title: E14.5Ngn3fbL_12_53


title: Ngn3CreNeurod1OEHZ_E15.5_99

status: Public on Feb 15 2025

type: SRA

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

country: China

institute: Peking University

description:
Smartseq3 scRNA-seq
sm3_rc.cell.tsv
sm3_rc.gene.tsv
sm3_rc.mtx

library_source: transcriptomic single cell

data_processing:
For CUT&RUN data, overrepresented sequences were identified using FastQC (v0.11.3), and then removed along with sequencing adaptors, primers, and other overrepresented sequences using Trimmomatic (v0.38). The remaining sequencing reads were aligned to the Mus musculus genome (mm10) using bowtie2 (v2.2.5) with default parameters. PCR duplicate reads were subsequently removed using samtools (v1.3.1), and only reads with a mapping quality score ≥30 were retained for downstream analysis.  Peak calling was performed on individual samples using MACS2 (v2.2.6), retaining peaks with a P value less than 10-3. Reproducibility between two biological replicates was assessed using idr (v2.0.4.2). Different irreproducible discovery rate (IDR) thresholds were applied depending on the CUT&RUN targets. For CUT&RUN targeting NGN3 in Ngn3low cells, peaks with an IDR larger than 250 were retained for downstream analysis. For CUT&RUN targeting NGN3 in Ngn3high cells and NEUROD1, the threshold was set to 400. Genome regions overlapping with the ENCODE blacklist were filtered out from the final identified peaks. Tag intensities were calculated as Tags per ten million (TP10M) values and stored in bedGraph files using Homer (v4.7.2).
For bulk-cell ATAC-seq data, Overrepresented sequences were identified using FastQC (v0.11.3), and then removed along with sequencing adaptors, primers, and other overrepresented sequences using Trimmomatic (v0.38). The remaining sequencing reads were aligned to the Mus musculus genome (mm10) using bowtie2 (v2.2.5) with default parameters. PCR duplicate reads were subsequently removed using samtools (v1.3.1), and only reads with a mapping quality score ≥30 were retained for downstream analysis.  Prior to peak calling, reads generated from biological replicates were combined. ATAC-seq peaks were then identified using MACS2 (v2.2.6), retaining peaks with a false discovery rate (FDR) less than 0.01. Genome regions overlapping with the ENCODE blacklist were excluded from further analysis. Tag intensities were calculated as TP10M values and stored in bedGraph files using Homer (v4.7.2).
For snATAC-seq, preprocessing was conducted using cellranger-atac (v1.2.0) with default parameters against the refdata-cellranger-atac-mm10-1.2.0 genome. Cells with detected UMI counts greater than 1,000 and reads in promoter regions (RIPR) between 15% and 45% were retained for downstream analysis. The mm10 genome was segmented into discrete 5 kb intervals, serving as bins for each cell. The tag intensities for each bin were calculated based on the frequency of sequence tags and imported into the R package Signac (v1.3.0) for downstream analysis.
For smart-seq2 snRNA-seq, sequencing reads were aligned to the mm10 mouse genome assembly using TopHat (v2.1.0). Gene-level quantification of mapped reads was performed with HTSeq (v0.6.6) using the parameters “-s no -a 30”. Cells exhibiting fewer than 0.2 million mapped reads or fewer than 4,000 detected genes were excluded from further analysis. Gene expression levels were quantified using TPM (transcripts per million).
For smart-seq3 snRNA-seq, Trimmomatic (v0.39) was utilized to remove primer and adaptor sequences from the reads. Subsequently, the trimmed forward reads (Read 1) were aligned to the mm10 mouse genome using HISAT2 (v2.1.0). The resulting aligned reads were annotated to gene features using featureCounts (v2.0.0), considering both the 5' and internal fragments. Cells were filtered out if they exhibited fewer than 4,000 detected genes. Gene expression levels were quantified using TPM.
For 10x Genomics scRNA-seq, preprocessing was conducted using Cell Ranger (v3.0.1) with default parameters aligned to the refdata-cellranger-mm10-1.2.0 reference genome. The “filtered_feature_bc_matrix” output from Cell Ranger was imported into the Seurat package (version 4.1.1) for downstream analysis in R. WT and CKO or OE cells within the same sample were initially distinguished based on TP10K (transcripts per 10 thousand) values of Uty, Eif2s3y, and Ddx3y for male cells, and the TP10K value of Xist for female cells. These values were log-transformed, with cells exhibiting male-related values greater than 0.2 and female-related values equal to 0 classified as male, while cells with female-related values greater than 1 and male-related values equal to 0 classified as female. The downstream analysis, including dimensional reduction, cell clustering, and differential expression analysis, was conducted using the standard Seurat pipeline.
Assembly: mm10
Supplementary files format and content: Sparce matrix, Bedgraph

molecule: polyA RNA

organism: Mus musculus

source_name: fetal pancreas

extract_protocol:
For Smart-seq2 scRNA-seq, single cells were manually picked from FACS-purified bulk cells using a mouth pipette. cDNA synthesis and amplification were performed following the protocol by Picelli et al. For Smart-seq3 scRNA-seq, single cells were directly sorted into 384-well plates containing lysis buffer. cDNA synthesis and amplification were carried out according to the Smart-seq3 protocol .For 10x Genomics scRNA-seq, the procedure was performed according to the manufacturer’s instructions using the Single Cell 3′ Reagent Kit v3.1. Sorted EpCAM+ pancreatic cells from wild-type (WT), conditional knockout (CKO), or overexpression (OE) embryos of different genders were pooled and processed as one sample. For NGN3-CKO samples, E14.5 EpCAM+ pancreatic cells were pooled per replicate: replicate 1 consisted of two WT male litters and one CKO female litter, and replicate 2 consisted of three WT male litters and three CKO female litters. For NGN3-OE samples, E14.5 EpCAM+ pancreatic cells were pooled from four WT female litters and four OE male litters, and E17.5 EpCAM+ pancreatic cells were pooled from two WT female litters and three OE male litters. For NeuroD1-CKO samples, E15.5 EpCAM+ pancreatic cells were pooled per replicate: replicate 1 consisted of one WT male litter and one CKO female litter, and replicate 2 consisted of two WT female litters and one CKO male litter. The gender of the embryos was determined by genotyping for Y-chromosome-associated gene Sry.
For Smart-seq2 scRNA-seq, libraries were prepared with 2 ng of cDNA using the TruePrep DNA Library Prep Kit (Vazyme, TD502), and sequenced on the Illumina HiSeq 4000 system, generating 150 bp paired-end reads. For Smart-seq3 scRNA-seq, libraries were constructed using the TruePrep DNA Library Prep Kit V2 for lllumina (Vazyme, TD501), and sequencing was conducted on the MGIseq-2000 platform, generating 100 bp paired-end reads. For 10x Genomics scRNA-seq, libraries were sequenced as 150-bp paired-end reads on an Illumina HiSeq 4000 system.
CUT&RUN was conducted following the published protocol with modifications in DNA purification and library construction steps. We used 30,000 cells per CUR&RUN assay with primary antibodies against FLAG (1:25, CST, 2368S), p300 (1;100, CST, 54062S), and NeuroD1 (1:100, Millpore, ABE991). DNA was purified using a spin column (VISTECH, DC2005) and processed for library construction with KAPA Hyper Prep Kit (KAPA biosystems, KK8502). Briefly, after end repair and adaptor ligation, the reaction was purified using VAHTS DNA Clean Beads (Vazyme, N411-03-AA) and subjected to PCR amplification with 2× KAPA HiFi HotStart ReadyMix (KAPA Biosystems, KM2602) and Illumina universal primers. The PCR program was: 98°C for 45 seconds, followed by 19 cycles of 98°C for 15 seconds, 60°C for 10 seconds, and 72°C for 1 minute, with a final extension at 72°C for 5 minutes. The final DNA was purified using 1× VAHTS DNA Clean Beads.
CUT&RUN libraries were subjected to 150 bp paired-end sequencing or 51 bp single-end sequencing on the Illumina NovaSeq 6000 or Illumina Hiseq 2500 platform.
Bulk-cell ATAC-seq was conducted following the published protocol  with modifications in cell sorting and nuclei preparation. Specifically, 2,000 cells per ATAC-seq were directly sorted into 50 ul lysis buffer in a 200 ul tube for nuclei preparation. Libraries were constructed using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD502). PCR amplification was performed for 12 cycles under the following conditions: 72°C for 3 minutes, 98°C for 30 seconds, then 12 cycles of 98°C for 15 seconds, 60°C for 30 seconds, and 72°C for 3 minutes, followed by a final extension at 72°C for 5 minutes.
The final DNA was purified using 1× VAHTS DNA Clean Beads and sequenced as 150 bp paired-end reads on the Illumina NovaSeq 6000 platform.
For snATAC-seq, the procedure was performed according to the manufacturer’s instructions using the Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 (10x Genomics). For the Ngn3-CKO samples, E14.5 EpCAM+ pancreatic cells of WT and CKO embryos with different genders (two WT male litters and two CKO female litters) were pooled and loaded as one sample. To ensure experimental success and an adequate number of nuclei, extra pancreatic cells from WT embryos were included, with a ratio of to EpCAM+ cells of 1:4. For the NeuroD1-CKO samples, E15.5 EpCAM+ pancreatic cells of WT and CKO embryos with different genders (two WT female litters and three CKO male litters) were pooled and loaded as one sample.
Libraries were sequenced as 50-bp paired-end reads on an NovaSeq 6000 system.
snATAC-seq

tag: tissue

value: fetal pancreas

tag: time

tag: genotype

tag: dataset


title: Ngn3CreNeurod1OEHZ_E15.5_88


title: E14.5Ngn3fbH_23_53

description:
Smartseq2 scRNA-seq
sm2_Ngn3fbGFP_validation.rc.csv


title: E14.5Ngn3fbH_22_53


title: Ngn3CreNeurod1OEHZ_E15.5_87


title: E14.5Ngn3fbH_21_53


title: Ngn3CreNeurod1OEHZ_E15.5_86


title: E14.5Ngn3fbH_19_53


title: E14.5Ngn3fbH_18_53


title: Ngn3CreNeurod1OEHZ_E15.5_85


title: E14.5Ngn3fbH_16_53


title: Ngn3CreNeurod1OEHZ_E15.5_84


title: E14.5Ngn3fbH_17_53


title: Ngn3CreNeurod1OEHZ_E15.5_83


title: Ngn3CreNeurod1OEHZ_E15.5_81


title: Ngn3CreNeurod1OEHZ_E15.5_82


title: E14.5Ngn3fbL_03_53


title: Ngn3CreNeurod1OEHZ_E15.5_80


title: E14.5Ngn3fbH_15_53


title: E14.5Ngn3fbH_24_53


title: Ngn3CreNeurod1OEHZ_E15.5_79


title: E14.5Ngn3fbH_13_53


title: E14.5Ngn3fbH_12_53


title: E14.5Ngn3fbH_11_53


title: Ngn3CreNeurod1OEHZ_E15.5_77


title: Ngn3CreNeurod1OEHZ_E15.5_78


title: Ngn3CreNeurod1OEHZ_E15.5_76


title: E14.5Ngn3fbH_09_53


title: Ngn3CreNeurod1OEHZ_E15.5_75


title: Ngn3CreNeurod1OEHZ_E15.5_72


title: E14.5Ngn3fbH_06_53


title: E14.5Ngn3fbH_07_53


title: E14.5Ngn3fbH_08_53


title: E14.5Ngn3fbH_04_53


title: E14.5Ngn3fbH_05_53


title: Ngn3CreNeurod1OEHZ_E15.5_73


title: Ngn3CreNeurod1OEHZ_E15.5_71


title: Ngn3CreNeurod1OEHZ_E15.5_74


title: Ngn3CreNeurod1OEHZ_E15.5_70


title: Ngn3CreNeurod1OEHZ_E15.5_69


title: E14.5Ngn3fbH_03_53


title: E14.5Ngn3fbH_01_53


title: E14.5Ngn3fbH_02_53


title: E13_5_Ngn3_KO_2_9_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E14.5Ngn3fbH_14_53


title: Ngn3CreNeurod1OEHZ_E15.5_67


title: Ngn3CreNeurod1OEHZ_E15.5_68


title: E13_5_Ngn3_KO_2_8_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Ngn3CreNeurod1OEHZ_E15.5_65


title: E13_5_Ngn3_KO_2_7_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E13_5_Ngn3_KO_2_6_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: 1Gy_rep2

type: RNA

city: Hirosaki

first: Satoru

last: Monzen

state: Aomori

address: Hon-cho 66-1

country: Japan

institute: Hirosaki University

hyb_protocol: A SurePrint G3 Mouse miRNA microarray slide 8x60K (Agilent Technologies) was hybridised with the Cy3 labelled miRNA in a hybridisation solution prepared with a Gene Expression Hybridisation Kit (Agilent Technologies Inc.), following the manufacturer’s instructions.

