title: SCTCR_COH4_84

description: 10x Genomics


title: C-8_A_control_primodial_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-seq56
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 204 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).

tag: genotype

value: wild-type

tag: developmental stage

tag: cell type

value: oocyte


title: C-88_C_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq54
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 202 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: C-87_C_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq53
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 201 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: T-2_a_Tcf3_12_dKO_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq67
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 215 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).

value: Tcf3/12 KO


title: C-86_C_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq52
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 200 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: C-85_C_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq51
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 199 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: C-7_A_control_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq50
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 198 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: C-76_C_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq49
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 197 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: C-75_C_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq48
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 196 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: C-74_C_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq47
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 195 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: tubal_infertility-2

type: RNA

city: Xiamen

first: Que

last: Xiaohong

state: None Selected

address: No. 24, Bai Lu Road, Siming District

institute: Fujian Medical University

description: LncRNA expression data from endometrial tissue of infertile women with tubal disease.

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays (4x44K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The lncRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed lncRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information.

organism: Homo sapiens

source_name: endometrium

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: Put into low-temperature medium containing fetal bovine serum for brief preservation.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Tissue was obtained by endometrial curettage and promptly cooled in a -80°C refrigerator.

tag: tissue

value: endometrium

tag: disease state

value: tubul disease infertility


title: tubal_infertility-3


title: Motor Neuron, TDP-43ΔNLS:YFP ATXN2 Knockout, Day 12, Bio Rep 4 [N_AKO4]

city: Cambridge

first: Kristina

middle: M

last: Holton

state: MA

address: 7 Divinity Ave

department: HSCRB

country: USA

institute: Harvard University

description:
N_AKO4
Day 12 11a Motor Neuron ATXN2 Knockout TDP-43ΔNLS Rep 4

data_processing:
bcl2fastq v2.20
fastqc 0.11.9
multiqc 1.13.0
STAR aligner 2.7.1a, sjdb 100 (read length-1) ; --outSAMtype BAM SortedByCoordinate \--outSAMunmapped Within \--outSAMattributes NH HI NM MD AS \--outReadsUnmapped Fastx \--quantMode GeneCounts; MultiQC post-alignment:>80% uniquely mapped reads, low duplication levels
Assembly: Ensemble GRCh38 r109, with YFP chromosome added; Gene Symbol from org.Hs.eg.db
Supplementary files format and content: counts_unnorm.txt ; Tab Delimited file of read counts by gene symbol in all 32 samples

molecule: polyA RNA

source_name: Spinal Cord

growth_protocol: Motor neurons were produced by differentiation from 11a iPSCs previously transduced with Neurogenin 2 Doxycycline inducible overexpression construct. Cells were differentiated using an accelerated motor neuron differentiation protocol that couples NGN2 overexpression with exposure to patterning factors to direct differentiation to spinal cord motor neurons. The full protocol and characterization of the method can be located in Limone, et. al 2023. Neurons were cultured without a mouse glia baselayer. The 11a iPSC line was derived from a biopsy from a 37-year-old healthy male patient as previously described in Boulting et al. 2011. Neurons were maintained for 5 days following completion of the differentiation protocol before harvesting RNA, for a total of 12 days in culture.

extract_protocol:
Homogenization of samples prior to column extraction was performed using Qiagen Qiashredder columns. RNA extraction was performed using Qiagen Mini RNEasy Plus Kits accoding to manufacturer's instructions.
Kapa mRNA Hyperprep

treatment_protocol: ATXN2 knockout was conferred to 11a iPSCs using CRISPR and single-cell cloning before transduction with inducible TDP-43 perturbations. TDP-43 perturbations were conferred in ATXN2 intact and knockout via recombination at the AAVS1 safe harbor locus with a plasmid harboring a doxycycline inducible expression cassette.

value: Spinal Cord

tag: cell line

value: Motor Neuron

value: ATXN2 -/-


title: ems-3

description: LncRNA expression data from endometrial tissue of infertile women with endometriosis.

