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Sample GSM3261830 Query DataSets for GSM3261830
Status Public on Feb 06, 2020
Title GS RA24h RNA
Sample type SRA
Source name GS RA24h
Organism Mus musculus
Characteristics cell type: Germline stem (GS) cell line
Sex: male
treatment: 100 nM retinoic acid for 24 hours
Treatment protocol 100 nM retinoic acid was added to the culture media for times indicated in the file names. BAX shRNA lentivirus vectors (GAGATGAACTGGACAGCAATA, TCAAGGCCCTGTGCACTAAAG) were transduced to GS cells in order to suppress apoptosis in response to retinoic acid.
Growth protocol Germline stem (GS) cells (kindly provided by Dr Takashi Shinohara) were cultured on mitomycin C treated primary embryonic fibroblast (PEF) cells according to the previous report (Kanatsu-Shinohara et al., Biol Reprod., 2003, 69, 612-616) with minor modifications. Before GS cell sampling, PEF cells were removed by a differential attachment method to gelatin coated dishes following standard procedures. Embryonic stem (ES) cells (kindly provided by Dr Junichi Takeda) were grown in feeder-free naive state (2iLIF) conditions according to the previous report (Ying et al., Nature, 2008, 453, 519-523) with minor modifications. Primary embryonic fibroblast (PEF) cells were prepared from mouse embryos according to standard procedures and used for experiments at three to five passages .
Extracted molecule polyA RNA
Extraction protocol Total RNAs were extracted with Trizol reagent (Invitrogen) according to the manufacturer's instructions. Agilent 2100 bioanalyzer was used to assess the quality of total RNAs (RIN > 8).
Libraries were constructed from one microgram of total RNA using TruSeq RNA Sample Preparation Kit v2 (illumina) and sequenced by MiSeq with MiSeq Reagent Kit v2 (Illumina) .
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
Data processing RNA-seq reads were aligned to the mouse genome (mm10) using Hisat2 2.1.0.
Fragments per kilobase of exon per million mapped fragments (FPKM) were calculated by Cufflinks 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: Text files including FPKM values calculated by Cufflinks 2.2.1.
Submission date Jul 09, 2018
Last update date Feb 07, 2020
Contact name Shinichiro Chuma
Phone +81-75-751-3821
Organization name Kyoto university
Department Institute for Frontier Life and Medical Sciences
Lab Laboratory of Developmental Epigenome
Street address 53 Kawahara-cho, Shogoin, Sakyo-ku
City Kyoto
State/province Kyoto
ZIP/Postal code 606-8507
Country Japan
Platform ID GPL16417
Series (2)
GSE116779 Transcriptomic and epigenetic profiling of genome control in the germline stem cell cycle in mice [RNA-seq]
GSE116798 Transcriptomic and epigenetic profiling of genome control in the germline stem cell cycle in mice
BioSample SAMN09631361
SRA SRX4368809

Supplementary file Size Download File type/resource
GSM3261830_GS_RA24h_RNA_genes.fpkm_tracking.gz 1.4 Mb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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