scan_protocol: Cy3 fluorescence signal images on the slide were obtained by a microarray scanner (Agilent SureScan Microarray Scanner G 2600 D; Agilent Technologies Inc.) and processed using the Feature Extraction version 10.7 software based on the instructions from Agilent Technologies.

data_processing: The scanned images were analyzed with Feature Extraction version 10.7 software (Agilent Technologies Inc.). To identify only signals that differed from the background, Fetures flagged in  glsPosAndSignif were included in the analysis. In addition, features flagged glsSaturated, glsFeatNonUnifOL, and glsFeatPopnOL were excluded in order to identify only features that were not saturated and that were uniform across multiple identical sequences in the array. These analyses were performed using Microsoft Excel software (Microsoft office 365). Then, the obtain data were normalized by quantile normalization, and signal intensities for each probe were calculated.

molecule: total RNA

source_name: osteoblasts

label_protocol: Cyanine-3 (Cy3) labeled miRNA was synthesized using the miRNA Complete Labelling Reagent and Hyb kit (Agilent Technologies Inc.).

growth_protocol: MC3T3-E1 cells were mainteined MEMα supplemented 10% heat-inactivated fetal bovine serum and 1% penicillin/streptomycin. The cultures were incubated in a 5% CO2 incubator at 37℃.

extract_protocol: Total RNAs were extracted using RNeasy® Plus Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's instructions. And then, total RNA quality was confirmed using a 2100 Bioanalyzer (Agilent Technologies Inc.).

treatment_protocol: The cell was exposed to 0.223 Gy/min alpha particles (total dose: 0.5 Gy and 1 Gy)

tag: cell line

tag: treatment


title: Ngn3CreNeurod1OEHZ_E15.5_64


title: E13_5_Ngn3_KO_2_64_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: 1Gy_rep1


title: E13_5_Ngn3_KO_2_63_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Ngn3CreNeurod1OEHZ_E15.5_63


title: FAC-sorted RGCs at 14dpi_biological replicate 6

city: Leuven

first: Anyi

last: Zhang

address: Naamsestraat 61/bus 4049

country: Belgium

institute: KU Leuven

description: Library name: 14dpi_6

library_source: transcriptomic

data_processing:
Technical replicates of RNA-seq samples were merged post-sequencing, and adapter sequences were removed using TrimGalore (v0.6.7).
Quality control was conducted using FastQC (v0.11.5).
Sequencing reads were aligned to the zebrafish reference genome (Ensembl-GRCz11) using the STAR aligner.
Genes with low expression were filtered out using a custom-developed R script.
Batch effects were corrected with pyCombat.
Assembly: Ensembl-GRCz11
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Filtered and batch effects corrected counts for all samples

organism: Danio rerio

source_name: Retinal ganglion cells

extract_protocol:
RNA was extracted in two separate batches using the Quick-RNA Microprep kit according to the manufacturer’s instructions.
Libraries were prepared using the Smart-Seq2 method (RGC samples, Nextera XT DNA, Illumina, San Diego, CA, USA

tag: cell type

value: Retinal ganglion cells

value: optic nerve crush

tag: batch

value: RNA extraction batch 2


title: FAC-sorted RGCs at 14dpi_biological replicate 5

description: Library name: 14dpi_5


title: Ngn3CreNeurod1OEHZ_E15.5_62


title: FAC-sorted RGCs at 14dpi_biological replicate 4

description: Library name: 14dpi_4


title: E13_5_Ngn3_KO_2_62_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Ngn3CreNeurod1OEHZ_E15.5_66


title: FAC-sorted RGCs at 14dpi_biological replicate 2

description: Library name: 14dpi_2

value: RNA extraction batch 1


title: E13_5_Ngn3_KO_2_61_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Ngn3CreNeurod1OEHZ_E15.5_61


title: Ngn3CreNeurod1OEHZ_E15.5_60


title: FAC-sorted RGCs at 14dpi_biological replicate 3

description: Library name: 14dpi_3


title: FAC-sorted RGCs at 14dpi_biological replicate 1

description: Library name: 14dpi_1


title: E13_5_Ngn3_KO_2_60_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Ngn3CreNeurod1OEHZ_E15.5_59


title: FAC-sorted RGCs at 10dpi_biological replicate 4

description: Library name: 10dpi_4


title: FAC-sorted RGCs at 10dpi_biological replicate 5

description: Library name: 10dpi_5


title: FAC-sorted RGCs at 10dpi_biological replicate 3

description: Library name: 10dpi_3


title: E13_5_Ngn3_KO_2_5_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: FAC-sorted RGCs at 10dpi_biological replicate 2

description: Library name: 10dpi_2


title: 0Gy_rep1

value: no radiation


title: Ngn3CreNeurod1OEHZ_E15.5_58


title: 0.5Gy_rep2


title: 0.5Gy_rep1


title: 0Gy_rep2


title: FAC-sorted RGCs at 10dpi_biological replicate 1

description: Library name: 10dpi_1


title: E13_5_Ngn3_KO_2_59_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: FAC-sorted RGCs at 6dpi_biological replicate 5

description: Library name: 6dpi_5


title: FAC-sorted RGCs at 6dpi_biological replicate 4

description: Library name: 6dpi_4


title: E13_5_Ngn3_KO_2_58_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Ngn3CreNeurod1OEHZ_E15.5_57


title: FAC-sorted RGCs at 6dpi_biological replicate 2

description: Library name: 6dpi_2


title: FAC-sorted RGCs at 6dpi_biological replicate 1

description: Library name: 6dpi_1


title: Ngn3CreNeurod1OEHZ_E15.5_56


title: FAC-sorted RGCs at 6dpi_biological replicate 3

description: Library name: 6dpi_3


title: FAC-sorted RGCs at 3dpi_biological replicate 6

description: Library name: 3dpi_6


title: E13_5_Ngn3_KO_2_57_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E13_5_Ngn3_KO_2_55_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: FAC-sorted RGCs at 3dpi_biological replicate 5

description: Library name: 3dpi_5


title: Ngn3CreNeurod1OEHZ_E15.5_53


title: Ngn3CreNeurod1OEHZ_E15.5_55


title: FAC-sorted RGCs at 3dpi_biological replicate 4

description: Library name: 3dpi_4


title: E13_5_Ngn3_KO_2_56_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: FAC-sorted RGCs at 3dpi_biological replicate 3

description: Library name: 3dpi_3


title: FAC-sorted RGCs at 3dpi_biological replicate 2

description: Library name: 3dpi_2


title: FAC-sorted RGCs at 3dpi_biological replicate 1

description: Library name: 3dpi_1


title: Ngn3CreNeurod1OEHZ_E15.5_52


title: FAC-sorted RGCs at 1dpi_biological replicate 6

description: Library name: 1dpi_6


title: E13_5_Ngn3_KO_2_53_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E13_5_Ngn3_KO_2_54_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E13_5_Ngn3_KO_2_52_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Ngn3CreNeurod1OEHZ_E15.5_51


title: FAC-sorted RGCs at 1dpi_biological replicate 4

description: Library name: 1dpi_4


title: FAC-sorted RGCs at 1dpi_biological replicate 5

description: Library name: 1dpi_5


title: FAC-sorted RGCs at 1dpi_biological replicate 7

description: Library name: 1dpi_7


title: Ngn3CreNeurod1OEHZ_E15.5_50


title: FAC-sorted RGCs at 1dpi_biological replicate 3

description: Library name: 1dpi_3


title: FAC-sorted RGCs at 1dpi_biological replicate 2

description: Library name: 1dpi_2


title: Ngn3CreNeurod1OEHZ_E15.5_49


title: Ngn3CreNeurod1OEHZ_E15.5_54


title: FAC-sorted RGCs at naive condition_biological replicate 6

description: Library name: naive_6

value: Non-injured


title: E13_5_Ngn3_KO_2_51_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E13_5_Ngn3_KO_2_50_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Ngn3CreNeurod1OEHZ_E15.5_48


title: E13_5_Ngn3_KO_2_4_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: FAC-sorted RGCs at naive condition_biological replicate 3

description: Library name: naive_3


title: E13_5_Ngn3_KO_2_49_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Ngn3CreNeurod1OEHZ_E15.5_47


title: FAC-sorted RGCs at naive condition_biological replicate 2

description: Library name: naive_2


title: Ngn3CreNeurod1OEHZ_E15.5_46


title: FAC-sorted RGCs at naive condition_biological replicate 1

description: Library name: naive_1


title: E13_5_Ngn3_KO_2_47_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Ngn3CreNeurod1OEHZ_E15.5_45


title: CCl4, scRNA-seq

city: Daejeon

first: Kwon Yong

last: Tak

address: Gu Sung Street

country: South Korea

institute: KAIST

description:
Library name: CCl4
Control

data_processing:
The barcoded processing, sequence mapping and gene counting were done using the Cell Ranger software v 4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: tsv files and matrix files

source_name: liver

extract_protocol:
Liver was extracted from transcardiac perfused mouse and enzyme dissociated to cell level.
Library was performed according to the manufacter’s instructions (Chromium Single Cell 3′ Reagent Kit v3.1, 10x Genomics). Briefly, 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.

treatment_protocol: Mouse was IP jected with CCl4

value: liver

value: 4 months old


title: E13_5_Ngn3_KO_2_48_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E13_5_Ngn3_KO_2_46_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: F-CCl4, scRNA-seq

description:
Library name: F-CCl4
F- means our developed method 'FiNi-seq'


title: E13_5_Ngn3_KO_2_45_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Ngn3CreNeurod1OEHZ_E15.5_43


title: FAC-sorted RGCs at 1dpi_biological replicate 1

description: Library name: 1dpi_1


title: cKO_4

city: Guangzhou

first: Yan

state: Guangdong

address: No. 600 Tianhe Road

institute: The Third Affiliated Hospital of Sun Yat-Sen University

description:
Library name: sample8
KO_4

data_processing:
Sequence reads were aligned to the mouse genome version mm10 with using bowtie2 and RSEM.
Differentially expressed genes (DEGs) were calculated by DESeq2.
Assembly: mm10
Supplementary files format and content: tsv file containing ensembl gene accession number and raw counts for each sample.

growth_protocol: Mice of C57BL/6J background were housed under specific pathogen free conditions. Experiments were performed with animals under protocols approved by the Institutional Animal Care and Use Committee of The Third Affiliated Hospital of Sun Yat-sen University.

