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SRX23078013: GSM7999938: KAS-seq_GV SN_biol rep1_input; Mus musculus; OTHER
1 ILLUMINA (Illumina NovaSeq 6000) run: 36.4M spots, 10.9G bases, 3.6Gb downloads

External Id: GSM7999938_r1
Submitted by: nanjing medical university
Study: KAS-seq profiling captures transcription dynamics during oocyte maturation
show Abstracthide Abstract
In fully grown oocytes, the genome is considered to be globally transcriptionally silenced. However, this conclusion is primarily derived from the results obtained through immunofluorescence staining or inferred from the highly condensed state of chromosomes, lacking more direct evidence. Here, by using a kethoxal-assisted single-stranded DNA sequencing (KAS-seq) approach, we investigated the landscape of single-strand DNA (ssDNA) throughout the genome and provided a readout of the activity and dynamics of transcription during oocyte meiotic maturation. In non-surrounded nucleolus (NSN) oocytes, we observed a robust KAS-seq signal, indicating the high transcriptional activity. In surrounded nucleolus (SN) oocytes, the presence of ssDNA still persists although the KAS-seq signal was relatively weak, suggesting the presence of transcription. Accompanying with the meiotic resumption, the transcriptional activity gradually decreased, and global repression was detected in matured oocytes. Moreover, we preformed the integrative genomics analysis to dissect the transcriptional dynamics during mouse oocyte maturation. In sum, the present study delineates the detailed transcriptional activity during mammalian oocyte maturation. Overall design: We utilized the KAS-seq technique to construct libraries for various developmental stages of mouse oocytes (GV, GVBD, MII) to investigate the dynamic changes of ssDNA during oocytes maturation.
Sample: KAS-seq_GV SN_biol rep1_input
SAMN39229577 • SRS20036825 • All experiments • All runs
Organism: Mus musculus
Library:
Name: GSM7999938
Instrument: Illumina NovaSeq 6000
Strategy: OTHER
Source: GENOMIC
Selection: other
Layout: PAIRED
Construction 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).
Runs: 1 run, 36.4M spots, 10.9G bases, 3.6Gb
Run# of Spots# of BasesSizePublished
SRR2740202336,364,03610.9G3.6Gb2024-06-07

ID:
31171053

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