|
| Status |
Public on May 18, 2021 |
| Title |
Sample 19_female_H3K4me1_2nd |
| Sample type |
SRA |
| |
|
| Source name |
female_H3K4me1
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD1 (ICR)
Sex: female
embryonic day: E16.5
tissue/cell type: murine embryonic external genitalia (eExG)
chip antibody: Anti-Histone H3 (mono methyl K4) (Abcam: 8895)
|
| Treatment protocol |
None
|
| Growth protocol |
Pregnant ICR mice were housed in breeding cages followed with approved Wakayama Medical University guidelines. Noon on the day when the vaginal plug was detected was designed as E0.5.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
eExG were crosslinked with 20mM EGS (Thermo Fisher Scientific Inc.) and 1% formaldehyde. Cross-linked chromatin was digested by MNase (Takara) and sonicated.
Immunoprecipitated DNA library for Ion Torrent was prepared in accordance with NEB Next Fast DNA Library Prep Set for Ion Torrent (NEW ENGLAND BioLabs. Inc). Immunoprecipitated DNA library for NextSeq was prepared in accordance with KAPA LTP Library preparation Kit (KAPA), SeqCap Adaptor Kit A (Roche), and Agencourt AMPure XP Beads (Beckman Coulter). High-thoughput sequencing was performed by using Ion Proton system (Thermo Fisher Scientific) and NextSeq 500 Desktop Sequencer (Illumina).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Read quality was checked for each sample using FASTQC version 0.11.5.
Reads were mapped to the reference mouse genome UCSC version mm10 using option ‘-k 2’ in Bowtie2 version 2.3.2.
Duplicate reads were excluded with SAMtools version 1.5.
Peak detection was done using the MACS algorithm version 2.1.1.20160309 with option '--to-large --nomodel'.
Genome_build: mm10
Supplementary_files_format_and_content: The BED files were genrated utiizing MACS algorithm.
|
| |
|
| Submission date |
Sep 21, 2020 |
| Last update date |
May 19, 2021 |
| Contact name |
Gen Yamada |
| E-mail(s) |
genyama778899@gmail.com
|
| Organization name |
Wakayama Medical University
|
| Department |
Institute of Advanced Medicine
|
| Lab |
Department of Developmental Genetics
|
| Street address |
811–1 Kimiidera
|
| City |
Wakayama |
| ZIP/Postal code |
641–8509 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE158279 |
Genome-wide distribution of AR, Sp1, H3K27Ac, H3K4me1 in E16.5 embryonic external genitalia (eExG) |
|
| Relations |
| BioSample |
SAMN16231118 |
| SRA |
SRX9162531 |
