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Status |
Public on Apr 24, 2023 |
Title |
RNA_WT_E2C_rep2 |
Sample type |
SRA |
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Source name |
early 2-cell mouse embryos
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Organism |
Mus musculus |
Characteristics |
tissue: early 2-cell mouse embryos genotype: wild type treatment: none
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Treatment protocol |
siRNAs (25 uM for each) were injected into FGOs for maternal Obox KD and zygotes for zygotic Obox KD. For stacc-seq, Obox mRNA was injected into zygotes.
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Growth protocol |
2i ESCs were cultured on 0.1% gelatin pre-coated dishes in DMEM medium (Gibco, 11995-065) containing leukemia-inhibiting factor (LIF) (Millipore, ESG1107), 15% fetal bovine serum (FBS; Hyclone, SH30396.03), GlutaMAX (Gibco, 35050-061), penicillin/ streptomycin (Millipore, TMS-AB2-C), nucleosides (Millipore, ES-008-D), non-essential amino acids (Gibco, 25-025-CIR), and β-mercaptoethanol (Gibco, 21985- 023). Naïve mESCs (2i) mESCs were cultured on feeder-free dishes coated with 0.1% gelatin in the N2B27 medium supplemented with 1 μM PD035901, 3 μM Chir99021, and 1 × 103 units/mL LIF. The cells were passaged 1:10-1:20.
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Extracted molecule |
total RNA |
Extraction protocol |
For embryos, the zona pellucida was gently removed by treatment with Tyrode’s solution (Sigma, T1844). Then the embryos were lysed in lysis buffer containing RNase inhibitor. 2i ESCs were lysed in lysis buffer containing RNase inhibitor. The following steps followed the Smart-seq2 protocol as previously described (Picelli et al., 2014). For whole genome sequence, the tail tip DNA were extracted with isopropanol precipitation method. The Smart-seq2 libraries of embryos were prepared as previously described (Picelli et al., 2014). Embryos were lysed in lysis buffer containing RNase inhibitor according to the user manual. The library was quantified using Qubit and Agilent 2100 before being subjected to sequencing. For stacc-seq, the library was prepared following the protocol as descripted before (Liu et al., 2020). For ATAC-seq, the library was prepared following the protocol as descripted before (Buenrostro et al., 2013; Wu ET AL., 2016). The Smart-seq2, WGS (Picelli et al., 2014) and stacc-seq (Liu et al., 2020) library strategies were followed the protocols described.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
WT_E2C_rep2 Obox_RNASeq_FPKM.xlsx
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Data processing |
ATAC-Seq and 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 then mapped to 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 from UCSC genome annotation database. Assembly: mm9 Supplementary files format and content: Bigwig for Stacc-seq and ATAC-Seq signals Supplementary files format and content: gene expression FPKM table for RNA-seq data
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Submission date |
Oct 14, 2022 |
Last update date |
Apr 24, 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) |
GSE215813 |
OBOX regulates murine zygotic genome activation and early development |
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Relations |
BioSample |
SAMN31286212 |
SRA |
SRX17893696 |
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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