value: endometriosis


title: C-72_C_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq45
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 193 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: C-73_C_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq46
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 194 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: C-71_C_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq44
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 192 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: tubal_infertility-1


title: Motor Neuron, TDP-43ΔNLS:YFP ATXN2 Knockout, Day 12, Bio Rep 1 [N_AKO1]

description:
N_AKO1
Day 12 11a Motor Neuron ATXN2 Knockout TDP-43ΔNLS Rep 1


title: Motor Neuron, TDP-43:YFP ATXN2 Knockout, Day 12, Bio Rep 3 [T_AKO3]

description:
T_AKO3
Day 12 11a Motor Neuron ATXN2 Knockout TDP-43 Rep 3


title: C-70_C_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq43
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 191 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: Motor Neuron, TDP-43:YFP ATXN2 Knockout, Day 12, Bio Rep 4 [T_AKO4]

description:
T_AKO4
Day 12 11a Motor Neuron ATXN2 Knockout TDP-43 Rep 4


title: C-68_C_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq40
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 188 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: C-6_A_control_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq42
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 190 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: Motor Neuron, TDP-43:YFP ATXN2 Knockout, Day 12, Bio Rep 2 [T_AKO2]

description:
T_AKO2
Day 12 11a Motor Neuron ATXN2 Knockout TDP-43 Rep 2


title: ems-2


title: normal-3

description: LncRNA expression data from normal female endometrial tissue.

value: normal


title: Motor Neuron, TDP-43:YFP ATXN2 Knockout, Day 12, Bio Rep 1 [T_AKO1]

description:
T_AKO1
Day 12 11a Motor Neuron ATXN2 Knockout TDP-43 Rep 1


title: ems-1


title: normal-2


title: normal-1


title: Motor Neuron, YFP ATXN2 Knockout, Day 12, Bio Rep 4 [Y_AKO4]

description:
Y_AKO4
Day 12 11a Motor Neuron ATXN2 Knockout YFP Rep 4


title: C-66_C_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq38
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 186 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: Motor Neuron, TDP-43ΔNLS:YFP ATXN2 Knockout, Day 12, Bio Rep 3 [N_AKO3]

description:
N_AKO3
Day 12 11a Motor Neuron ATXN2 Knockout TDP-43ΔNLS Rep 3


title: Motor Neuron, YFP ATXN2 Knockout, Day 12, Bio Rep 3 [Y_AKO3]

description:
Y_AKO3
Day 12 11a Motor Neuron ATXN2 Knockout YFP Rep 3


title: C-65_C_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq37
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 185 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: ISO-HAS-B cells, Paclitaxel

city: Sapporo

first: Hideki

last: Tanizawa

state: Hokkaido

address: Kita 15, Nishi 7, Kita-ku

department: Institute for Genetic Medicine

country: Japan

institute: Hokkaido University

data_processing:
Sequenced reads were aligned to the human reference genome GRCh38 using the STAR aligner (version 2.7.10a) (Dobin et al., 2013).
The UMI Tools package (version 1.1.4) was used to demultiplex the pooled samples to obtain the above sequence files (Smith et al., 2017).
Sequenced data from respective samples were adjusted to 4.5 million reads by randomly selecting reads to minimize biases derived from variation in read numbers.
Reads aligned to multiple positions were discarded using the SAMtools (version 1.14) (Li et al., 2009).
Redudant reads containing the same unique molecule identifier (UMI) that reflect a potential PCR bias were removed by the UMI Tools package (version 1.1.4)  (Smith et al., 2017).
Aligned reads were counted using the htseq-count script (version 2.0.3) based on the GENCODE v44 gene annotation (Anders et al., 2015; Frankish et al., 2021).
The DESeq2 program (version 1.28.1) was employed to identify differentially expressed genes (Love et al., 2014).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: ISO-HAS-B

growth_protocol: Cells were cultured in DMEM (Wako) supplemented with 10% FBS (Corning) and 1% penicillin-streptomycin mixed solution (Nacalai Tesque, #26252-94) at 37℃ in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted using PureLink™ RNA Mini Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. The total RNA was treated with RQ1 RNase-Free DNase (Promega, #M6101) at 37°C for 40 minutes and purified by phenol/chloroform extraction and ethanol precipitation.
The 3'mRNA-seq library was prepared using the QIAseq UPX 3’ Transcriptome Kit from QIAGEN, following the manufacturer's instructions.

