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Sample GSM6641853 Query DataSets for GSM6641853
Status Public on Apr 24, 2023
Title RNA_mzKO_E2C_rep1
Sample type SRA
 
Source name early 2-cell mouse embryos
Organism Mus musculus
Characteristics tissue: early 2-cell mouse embryos
genotype: Obox mzKO
treatment: none
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.
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.
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description mzKO_E2C_rep1
Obox_RNASeq_FPKM.xlsx
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
 
Submission date Oct 14, 2022
Last update date Apr 24, 2023
Contact name Fengling Chen
E-mail(s) cfl15@tsinghua.org.cn
Organization name Tsinghua University
Street address 30 Shuangqing Rd.
City Beijing
State/province Beijing
ZIP/Postal code 100086
Country China
 
Platform ID GPL24247
Series (1)
GSE215813 OBOX regulates murine zygotic genome activation and early development
Relations
BioSample SAMN31286202
SRA SRX17893706

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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