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) according to manual instruction. Total RNA was qualified and quantified as follows: (1) RNA purity and concentration were then examined using NanoDrop 2000; (2) RNA integrity and quantity were measured using the Agilent 2100/4200 system.
mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library.

treatment_protocol: 6- to 8-week-old Control or liver-specific METTL3 inducible knockout (Mettl3 cKO) mice were hydrodynamic tail vein injected with c-MYC/sgP53 plasmids. Liver samples were collected  3 weeks after injection. Total RNA was extracted for RNA sequencing.

value: cKO

value: 3 weeks post-hydrodynamic tail vein injection of c-MYC/sgP53 plasmids


title: cKO_2

description:
Library name: sample6
KO_2


title: cKO_3

description:
Library name: sample7
KO_3


title: FAC-sorted RGCs at naive condition_biological replicate 5

description: Library name: naive_5


title: Control_2

description:
Library name: sample2
WT_2

value: wild-type control


title: Control_3

description:
Library name: sample3
WT_3


title: Ngn3CreNeurod1OEHZ_E15.5_40


title: E13_5_Ngn3_KO_2_43_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E13_5_Ngn3_KO_2_42_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Ngn3CreNeurod1OEHZ_E15.5_41


title: Control_1

description:
Library name: sample1
WT_1


title: Ngn3CreNeurod1OEHZ_E15.5_39


title: E13_5_Ngn3_KO_2_41_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, CTCFOE, rep3, RNA-seq

city: Shanghai

first: Yijun

address: 800 Dongchuan Rd

institute: Shanghai Jiao Tong University

description: Library name: Sample 18

data_processing:
Raw FASTQ data files were mapped to the mouse reference genome (GRCm38/mm10) using the HISAT2 (v2.2.1) with default parameters. Subsequently, Cufflinks (v2.2.1) was employed to estimate transcript expression levels in FPKM (Fragments Per Kilobase of exon per Million mapped fragments).
Gene expression analyses were conducted with a minimum of three replicates, presenting data as mean ± SEM. Statistical significance of gene expression changes was determined using unpaired Student’s t-test in GraphPad Prism (v8.4.2) and R (v4.1.1), with significance levels denoted as follows: ‘*’ for P ≤ 0.05, ‘**’ for P ≤ 0.01, and ‘***’ for P ≤ 0.001.
Assembly: GRCm38
Supplementary files format and content: The fpkm files include gene expression values for each sample.

source_name: Brain

growth_protocol: C57/BL6J and Institute of Cancer Research (ICR) mice were maintained at 23°C in an SPF (specific pathogen free) facility following a 12-h (7:00‒19:00) light and 12-h (19:00‒7:00) dark schedule. All animal experimental procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of Shanghai Jiao Tong University (protocol#: A2016041).

extract_protocol:
The P0 pups or adult mice were decapitated. The skin and skull of the head were carefully removed, and the brain was placed in the 35-mm dish filled with ice-cold PBS. The cortical or olfactory bulb tissues were then dissected out using fine forceps and immediately transferred to a new microcentrifuge tube containing ice-cold TRIzol Reagent. The sample was homogenized using a pestle and then centrifuged at 12,000 × g for 10 min at 4°C. The supernatant was transferred into a new microcentrifuge tube, and 100 l of chloroform was added. The sample was then incubated at room temperature for 3 min after vigorous shaking for 15 sec. After centrifuging at 12,000 × g for 15 min at 4°C, the upper aqueous phase was carefully transferred into a new RNase-free microcentrifuge tube, followed by the addition of 250 l of isopropanol. The mixture was inverted several times and incubated at room temperature for 10 min. After centrifuging at 12,000 × g for 10 min at 4°C, the supernatant was discarded, and the RNA pellet was washed once with 1 ml of freshly-made 75% ethanol, air-dried for 5 min, and dissolved in 30 l of nuclease-free water. The concentration of RNA was measured using the spectrophotometer. The high-quality RNA, with an A260/A280 ratio of ~2.0, is subjected to library preparation.
The polyadenylated mRNA was isolated using oligo(dT) coupled to magnetic beads from 1 g of total RNA and fragmented by heating at 94°C for 8 min. The first cDNA strand was synthesized by reverse transcription with a random primer (N6). After synthesizing the second strand DNA, the Y-shaped adapter-HTS was ligated to both ends. The ligated DNA was cleaned by AMPure XP Beads. Finally, the RNA-seq library was synthesized through PCR (98°C, 30 s; 98°C, 10 s, 60°C, 30 s, 72°C, 30 s for 10 cycles; and a final extension at 72°C, 5 min) by combining the reagents (2.5 l of P5 primer, 2.5 l of P7 primer, and 25 l of Amplification Mix). All RNA-seq libraries were sequenced on an Illumina NovaSeq 6000 platform.

value: Brain

value: Neuroblast

value: CTCF ADA mutation

value: CTCFOE


title: N2A, OECtr, rep2, RNA-seq

description: Library name: Sample 14

value: OECtr


title: N2A, CTCFOE, rep2, RNA-seq

description: Library name: Sample 17


title: Ngn3CreNeurod1OEHZ_E15.5_38

value: fetal pancreas


title: N2A, OECtr, rep1, RNA-seq

description: Library name: Sample 13


title: Control_4

description:
Library name: sample4
WT_4


title: E13_5_Ngn3_KO_2_40_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Ngn3CreNeurod1OEHZ_E15.5_42


title: N2A, shWAPL-3, rep3, RNA-seq

description: Library name: Sample 12

value: shWAPL


title: N2A, shWAPL-3, rep2, RNA-seq

description: Library name: Sample 11


title: Ngn3CreNeurod1OEHZ_E15.5_37


title: N2A, shWAPL-3, rep1, RNA-seq

description: Library name: Sample 10


title: E13_5_Ngn3_KO_2_44_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Ngn3CreNeurod1OEHZ_E15.5_36


title: E13_5_Ngn3_KO_2_39_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E13_5_Ngn3_KO_2_3_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, shWAPL-2, rep2, RNA-seq

description: Library name: Sample 8


title: N2A, shWAPL-2, rep3, RNA-seq

description: Library name: Sample 9


title: N2A, CTCFOE, rep1, RNA-seq

description: Library name: Sample 16


title: E13_5_Ngn3_KO_2_38_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Ngn3CreNeurod1OEHZ_E15.5_35


title: N2A, shWAPL-2, rep1, RNA-seq

description: Library name: Sample 7


title: N2A, OECtr, rep3, RNA-seq

description: Library name: Sample 15


title: N2A, shWAPL-1, rep3, RNA-seq

description: Library name: Sample 6


title: N2A, shWAPL-1, rep2, RNA-seq

description: Library name: Sample 5


title: E13_5_Ngn3_KO_2_37_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Ngn3CreNeurod1OEHZ_E15.5_33


title: N2A, shWAPL-1, rep1, RNA-seq

description: Library name: Sample 4


title: N2A, shCtr, rep3, RNA-seq

description: Library name: Sample 3

value: shCtr


title: Ngn3CreNeurod1OEHZ_E15.5_32


title: N2A, shCtr, rep2, RNA-seq

description: Library name: Sample 2


title: N2A, shCtr, rep1, RNA-seq

description: Library name: Sample 1


title: E13_5_Ngn3_KO_2_35_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E13_5_Ngn3_KO_2_36_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E13_5_Ngn3_KO_2_34_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, shWAPL-3, HS18, rep2, 4C-seq

description: Library name: Sample 30

library_source: genomic

data_processing:
Raw FASTQ files were mapped to the mouse reference genome (GRCm38/mm10) using Bowtie2 (v2.2.5) with default parameters. The reads per million (RPM) values were calculated using r3Cseq program (v1.20). Bedgraph files generated by r3Cseq (v1.20) were visualized in the UCSC genome browser.
Assembly: GRCm38
Supplementary files format and content: The bedgraph files detail pileup signals of DNA-DNA interactions.
Library strategy: 4C-Seq

molecule: genomic DNA

growth_protocol: Mouse Neuro-2a (N2a) cells were cultured in a modified Eagle’s medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, and 1% Non-Essential Amino Acids. Typically, N2a cells were incubated at 37°C in a humidified incubator with 5% (v/v) CO2.

extract_protocol:
Briefly, cortical tissues were dissected out using fine forceps and immediately transferred to a dish containing ice-cold NeuroBasal medium. The tissues were then torn into pieces using fine forceps and transferred to an Eppendorf tube containing 0.25% trypsin-EDTA. The sample was incubated at 37°C for 15 min with continuous shaking at 300 rpm. The trypsin digestion of tissues was quenched by the addition of 10% FBS in the PBS buffer. After filtering the dissociated tissues into a single-cell suspension, the volume was adjusted to 5 ml using 10% FBS in the PBS for crosslinking.
Quantitative high-resolution chromosome conformation capture copy (QHR-4C) experiments were performed as previously described with minor modifications. In brief, five million cells were harvested as described above. The cells were resuspended in MEM medium, and then crosslinked with 2% formaldehyde at room temperature with slow rotations for 10 min. The reaction was quenched by the addition of 2 M glycine. The fixed cells were spun down at 900 × g for 5 min at 4°C and then washed twice with 1 ml of ice-cold PBS. Cells were lysed twice with 1 ml of ice-cold 4C permeabilization buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.2% SDS, 0.5% NP40, 1% Triton X-100, and 1 × protease inhibitors) with slow rotations for 10 min at 4°C. Cells were then resuspended in nuclease-free water, followed by the addition of 10 × DpnII buffer and 10% SDS, and incubation at 37°C with constant shaking at 900 rpm. After 1 h, 20% Triton X-100 was added to the sample, and the sample was incubated at 37°C for an additional hour with constant shaking at 900 rpm. Next, DpnII was added to the sample, followed by an overnight incubation at 37°C with constant shaking at 900 rpm. The enzyme was heat-inactivated at 65°C for 20 min. The sample was centrifuged at 2,000 × g for 10 min, and the supernatant was carefully removed to not disturb the cell pellets. The cell pellets were then resuspended with nuclease-free water. The digested nuclei were ligated with T4 DNA ligase in a total ligation volume of 2 ml at 16°C for 12 h.
The next day, the ligated chromatin was digested with 10 mg/ml Protease K at 65°C for 2 h. The DNA was extracted using phenol-chloroform extraction, followed by ethanol precipitation as described above. The DNA pellet was then dissolved in nuclease-free water and sonicated using a Bioruptor system with a low energy setting. Sonication was performed in cycles of 30-sec on and 30-sec off for 12 cycles to obtain DNA fragments ranging from 200-600 bp. The concentration of the sonicated DNA was measured using the Qubit fluorescent dye. Next, DNA was used as a template for linear amplification with a specific 5’ biotin-tagged primer complementary to the viewpoint. The linear amplification was conducted in a total volume of 0.05 ml, including 2 × Buffer, dNTP, Polymerase, and 1 uM 5’ biotin-tagged primer, using the program (95°C, 2 min; 95°C, 15 s, 58°C, 25 s, 72°C, 1 min 30 s for 80 cycles; and a final extension at 72°C, 5 min). The amplified products were denatured at 95°C for 5 min and then chilled on ice to obtain biotinylated single-stranded DNA (ssDNA). The biotinylated ssDNA was ligated with 50 mM Adapter-4C adapters for 12 h at 16°C and purified by streptavidin magnetic C1 beads. The QHR-4C libraries were generated via PCR amplification (94°C, 2 min; 94°C, 10 s, 60°C, 15 s, 72°C, 1 min for 19 cycles; and a final extension at 72°C, 5 min) using high-fidelity DNA polymerase. The amplified PCR products were purified using the High-Pure PCR Product Purification kit and sequenced on an Illumina NovaSeq 6000 platform.