treatment_protocol: Cells were first cultured for 6 days in DMEM supplemented with chemotherapeutic drug (cisplatin and paclitaxel) and then cultured for 2 days in DMEM supplemented with senolytic agent (ABT-263) if described.

value: ISO-HAS-B

tag: treatment

value: Paclitaxel


title: ISO-HAS-B cells, Cisplatin + ABT-263

value: Cisplatin + ABT-263


title: C-5_A_control_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq36
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 184 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: Motor Neuron, TDP-43ΔNLS:YFP ATXN2 Knockout, Day 12, Bio Rep 2 [N_AKO2]

description:
N_AKO2
Day 12 11a Motor Neuron ATXN2 Knockout TDP-43ΔNLS Rep 2


title: ISO-HAS-B cells, Cisplatin, rep1

value: Cisplatin


title: Motor Neuron, YFP ATXN2 Knockout, Day 12, Bio Rep 1 [Y_AKO1]

description:
Y_AKO1
Day 12 11a Motor Neuron ATXN2 Knockout YFP Rep 1


title: Motor Neuron, YFP ATXN2 Knockout, Day 12, Bio Rep 2 [Y_AKO2]

description:
Y_AKO2
Day 12 11a Motor Neuron ATXN2 Knockout YFP Rep 2


title: ISO-HAS-B cells, Control, rep2

value: No treatment


title: ISO-HAS-B cells, Cisplatin, rep2


title: C-55_C_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq35
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 183 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: C-67_C_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq39
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 187 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: C-69_C_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq41
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 189 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: MO-LAS-B cells, Cisplatin + ABT-263

source_name: MO-LAS-B

value: MO-LAS-B


title: C-54_C_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq34
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 182 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: Motor Neuron, Empty Vector ATXN2 Knockout, Day 12, Bio Rep 4 [EV_AKO4]

description:
EV_AKO4
Day 12 11a Motor Neuron ATXN2 Knockout Empty Vector Rep 4


title: ISO-HAS-B cells, Control, rep1


title: Motor Neuron, Empty Vector ATXN2 Knockout, Day 12, Bio Rep 3 [EV_AKO3]

description:
EV_AKO3
Day 12 11a Motor Neuron ATXN2 Knockout Empty Vector Rep 3


title: MO-LAS-B cells, Cisplatin, rep1


title: MO-LAS-B cells, Cisplatin, rep2


title: C-53_C_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq33
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 181 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: Motor Neuron, Empty Vector ATXN2 Knockout, Day 12, Bio Rep 2 [EV_AKO2]

description:
EV_AKO2
Day 12 11a Motor Neuron ATXN2 Knockout Empty Vector Rep 2


title: MO-LAS-B cells, Paclitaxel, rep1


title: C-52_C_control_secondary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq32
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 180 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: Motor Neuron, Empty Vector ATXN2 Knockout, Day 12, Bio Rep 1  [EV_AKO1]

description:
EV_AKO1
Day 12 11a Motor Neuron ATXN2 Knockout Empty Vector Rep 1

data_processing:
bcl2fastq v2.20
fastqc 0.11.9
multiqc 1.13.0
STAR aligner 2.7.1a, sjdb 100 (read length-1) ; --outSAMtype BAM SortedByCoordinate \--outSAMunmapped Within \--outSAMattributes NH HI NM MD AS \--outReadsUnmapped Fastx \--quantMode GeneCounts; MultiQC post-alignment:>80% uniquely mapped reads, low duplication levels
Assembly: Ensemble GRCh38 r109, with YFP chromosome added; Gene Symbol from org.Hs.eg.db
Supplementary files format and content: counts_unnorm.txt ; Tab Delimited file of read counts by gene symbol in all 32 samples

extract_protocol:
Homogenization of samples prior to column extraction was performed using Qiagen Qiashredder columns. RNA extraction was performed using Qiagen Mini RNEasy Plus Kits accoding to manufacturer's instructions.
Kapa mRNA Hyperprep


title: MO-LAS-B cells, Control, rep1


title: KO [scRNA-seq]

