title: T-78_c_Tcf3_12_dKO_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq113
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 261 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-73_c_Tcf3_12_dKO_secondary_single_oocyte_RNA

status: Public on Mar 23 2024

type: SRA

city: Beijing

first: Bofeng

last: Liu

address: Haidian District

department: School of Life Science

country: China

institute: Tsinghua University

library_source: transcriptomic

data_processing:
library strategy: Smart-seq108
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

molecule: total RNA

organism: Mus musculus

source_name: Oocyte

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 256 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).

tag: genotype

value: Tcf3/12 KO

tag: developmental stage

tag: cell type

value: oocyte


title: T-75_c_Tcf3_12_dKO_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq110
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 258 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-74_c_Tcf3_12_dKO_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq109
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 257 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-76_c_Tcf3_12_dKO_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq111
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 259 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-70_c_Tcf3_12_dKO_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq105
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 253 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-69_c_Tcf3_12_dKO_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq103
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 251 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-71_c_Tcf3_12_dKO_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq106
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 254 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-90_c_Tcf3_12_dKO_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq117
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 265 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-6_a_Tcf3_12_dKO_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq104
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 252 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: C1: Mus musculus

first: Shuang

last: Li

state: Beijing

address: Biomedical engineering

department: Biomedical engineering

institute: Beihang university

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).  5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell line

value: Mouse Mononuclear Macrophages Cells

value: control


title: T-72_c_Tcf3_12_dKO_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq107
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 255 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: C3: Mus musculus


title: T-77_c_Tcf3_12_dKO_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq112
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 260 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-67_c_Tcf3_12_dKO_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq101
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 249 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-5_a_Tcf3_12_dKO_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq99
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 247 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-54_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq94
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 242 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-56_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq96
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 244 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-57_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq97
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 245 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-68_c_Tcf3_12_dKO_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq102
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 250 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-51_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq91
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 239 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-58_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq98
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 246 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-53_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq93
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 241 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-47_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq86
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 234 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-49_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq88
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 236 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-48_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq87
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 235 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-44_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq83
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 231 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-45_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq84
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 232 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-46_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq85
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 233 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-42_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq81
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 229 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-41_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq80
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 228 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-40_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq79
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 227 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-39_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq77
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 225 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-36_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq74
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 222 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-38_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq76
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 224 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-37_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq75
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 223 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-55_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq95
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 243 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-52_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq92
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 240 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-50_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq90
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 238 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-66_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq100
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 248 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-34_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq72
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 220 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: PTAFR_KO_Hyperoxia 2

city: Birmingham

first: Tamas

last: Jilling

state: AL

address: UAB Station

department: Department of Pediatrics

country: USA

institute: The University of Alabama at Birmingham

data_processing:
CLC Genomic Workbench (Qiagene)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content:   tab-delimited text files include TPM values for each Sample

source_name: Lung

growth_protocol: Timed-pregnant dams were housed two/cage until delivery and then until P3

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
Novogene

treatment_protocol: On P3, half the litter with one dam was moved to hyperoxia (FiO2=85%), the other half stayed at room air (Normoxia; FiO2=21%). Dams were switched daily.

tag: tissue

value: Lung

value: PTAFR KO

tag: treatment

value: Hyperoxia


title: PTAFR_KO_Hyperoxia 3


title: T-32_a_Tcf3_12_dKO_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq70
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 218 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: PTAFR_KO_Normoxia 2

value: Normoxia


title: T-31_a_Tcf3_12_dKO_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq69
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 217 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: PTAFR_KO_Hyperoxia 1


title: PTAFR_KO_Normoxia 3


title: T-3_a_Tcf3_12_dKO_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq78
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 226 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-43_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq82
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 230 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-30_a_Tcf3_12_dKO_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq68
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 216 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: PTAFR_KO_Normoxia 1


title: WT_Hyperoxia 3

value: Wild Type


title: T-29_a_Tcf3_12_dKO_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq66
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 214 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: WT_Hyperoxia 2


title: WT_Hyperoxia 1


title: WT_Normoxia 3


title: T-28_a_Tcf3_12_dKO_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq65
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 213 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-27_a_Tcf3_12_dKO_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq64
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 212 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-35_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq73
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 221 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: WT_Normoxia 2


title: WT_Normoxia 1


title: T-26_a_Tcf3_12_dKO_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq63
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 211 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-33_b_Tcf3_12_dKO_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq71
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 219 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-1_a_Tcf3_12_dKO_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq62
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 210 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: C-9_A_control_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq60
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 208 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).

value: wild-type


title: SCTCR_COH4_56

city: PARIS

first: Anne-laure

last: Le gac

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: 10x Genomics

data_processing:
For the single cells, the demultiplexing, barcoded processing, gene counting  were made using the Cell Ranger software version 7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
For the bulk TCR seq, Mixcr (version 4.4.2) was used to perform the alignment and assemble the reads with the following parameters: milab-human-rna-tcr-umi-multiplex.
Assembly: GRCh38-2020-A for the scRNA-seq and vdj_GRCh38_alts_ensembl-3.1.0-3.1.0 for sc V(D)J-seq.

organism: Homo sapiens

source_name: tumor

extract_protocol:
Trizol for bulk TCR
Human TCR RNA Multiplex-Thrm-001 Kit (MiLaboratories)  for bulk TCR,
10X
Other : CITE-seq, bulk TCRseq

treatment_protocol: FACS sorting for scRNAseq

value: tumor

value: T cells


title: T-10_a_Tcf3_12_dKO_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq61
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 209 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: SCTCR_COH4_76

description: 10x Genomics


title: HTO_COH4_76

description: 10x Genomics


title: C-92_D_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq59
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 207 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: C-91_D_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq58
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 206 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: C-90_D_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq57
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 205 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: HTO_COH4_84

description: 10x Genomics


title: HTO_COH4_56

description: 10x Genomics


title: C-89_C_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq55
Basecalls performed using CASAVA version 1.8
All RNA-Seq data were mapped to mm9 genome by Tophat (version 2.4.0) (Trapnell et al., 2012). The gene expression level was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) based on the annotation mm9 refFlat database from the UCSC genome browser. The expression matrix (FPKM) for Tcf3/12 DKO single-oocyte RNA-seq was produced in a manner akin to that of bulk RNA-seq data. Subsequently, it was imported into SEURAT (version 5.0.0) (Hao et al., 2021) to perform UMAP clustering and compute the average expression.
Assembly: mm9

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM EDTA, and 0.01% DNase I and incubated at 37°C for 10 min with gentle agitation. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS. The dissociated single-cell suspensions were transferred under the microscope (Nikon, SMZ1000), and single oocyte was washed three times with 0.1% BSA/PBS, each oocyte was transferred into 0.2 ml PCR tubes containing 2 μl lysis buffer. Transcriptome libraries were prepared following the Smart-seq2 protocol (Picelli et al., 2013). Sequencing libraries were constructed by using KAPA HyperPlus Kit (Kapa Biosystems) according to the manufacturer’s instructions. All libraries were sequenced on the Illumina NovaSeq 6,000 platform with 203 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).