|
| Status |
Public on Jul 21, 2022 |
| Title |
granulosa cells_12h_H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
mouse granulosa cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: wild type
age: post natal day 21-28
treatment/time point: 12 hours after hCG injection
tissue: ovary
cell type: mouse granulosa cells
chip antibody: H3K4me3 (generous gifts from Dr. H. Kimura, Osaka University, Osaka, Japan)
|
| Treatment protocol |
The ovaries were obtained before hCG (0), and 4, 12 hours (h) after hCG injection. The follicles were punctured to isolate GCs.
|
| Growth protocol |
C57BL/6 female mice were injected intraperitoneally with 4 IU of eCG to promote follicular growth followed by 5 IU of hCG injection to induce ovulation and luteinization.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonication/enzymatic digested nuclei and histone-DNA complexes were isolated with antibody. The ChIP DNA and the Input DNA ends were repaired using T4 DNA polymerase, Klenow enzyme, and T4 polynucleotide kinase(PNK) (New England Biolabs), followed by treatment with Klenow exo- to add an A base to the 3’ end. After ligation of the Solexa adaptor using TaKaRa ligation Mix (TaKaRa), the adaptor-ligated DNAs were amplified using Solexa PCR primers for 18 cycles, and the amplified library was isolated from an agarose gel. The samples were purified using the QIAquick MinElute kit (Qiagen) at each preparation step.
The purified library was used for cluster generation and sequencing analysis using the Genome Analyzer GAIIx (Illumina).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
C3-12h-H3K4me3_S34_L005
|
| Data processing |
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie version 2.2.3 with the default parameters
Data were filtered using the following specifications…
peaks were called using MACS version 2.0.9 with the following setting: effective genome size = 1.87x10^9 (Mus musculus); upper and lower limit for model building = 5 and 50; q-value cutoff = 0.05; bandwidth = 300; broad mode = “off” ; nolambda=”on”.
Genome_build: mm10
Supplementary_files_format_and_content: peak BED file
|
| |
|
| Submission date |
Mar 01, 2021 |
| Last update date |
Jul 21, 2022 |
| Contact name |
Yuichiro Shirafuta |
| E-mail(s) |
[email protected]
|
| Phone |
0836222288
|
| Organization name |
Yamaguchi university
|
| Street address |
1-1-1, minami-kogushi
|
| City |
Ube |
| State/province |
Yamaguchi |
| ZIP/Postal code |
7558505 |
| Country |
Japan |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE167938 |
Integrated analysis of transcriptome and histone modifications in granulosa cells during ovulation in female mice [ChIP-seq] |
| GSE167940 |
Integrated analysis of transcriptome and histone modifications in granulosa cells during ovulation in female mice |
|
| Relations |
| BioSample |
SAMN18093702 |
| SRA |
SRX10194327 |