city: Lyon

first: Pauline

last: GARCIA

address: 8 avenue Rockefeller

country: France

institute: INMG

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
STARsolo v2.7.9a
Sequencing reads were processed with STAR (v.2.7.8a) to align and count data for each sample.
The downstream analysis was carried to Seurat package (v.4.0.1).
Each of the 4 datasets was first analyzed independently before combining datasets. Features in canonical chromosomes (1 to 19, X, Y and mitochondrial), identified as protein coding in Ensembl databases and expressed at minimum in 10 “cells” were conserved.
For each sample, SCTransform and RunPCA from Seurat package performed to allow used DoubletFinder (v.2.0.3) and to identify and to remove cell doublets.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skeletal muscle

extract_protocol:
TA injured muscles  were dissected and places in a sterile Petri dish containing PBS. Mechanic dissection was performed with sissors to have a pulp of muscle. The pulp was digested in a bath of Collagenase II (Gibco™ 17101015) solution diluted in Ham’s F10 Nutrient Mix  (Gibco™ 11550043) during 1 hour at 37°C. A second digestion is performed during 30 min containing Collagenase II (Gibco™ 17101015) and Dispase (Gibco™ 17105041) at 37°C. The pulp is then filtered (0.22 μm) followed by a step of trituration using seringe and 0.2G. Washes Hindlimbs muscles from both legs were dissected and places in a sterile Petri dish containing PBS. Mechanic dissection was performed with sissors to have a pulp of muscle. The pulp was digested in a bath of Collagenase II (Gibco™ 17101015) solution diluted in Ham’s F10 Nutrient Mix  (Gibco™ 11550043) during 1 hour at 37°C. A second digestion is performed during 30 min containing Collagenase II (Gibco™ 17101015) and Dispase (Gibco™ 17105041) at 37°C. The pulp is then filtered (0.22 μm) followed by a step of trituration using seringe and 0.2G. Washes were done with 5% bovine Serum Albumin (BSA), 3mM EDTA diluted in phosphate buffer saline (PBS) (Gibco™ 14200075)ith 5% bovine Serum Albumin (BSA), 3mM EDTA diluted in phosphate buffer saline (PBS) (Gibco™ 14200075). Cells were selected at the FACS plateform from the CRCL stained with Hoeschst and Propidium Iodide.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, skeletal muscle cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: skeletal muscle cells

value: Skeletal muscle

tag: age

value: 8-12 weeks old


title: MO-LAS-B cells, Control, rep2


title: C-51_B_control_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq31
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 179 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).

value: wild-type

value: oocyte


title: Motor Neuron, TDP-43ΔNLS:YFP Overexpression, Day 12, Bio Rep 3 [N3]

description:
N3
Day 12 11a Motor Neuron TDP-43ΔNLS Rep 3

value: Wild Type


title: C-49_B_control_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq29
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 177 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: Setdb1_KO_TAM_biol rep1

description:
SETDB1TAMO263_S7
counts_unormalized.csv

data_processing:
nf-core/rnaseq v.3.11.2
Nf-core/rnaseq v3.2 was used on a conda container, the raw fastq reads aligned with STAR and to project the alignments onto the transcriptome and to perform the downstream BAM-level quantification with Salmon.
Data were filtered to conserve only features in canonical chromosomes (1 to 19, X, Y and mitochondrial) identified as protein coding in Ensembl databases. Differential analysis was performed with DEseq2 package (v1.34.0).
Gene set enrichment analysis was computed by fgsea package (v1.20.0) on genes ranked by the sign of Log2 Fold Change * log10(p-adjusted by BH). The gProfiler2 package (v.0.2.1) was used to compute and compare multiple input collections from MH, M2:CP, KEGG, M5:GO on genes ranked by the sign of Log2 Fold Change * log10(p-adjusted by BH).
Assembly: GRCm38

source_name: Muscle stem cells

extract_protocol:
RNA was prepared as described for RNA extraction and sent to the Genom’IC (Institut Cochin) genomic platform. Libraries were prepared with TruSeq Stranded Total Library preparation kit according to supplier recommendations. The important steps of this protocol are the removal of ribosomal RNA fraction from 400 ng of total RNA using the Ribo-Zero Gold Kit; fragmentation using divalent cations under elevated temperature to obtain ~300 bp pieces; double strand cDNA synthesis using reverse transcriptase and random primers, and finally Illumina adapters ligation and cDNA library amplification by PCR for sequencing. Sequencing was carried out on pair-end 75 bp of Illumina NextSeq500.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: 10 weeks old

