|
| Status |
Public on May 25, 2022 |
| Title |
NM_Epi_K4.3 |
| Sample type |
SRA |
| |
|
| Source name |
Epi
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody: H3K4me3 antibody (Cell signaling Technology, 9727S, USA)
fertilization: NM
strain: B6D2F1
developmental stage: embryonic day 7.5 (E7.5)
|
| Treatment protocol |
Single cell of pre-implatation embryos was collected without polar body by removing zone pellucida with 20mg/ml PE (Pronase E, Sigma), incubating in CZB without Ca2+ and gently pipetting with a firepolished glass tube. Single cell of E7.5 embryos (EXE, Epi) was collected by separating from decidua and digestng with 0.05% TE (Trypsin-EDTA, Gibco, 25300062). All the cells were washed at least three times with 0.5% BSA-PBS (MP Biomedicals ,USA) solution before used.
|
| Growth protocol |
The BDF1 (C57BL/6N female × DBA2 male) mice were used to obtain embryos (the in vitro fertilization and in vitro culture embryos were defined as IVF embryos, the natural mating and in vivo development embryos were defined as NM embryos.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
About 500-1000 cells were used per library and about 1µg histone H3K4me3 antibody (Cell signaling Technology, 9727S, USA) or histone H3K27me3 antibody (Diagnode, C15410195, Belgium) were used for immunoprecipitation reaction.
The sequence libraries were generated by Kapa Hyper Prep Kit (KAPA, KK8504, Switzerland).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
NM_IF_EPI_segments.bed
NM_IF_EPI_K4.logFE.bw
|
| Data processing |
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome using bwa mem (0.7.12-r1039) with default paraments.
PCR duplicates were removed and only the reads with high quality (MAPQ>20) were retained for futher analysis.
Chromatin states were defined using ChromHMM (Version 1.15) with paraments -b 500 -center.
The signal trackings were normalized by input values using macs2 (2.1.2) bdgcmp with paraments -m logFE -p 1
Genome_build: mm10
Supplementary_files_format_and_content: bed
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Mar 04, 2021 |
| Last update date |
May 25, 2022 |
| Contact name |
Jin Sun |
| E-mail(s) |
[email protected]
|
| Organization name |
Tongji University
|
| Department |
life science and technology
|
| Lab |
Jiang
|
| Street address |
siping1239
|
| City |
shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE168269 |
Ectopic histone modification in extra-embryonic tissues influence implantation and placenta development of IVF embryos (ChIP-Seq) |
| GSE168274 |
Ectopic histone modification in extra-embryonic tissues influence implantation and placenta development of IVF embryos |
|
| Relations |
| BioSample |
SAMN18141047 |
| SRA |
SRX10240044 |
