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Sample GSM2673310 Query DataSets for GSM2673310
Status Public on Dec 25, 2022
Title TR10 RNA-seq rep1
Sample type SRA
 
Source name ES Cell
Organism Mus musculus
Characteristics cell type: ESC
genotype: Terc rescued
strain: C57BL/6
chip antibody: none
Growth protocol The embryonic stem cells were cultured on feeder in medium consisted of knock-out DMEM (Invitrogen) containing 20% FBS (HyClone), 1,000 U/ml mouse leukemia inhibitory factor (LIF; ESG1107, Millipore), 0.1 mM non-essential amino acids, 0.1 mM β-mercaptoethanol, 1 mM L-glutamine, penicillin (100 U/ml) and streptomycin (100 μg/ml). For the culture of ESCs, the medium was changed daily, and cells were routinely passaged every two days.
Extracted molecule total RNA
Extraction protocol For RNA-seq, total RNA was purified using an RNA mini kit (Qiagen) and treated with DNase I (Qiagen).
For RNA-seq, total RNA were poly(A) enriched with oligo(T) beads and RNA libraries were prepared for sequencing using standard Illumina protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Raw RNA-seq reads were firstly aligned to the mouse genome (version: UCSC mm10) using STAR (version 2.5.1). To study the expression of repeat elements, for read with multiple hits, only one hit was randomly picked as final alignment by setting STAR parameter as “—outSAMprimaryFlag AllBestScore –outSAMmultNmax 1”. The CUFFDIFF (v2.2.1) was used to identify differential gene expression.
genome build: mm10
processed data files format and content: bedgraph file generated using Bedtools
 
Submission date Jun 19, 2017
Last update date Dec 25, 2022
Contact name Xinyi Lu
E-mail(s) rnagenomics@foxmail.com
Organization name Nankai University
Street address 94 Weijin Road
City Tianjin
ZIP/Postal code 300071
Country China
 
Platform ID GPL21273
Series (2)
GSE100168 Telomeres suppress the activity of retrotransposons in pluripotent stem cells [exp1]
GSE118027 Telomeres suppress the activity of retrotransposons in pluripotent stem cells
Relations
BioSample SAMN07252381
SRA SRX2931284

Supplementary file Size Download File type/resource
GSM2673310_TelRec_rep1_R1.bedgraph.gz 173.6 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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