value: Muscle stem cells

value: KO

value: Tamoxifen

tag: time

value: 60h after CTX


title: Motor Neuron, TDP-43ΔNLS:YFP Overexpression, Day 12, Bio Rep 4 [N4]

description:
N4
Day 12 11a Motor Neuron TDP-43ΔNLS Rep 4

value: Spinal Cord

value: Motor Neuron


title: Setdb1_KO_TAM_biol rep3

description:
SETDB1TAMO275_S10
counts_unormalized.csv


title: WT [scRNA-seq]

description: 10x Genomics


title: Motor Neuron, TDP-43ΔNLS:YFP Overexpression, Day 12, Bio Rep 2 [N2]

description:
N2
Day 12 11a Motor Neuron TDP-43ΔNLS Rep 2


title: Control_OIL_biol rep 2

description:
SETDB1OIL274_S8
counts_unormalized.csv

value: WT

value: Oil


title: C-48_B_control_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq28
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 176 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: C-50_B_control_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq30
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 178 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: MO-LAS-B cells, Paclitaxel, rep2

value: Paclitaxel


title: Setdb1_KO_TAM_biol rep2

description:
SETDB1TAMO265_S9
counts_unormalized.csv


title: Control_OIL_biol rep 1

description:
OSETDB1OIL273_S12
counts_unormalized.csv


title: sperm_H3K27ac_rep2

description: STAR ChIP-seq

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.
STAR ChIP-seq reads were aligned to the mm9 genome using bowtie 2.2.2. Replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome.
Assembly: mm9
Supplementary files format and content: bed file

molecule: genomic DNA

source_name: Sperm

extract_protocol: STAR ChIP-seq was performed as previously described (Zhang et al., 2016). Briefly, samples were lysed followed by fragmented by micrococcal nuclease (MNase, Sigma, N3755-200UN) at 37 °C for 5 min. After being terminated, the supernatant containing chromatin was incubated with the primary antibody at 4 °C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific) was added to each sample and incubated at 4 °C for 2–3 h with rotation. The beads were then washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 28 μl H2O, 1 μl 10× Ex-Taq buffer (Takara, RR006B) and 1 μl proteinase K (NEB, P8107S) and incubated at 55 °C for 90 min, followed by incubation at 72 °C for 40 min to inactivate the proteinase K. Samples were then subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). STAR ChIP-seq libraries were sequenced using the HiSeq X Ten system or NovaSeq (Illumina) according to the manufacturer’s protocol.

value: Sperm

tag: antibody

value: H3K27ac (Active Motif 39133)


title: C-47_B_control_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq27
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 175 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: Control_OIL_biol rep 3

description:
SETDB1OIL276_S11
counts_unormalized.csv


title: sperm_H3K27ac_rep1

description: STAR ChIP-seq


title: Motor Neuron, TDP-43:YFP Overexpression, Day 12, Bio Rep 3 [T3]

description:
T3
Day 12 11a Motor Neuron TDP-43 Rep 3


title: C-46_B_control_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq26
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 174 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: PN5_H3K27ac_rep1

description: STAR ChIP-seq

source_name: Preimplantation embryo

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. PN5 embryos were harvested in M2 medium 30 h after hCG.
STAR ChIP-seq was performed as previously described (Zhang et al., 2016). Briefly, samples were lysed followed by fragmented by micrococcal nuclease (MNase, Sigma, N3755-200UN) at 37 °C for 5 min. After being terminated, the supernatant containing chromatin was incubated with the primary antibody at 4 °C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific) was added to each sample and incubated at 4 °C for 2–3 h with rotation. The beads were then washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 28 μl H2O, 1 μl 10× Ex-Taq buffer (Takara, RR006B) and 1 μl proteinase K (NEB, P8107S) and incubated at 55 °C for 90 min, followed by incubation at 72 °C for 40 min to inactivate the proteinase K. Samples were then subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). STAR ChIP-seq libraries were sequenced using the HiSeq X Ten system or NovaSeq (Illumina) according to the manufacturer’s protocol.

