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Sample GSM2808237 Query DataSets for GSM2808237
Status Public on Oct 10, 2018
Title Cont_LEC
Sample type SRA
 
Source name Lymphatic endothelial cell
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Skin
age: E15.5
genotype: Wild type
Growth protocol Primary mouse dermal LECs derived from C57BL/6 embryos were obtained and maintained in complete mouse endothelial cell media with supplements (C57-6064L & M1168, Cell Biologics). All the in vitro cell culture experiments was performed within passage 5.
Extracted molecule total RNA
Extraction protocol RNA-Seq experiments with pooled RNA samples extracted from 2-3 biological replicates were performed. Total RNA was extracted from control and Dot1lΔEC skin LECs using RNeasy Plus Mini Kit (74134, Qiagen) and its amount and quality of the total RNA were evaluated using Bioanalyzer (Agilent). RNA samples with >7.0 RNA Integrity Number (RIN) value were used for RNA-Seq library preparation with the ScriptSeq v2 kit (Illumina) according to manufacturer’s instruction.
Libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
 
Data processing Paired-end sequencing reads were mapped to mm9 mouse genome using STAR tool(v2.5.2b).
After mapping, fragments per kilobase million (FPKM) was calculated by Cufflinks (v2.2.1) tool using the following strand-specific Cuffnorm option: --library-type=fr-second strand.
Functional annotation of differentially expressed genes (DEGs) and enrichment analyses were performed using DAVID (v6.8) and Gene Set Enrichment Analysis (GSEA, v2.2.4), respectively, and genes were considered differentially expressed at the fold change > 3 and FPKM > 5. R (v3.3.2) package was used for statistical analyses and scatter plot generation, and RNA-Seq results were visualized using Integrative Genomics Viewer (IGV).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
 
Submission date Oct 11, 2017
Last update date May 15, 2019
Contact name Chanhyeok Park
E-mail(s) chpark0729@gmail.com
Organization name Konkuk University
Department Stem cell and regeneration biotechnology
Lab Hong lab
Street address 120, Neungdong-ro
City Seoul
ZIP/Postal code 05066
Country South Korea
 
Platform ID GPL16417
Series (2)
GSE104810 Genome-wide mapping of H3K79me2 in EPZ5676-treated lymphatic endothelial cells [RNA-Seq]
GSE104811 Genome-wide mapping of H3K79me2 in EPZ5676-treated lymphatic endothelial cells
Relations
BioSample SAMN07774292
SRA SRX3269794

Supplementary file Size Download File type/resource
GSM2808237_Cont_LEC.txt.gz 136.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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