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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 16, 2018 |
| Title |
E7-5-A-RRBS-rep2 |
| Sample type |
SRA |
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| Source name |
mouse embryos
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| Organism |
Mus musculus |
| Characteristics |
strain: ICR
developmental stage: 7.5 dpc
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| 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.
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| Growth protocol |
Embryo were collected from pregnant mice at 6.5, 7.0 and 7.5 dpc
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| Extracted molecule |
genomic DNA |
| 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).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
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| 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.
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| Submission date |
Oct 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Naihe Jing |
| E-mail(s) |
njing@sibcb.ac.cn
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| Organization name |
shanghai institute of biochemistry and cell biology
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| Street address |
Yueyang Road 320
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| City |
Shanghai City |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE104243 |
Distinct distribution of H3K27me3 and DNA methylation stabilizes the segregation of extraembryonic and embryonic lineages |
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| Relations |
| BioSample |
SAMN07735608 |
| SRA |
SRX3241631 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2803353_E7-5-A_RRBS_R2.bw |
6.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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