 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 07, 2024 |
| Title |
KAS-seq_GVBD_biol rep2 |
| Sample type |
SRA |
| |
|
| Source name |
oocyte
|
| Organism |
Mus musculus |
| Characteristics |
cell type: oocyte
developmental stage: GVBD
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Oocytes were labeled with N3-Kethxal (5 mM), and labeled genomic DNA (gDNA 9.5 µL) was subsequently extracted using the Quick-DNA Microprep Plus Kit (Zymo D4074)
After labeling, gDNA was fragmented using Tn5 transposase (Vazyme TD501).Following fragmentation, biotinylation labeling was performed using DBCO-PEG4-biotin (20 mM, DMSO solution, Sigma 760749). The biotinylated DNA was then cleaned up using DNA Clean & Concentrator-5 kit (Zymo, D4013), and 5 µL of labeled DNA was retained as input, while the remaining 50 µL of DNA was used for enrichment.The Dynabeads™ MyOne™ Streptavidin C1 (Thermo 65001) were mixed with the 50 µL fragmented DNA obtained from the previous steps and rotated slowly at room temperature for 15 min.DNA-conjugated beads and their corresponding inputs were used for library PCR using i5 and i7 index primers (Vazyme TD205) and VAHTS HiFi Amplification Mix (Vazyme N616). The PCR reactions were initiated with a 5-min incubation at 72°C, followed by 10 min at 95°C, and then amplified for 17 cycles (10 s at 98°C, 30 s at 60°C, 1 min at 72°C). Finally, the libraries were cleaned up by using DNA Clean & Concentrator-5 kit (Zymo, D4013).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Paired-end reads of 150-bp were generated on the Illumina novaseq 6000 platform in this study (sequenced by Annoroad). For KAS-seq data, raw reads were trimmed using trim galore (v0.6.10) (parameters: --quality 20 --phred33 –length 30 –stringency 3 --paired) and mapped to mouse reference genome (GRcm38) using Bowtie2 (v2.5.1) (parameters: -X 2000 -I 10). All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. The signal tracks and heatmap were both generated by deeptools (v3.5.2). The MACS2 (macs2 2.2.7.1) were used for peak calling (parameters: --broad). HOMER (v4.10) was used for motif enrichment analysis. Annotation of peaks was performed using ChIPseeker (v1.36.0).
Assembly: GRcm38
Supplementary files format and content: bigwig
Library strategy: KAS-Seq
|
| |
|
| Submission date |
Jan 02, 2024 |
| Last update date |
Jun 07, 2024 |
| Contact name |
huiqing an |
| E-mail(s) |
hongzheng360@gmail.com
|
| Organization name |
Nanjing Medical University
|
| Street address |
101 Longmian Rd, Nanjing, Jiangsu, China
|
| City |
Nanjing |
| ZIP/Postal code |
211166 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE252350 |
KAS-seq profiling captures transcription dynamics during oocyte maturation |
|
| Relations |
| BioSample |
SAMN39229572 |
| SRA |
SRX23078018 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7999943_GVBD-2-Sample.bw |
64.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
