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Sample GSM2341388 Query DataSets for GSM2341388
Status Public on Jun 12, 2017
Title FGSCs rep3
Sample type SRA
 
Source name FGSCs
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: ovary
cell type: germline stem cells
age: 6 days
Extracted molecule total RNA
Extraction protocol Total RNA from the SSCs and FGSCs were isolated using TRIzol reagent (Invitrogen, life Technologies, USA) according to the manufacturer's protocol. Total RNA from each sample was quantified using Agilent 2100, and RNA integrity was assessed using Agilent 2100.
After extracting the total RNA from samples, mRNA and non-coding RNAs are enriched by removing rRNA from the total RNA with kit. By using the fragmentation buffer, the mRNAs and non-coding RNAs are fragmented into short fragments (about 200~500nt), then the first-strand cDNA is synthesized by random hexamer-primer using the fragments as templates, and dTTP is substituted by dUTP during the synthesis of the second strand. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters, then the second strand is degraded using UNG(Uracil-N-Glycosylase) finally. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000 when necessary.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Alignment/mapping reads to reference genome by TopHat2
Transcripts assembling by Cufflinks
Merge assembles by Cuffmege
Coding potential calculation by CNCI and CPC
The genes expression levels were estimated by FPKM (fragments per kilobase of exon per million fragments mapped) and assessed using Cuffdiff v2.1.1
Genome_build: UCSC mm10
Supplementary_files_format_and_content: RPKM values for novel lncRNAs
 
Submission date Oct 11, 2016
Last update date May 15, 2019
Contact name Ji Wu
E-mail(s) jiwu@sjtu.edu.cn
Organization name Shanghai Jiao Tong University
Street address No.800, Dongchuan Road, Minhang District
City Shanghai
ZIP/Postal code 200240
Country China
 
Platform ID GPL13112
Series (1)
GSE87824 Systematic identification and comparison of expressed profiles of lncRNAs and circRNAs in male and female germline stem cells
Relations
BioSample SAMN05894736
SRA SRX2236906

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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