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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 11, 2024 |
| Title |
17hpi_CHX-treated_rep1 |
| Sample type |
SRA |
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| Source name |
17hpi_zygotes
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| Organism |
Mus musculus |
| Characteristics |
cell type: 17hpi_zygotes
strain: ICR
developmental stage: embryo
genotype: wild type
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| Treatment protocol |
Embryos in this study were derived from IVF( In Vitro Fertilization). Female mice were superovulated by 5 IU PMSG injection, followed by 5 IU hCG injection 48 h later. COCs were isolated. Embryos at different stages were collected after adding the sperm of wild type male mice at different time periods.
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| Growth protocol |
Mice were housed under SPF environmental conditions with free access to water and food, 20–22°C ,50–70% humidity, and a 12/12-hour light and dark cycle in the Animal Core Facility of Nanjing Medical University. Animal care and experimental procedures were conducted according to the guidelines of the Animal Research Committee of Nanjing Medical University.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
For RNA-seq, the collected embryos were washed twice with 1xPBS and then immediately placed in lysis buffer( Combine 0.2% (vol/vol) Triton X-100 and 2 U µl–1 RNase inhibitor);For Stacc-seq, embryos were collected and transferred into a 200-μl low-binding tube (total volume with buffer less than 1 μl). Six microlitres of DB-1 (10 mM Tris-HCl pH = 7.4, 150 mM NaCl, 0.5 mM spermidine, 1 × EDTA-free Roche complete protease inhibitor, 0.005% digitonin (Sigma, D141)) buffer was added.
For RNA-seq, samples were taken out from -80℃ freezer, and thawed on ice, 1μl of 10μM oligo-dT primer, 1μl of 10 mM dNTP mix were added to the lysis buffer. cDNA synthesis and amplification were performed following the Smart-seq2 ; Stacc-seq was performed following the previously reported protocol designed by Bofeng Liu etc. pG–Tn5 (Vazyme,TD901) and RNA pol ll antibody (Active motif,39097,lot102660) was used. The precipitated DNA was processed into sequencing libraries using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme,TD903 )following the manufacturer's instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
RNA-seq reads were mapped to the mm9 genome by STAR v2.5.0a
stacc-seq reads were mapped to mm10 whole genome using bowtie v1.3.0 with parameters --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 --no-unal -I 10 -X 700
replicates of same stage were pooled together and RPKM in wiggle files were counted by the number of reads falling into 100bp bin in the genome
FPKM_count.py is used to calculate the reads FPKM of each exon
Assembly: mm10
Supplementary files format and content: plain txt file, each contains two column. First column means the gene ID, the second column means sample's FPKM
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| Submission date |
Aug 23, 2022 |
| Last update date |
Jan 11, 2024 |
| Contact name |
Wenjie Shu |
| E-mail(s) |
shuwj@bmi.ac.cn
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| Organization name |
Beijing Institute of Radiation Medicine
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| Street address |
Taiping Road 27
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| City |
Beijing |
| ZIP/Postal code |
100850 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE211845 |
Maternal KLF17 regulates zygotic genome activation in the mouse |
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| Relations |
| BioSample |
SAMN30465809 |
| SRA |
SRX17238087 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6503244_17hpi_CHX-1_FPKM.txt.gz |
369.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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