value: Preimplantation embryo

value: 1-cell PN5


title: Motor Neuron, TDP-43:YFP Overexpression, Day 12, Bio Rep 4 [T4]

description:
T4
Day 12 11a Motor Neuron TDP-43 Rep 4


title: C-45_B_control_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq25
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 173 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).

value: wild-type


title: PN5_H3K27ac_rep2

description: STAR ChIP-seq


title: Motor Neuron, TDP-43:YFP Overexpression, Day 12, Bio Rep 2 [T2]

description:
T2
Day 12 11a Motor Neuron TDP-43 Rep 2


title: MII_H3K27ac_rep1

description: STAR ChIP-seq

data_processing:
Basecalls performed using CASAVA version 1.8.
STAR ChIP-seq reads were aligned to the mm9 genome using bowtie 2.2.2. Replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome.
Assembly: mm9
Supplementary files format and content: bigWig files

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG. MII oocytes were harvested in M2 medium 13 h after hCG.
STAR ChIP-seq was performed as previously described (Zhang et al., 2016). Briefly, samples were lysed followed by fragmented by micrococcal nuclease (MNase, Sigma, N3755-200UN) at 37 °C for 5 min. After being terminated, the supernatant containing chromatin was incubated with the primary antibody at 4 °C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific) was added to each sample and incubated at 4 °C for 2–3 h with rotation. The beads were then washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 28 μl H2O, 1 μl 10× Ex-Taq buffer (Takara, RR006B) and 1 μl proteinase K (NEB, P8107S) and incubated at 55 °C for 90 min, followed by incubation at 72 °C for 40 min to inactivate the proteinase K. Samples were then subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). STAR ChIP-seq libraries were sequenced using the HiSeq X Ten system or NovaSeq (Illumina) according to the manufacturer’s protocol.

value: Oocyte

value: MII oocyte


title: MII_H3K27ac_rep2

description: STAR ChIP-seq


title: C-44_B_control_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq24
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 172 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).

value: oocyte


title: Motor Neuron, TDP-43ΔNLS:YFP Overexpression, Day 12, Bio Rep 1 [N1]

description:
N1
Day 12 11a Motor Neuron TDP-43ΔNLS Rep 1

value: Wild Type


title: Motor Neuron, TDP-43:YFP Overexpression, Day 12, Bio Rep 1 [T1]

description:
T1
Day 12 11a Motor Neuron TDP-43 Rep 1


title: mESC_H3K27ac_500_rep1

description: STAR ChIP-seq

source_name: Embryonic stem cell

value: Embryonic stem cell


title: mESC_H3K27ac_500_rep2

description: STAR ChIP-seq


title: Motor Neuron, YFP only, Day 12, Bio Rep 4 [Y4]

description:
Y4
Day 12 11a Motor Neuron YFP Rep 4


title: ICM_H3K27ac_rep1

description: STAR ChIP-seq

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. Embryos were harvested in M2 medium 98 h after hCG.
STAR ChIP-seq was performed as previously described (Zhang et al., 2016). Briefly, samples were lysed followed by fragmented by micrococcal nuclease (MNase, Sigma, N3755-200UN) at 37 °C for 5 min. After being terminated, the supernatant containing chromatin was incubated with the primary antibody at 4 °C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific) was added to each sample and incubated at 4 °C for 2–3 h with rotation. The beads were then washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 28 μl H2O, 1 μl 10× Ex-Taq buffer (Takara, RR006B) and 1 μl proteinase K (NEB, P8107S) and incubated at 55 °C for 90 min, followed by incubation at 72 °C for 40 min to inactivate the proteinase K. Samples were then subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). STAR ChIP-seq libraries were sequenced using the HiSeq X Ten system or NovaSeq (Illumina) according to the manufacturer’s protocol.

