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| Status |
Public on Jan 26, 2023 |
| Title |
xenopus tropicalis sperm-ATAC_rep2 |
| Sample type |
SRA |
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| Source name |
xenopus tropicalis sperm
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| Organism |
Xenopus tropicalis |
| Characteristics |
tissue: sperm
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| 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.
About 50000 sperms were lysed in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and 0.5% NP-40) for 10 min on ice to prepare the nuclei. Then, nuclei were spun at 1500g for 5 min to remove the supernatant. Nuclei were then incubated with the Tn5 transposome and tagmentation buffer at 37 °C for 30 min (Vazyme，TD501). Following incubation, sperm were treated with Proteinase K at 63°C for 2 hr, and gDNA was purified with the 1.2× DNA clean beads. PCR was performed to amplify the library for 12 cycles and libraries were purified with the 1.2×DNA clean beads. Amplified ATAC libraries were sequenced on the Illumina HiSeq X10 platform.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Raw fastq ATAC-seq reads were trimmed and aligned to X.tropicalis v10.0 genome using bwa. ATAC-seq signal tracks for visualization were also generated by bamCoverage with option “--normalizeUsing RPKM”.
Genome_build: xv10
Supplementary_files_format_and_content: bigWig
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| Submission date |
Mar 03, 2022 |
| Last update date |
Jan 26, 2023 |
| Contact name |
Chuihui Hou |
| E-mail(s) |
houch@sustech.edu.cn
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| Organization name |
Southern University of Science and Technology
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| Street address |
Xueyuan Avenue
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| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518055 |
| Country |
China |
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| Platform ID |
GPL30213 |
| Series (2) |
| GSE197867 |
Super-sized clustered loops anchored at transposon Helitrons in Xenopus tropicalis sperm associate with late gene expression during embryogenesis [ATAC-Seq] |
| GSE197877 |
Super-sized clustered loops anchored at transposon Helitrons in Xenopus tropicalis sperm associate with late gene expression during embryogenesis |
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| Relations |
| BioSample |
SAMN26419484 |
| SRA |
SRX14360135 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5931494_xt_sperm_ATAC_rep2.bw |
178.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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