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Sample GSM2803362

Query DataSets for GSM2803362

Status

Public on Mar 16, 2018

Title

Y27_ExE_EPZ_RNA

Sample type

SRA

Source name

mouse embryos

Organism

Mus musculus

Characteristics

strain: ICR
treatment: specific inhibitor of EZH2, EPZ005687 (Selleck, S7004)

Treatment protocol

For samples from Y25,Y26,Y27, the specific inhibitor of EZH2, EPZ005687 (Selleck, S7004), were added in the explant culture of mouse embryo. Embryos are cultured in N2B27 medium for 48 hrs. For samples from Y34, Y35, Y36, equivalent volume of DMSO were added as control group.

Growth protocol

Embryo were collected from pregnant mice at 6.5, 7.0 and 7.5 dpc

Extracted molecule

polyA RNA

Extraction protocol

RNA from embryo samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier; Genomic DNA acquired from ChIP assay (H3K27me3, merck millipore, catlog number: 07-449, lot number: 2275589) of embryo samples were separated and extracted by microChIP. Genomic DNA acquired from embryos were separated and extracted followed by bisulfite sequencing
Libraries of genomic DNA were construted by using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #7370L); libraries of genomic DNA were construted by using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #7370L); libraries of single cell based bisulfite seq were constructed according to the protocol described in (H Guo et al, Nature Protocol 10(5):645-59).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
For RNA-seq data, trimmed clean reads were aligned to mouse reference genome (mm10) using TopHat (v2.0.9) with the default parameters
For Bisulfite seq, the trimmed reads were mapped to mm10 mouse genome following our modified bisulfite sequencing pipeline.(H Guo et al, Nature Protocol 10(5):645-59)
For the ChIP-seq data, the trimmed reads were mapped to the mouse genome (mm10 assembly) using BWA sligner (version 0.7.5a-r405) with the options "-I 15 -q 10 -t 4"
Genome_build: mm10
Supplementary_files_format_and_content: The bigwig files for RRBS data include the DNA methylation level of each single CpG site. The tagAlign files show the bed files for aligned reads.

Submission date

Oct 03, 2017

Last update date

May 15, 2019

Contact name

Naihe Jing

E-mail(s)

njing@sibcb.ac.cn

Organization name

shanghai institute of biochemistry and cell biology

Street address

Yueyang Road 320