value: ICM


title: Motor Neuron, YFP only, Day 12, Bio Rep 3 [Y3]

description:
Y3
Day 12 11a Motor Neuron YFP Rep 3


title: GO_P7_H3K27ac_rep2

description: STAR ChIP-seq

extract_protocol:
P7 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
STAR ChIP-seq was performed as previously described (Zhang et al., 2016). Briefly, samples were lysed followed by fragmented by micrococcal nuclease (MNase, Sigma, N3755-200UN) at 37 °C for 5 min. After being terminated, the supernatant containing chromatin was incubated with the primary antibody at 4 °C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific) was added to each sample and incubated at 4 °C for 2–3 h with rotation. The beads were then washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 28 μl H2O, 1 μl 10× Ex-Taq buffer (Takara, RR006B) and 1 μl proteinase K (NEB, P8107S) and incubated at 55 °C for 90 min, followed by incubation at 72 °C for 40 min to inactivate the proteinase K. Samples were then subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). STAR ChIP-seq libraries were sequenced using the HiSeq X Ten system or NovaSeq (Illumina) according to the manufacturer’s protocol.

value: Growing oocyte P7


title: Motor Neuron, YFP only, Day 12, Bio Rep 2 [Y2]

description:
Y2
Day 12 11a Motor Neuron YFP Rep 2

value: Spinal Cord


title: mESC_Dnmt3ab_Setd2_tKO_H3K4me3_rep1

description: STAR ChIP-seq

value: Dnmt3a/b KO


title: C-38_B_control_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq21
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 169 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: GO_P10_H3K27ac_rep2

description: STAR ChIP-seq

extract_protocol:
P10 female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
STAR ChIP-seq was performed as previously described (Zhang et al., 2016). Briefly, samples were lysed followed by fragmented by micrococcal nuclease (MNase, Sigma, N3755-200UN) at 37 °C for 5 min. After being terminated, the supernatant containing chromatin was incubated with the primary antibody at 4 °C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific) was added to each sample and incubated at 4 °C for 2–3 h with rotation. The beads were then washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 28 μl H2O, 1 μl 10× Ex-Taq buffer (Takara, RR006B) and 1 μl proteinase K (NEB, P8107S) and incubated at 55 °C for 90 min, followed by incubation at 72 °C for 40 min to inactivate the proteinase K. Samples were then subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). STAR ChIP-seq libraries were sequenced using the HiSeq X Ten system or NovaSeq (Illumina) according to the manufacturer’s protocol.

value: Growing oocyte P10


title: C-37_B_control_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq20
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 168 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: GO_P10_H3K27ac_rep1

description: STAR ChIP-seq


title: FGO_H3K27ac_rep2

description: STAR ChIP-seq

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
STAR ChIP-seq was performed as previously described (Zhang et al., 2016). Briefly, samples were lysed followed by fragmented by micrococcal nuclease (MNase, Sigma, N3755-200UN) at 37 °C for 5 min. After being terminated, the supernatant containing chromatin was incubated with the primary antibody at 4 °C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific) was added to each sample and incubated at 4 °C for 2–3 h with rotation. The beads were then washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 28 μl H2O, 1 μl 10× Ex-Taq buffer (Takara, RR006B) and 1 μl proteinase K (NEB, P8107S) and incubated at 55 °C for 90 min, followed by incubation at 72 °C for 40 min to inactivate the proteinase K. Samples were then subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). STAR ChIP-seq libraries were sequenced using the HiSeq X Ten system or NovaSeq (Illumina) according to the manufacturer’s protocol.

value: Full grown oocyte


title: Motor Neuron, YFP only, Day 12, Bio Rep 1  [Y1]

description:
Y1
Day 12 11a Motor Neuron YFP Rep 1

extract_protocol:
Homogenization of samples prior to column extraction was performed using Qiagen Qiashredder columns. RNA extraction was performed using Qiagen Mini RNEasy Plus Kits accoding to manufacturer's instructions.
Kapa mRNA Hyperprep

