|
| Status |
Public on Sep 22, 2021 |
| Title |
ChIPseq_H3K27ac_TT2_GLN_KO_C43_P7_paied_end |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
chip-seq antibody: H3K27ac (Active Motif: 39133)
strain: C57BL/6xCBA
cell line: TT2
genotype: GLN KO
|
| Treatment protocol |
Cells were crosslinked using 1% formaldehyde for 13minutes at room temperature then quenched with glycine.
|
| Growth protocol |
mESCs were grown on 0.1% gelatinized plate supplemented with 15% certified FBS (Life Technologies), 20mM HEPES, 0.1mM non-essential amino acids, 0.1mM 2-mercaptoethanol, 100U/ml penicillin, 0.05mM streptomycin, 1U/ul Leukemia-inhibitory factor(LIF) and 2mM glutamine. Cells were passage at 83% confluency.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin were extracted by lysing the cells and fragmented with sonication. The histone-DNA complexes were then isolated with antibodies.
ChIP libraries were prepared for sequencing using KAPA Hyper Prep Kit (Roche) according to manufacturer protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were aligned to GRCm38/mm10 genome assembly by Bowtie 2 with parameters -q -N 1 -L 25 -X 500 --no-discordant --no-mixed
Duplicates were then removed by Picard MarkDuplicates v2.9.0
Input-subtracted reads per kilobase per million (RPKM) values per 100bp bin were generated as previously described (Hawkins et al., 2013).
supplementary_files_format_and_content:BigWig files were generated by UCSC utilites; Scores represent input-subtracted RPKM for each 100bp bin.
|
| |
|
| Submission date |
Sep 21, 2021 |
| Last update date |
Sep 22, 2021 |
| Contact name |
Danny Leung |
| E-mail(s) |
dcyleung@ust.hk
|
| Organization name |
HONG KONG UNIV OF SCIENCE & TECHNOLOGY
|
| Street address |
Clear Water Bay
|
| City |
HONG KONG |
| State/province |
HONG KONG |
| ZIP/Postal code |
999077 |
| Country |
China |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE165214 |
Polymorphic endogenous retroviral element gives rise to differential epigenomic states and gene expression between distinct genetic backgrounds |
|
| Relations |
| BioSample |
SAMN21537633 |
| SRA |
SRX12286026 |
