|
| Status |
Public on Jan 26, 2023 |
| Title |
xenopus tropicalis sperm-H3K27ac_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
xenopus tropicalis sperm
|
| Organism |
Xenopus tropicalis |
| Characteristics |
tissue: sperm
antibody: H3K27ac
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Male Xenopus tropicalis were injected with 150 U HCG. After 2 hours, two X. tropicalis testes collected in 1 ml 1xMBS and homogenized using razor blades. The solution was filtered with 40um strainer and its volume was brought down to 14ml. Then, through twice 180G horizontal centrifugation, we can obtain pure sperm in the supernatant.
The ChIP assay was performed as described. Briefly, 5-20 millions sperm were crosslinked with 1% formaldehyde for 10 min using vacuum infiltration. Chromatin was sheared to an average size of 150 bp using a sonicator (Bioruptor Pico, Diagenode). Sonicated chromatin fragments were immunoprecipitated with 3-5 μg of antibody. Chromatin-bound antibodies were recovered with 30μl Protein A/G magnetic beads (Millipore 16-663). After reverse crosslinking, ChIPed DNA was recovered using the MinElute Reaction Cleanup Kit (Qiagen 28206) and amplified with the VAHTS® Universal DNA Library Prep Kit for Illumina V3 (Vazyme ND607). Amplified ChIP libraries were sequenced on the Illumina HiSeq X10 platform.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Low-quality raw ChIP reads and adapter sequences were removed by Trimmomatic v0.38. Clean reads were then aligned to the X.tropicalis v10.0 reference genome using bwa with default parameters. ChIP-seq signal tracks for visualization were also generated by bamCoverage with options “--binSize 10 --extendReads --minMappingQuality 20 --ignoreDuplicates --normalizeUsing RPKM”.
Genome_build: xv10
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Mar 03, 2022 |
| Last update date |
Jan 26, 2023 |
| Contact name |
Chuihui Hou |
| E-mail(s) |
houch@sustech.edu.cn
|
| Organization name |
Southern University of Science and Technology
|
| Street address |
Xueyuan Avenue
|
| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518055 |
| Country |
China |
| |
|
| Platform ID |
GPL30213 |
| Series (2) |
| GSE197866 |
Super-sized clustered loops anchored at transposon Helitrons in Xenopus tropicalis sperm associate with late gene expression during embryogenesis [ChIP-Seq] |
| GSE197877 |
Super-sized clustered loops anchored at transposon Helitrons in Xenopus tropicalis sperm associate with late gene expression during embryogenesis |
|
| Relations |
| BioSample |
SAMN26419684 |
| SRA |
SRX14360622 |
