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| Status |
Public on Oct 07, 2019 |
| Title |
E7-0-ExE-INPUT_rep2 |
| Sample type |
SRA |
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| Source name |
mouse embryos
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| Organism |
Mus musculus |
| Characteristics |
antibody: none
strain: ICR
devlopmental stage: 7.0 dpc
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| Growth protocol |
Embryo were collected from pregnant mice at 6.5, 7.0 and 7.5 dpc; stem cells were cultured under regular condition.
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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 from embryo samples were separated and extracted by modified microChIP or single cell based bisulfite seq.
Libraries of RNA samole were generated by using illumina Nextera XT DNA sample preparation kit; 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,2015).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| 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 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"
For the integrated HMM_state_15.enhancerRegion processed data, we show genome-wide 200bp tiles of ChromHMM results for enhancers. Only 4 types of enhancers identified by ChromHMM were annotated, 1 for bivalent, 2 for poised, 3 for active and 4 for double acylated enhancers. Other types were annotated as 0.
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. The "merge.dexseq_clean_refseq.gene.all.xls" file include the expression (FPKM) of all the RefSeq genes for eaach sample. The bigwig files for ChIP-Seq show the genome wide coverge minus the input. The "HMM_state_15.enhancerRegion.kmeans.subKmeans.mergeAll.xls.gz" file includes the integrated analysis of all the sequenced epigenetic markers of this project.
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| Submission date |
Apr 24, 2017 |
| Last update date |
Oct 07, 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) |
| GSE98101 |
Spatial-temporal epigenetic landscape of mouse gastrula |
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| Relations |
| BioSample |
SAMN06827119 |
| SRA |
SRX2761275 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2587130_E7-0-ExE-INPUT_rep2.sort.tagAlign.gz |
192.3 Mb |
(ftp)(http) |
TAGALIGN |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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