value: Motor Neuron


title: FGO_H3K27ac_rep1

description: STAR ChIP-seq


title: 8cell_H3K27ac_rep1

description: STAR ChIP-seq

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. Embryos were harvested in M2 medium 65 h after hCG.
STAR ChIP-seq was performed as previously described (Zhang et al., 2016). Briefly, samples were lysed followed by fragmented by micrococcal nuclease (MNase, Sigma, N3755-200UN) at 37 °C for 5 min. After being terminated, the supernatant containing chromatin was incubated with the primary antibody at 4 °C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific) was added to each sample and incubated at 4 °C for 2–3 h with rotation. The beads were then washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 28 μl H2O, 1 μl 10× Ex-Taq buffer (Takara, RR006B) and 1 μl proteinase K (NEB, P8107S) and incubated at 55 °C for 90 min, followed by incubation at 72 °C for 40 min to inactivate the proteinase K. Samples were then subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). STAR ChIP-seq libraries were sequenced using the HiSeq X Ten system or NovaSeq (Illumina) according to the manufacturer’s protocol.


title: C-3_A_control_primodial_single_oocyte_RNA

data_processing:
library strategy: Smart-seq23
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 171 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: 2cell_late_H3K27ac_rep1

description: STAR ChIP-seq

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. Embryos were harvested in M2 medium 48 h after hCG.
STAR ChIP-seq was performed as previously described (Zhang et al., 2016). Briefly, samples were lysed followed by fragmented by micrococcal nuclease (MNase, Sigma, N3755-200UN) at 37 °C for 5 min. After being terminated, the supernatant containing chromatin was incubated with the primary antibody at 4 °C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific) was added to each sample and incubated at 4 °C for 2–3 h with rotation. The beads were then washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 28 μl H2O, 1 μl 10× Ex-Taq buffer (Takara, RR006B) and 1 μl proteinase K (NEB, P8107S) and incubated at 55 °C for 90 min, followed by incubation at 72 °C for 40 min to inactivate the proteinase K. Samples were then subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). STAR ChIP-seq libraries were sequenced using the HiSeq X Ten system or NovaSeq (Illumina) according to the manufacturer’s protocol.

value: late 2-cell


title: C-35_B_control_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq18
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 166 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: Motor Neuron, Empty Vector Unpreturbed, Day 12, Bio Rep 3 [EV3]

description:
EV3
Day 12 11a Motor Neuron Empty Vector Rep 3

data_processing:
bcl2fastq v2.20
fastqc 0.11.9
multiqc 1.13.0
STAR aligner 2.7.1a, sjdb 100 (read length-1) ; --outSAMtype BAM SortedByCoordinate \--outSAMunmapped Within \--outSAMattributes NH HI NM MD AS \--outReadsUnmapped Fastx \--quantMode GeneCounts; MultiQC post-alignment:>80% uniquely mapped reads, low duplication levels
Assembly: Ensemble GRCh38 r109, with YFP chromosome added; Gene Symbol from org.Hs.eg.db
Supplementary files format and content: counts_unnorm.txt ; Tab Delimited file of read counts by gene symbol in all 32 samples


title: 2cell_late_H3K27ac_rep2

description: STAR ChIP-seq

value: H3K27ac (Active Motif 39133)


title: C-34_B_control_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq17
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 165 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).


title: 2cell_early_H3K27ac_rep1

description: STAR ChIP-seq

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. Embryos were harvested in M2 medium 36 h after hCG.
STAR ChIP-seq was performed as previously described (Zhang et al., 2016). Briefly, samples were lysed followed by fragmented by micrococcal nuclease (MNase, Sigma, N3755-200UN) at 37 °C for 5 min. After being terminated, the supernatant containing chromatin was incubated with the primary antibody at 4 °C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific) was added to each sample and incubated at 4 °C for 2–3 h with rotation. The beads were then washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 28 μl H2O, 1 μl 10× Ex-Taq buffer (Takara, RR006B) and 1 μl proteinase K (NEB, P8107S) and incubated at 55 °C for 90 min, followed by incubation at 72 °C for 40 min to inactivate the proteinase K. Samples were then subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). STAR ChIP-seq libraries were sequenced using the HiSeq X Ten system or NovaSeq (Illumina) according to the manufacturer’s protocol.

value: Preimplantation embryo

value: early 2-cell


title: C-33_B_control_primary_single_oocyte_RNA

data_processing:
library strategy: Smart-seq16
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 164 bp paired-end mode at the Annoroad Genomics Company (Beijing, China).

value: wild-type