value: HS18 enrichment


title: N2A, shWAPL-3, HS19-20, rep2, 4C-seq

description: Library name: Sample 32

value: HS19-20 enrichment


title: N2A, shWAPL-3, HS19-20, rep1, 4C-seq

description: Library name: Sample 31


title: N2A, shWAPL-3, HS18, rep1, 4C-seq

description: Library name: Sample 29


title: E13_5_Ngn3_KO_2_33_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, shWAPL-3, HS51bL, rep2, 4C-seq

description: Library name: Sample 28

value: HS51bL enrichment


title: Ngn3CreNeurod1OEHZ_E15.5_30


title: Ngn3CreNeurod1OEHZ_E15.5_31


title: N2A, shWAPL-3, HS51bL, rep1, 4C-seq

description: Library name: Sample 27


title: Ngn3CreNeurod1OEHZ_E15.5_34


title: Ngn3CreNeurod1OEHZ_E15.5_44


title: N2A, shWAPL-3, HS51, rep2, 4C-seq

description: Library name: Sample 26

value: HS51 enrichment


title: Ngn3CreNeurod1OEHZ_E15.5_28


title: Ngn3CreNeurod1OEHZ_E15.5_29


title: E13_5_Ngn3_KO_2_32_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, shWAPL-3, HS51, rep1, 4C-seq

description: Library name: Sample 25


title: E13_5_Ngn3_KO_2_31_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, shWAPL-2, HS19-20, rep2, 4C-seq

description: Library name: Sample 24


title: Ngn3CreNeurod1OEHZ_E15.5_27


title: E13_5_Ngn3_KO_2_30_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, shWAPL-2, HS19-20, rep1, 4C-seq

description: Library name: Sample 23


title: N2A, shWAPL-2, HS18, rep2, 4C-seq

description: Library name: Sample 22


title: N2A, shWAPL-2, HS18, rep1, 4C-seq

description: Library name: Sample 21


title: Ngn3CreNeurod1OEHZ_E15.5_26


title: N2A, shWAPL-2, HS51bL, rep2, 4C-seq

description: Library name: Sample 20


title: Ngn3CreNeurod1OEHZ_E15.5_25


title: E13_5_Ngn3_KO_2_2_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, shWAPL-2, HS51bL, rep1, 4C-seq

description: Library name: Sample 19


title: N2A, shWAPL-2, HS51, rep2, 4C-seq

description: Library name: Sample 18


title: Ngn3CreNeurod1OEHZ_E15.5_24


title: E13_5_Ngn3_KO_2_29_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, shWAPL-1, HS19-20, rep2, 4C-seq

description: Library name: Sample 16


title: N2A, shWAPL-1, HS19-20, rep1, 4C-seq

description: Library name: Sample 15


title: Ngn3CreNeurod1OEHZ_E15.5_23


title: N2A, shWAPL-2, HS51, rep1, 4C-seq

description: Library name: Sample 17


title: E13_5_Ngn3_KO_2_27_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, shWAPL-1, HS18, rep2, 4C-seq

description: Library name: Sample 14


title: Ngn3CreNeurod1OEHZ_E15.5_22


title: N2A, shWAPL-1, HS51bL, rep2, 4C-seq

description: Library name: Sample 12


title: Ngn3CreNeurod1OEHZ_E15.5_21


title: E13_5_Ngn3_KO_2_26_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E13_5_Ngn3_KO_2_25_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, shWAPL-1, HS51bL, rep1, 4C-seq

description: Library name: Sample 11


title: N2A, shWAPL-1, HS51, rep2, 4C-seq

description: Library name: Sample 10


title: Ngn3CreNeurod1OEHZ_E15.5_20


title: N2A, shWAPL-1, HS51, rep1, 4C-seq

description: Library name: Sample 9


title: E13_5_Ngn3_KO_2_24_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, shCtr, HS19-20, rep2, 4C-seq

description: Library name: Sample 8


title: Ngn3CreNeurod1OEHZ_E15.5_19


title: N2A, shCtr, HS19-20, rep1, 4C-seq

description: Library name: Sample 7


title: E13_5_Ngn3_KO_2_28_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E13_5_Ngn3_KO_2_23_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, shCtr, HS18, rep2, 4C-seq

description: Library name: Sample 6


title: N2A, shCtr, HS18, rep1, 4C-seq

description: Library name: Sample 5


title: E13_5_Ngn3_KO_2_22_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, shCtr, HS51bL, rep2, 4C-seq

description: Library name: Sample 4


title: N2A, shCtr, HS51bL, rep1, 4C-seq

description: Library name: Sample 3


title: Ngn3CreNeurod1OEHZ_E15.5_17


title: Ngn3CreNeurod1OEHZ_E15.5_16


title: N2A, shCtr, HS51, rep1, 4C-seq

description: Library name: Sample 1


title: E13_5_Ngn3_KO_2_21_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E13_5_Ngn3_KO_2_20_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: FAC-sorted RGCs at naive condition_biological replicate 4

description: Library name: naive_4

value: Retinal ganglion cells

value: Non-injured

value: RNA extraction batch 2


title: N2A, shCtr, HS51, rep2, 4C-seq

description: Library name: Sample 2


title: CD4 T cells TCR_Library

city: Boston

first: Hengcheng

state: Boston

address: 221 Longwood Ave

department: Medicine/Renal

country: USA

institute: Brigham and Women's Hospital

description: Library name: Sample2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Mouse CD4 T cells

extract_protocol:
Balb/c kidneys were transplanted into Foxp3IRES-GFP mice. 20 days post-transplantation, CD4+CD19-CXCR5+FoxP3+ Tfr and CD4+CD19-CXCR5-FoxP3+ Treg cells from the dLN of allogeneic kidney transplant recipients were sorted.
Cells were resuspended in 0.4% BSA in PBS at a concentration of 2,000 cells per μl, then loaded onto a single lane (Chromium chip K, 10X Genomics) followed by encapsulation in a lipid droplet (Single Cell 5′kit V2, 10X Genomics) followed by cDNA and library generation according to the manufacturer’s protocol. 5’ mRNA library was sequenced to an average of 50,000 reads per cell, V(D)J library and HTO (Cell Hashing antibodies) library sequenced to an average of 5,000 reads per cell, all using Illumina Novaseq.

value: CD4 T cells

tag: age

value: 6-8 weeks


title: Ngn3CreNeurod1OEHZ_E15.5_15


title: E13_5_Ngn3_KO_2_1_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, ADA-Clone2, HS19-20, rep2, 4C-seq

description:
Library name: Sample 24
N2A_ADA-Clone2_HS19-20.merge.RPMs.bedGraph.gz

data_processing:
Raw FASTQ files were mapped to the mouse reference genome (GRCm38/mm10) using Bowtie2 (v2.2.5) with default parameters. The reads per million (RPM) values were calculated using r3Cseq program (v1.20). Bedgraph files generated by r3Cseq (v1.20) were visualized in the UCSC genome browser.
Assembly: GRCm38
Supplementary files format and content: The bedgraph files detail pileup signals of DNA-DNA interactions.
Library strategy: 4C-seq

value: Brain

value: Homozygous


title: E13_5_Ngn3_KO_2_19_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Ngn3CreNeurod1OEHZ_E15.5_18


title: N2A, ADA-Clone2, HS19-20, rep1, 4C-seq

description:
Library name: Sample 23
N2A_ADA-Clone2_HS19-20.merge.RPMs.bedGraph.gz

value: Neuroblast


title: Ngn3CreNeurod1OEHZ_E15.5_14


title: E13_5_Ngn3_KO_2_18_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, ADA-Clone2, HS18, rep1, 4C-seq

description:
Library name: Sample 21
N2A_ADA-Clone2_HS18.merge.RPMs.bedGraph.gz


title: Ngn3CreNeurod1OEHZ_E15.5_12


title: E13_5_Ngn3_KO_2_17_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, ADA-Clone2, HS51bL, rep2, 4C-seq

description:
Library name: Sample 20
N2A_ADA-Clone2_HS51bL.merge.RPMs.bedGraph.gz


title: N2A, ADA-Clone2, HS51, rep2, 4C-seq

description:
Library name: Sample 18
N2A_ADA-Clone2_HS51.merge.RPMs.bedGraph.gz


title: N2A, ADA-Clone2, HS51bL, rep1, 4C-seq

description:
Library name: Sample 19
N2A_ADA-Clone2_HS51bL.merge.RPMs.bedGraph.gz


title: Ngn3CreNeurod1OEHZ_E15.5_11


title: E13_5_Ngn3_KO_2_16_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, ADA-Clone1, HS19-20, rep2, 4C-seq

description:
Library name: Sample 16
N2A_ADA-Clone1_HS19-20.merge.RPMs.bedGraph.gz


title: N2A, ADA-Clone1, HS19-20, rep1, 4C-seq

description:
Library name: Sample 15
N2A_ADA-Clone1_HS19-20.merge.RPMs.bedGraph.gz


title: E13_5_Ngn3_KO_2_15_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: CD4 T cells GEX_HTO_Library

description: Library name: Sample1


title: Ngn3CreNeurod1OEHZ_E15.5_10


title: N2A, ADA-Clone1, HS18, rep2, 4C-seq

description:
Library name: Sample 14
N2A_ADA-Clone1_HS18.merge.RPMs.bedGraph.gz


title: N2A, ADA-Clone1, HS18, rep1, 4C-seq

description:
Library name: Sample 13
N2A_ADA-Clone1_HS18.merge.RPMs.bedGraph.gz


title: Ngn3CreNeurod1OEHZ_E15.5_9


title: E13_5_Ngn3_KO_2_14_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, ADA-Clone1, HS51bL, rep2, 4C-seq

description:
Library name: Sample 12
N2A_ADA-Clone1_HS51bL.merge.RPMs.bedGraph.gz


title: N2A, ADA-Clone2, HS18, rep2, 4C-seq

description:
Library name: Sample 22
N2A_ADA-Clone2_HS18.merge.RPMs.bedGraph.gz


title: Ngn3CreNeurod1OEHZ_E15.5_13


title: N2A, ADA-Clone1, HS51, rep2, 4C-seq

description:
Library name: Sample 10
N2A_ADA-Clone1_HS51.merge.RPMs.bedGraph.gz


title: N2A, ADA-Clone1, HS51, rep1, 4C-seq

description:
Library name: Sample 9
N2A_ADA-Clone1_HS51.merge.RPMs.bedGraph.gz


title: Ngn3CreNeurod1OEHZ_E15.5_7

description:
Smartseq3 scRNA-seq
sm3_rc.cell.tsv
sm3_rc.gene.tsv
sm3_rc.mtx


title: E13_5_Ngn3_KO_2_12_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, ADA-Clone2, HS51, rep1, 4C-seq

description:
Library name: Sample 17
N2A_ADA-Clone2_HS51.merge.RPMs.bedGraph.gz


title: N2A, shWAPL-1, HS18, rep1, 4C-seq

description: Library name: Sample 13

value: CTCF ADA mutation


title: N2A, WT, HS19-20, rep1, 4C-seq

description:
Library name: Sample 7
N2A_WT_HS19-20.merge.RPMs.bedGraph.gz

value: Wild type


title: N2A, WT, HS18, rep2, 4C-seq

description:
Library name: Sample 6
N2A_WT_HS18.merge.RPMs.bedGraph.gz


title: E13_5_Ngn3_KO_2_11_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv

value: fetal pancreas


title: Ngn3CreNeurod1OEHZ_E15.5_6


title: Ngn3CreNeurod1OEHZ_E15.5_5


title: E13_5_Ngn3_KO_2_10_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, WT, HS51bL, rep2, 4C-seq

description:
Library name: Sample 4
N2A_WT_HS51bL.merge.RPMs.bedGraph.gz


title: Ngn3CreNeurod1OEHZ_E15.5_4


title: N2A, WT, HS51bL, rep1, 4C-seq

description:
Library name: Sample 3
N2A_WT_HS51bL.merge.RPMs.bedGraph.gz


title: Ngn3CreNeurod1OEHZ_E15.5_3


title: E13_5_Ngn3_KO_1_9_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Ngn3CreNeurod1OEHZ_E15.5_8


title: N2A, ADA-Clone2, RAD21, rep2, ChIP-seq

description:
Library name: Sample 20
N2A_ADA-Clone_Rad21.bw
N2A_ADA-Clone_Rad21_rep2.bw

data_processing:
The raw sequencing data were mapped to the mouse reference genome (GRCm38/mm10) using Bowtie2 (v2.2.5) with default settings. Samtools (v1.15.1) was utilized to convert the Sequence Alignment/Map (SAM) format into a Binary Alignment/Map (BAM) format and to index the resulting BAM files. Subsequently, the BAM files were normalized to RPKM (Reads Per Kilobase per Million mapped reads) for comparative analysis of occupancy levels across samples, utilizing the bamCoverage module of the deepTools suite. The bedGraph files, generated from the deepTools program, were then uploaded to the UCSC Genome Browser for visualization of genomic regions of interest. Peak calling was conducted using MACS2 (v2.2.7.1) with default parameters.
Assembly: GRCm38
Supplementary files format and content: The bigwig files describe pileup signals of DNA-protein interactions.

