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Sample GSM5060377 Query DataSets for GSM5060377
Status Public on Sep 15, 2021
Title ES Control_2
Sample type SRA
 
Source name ES cells
Organism Mus musculus
Characteristics cell type: ICM-derived ES cells
treatment: untreated
Treatment protocol ES cells was treated with CX-5461
Growth protocol Mouse ES cells and iPS cells were cultured on 0.1% gelatin-coated plates with MEF feeder cells in LIF/2i media for 2 days.
Extracted molecule total RNA
Extraction protocol Cells were dissociated with Trypsin for 5 min, stopped with serum containing media, and depleted with MEF for at least half-an-hour, and total RNA was extracted by TRIzon
A total amount of 2 μg RNA per sample was used as input materials for the RNA sample preparation. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Purified mRNA was fragmentated at 94 °C for 15 min by using divalent cations under elevated temperature in NEBNext first strand synthesis reaction buffer (5X). First strand cDNA was synthesized using random primer and ProtoScript II reverse transcriptase in a preheated thermal cycler as follows: 10 min at 25 °C; 15 min at 42 °C; 15 min at 70 °C. Immediately finished, second strand synthesis reaction was performed by using second strand synthesis reaction buffer (10X) and enzyme mix at 16 °C for 1 hr. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair, A-tailing and adapter added were implemented. The products were retrieved and PCR was performed for library enrichment. The libraries were sequenced on an Illumina platform.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description gene_TPM_ES.xlsx
Data processing Basecalls performed using CASAVA version 1.8
All bulk RNA-seq reads were trimmed using Trimmomatic software with the following parameters “ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36” (Version 0.36). and were further quality-filtered using FASTX Toolkit’s fastq_quality_trimmer command (Version 0.0.13, http://hannonlab.cshl.edu/fastx_toolkit/) with the minimum quality score 20 and minimum percent of 80% bases that has a quality score larger than this cutoff value.
The high-quality reads were mapped to the mm10 genome by HISAT2, a fast and sensitive spliced alignment program for mapping RNA-seq reads, with -dta paramenter. PCR duplicate reads were removed using Picard tools and only uniquely mapped reads were kept for further analysis.
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: mm10
Supplementary_files_format_and_content: xlsx, gene expression level (TPM)
 
Submission date Feb 02, 2021
Last update date Sep 15, 2021
Contact name Hua Yu
E-mail(s) huayu@zju.edu.cn
Phone 18758008246
Organization name Zhejiang University
Street address 866 Yuhangtang Rd
City Hangzhou
ZIP/Postal code 310058
Country China
 
Platform ID GPL17021
Series (2)
GSE166025 rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin [RNA-seq]
GSE166041 rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin
Relations
BioSample SAMN17764418
SRA SRX10008314

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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