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| Growth protocol |
Human pericytes (passages 2-9; from ScienCell, Carlsbad, CA, USA) were cultured as recommended by the manufacturer. Cells were kept at 5% CO2, 20% O2, 37°C and humidified atmosphere. Pericyte medium consisted of DMEM Glutamax (Gibco, Life Technologies, Carlsbad, CA, USA) supplemented with Penicillin/Streptomycin (Roche Diagnostics) and 10% fetal calf serum. Primary mouse brain pericytes were isolated and cultured as documented in detail (Tigges et al. Microvascular Research 84 (2012) 74–80).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA deep sequencing was performed by analyzing ribosomal depleted total RNA from human pericytes. RNA was isolated using a RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions including DNA digestion.
RNA was fragmented and primed for cDNA synthesis. Human samples: Libraries were created using a NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina as recommended by the manufacturer. Mouse sample libraries were created using a Scriptseq v2 Kit from Illumina SSV21124 as recommended by the manufacturer.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
total RNA ribosomal depleted
HypERrlnc knockdown with LNA GapmeR
human PC HypERrlnc KD_FPKM.txt
hPC_1KD
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| Data processing |
(RNA-SEQ) Reads were mapped with Tophat default parameters to MM10 (mouse brain primary pericytes), or GRCH38 (human primary pericytes). Afterwards Cufflinks was utilized with the default attributes for gene quantification.
Genome_build: MM10 (mouse brain primary pericytes), or GRCH38 (human primary pericytes)
Supplementary_files_format_and_content: Tab delimited text file which includes FPKM values for each sample
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| Submission date |
Dec 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Christoph Michael Zehendner |
| Organization name |
Goethe University
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| Street address |
Theodor Stern Kai 7
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| City |
Frankfurt am Main |
| ZIP/Postal code |
60590 |
| Country |
Germany |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE92887 |
Impact of HypERrlnc Knockdown on the human pericyte transcriptome |
| GSE92888 |
Long non-coding control of pericyte function |
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| Relations |
| BioSample |
SAMN06179974 |
| SRA |
SRX2443293 |
| 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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