extract_protocol:
Briefly, cortical tissues were dissected out using fine forceps and immediately transferred to a dish containing ice-cold NeuroBasal medium. The tissues were then torn into pieces using fine forceps and transferred to an Eppendorf tube containing 0.25% trypsin-EDTA. The sample was incubated at 37°C for 15 min with continuous shaking at 300 rpm. The trypsin digestion of tissues was quenched by the addition of 10% FBS in the PBS buffer. After filtering the dissociated tissues into a single-cell suspension, the volume was adjusted to 5 ml using 10% FBS in the PBS for crosslinking.
The purified DNA was subjected to high-throughput library preparation following the protocol recommended by the manufacturer. Briefly, 10 ng of purified DNA was used as a template and combined with End Prep Mix on ice. The reaction was incubated using the following program (20°C, 15 min; 65°C, 15 min). Next, the sample was directly proceeded to adapter ligation and mixed with Rapid Ligation buffer, Rapid DNA ligase, and Adapter-HTS. The sample was then incubated at 20°C for 15 min. Next, the ligated DNA was purified using well-mixed AMPure XP Beads. The DNA purification process was consistent with that described in RNA-seq. Finally, the purified product was amplified using the following mixture (P5 primer, P7 primer, and Amplification Mix ) and proceeded to PCR (95°C, 3 min; 98°C, 20 s, 60°C, 15 s, 72°C, 30 s for 11 cycles; and a final extension at 72°C, 5 min) with P5 and P7 primers for sequencing. The PCR products were also purified using well-mixed AMPure XP Beads. All ChIP-seq libraries were sequenced on an Illumina NovaSeq 6000 platform.

tag: chip antibody


title: Ngn3CreNeurod1OEHZ_E15.5_2


title: E13_5_Ngn3_KO_1_8_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, WT, HS51, rep1, 4C-seq

description:
Library name: Sample 1
N2A_WT_HS51.merge.RPMs.bedGraph.gz


title: N2A, ADA-Clone1, HS51bL, rep1, 4C-seq

description:
Library name: Sample 11
N2A_ADA-Clone1_HS51bL.merge.RPMs.bedGraph.gz


title: N2A, ADA-Clone2, RAD21, rep1, ChIP-seq

description:
Library name: Sample 19
N2A_ADA-Clone_Rad21.bw
N2A_ADA-Clone_Rad21_rep2.bw


title: E13_5_Ngn3_KO_1_7_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E13_5_Ngn3_KO_2_13_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, ADA-Clone1, RAD21, rep2, ChIP-seq

description:
Library name: Sample 18
N2A_ADA-Clone_Rad21.bw
N2A_ADA-Clone_Rad21_rep1.bw


title: Ngn3CreNeurod1OEHZ_E15.5_1


title: N2A, ADA-Clone1, RAD21, rep1, ChIP-seq

description:
Library name: Sample 17
N2A_ADA-Clone_Rad21.bw
N2A_ADA-Clone_Rad21_rep1.bw


title: N2A, WT, HS19-20, rep2, 4C-seq

description:
Library name: Sample 8
N2A_WT_HS19-20.merge.RPMs.bedGraph.gz


title: N2A, WT, HS18, rep1, 4C-seq

description:
Library name: Sample 5
N2A_WT_HS18.merge.RPMs.bedGraph.gz


title: N2A, WT, RAD21, rep2, ChIP-seq

description:
Library name: Sample 16
N2A_WT_Rad21.bw


title: E17_5Ngn3CreNgn3OE

description: 10x genomics scRNA-seq


title: N2A, ADA-Clone2, CTCF, rep2, ChIP-seq

description:
Library name: Sample 14
N2A_ADA-Clone_CTCF.bw

value: CTCF


title: E13_5_Ngn3_KO_1_5_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, ADA-Clone2, CTCF, rep1, ChIP-seq

description:
Library name: Sample 13
N2A_ADA-Clone_CTCF.bw


title: E15_5Neurod1KO_2

description: 10x genomics scRNA-seq


title: E13_5_Ngn3_KO_1_56_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, WT, HS51, rep2, 4C-seq

description:
Library name: Sample 2
N2A_WT_HS51.merge.RPMs.bedGraph.gz


title: N2A, ADA-Clone1, CTCF, rep2, ChIP-seq

description:
Library name: Sample 12
N2A_ADA-Clone_CTCF.bw


title: cKO_1

description:
Library name: sample5
KO_1

value: liver

value: cKO

value: 3 weeks post-hydrodynamic tail vein injection of c-MYC/sgP53 plasmids


title: E15_5Neurod1KO_1

description: 10x genomics scRNA-seq


title: N2A, ADA-Clone1, CTCF, rep1, ChIP-seq

description:
Library name: Sample 11
N2A_ADA-Clone_CTCF.bw


title: N2A, WT, CTCF, rep2, ChIP-seq

description:
Library name: Sample 10
N2A_WT_CTCF.bw


title: E13_5_Ngn3_KO_1_55_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E14_5Ngn3CreNgn3OE

description: 10x genomics scRNA-seq


title: E13_5_Ngn3_KO_1_54_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, WT, CTCF, rep1, ChIP-seq

description:
Library name: Sample 9
N2A_WT_CTCF.bw


title: E14_5Ngn3CreNgn3KO_2

description: 10x genomics scRNA-seq


title: E13_5_Ngn3_KO_1_53_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Adult_cortex, HET, RAD21, rep1, ChIP-seq

description:
Library name: Sample 7
HET_Cortex_Rad21.bw

value: Cortical neuron

value: Neuron

value: Heterozygous


title: Adult_cortex, WT, RAD21, rep2, ChIP-seq

description:
Library name: Sample 6
WT_Cortex_Rad21.bw


title: E13_5_Ngn3_KO_1_6_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Adult_cortex, WT, RAD21, rep1, ChIP-seq

description:
Library name: Sample 5
WT_Cortex_Rad21.bw


title: E14_5Ngn3CreNgn3KO_1

description: 10x genomics scRNA-seq


title: N2A, WT, RAD21, rep1, ChIP-seq

description:
Library name: Sample 15
N2A_WT_Rad21.bw


title: E15.5_Neurod1KO

description: 10x genomics snATAC-seq

library_source: genomic single cell


title: E13_5_Ngn3_KO_1_51_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Adult_cortex, HET, CTCF, rep1, ChIP-seq

description:
Library name: Sample 3
HET_Cortex_Ctcf.bw


title: Adult_cortex, WT, CTCF, rep2, ChIP-seq

description:
Library name: Sample 2
WT_Cortex_Ctcf.bw


title: E14.5_Ngn3CreNgn3KO

description: 10x genomics snATAC-seq


title: E13_5_Ngn3_KO_1_4_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Adult_cortex, WT, CTCF, rep1, ChIP-seq

description:
Library name: Sample 1
WT_Cortex_Ctcf.bw


title: E13_5_Ngn3_KO_1_52_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, ADA-Clone2, rep2, RNA-seq

description:
Library name: Sample 28
N2A_Ctcfmut_raw_counts.txt
N2A_ADA-Clone2_rep2.R1.fastq.gz

data_processing:
Raw FASTQ data files were mapped to the mouse reference genome (GRCm38/mm10) using the HISAT2 (v2.2.1) with default parameters. Subsequently, Cufflinks (v2.2.1) was employed to estimate transcript expression levels in FPKM (Fragments Per Kilobase of exon per Million mapped fragments).
Gene expression analyses were conducted with a minimum of three replicates, presenting data as mean ± SEM. Statistical significance of gene expression changes was determined using unpaired Student’s t-test in GraphPad Prism (v8.4.2) and R (v4.1.1), with significance levels denoted as follows: ‘*’ for P ≤ 0.05, ‘**’ for P ≤ 0.01, and ‘***’ for P ≤ 0.001.
Assembly: GRCm38
Supplementary files format and content: The raw counts file contains all the gene count data.
Supplementary files format and content: The fpkm files include gene expression values for each sample.


title: N2A, ADA-Clone2, rep1, RNA-seq

description:
Library name: Sample 27
N2A_Ctcfmut_raw_counts.txt
N2A_ADA-Clone2_rep1.R1.fastq.gz


title: N2A, ADA-Clone2, rep3, RNA-seq

description:
Library name: Sample 29
N2A_Ctcfmut_raw_counts.txt
N2A_ADA-Clone2_rep3.R1.fastq.gz


title: E13_5_Ngn3_KO_1_49_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, ADA-Clone1, rep3, RNA-seq

description:
Library name: Sample 26
N2A_Ctcfmut_raw_counts.txt
N2A_ADA-Clone1_rep3.R1.fastq.gz


title: E16.5_Ngn3CreER

description: 10x genomics snATAC-seq


title: N2A, ADA-Clone1, rep2, RNA-seq

description:
Library name: Sample 25
N2A_Ctcfmut_raw_counts.txt
N2A_ADA-Clone1_rep2.R1.fastq.gz


title: E13_5_Ngn3_KO_1_48_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E15.5_Ngn3CreER

description: 10x genomics snATAC-seq


title: E15.5_Pdx1Cre

description: 10x genomics snATAC-seq


title: N2A, ADA-Clone1, rep1, RNA-seq

description:
Library name: Sample 24
N2A_Ctcfmut_raw_counts.txt
N2A_ADA-Clone1_rep1.R1.fastq.gz


title: Adult_cortex, HET, RAD21, rep2, ChIP-seq

description:
Library name: Sample 8
HET_Cortex_Rad21.bw


title: N2A, WT, rep3, RNA-seq

description:
Library name: Sample 23
N2A_Ctcfmut_raw_counts.txt
N2A_WT_rep3.R1.fastq.gz

value: No treatment


title: N2A, WT, rep2, RNA-seq

description:
Library name: Sample 22
N2A_Ctcfmut_raw_counts.txt
N2A_WT_rep2.R1.fastq.gz


title: E14.5_Ngn3CreER

description: 10x genomics snATAC-seq


title: E13_5_Ngn3_KO_1_46_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Adult_cortex, HET, CTCF, rep2, ChIP-seq

description:
Library name: Sample 4
HET_Cortex_Ctcf.bw


title: E13_5_Ngn3_KO_1_47_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: N2A, WT, rep1, RNA-seq

