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Sample GSM3581271 Query DataSets for GSM3581271
Status Public on Jan 29, 2019
Title mcBKSM_clone_1
Sample type SRA
Source name induced neural stem cell
Organism Mus musculus
Characteristics strain: C57BL/6-Pou5f1 x 129X1/SvJ
tissue: Embryonic fibroblast
age: E13.5
genotype: Oct4-CreER x Rosa26-loxSTOPlox-EYFP mouse
Growth protocol Mouse embryonic fibroblasts(MEFs) were derived from genetically modifed mouse embryos at embryonic day 13.5 after carefully removing the head and all the internal organs including the spinal cord. Control neural stem cell(cNSCs) were extracted from cerebral cortex of embryo at embryonic day 13.5. induced iNSCs were generated by using polycistronic vector or monocistronic vector. MEFs were infected with lentivirus or retrovirus and induced with neural stem cell medium.
Extracted molecule total RNA
Extraction protocol RNA-Seq experiments with pooled RNA samples extracted from 2-3 biological replicates
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 mm10 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: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Submission date Jan 28, 2019
Last update date Feb 04, 2019
Contact name Chanhyeok Park
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 (1)
GSE125740 Fusion of reprogramming factors alters trajectory of somatic lineage conversion
BioSample SAMN10830155
SRA SRX5299574

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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