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Status |
Public on Jun 23, 2023 |
Title |
RNA_1C_KO_rep2 |
Sample type |
SRA |
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Source name |
Zygotes
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Organism |
Mus musculus |
Characteristics |
tissue: Zygotes antibody: none genotype: TDP-43 oocyte knockout
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Treatment protocol |
Oocytes or enbryos were isolated from 7-8-week-old female mice after intraperitoneal injection PMSG or HCG. For FGO, PMSG48h;For MII oocytes, HCG 13h;For embryos, 30h, 36h and 48h.The zona pellucida of oocytes and embryos were removed using Tyrode’s solution before they were collected.
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Growth protocol |
TDP-43 mice were maintained in a hybrid background of C57BL/6J and ICR under guidelines of the Animal Care and Use Committee of the Institute of Zoology, Chinese Academy of Sciences.Oocytes and embryos were isolated in M2 medium, early embryos were culture in KOSM meduim.
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Extracted molecule |
total RNA |
Extraction protocol |
The oocytes and embryos were collected as Smart-seq2 or Stacc-seq protocols in the paper, and the extraction was amplificated or used for the library directly as in the paper. For RNA-seq, RNA libraries for RNA-seq were prepared using a kit of Vazyme (TD502) and performed as the protocol of manufacture. For stacc-seq, Stacc-seq libraries performed according to the previous report.1 μl fully dissolved 5% digitonin was added to Buffer1 (10 mM Tris-HCl pH = 7.4, 150 mM NaCl, 0.5 mM spermidine, 1 × EDTA-free Roche complete protease inhibitor). 0.5 μl PA/G-Tn5 and 0.5 μg TDP-43 or Pol II antibody was added to prepared Buffer1 and incubated at 4℃ for 30 min. Meanwhile, oocytes and embryos were treated gently with Tyrode’s solution for removing the zona pellucida, then were put into 200ml low-binding tube contained 6ml prepared Buffer1 and incubate 4℃ for 10 min . Then 35 ml the prepared Buffer1, mixture of PA/G-Tn5, and the antibody and 12.5 ml TTBL were added for cleaving the chromatin around the binding sites and transposing with adaptors. Then the DNA were purified and PCR as the stacc-seq steps in previously reported
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
RNA_1C_KO_rep2
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Data processing |
Stacc-seq reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM. RNA-seq reads were trimmed by Trim Galore v0.6.6 and then mapped to the mm9 genome by HISAT2 v2.2.1(Kim et al., 2019). StringTie v2.1.2(Pertea et al., 2016) was used to calculate the FPKM per gene based on mm9 refFlat annotation from the UCSC genome annotation database. Assembly: mm9 Supplementary files format and content: Bigwig for Stacc-seq signals Supplementary files format and content: gene expression FPKM table for RNA-seq data
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Submission date |
Jan 01, 2023 |
Last update date |
Jun 23, 2023 |
Contact name |
Fengling Chen |
E-mail(s) |
cfl15@tsinghua.org.cn
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Organization name |
Tsinghua University
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Street address |
30 Shuangqing Rd.
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City |
Beijing |
State/province |
Beijing |
ZIP/Postal code |
100086 |
Country |
China |
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Platform ID |
GPL24247 |
Series (1) |
GSE221985 |
Maternal TDP-43 interacts with RNA Pol II and regulates zygotic genome activation |
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Relations |
BioSample |
SAMN32527232 |
SRA |
SRX18901416 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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