description:
Library name: Sample 21
N2A_Ctcfmut_raw_counts.txt
N2A_WT_rep1.R1.fastq.gz


title: E13_5_Ngn3_KO_1_45_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Adult_ob, HET, rep2, RNA-seq

description:
Library name: Sample 19
Adult_ob_raw_counts.txt
Adult_ob_HET_rep2

value: Olfactory bulb


title: Adult_ob, HET, rep3, RNA-seq

description:
Library name: Sample 20
Adult_ob_raw_counts.txt
Adult_ob_HET_rep3


title: ATAC_E17.5WT_3

description: Bulk cell ATAC-seq


title: Adult_ob, HET, rep1, RNA-seq

description:
Library name: Sample 18
Adult_ob_raw_counts.txt
Adult_ob_HET_rep1


title: E13_5_Ngn3_KO_1_44_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E13.5_Pdx1Cre

description: 10x genomics snATAC-seq


title: ATAC_E17.5WT_2

description: Bulk cell ATAC-seq


title: E13_5_Ngn3_KO_1_43_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Adult_ob, WT, rep3, RNA-seq

description:
Library name: Sample 17
Adult_ob_raw_counts.txt
Adult_ob_WT_rep3


title: Adult_ob, WT, rep1, RNA-seq

description:
Library name: Sample 15
Adult_ob_raw_counts.txt
Adult_ob_WT_rep1


title: E13_5_Ngn3_KO_1_42_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: ATAC_E17.5WT_1

description: Bulk cell ATAC-seq


title: Adult_cortex, HET, rep3, RNA-seq

description:
Library name: Sample 14
Adult_cortex_raw_counts.txt
Adult_cortex_HET_rep3


title: Adult_cortex, HET, rep1, RNA-seq

description:
Library name: Sample 12
Adult_cortex_raw_counts.txt
Adult_cortex_HET_rep1


title: Adult_cortex, HET, rep2, RNA-seq

description:
Library name: Sample 13
Adult_cortex_raw_counts.txt
Adult_cortex_HET_rep2


title: ATAC_E17.5Neurod1KO_3

description: Bulk cell ATAC-seq


title: E13_5_Ngn3_KO_1_41_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Adult_cortex, WT, rep3, RNA-seq

description:
Library name: Sample 11
Adult_cortex_raw_counts.txt
Adult_cortex_WT_rep3


title: ATAC_E17.5Neurod1KO_2

description: Bulk cell ATAC-seq


title: E13_5_Ngn3_KO_1_40_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Adult_cortex, WT, rep2, RNA-seq

description:
Library name: Sample 10
Adult_cortex_raw_counts.txt
Adult_cortex_WT_rep2


title: P0_cortex, HET, rep4, RNA-seq

description:
Library name: Sample 8
P0_cortex_raw_counts.txt
P0_cortex_HET_rep4


title: E13_5_Ngn3_KO_1_39_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: ATAC_E17.5Neurod1KO_1

description: Bulk cell ATAC-seq


title: P0_cortex, HET, rep3, RNA-seq

description:
Library name: Sample 7
P0_cortex_raw_counts.txt
P0_cortex_HET_rep3


title: ATAC_E15.5WT_3

description: Bulk cell ATAC-seq


title: P0_cortex, HET, rep2, RNA-seq

description:
Library name: Sample 6
P0_cortex_raw_counts.txt
P0_cortex_HET_rep2


title: Adult_ob, WT, rep2, RNA-seq

description:
Library name: Sample 16
Adult_ob_raw_counts.txt
Adult_ob_WT_rep2


title: E13_5_Ngn3_KO_1_37_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: ATAC_E15.5WT_2

description: Bulk cell ATAC-seq


title: P0_cortex, HET, rep1, RNA-seq

description:
Library name: Sample 5
P0_cortex_raw_counts.txt
P0_cortex_HET_rep1


title: P0_cortex, WT, rep4, RNA-seq

description:
Library name: Sample 4
P0_cortex_raw_counts.txt
P0_cortex_WT_rep4


title: E13_5_Ngn3_KO_1_38_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: ATAC_E15.5Pdx1CreERNgn3KONeurod1OE_2

description: Bulk cell ATAC-seq


title: E13_5_Ngn3_KO_1_36_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: ATAC_E15.5Pdx1CreERNgn3KONeurod1OE_1

description: Bulk cell ATAC-seq


title: P0_cortex, WT, rep2, RNA-seq

description:
Library name: Sample 2
P0_cortex_raw_counts.txt
P0_cortex_WT_rep2


title: E13_5_Ngn3_KO_1_35_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: P0_cortex, WT, rep3, RNA-seq

description:
Library name: Sample 3
P0_cortex_raw_counts.txt
P0_cortex_WT_rep3


title: ATAC_E15.5Pdx1CreERNeurod1OE_2

description: Bulk cell ATAC-seq


title: ATAC_E15.5Pdx1CreERNeurod1OE_1

description: Bulk cell ATAC-seq


title: HiC_E14.5Ngn3flGFPH

description: Library name: HiC_E14.5Ngn3flGFPH

data_processing:
For HiC, preprocessing of Hi-C data was performed using juicer (v1.6) with default parameters aligned to the mm10 reference genome. Topologically associating domains (TADs) were identified using the “hicFindTADs” function in HiCExplorer (v2.1.1). Genomic regions where both promoter and enhancer elements of a gene were located within a single TAD were identified as potential promoter-enhancer loops. Hi-C contact maps were normalized using the “coverage” method in juicer and visualized to assess chromatin interactions.
Assembly: mm10
Supplementary files format and content: hic

extract_protocol:
Hi-C was performed with modifications to the DNA fragmentation and library construction steps. Briefly, E14.5 Ngn3high cells were fixed with 1% formaldehyde at room temperature (RT) for 10 minutes, and the crosslinking reaction was quenched with glycine for 10 minutes at RT. Cells were washed with 1 × PBS and lysed in 50 μl lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 0.1 mM EDTA, 0.5% NP-40, and protease inhibitors) on ice for 50 minutes. After centrifugation at 3,000 r.p.m. at 4 °C for 5 minutes, the supernatant was carefully discarded. Chromatin was solubilized in 10 μl 0.5% SDS and incubated at 62 °C for 10 minutes, followed by quenching with 5 μl 10% Triton X-100 at 37 °C for 30 minutes. The nuclei were digested with 50 U MboI at 37 °C overnight with rotation in a final volume of 50 μl. MboI was inactivated at 62 °C for 20 minutes. For biotin labeling, 1.5 μl 1 mM dATP, 1.5 μl 1 mM dGTP, 1.5 μl 1 mM dTTP, 3.75 μl 0.4 mM biotin-14-dCTP, and 10 U Klenow enzyme were added, and the reaction was incubated at 37 °C for 1.5 hours with rotation.        Ligation was performed by adding 60 μl ligation mix (38.8 μl water, 12 μl 10 × NEB T4 DNA ligase buffer, 7 μl 10% Triton X-100, 1.2 μl 10 mg/ml BSA, and 1 μl 400 U/μl T4 DNA ligase) and incubating at RT for 6 hours with rotation. Crosslinking was reversed, and the DNA was purified. DNA was sheared to 300–500 bp using a Q800R3 sonicator. Biotin-labeled DNA fragments were captured with 10 μl Dynabeads MyOne Streptavidin C1 (Life Technologies).
The libraries were subjected to 150 bp paired-end sequencing on the Illumina NovaSeq 6000


title: Adult_cortex, WT, rep1, RNA-seq

description:
Library name: Sample 9
Adult_cortex_raw_counts.txt
Adult_cortex_WT_rep1


title: P0_cortex, WT, rep1, RNA-seq

description:
Library name: Sample 1
P0_cortex_raw_counts.txt
P0_cortex_WT_rep1


title: ATAC_E15.5Ngn3CreNgn3KONeurod1OE_2

description: Bulk cell ATAC-seq


title: E13_5_Ngn3_KO_1_32_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: H3K4me1_E11.5Pdx1H_1

description: Library name: H3K4me1_E11.5Pdx1H_1

data_processing:
For ChIP-seq, the sequencing reads were aligned to the Mus musculus genome (mm10) using Bowtie2 (v2.2.5) with default parameters, and only reads with a mapping quality score ≥30 were retained for downstream analysis. PCR duplicate reads were removed using SAMtools (v1.3.1) with the commands: samtools sort in_bam | samtools rmdup -s - out_bam. Reads from biological replicates were pooled to increase coverage. TP10M (tags per 10 million) values were calculated and stored in the bedGraph format using Homer with the following parameters: makeUCSCfile out_dir –o out.bdg –name sample_name -color track_color –fragLength 150 –avg -fsize 1e20. The input TP10M signal values were subtracted from the ChIP TP10M to generate normalized signal intensity tracks for downstream analyses.
Assembly: mm10
Supplementary files format and content: Bedgraph

extract_protocol:
For ChIP-seq, Approximately 1.5 × 10⁴ cells were used per ChIP, with 1 ng of primary antibody specific for H3K4me1 (Millipore, 07-436, Lot: 2343581). Libraries were prepared using the Ultra DNA Library Prep Kit for Illumina (NEB, E7370) according to the manufacturer’s instructions.
The final DNA was sequenced as 150 bp paired-end reads on the Illumina NovaSeq 6000 platform.


title: H3K4me1_E11.5Pdx1H_2

description: Library name: H3K4me1_E11.5Pdx1H_2


title: E13_5_Ngn3_KO_1_31_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: ATAC_E15.5Ngn3CreNgn3KONeurod1OE_1

description: Bulk cell ATAC-seq


title: E13_5_Ngn3_KO_1_30_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: D4_GE, replicate 2, scRNA-seq

city: Jinan

first: Zhaoyu

last: Jia

state: Shandong

address: 44 Wenhua Xi Road

department: Advanced Medical Research Institute

institute: Shandong University

description: 10X Genomics

data_processing:
Raw reads were processed by Cell Ranger with default setting.
Assembly: mm10
Supplementary files format and content: The Seurat object of all cells was generated from Seurat R package with standard workflow.

source_name: uterus

extract_protocol:
The uterine tissue was extracted and cut into 2–3 mm fragments, which were then subjected to digestion at 37 °C for 1 h using pancreatin and dispase. Subsequently, the epithelial layer was carefully separated from the middle of the tissue fragments under a stereomicroscope, followed by rinsing with 1× PBS. The remaining tissue fragments were subjected to Accumax solution digestion, and the resulting cell suspension was filtered through a nylon mesh to remove excess cell debris and muscle layer. After separating the epithelial layer and muscle layer, red fluorescent positive cells, namely glandular epithelial cells, were obtained through flow cytometry sorting.
Single-cell suspensions were loaded to 10x Chromium to capture single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3). The following cDNA amplification and library construction steps were performed according to the standard protocol.

value: uterus

tag: Sex

value: female

tag: pregnancy day

value: Pregnant day 4

value: Rosa26tdTomato LtfCre/+


title: ATAC_E15.5Neurod1KO_3

description: Bulk cell ATAC-seq


title: ATAC_E15.5Neurod1KO_2

description: Bulk cell ATAC-seq


title: BRCA1+/- olaparib injected ovary 1

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

institute: Nagoya University

hyb_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Version 6.9, May 2017).

scan_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Version 6.9, May 2017, Agilent C Scanner Settings).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 074036_D_F_20180103) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Rattus norvegicus

source_name: Ovary, BRCA1+/- Sprague-Dawley rat (CLEA Japan)

extract_protocol: Total RNA was extracted using RNeasy Mini(QIAGEN).

