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| Status |
Public on Oct 07, 2019 |
| Title |
Spatial-temporal epigenetic landscape of mouse gastrula |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
|
| Summary |
Regionalized lineage progenitor cells emerged from the onset of gastrulation would facilitate mouse embryonic patterning and build a blueprint for future development. However, the molecular mechanism especially the epigentic mechanism underlying the formation and development of lineage restricted cells has not been fully unveiled. Here,we present a comprehensive landscape of H3K4me3, H3K4me1, H3K9ac, H3K27ac, H3K27me3 and DNA methylation pattern in mouse embryo from pre-streak stage to late-streak stage, and fully analyze the epigenetic mechansim driving the embryonic patterning of mouse gastrula
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| Overall design |
To obtain a comprehensive epigenetic landscape of mouse gastrulation and the corresponding lineage development process, we have dissected mouse gastrula from pre-steak stage (E6.5) to late streak stage (E7.5)19 into extra-embryonic (ExE) and embryonic parts, and embryonic parts of E7.0 and E7.5 embryos will be further divided into sub-regions (A, P, AM) due to the emergence of embryo asymmetry.
|
| Web link |
https://www.nature.com/articles/s41422-019-0234-8
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| |
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| Contributor(s) |
Yang X, Hu B, Hou Y, Qiao Y, Tang F, Jiang N |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Apr 24, 2017 |
| Last update date |
Jul 25, 2021 |
| 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
|
| City |
Shanghai City |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (120)
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|
| Relations |
| BioProject |
PRJNA384051 |
| SRA |
SRP105106 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE98101_E6-5-Epi-K27ac.tagAlign.fc.signal.bw |
1.1 Gb |
(ftp)(http) |
BW |
| GSE98101_E6-5-Epi-K4M3.tagAlign.fc.signal.bw |
625.9 Mb |
(ftp)(http) |
BW |
| GSE98101_E6-5-Epi-K4me1.tagAlign.fc.signal.bw |
1.3 Gb |
(ftp)(http) |
BW |
| GSE98101_E6-5-Epi-K9ac.tagAlign.fc.signal.bw |
1.2 Gb |
(ftp)(http) |
BW |
| GSE98101_E6-5-ExE-K27ac.tagAlign.fc.signal.bw |
1.1 Gb |
(ftp)(http) |
BW |
| GSE98101_E6-5-ExE-K4M3.tagAlign.fc.signal.bw |
602.1 Mb |
(ftp)(http) |
BW |
| GSE98101_E6-5-ExE-K4me1.tagAlign.fc.signal.bw |
1.2 Gb |
(ftp)(http) |
BW |
| GSE98101_E6-5-ExE-K9ac.tagAlign.fc.signal.bw |
1020.1 Mb |
(ftp)(http) |
BW |
| GSE98101_E7-0-A-K27ac.tagAlign.fc.signal.bw |
1.1 Gb |
(ftp)(http) |
BW |
| GSE98101_E7-0-A-K4M3.tagAlign.fc.signal.bw |
507.2 Mb |
(ftp)(http) |
BW |
| GSE98101_E7-0-A-K4me1.tagAlign.fc.signal.bw |
1.1 Gb |
(ftp)(http) |
BW |
| GSE98101_E7-0-A-K9ac.tagAlign.fc.signal.bw |
947.1 Mb |
(ftp)(http) |
BW |
| GSE98101_E7-0-ExE-K27ac.tagAlign.fc.signal.bw |
1.1 Gb |
(ftp)(http) |
BW |
| GSE98101_E7-0-ExE-K4M3.tagAlign.fc.signal.bw |
568.4 Mb |
(ftp)(http) |
BW |
| GSE98101_E7-0-ExE-K4me1.tagAlign.fc.signal.bw |
1.1 Gb |
(ftp)(http) |
BW |
| GSE98101_E7-0-ExE-K9ac.tagAlign.fc.signal.bw |
1.1 Gb |
(ftp)(http) |
BW |
| GSE98101_E7-0-P-K27ac.tagAlign.fc.signal.bw |
1.1 Gb |
(ftp)(http) |
BW |
| GSE98101_E7-0-P-K4M3.tagAlign.fc.signal.bw |
660.1 Mb |
(ftp)(http) |
BW |
| GSE98101_E7-0-P-K4me1.tagAlign.fc.signal.bw |
1.2 Gb |
(ftp)(http) |
BW |
| GSE98101_E7-0-P-K9ac.tagAlign.fc.signal.bw |
911.3 Mb |
(ftp)(http) |
BW |
| GSE98101_E7-5-A-K27ac.tagAlign.fc.signal.bw |
1.2 Gb |
(ftp)(http) |
BW |
| GSE98101_E7-5-A-K4M3.tagAlign.fc.signal.bw |
1019.1 Mb |
(ftp)(http) |
BW |
| GSE98101_E7-5-A-K4me1.tagAlign.fc.signal.bw |
1.1 Gb |
(ftp)(http) |
BW |
| GSE98101_E7-5-A-K9ac.tagAlign.fc.signal.bw |
1.1 Gb |
(ftp)(http) |
BW |
| GSE98101_E7-5-AM-K27ac.tagAlign.fc.signal.bw |
1.0 Gb |
(ftp)(http) |
BW |
| GSE98101_E7-5-AM-K4M3.tagAlign.fc.signal.bw |
434.7 Mb |
(ftp)(http) |
BW |
| GSE98101_E7-5-AM-K4me1.tagAlign.fc.signal.bw |
1.2 Gb |
(ftp)(http) |
BW |
| GSE98101_E7-5-AM-K9ac.tagAlign.fc.signal.bw |
896.3 Mb |
(ftp)(http) |
BW |
| GSE98101_E7-5-ExE-K27ac.tagAlign.fc.signal.bw |
1.2 Gb |
(ftp)(http) |
BW |
| GSE98101_E7-5-ExE-K4M3.tagAlign.fc.signal.bw |
648.2 Mb |
(ftp)(http) |
BW |
| GSE98101_E7-5-ExE-K4me1.tagAlign.fc.signal.bw |
1.2 Gb |
(ftp)(http) |
BW |
| GSE98101_E7-5-ExE-K9ac.tagAlign.fc.signal.bw |
1.2 Gb |
(ftp)(http) |
BW |
| GSE98101_E7-5-P-K27ac.tagAlign.fc.signal.bw |
1.2 Gb |
(ftp)(http) |
BW |
| GSE98101_E7-5-P-K4M3.tagAlign.fc.signal.bw |
652.7 Mb |
(ftp)(http) |
BW |
| GSE98101_E7-5-P-K4me1.tagAlign.fc.signal.bw |
1.1 Gb |
(ftp)(http) |
BW |
| GSE98101_E7-5-P-K9ac.tagAlign.fc.signal.bw |
1.1 Gb |
(ftp)(http) |
BW |
| GSE98101_Enh9E_KO-merge.dexseq_clean_refseq.gene.txt.gz |
342.5 Kb |
(ftp)(http) |
TXT |
| GSE98101_RAW.tar |
3.4 Gb |
(http)(custom) |
TAR (of BW, TAGALIGN) |
| GSE98101_merge.dexseq_clean_refseq.gene.all.xls.gz |
659.2 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
| Processed data are available on Series record |
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