treatment_protocol: Female wild-type and BRCA1+/-  rats at 3 weeks of age were injected subcutaneously with olaparib one daily for 14 days by the dose of 50 mg/kg. The rats were euthanized 24 h after the final injection.  The fresh ovary tissues were excised and processed.

value: Ovary

value: Jcl:SD BRCA1+/-


title: BRCA1+/- olaparib injected ovary 4

label_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Version 6.9, May 2017).


title: D4_GE, replicate 1, scRNA-seq

description: 10X Genomics


title: BRCA1+/- vehicle ovary 4


title: E13_5_Ngn3_KO_1_34_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: BRCA1+/- olaparib injected ovary 3


title: E13_5_Ngn3_KO_1_33_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E13_5_Ngn3_KO_1_2_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E13_5_Ngn3_KO_1_29_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: ATAC_E13.5Ngn3KI_2

description: Bulk cell ATAC-seq


title: D4_Stroma, scRNA-seq

description: 10X Genomics


title: BRCA1+/- vehicle ovary 3


title: BRCA1+/- vehicle ovary 1


title: BRCA1+/- vehicle ovary 2


title: D4_Epi, scRNA-seq

description: 10X Genomics


title: ATAC_E13.5Ngn3H_1

description: Bulk cell ATAC-seq


title: BRCA1+/- olaparib injected ovary 2


title: E13_5_Ngn3_KO_1_27_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: iWAT of Atf4AKO mice_3

city: 천안시

first: Rehna

middle: Paula

last: Ginting

state: 충청남도

address: 25 Bongjeong-ro, Dongnam-gu

department: Integrated Biomedical Science

institute: Soonchunhyang University

data_processing:
mRNA was purified and fragmented from total RNA (1ug) using poly-T oligo-attached magnetic beads using two rounds of purification.
Cleaved RNA Fragments primed with random hexamers were reverse transcribed into first strand cDNA using reverse transcriptase, random primers, dUTP in place of dTTP. (The incorporation of dUTP quenches the second strand during amplification, because the polymerase does not incorporate past this nucleotide.)
These cDNA fragments then had the addition of a single ‘A’ base and subsequent ligation of the adapter. The products were purified and enriched with PCR to create the final strand specific cDNA library. The quality of the amplified libraries was verified by capillary electrophoresis (Bioanalyzer, Agilent).
After QPCR using SYBR Green PCR Master Mix (Applied Biosystems), we combined libraries that index tagged in equimolar amounts in the pool.
Cluster generation occurred in the flow cell on the cBot automated cluster generation system (illumina). And then the flow cell loaded on Novaseq 6000 sequencing system (Illumina) , performed sequencing with 2x100bp read length.
Assembly: mm10
Supplementary files format and content: microsoft excel worksheet (.xlsx) files include FPKM values for each sample

source_name: iWAT

extract_protocol:
Total RNA was extracted from homogenized tissues using TRIzol reagent. The isolated RNA was purified using Oligo Clean and Concentrator (Zymo Research). 1µg of total RNA was used for the construction of sequencing libraries
mRNA sequencing libraries were prepared using Illumina Truseq stranded mRNA library prep kit according to the manufacturer's instructions

treatment_protocol: Both of mice genotype are housed at 22˚C under a 12-h light/dark cycle before the experiment. At day of experiment 7am, both of mice genotype are housed at 5˚C for 12 hours. At the end of experiment, adipose tissues were collected and freeze with liquid nitrogen and store in 80˚C for further analysis

value: iWAT

value: adipocyte specific knockout

value: cold exposure

value: 12 hours


title: E13_5_Ngn3_KO_1_26_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv

value: fetal pancreas


title: wild-type olaparib injected ovary 3

source_name: Ovary, wild-type Sprague-Dawley rat (CLEA Japan)

value: Jcl:SD wild-type


title: wild-type olaparib injected ovary 4


title: iWAT of Atf4AKO mice_1


title: Neurod1_E15.5Pdx1CreERNeurod1OE_1

description: CUT&RUN

data_processing:
For CUT&RUN data, overrepresented sequences were identified using FastQC (v0.11.3), and then removed along with sequencing adaptors, primers, and other overrepresented sequences using Trimmomatic (v0.38). The remaining sequencing reads were aligned to the Mus musculus genome (mm10) using bowtie2 (v2.2.5) with default parameters. PCR duplicate reads were subsequently removed using samtools (v1.3.1), and only reads with a mapping quality score ≥30 were retained for downstream analysis.  Peak calling was performed on individual samples using MACS2 (v2.2.6), retaining peaks with a P value less than 10-3. Reproducibility between two biological replicates was assessed using idr (v2.0.4.2). Different irreproducible discovery rate (IDR) thresholds were applied depending on the CUT&RUN targets. For CUT&RUN targeting NGN3 in Ngn3low cells, peaks with an IDR larger than 250 were retained for downstream analysis. For CUT&RUN targeting NGN3 in Ngn3high cells and NEUROD1, the threshold was set to 400. Genome regions overlapping with the ENCODE blacklist were filtered out from the final identified peaks. Tag intensities were calculated as Tags per ten million (TP10M) values and stored in bedGraph files using Homer (v4.7.2).
For bulk-cell ATAC-seq data, Overrepresented sequences were identified using FastQC (v0.11.3), and then removed along with sequencing adaptors, primers, and other overrepresented sequences using Trimmomatic (v0.38). The remaining sequencing reads were aligned to the Mus musculus genome (mm10) using bowtie2 (v2.2.5) with default parameters. PCR duplicate reads were subsequently removed using samtools (v1.3.1), and only reads with a mapping quality score ≥30 were retained for downstream analysis.  Prior to peak calling, reads generated from biological replicates were combined. ATAC-seq peaks were then identified using MACS2 (v2.2.6), retaining peaks with a false discovery rate (FDR) less than 0.01. Genome regions overlapping with the ENCODE blacklist were excluded from further analysis. Tag intensities were calculated as TP10M values and stored in bedGraph files using Homer (v4.7.2).
For snATAC-seq, preprocessing was conducted using cellranger-atac (v1.2.0) with default parameters against the refdata-cellranger-atac-mm10-1.2.0 genome. Cells with detected UMI counts greater than 1,000 and reads in promoter regions (RIPR) between 15% and 45% were retained for downstream analysis. The mm10 genome was segmented into discrete 5 kb intervals, serving as bins for each cell. The tag intensities for each bin were calculated based on the frequency of sequence tags and imported into the R package Signac (v1.3.0) for downstream analysis.
For smart-seq2 snRNA-seq, sequencing reads were aligned to the mm10 mouse genome assembly using TopHat (v2.1.0). Gene-level quantification of mapped reads was performed with HTSeq (v0.6.6) using the parameters “-s no -a 30”. Cells exhibiting fewer than 0.2 million mapped reads or fewer than 4,000 detected genes were excluded from further analysis. Gene expression levels were quantified using TPM (transcripts per million).
For smart-seq3 snRNA-seq, Trimmomatic (v0.39) was utilized to remove primer and adaptor sequences from the reads. Subsequently, the trimmed forward reads (Read 1) were aligned to the mm10 mouse genome using HISAT2 (v2.1.0). The resulting aligned reads were annotated to gene features using featureCounts (v2.0.0), considering both the 5' and internal fragments. Cells were filtered out if they exhibited fewer than 4,000 detected genes. Gene expression levels were quantified using TPM.
For 10x Genomics scRNA-seq, preprocessing was conducted using Cell Ranger (v3.0.1) with default parameters aligned to the refdata-cellranger-mm10-1.2.0 reference genome. The “filtered_feature_bc_matrix” output from Cell Ranger was imported into the Seurat package (version 4.1.1) for downstream analysis in R. WT and CKO or OE cells within the same sample were initially distinguished based on TP10K (transcripts per 10 thousand) values of Uty, Eif2s3y, and Ddx3y for male cells, and the TP10K value of Xist for female cells. These values were log-transformed, with cells exhibiting male-related values greater than 0.2 and female-related values equal to 0 classified as male, while cells with female-related values greater than 1 and male-related values equal to 0 classified as female. The downstream analysis, including dimensional reduction, cell clustering, and differential expression analysis, was conducted using the standard Seurat pipeline.
Assembly: mm10
Supplementary files format and content: Sparce matrix, Bedgraph
Library strategy: CUT&RUN


title: iWAT of Atf4AKO mice_2


title: ATAC_E13.5Ngn3KI_1

description: Bulk cell ATAC-seq

data_processing:
For CUT&RUN data, overrepresented sequences were identified using FastQC (v0.11.3), and then removed along with sequencing adaptors, primers, and other overrepresented sequences using Trimmomatic (v0.38). The remaining sequencing reads were aligned to the Mus musculus genome (mm10) using bowtie2 (v2.2.5) with default parameters. PCR duplicate reads were subsequently removed using samtools (v1.3.1), and only reads with a mapping quality score ≥30 were retained for downstream analysis.  Peak calling was performed on individual samples using MACS2 (v2.2.6), retaining peaks with a P value less than 10-3. Reproducibility between two biological replicates was assessed using idr (v2.0.4.2). Different irreproducible discovery rate (IDR) thresholds were applied depending on the CUT&RUN targets. For CUT&RUN targeting NGN3 in Ngn3low cells, peaks with an IDR larger than 250 were retained for downstream analysis. For CUT&RUN targeting NGN3 in Ngn3high cells and NEUROD1, the threshold was set to 400. Genome regions overlapping with the ENCODE blacklist were filtered out from the final identified peaks. Tag intensities were calculated as Tags per ten million (TP10M) values and stored in bedGraph files using Homer (v4.7.2).
For bulk-cell ATAC-seq data, Overrepresented sequences were identified using FastQC (v0.11.3), and then removed along with sequencing adaptors, primers, and other overrepresented sequences using Trimmomatic (v0.38). The remaining sequencing reads were aligned to the Mus musculus genome (mm10) using bowtie2 (v2.2.5) with default parameters. PCR duplicate reads were subsequently removed using samtools (v1.3.1), and only reads with a mapping quality score ≥30 were retained for downstream analysis.  Prior to peak calling, reads generated from biological replicates were combined. ATAC-seq peaks were then identified using MACS2 (v2.2.6), retaining peaks with a false discovery rate (FDR) less than 0.01. Genome regions overlapping with the ENCODE blacklist were excluded from further analysis. Tag intensities were calculated as TP10M values and stored in bedGraph files using Homer (v4.7.2).
For snATAC-seq, preprocessing was conducted using cellranger-atac (v1.2.0) with default parameters against the refdata-cellranger-atac-mm10-1.2.0 genome. Cells with detected UMI counts greater than 1,000 and reads in promoter regions (RIPR) between 15% and 45% were retained for downstream analysis. The mm10 genome was segmented into discrete 5 kb intervals, serving as bins for each cell. The tag intensities for each bin were calculated based on the frequency of sequence tags and imported into the R package Signac (v1.3.0) for downstream analysis.
For smart-seq2 snRNA-seq, sequencing reads were aligned to the mm10 mouse genome assembly using TopHat (v2.1.0). Gene-level quantification of mapped reads was performed with HTSeq (v0.6.6) using the parameters “-s no -a 30”. Cells exhibiting fewer than 0.2 million mapped reads or fewer than 4,000 detected genes were excluded from further analysis. Gene expression levels were quantified using TPM (transcripts per million).
For smart-seq3 snRNA-seq, Trimmomatic (v0.39) was utilized to remove primer and adaptor sequences from the reads. Subsequently, the trimmed forward reads (Read 1) were aligned to the mm10 mouse genome using HISAT2 (v2.1.0). The resulting aligned reads were annotated to gene features using featureCounts (v2.0.0), considering both the 5' and internal fragments. Cells were filtered out if they exhibited fewer than 4,000 detected genes. Gene expression levels were quantified using TPM.
For 10x Genomics scRNA-seq, preprocessing was conducted using Cell Ranger (v3.0.1) with default parameters aligned to the refdata-cellranger-mm10-1.2.0 reference genome. The “filtered_feature_bc_matrix” output from Cell Ranger was imported into the Seurat package (version 4.1.1) for downstream analysis in R. WT and CKO or OE cells within the same sample were initially distinguished based on TP10K (transcripts per 10 thousand) values of Uty, Eif2s3y, and Ddx3y for male cells, and the TP10K value of Xist for female cells. These values were log-transformed, with cells exhibiting male-related values greater than 0.2 and female-related values equal to 0 classified as male, while cells with female-related values greater than 1 and male-related values equal to 0 classified as female. The downstream analysis, including dimensional reduction, cell clustering, and differential expression analysis, was conducted using the standard Seurat pipeline.
Assembly: mm10
Supplementary files format and content: Sparce matrix, Bedgraph


title: iWAT of Atf4WT mice_3

value: wild type


title: Neurod1_E15.5Ngn3CreNgn3KONeurod1OE_1

description: CUT&RUN


title: iWAT of Atf4WT mice_2


title: E13_5_Ngn3_KO_1_24_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E13_5_Ngn3_KO_1_28_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: wild-type olaparib injected ovary 2


title: iWAT of Atf4WT mice_1


title: DGF_007

city: Sacramento

first: Yongheng

last: Wang

state: CA

address: 3101 Clinical Lab Building (Research II), UC Davis Medical Center, 4625 2nd Ave.

institute: University of California Davis

description:
raw data file: slide4.tar
CosMx 6000 human gene panel

hyb_protocol: Sample processing followed NanoString's standard protocol, utilizing a pre-made 6175-gene panel to detect the spatial location and expression levels of each gene, without any additional custom probes.

scan_protocol: Sample processing and imaging followed NanoString's standard protocol, utilizing a pre-made 6175-gene panel to detect the spatial location and expression levels of each gene, without any additional custom probes.

data_processing: Data was processed using AtoMx

label: Flurorescent probes (red, green, blue, yellow)

organism: Homo sapiens

source_name: Delay graft function allograft

treatment_protocol: Kidneys were collected from donors and transplanted to the recipients. Human kidney biopsies collected one hour post-transplantation.

tag: subject

value: Patient 7 DGF 007

value: kidney

tag: condition

value: Delay graft function allograft

value: 58 years

value: Male


title: E13_5_Ngn3_KO_1_22_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Neurod1_E15.5Neurod1WT_1

description: CUT&RUN


title: Neurod1_E15.5Neurod1WT_2

description: CUT&RUN


title: Neurod1_E15.5Pdx1CreERNeurod1OE_2

description: CUT&RUN


title: DGF_008

label_protocol: Sample processing followed NanoString's standard protocol, utilizing a pre-made 6175-gene panel to detect the spatial location and expression levels of each gene, without any additional custom probes.

value: Patient 8 DGF 008

value: 56 years

value: Female


title: E13_5_Ngn3_KO_1_21_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: wild-type olaparib injected ovary 1

value: Ovary


title: wild-type vehicle ovay 4


title: IVD, scRNA seq

first: Yuchen

last: Liu

state: Massachusetts

address: 188 Longwood Avenue, REB 514B

institute: Harvard school of dental medicine

description: 10X Genomics

data_processing:
Cell Ranger was used to compare the original FASTQ sequencing data to the reference genome (mm10), perform gene expression quantification, and generate a cell-gene expression matrix.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Intervertebral disc

extract_protocol:
NP tissue was meticulously extracted from the lumbar and tail IVDs under a microscope, digested with 0.1% pronase (Sigma-Aldrich, Burlington, MA, USA) at 37°C for 30 minutes, and further digested with 0.2% collagenase type 2 (Sigma-Aldrich, Burlington, MA, USA) at 37°C for 2 hours.Then CD45+ immune cells were removed by FACS wtih APC/Cyanine7 anti-mouse CD45 Antibody(Biolegend, USA).
Approximately 16,000 cells were loaded into microfluidic chips to generate single-cell gel beads in emulsion by using a commercial kit (Chromium Next GEM Single Cell 5ʹ GEM Kit v2, 10X Genomic, Pleasanton, USA,). Subsequent cDNA amplification, quality control and library construction were carried out in accordance with standard guidelines.

value: Intervertebral disc

value: Stromal cell

value: Shh-CreER; Rosa26tdTomato

value: 6 week

value: Tamoxifen injection


title: wild-type vehicle ovay 2


title: E13_5_Ngn3_KO_1_25_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv

value: fetal pancreas


title: Neurod1_E14.5Ngn3H_2

description: CUT&RUN


title: Neurod1_E15.5Ngn3CreNgn3KONeurod1OE_2

description: CUT&RUN


title: wild-type vehicle ovay 3

value: Jcl:SD wild-type


title: DGF_009

extract_protocol: Sample processing followed NanoString's standard protocol, utilizing a pre-made 6175-gene panel to detect the spatial location and expression levels of each gene, without any additional custom probes.

value: Patient 9 DGF 009

value: 38 years


title: E13_5_Ngn3_KO_1_23_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: KO-Py-rep3

city: Iowa City

first: Noah

middle: S

last: Butler

state: IA

address: 4-350 BSB, 51 Newton Road

department: Department of Microbiology and Immunology

institute: University of Iowa

data_processing:
Sequence reads were trimmed for adaptor, poly-N, low-quality sequence (Base Quality less than 5) .
High quality reads were mapped to mouse reference genome (mm10) using HISAT2 (2.0.5)
Read counts for genes were obtained by featureCounts (1.5.0-p3) with GENCODE annotation database (vM25)
Differentially expressed genes (DEG) were identified using DESeq2 (1.20.0) by the criteria of ≥ 2-fold changes and adjusted p value of <0.05.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: spleen

extract_protocol:
Total RNA was extracted by Trizol, and purified with NucleoSpin RNA column (Takara)
Directional mRNA library (poly A enrichment) was constructed by Novoseq company

treatment_protocol: WT and tamoxifen-inducible deletion of TRAF3 (iTraf3−/−) SMARTA or PbTII cells were transferred to recipient mice, followed by infection with LCMV armstrong or Plasmodium yoelii. On day 8 post-infection, WT or iTraf3−/− PbTII CXCR5+SLAMlo TFH cells were sorted into Trizol or RP10 medium.

value: spleen

value: PbTII TFH cells

value: ERT2cre+, Traf3fl/fl

value: tamoxifen, P.yoelii  infection

value: day 8 post-infection


title: KO-Py-rep2


title: Neurod1_E14.5Ngn3H_1

description: CUT&RUN

extract_protocol:
For Smart-seq2 scRNA-seq, single cells were manually picked from FACS-purified bulk cells using a mouth pipette. cDNA synthesis and amplification were performed following the protocol by Picelli et al. For Smart-seq3 scRNA-seq, single cells were directly sorted into 384-well plates containing lysis buffer. cDNA synthesis and amplification were carried out according to the Smart-seq3 protocol .For 10x Genomics scRNA-seq, the procedure was performed according to the manufacturer’s instructions using the Single Cell 3′ Reagent Kit v3.1. Sorted EpCAM+ pancreatic cells from wild-type (WT), conditional knockout (CKO), or overexpression (OE) embryos of different genders were pooled and processed as one sample. For NGN3-CKO samples, E14.5 EpCAM+ pancreatic cells were pooled per replicate: replicate 1 consisted of two WT male litters and one CKO female litter, and replicate 2 consisted of three WT male litters and three CKO female litters. For NGN3-OE samples, E14.5 EpCAM+ pancreatic cells were pooled from four WT female litters and four OE male litters, and E17.5 EpCAM+ pancreatic cells were pooled from two WT female litters and three OE male litters. For NeuroD1-CKO samples, E15.5 EpCAM+ pancreatic cells were pooled per replicate: replicate 1 consisted of one WT male litter and one CKO female litter, and replicate 2 consisted of two WT female litters and one CKO male litter. The gender of the embryos was determined by genotyping for Y-chromosome-associated gene Sry.
For Smart-seq2 scRNA-seq, libraries were prepared with 2 ng of cDNA using the TruePrep DNA Library Prep Kit (Vazyme, TD502), and sequenced on the Illumina HiSeq 4000 system, generating 150 bp paired-end reads. For Smart-seq3 scRNA-seq, libraries were constructed using the TruePrep DNA Library Prep Kit V2 for lllumina (Vazyme, TD501), and sequencing was conducted on the MGIseq-2000 platform, generating 100 bp paired-end reads. For 10x Genomics scRNA-seq, libraries were sequenced as 150-bp paired-end reads on an Illumina HiSeq 4000 system.
CUT&RUN was conducted following the published protocol with modifications in DNA purification and library construction steps. We used 30,000 cells per CUR&RUN assay with primary antibodies against FLAG (1:25, CST, 2368S), p300 (1;100, CST, 54062S), and NeuroD1 (1:100, Millpore, ABE991). DNA was purified using a spin column (VISTECH, DC2005) and processed for library construction with KAPA Hyper Prep Kit (KAPA biosystems, KK8502). Briefly, after end repair and adaptor ligation, the reaction was purified using VAHTS DNA Clean Beads (Vazyme, N411-03-AA) and subjected to PCR amplification with 2× KAPA HiFi HotStart ReadyMix (KAPA Biosystems, KM2602) and Illumina universal primers. The PCR program was: 98°C for 45 seconds, followed by 19 cycles of 98°C for 15 seconds, 60°C for 10 seconds, and 72°C for 1 minute, with a final extension at 72°C for 5 minutes. The final DNA was purified using 1× VAHTS DNA Clean Beads.
CUT&RUN libraries were subjected to 150 bp paired-end sequencing or 51 bp single-end sequencing on the Illumina NovaSeq 6000 or Illumina Hiseq 2500 platform.
Bulk-cell ATAC-seq was conducted following the published protocol  with modifications in cell sorting and nuclei preparation. Specifically, 2,000 cells per ATAC-seq were directly sorted into 50 ul lysis buffer in a 200 ul tube for nuclei preparation. Libraries were constructed using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD502). PCR amplification was performed for 12 cycles under the following conditions: 72°C for 3 minutes, 98°C for 30 seconds, then 12 cycles of 98°C for 15 seconds, 60°C for 30 seconds, and 72°C for 3 minutes, followed by a final extension at 72°C for 5 minutes.
The final DNA was purified using 1× VAHTS DNA Clean Beads and sequenced as 150 bp paired-end reads on the Illumina NovaSeq 6000 platform.
For snATAC-seq, the procedure was performed according to the manufacturer’s instructions using the Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 (10x Genomics). For the Ngn3-CKO samples, E14.5 EpCAM+ pancreatic cells of WT and CKO embryos with different genders (two WT male litters and two CKO female litters) were pooled and loaded as one sample. To ensure experimental success and an adequate number of nuclei, extra pancreatic cells from WT embryos were included, with a ratio of to EpCAM+ cells of 1:4. For the NeuroD1-CKO samples, E15.5 EpCAM+ pancreatic cells of WT and CKO embryos with different genders (two WT female litters and three CKO male litters) were pooled and loaded as one sample.
Libraries were sequenced as 50-bp paired-end reads on an NovaSeq 6000 system.
snATAC-seq


title: P300_E13.5Ngn3L_2

description: CUT&RUN


title: DGF_006

description:
raw data file: slide3.tar
CosMx 6000 human gene panel

value: Patient 6 DGF 006

value: kidney

value: Delay graft function allograft

value: 49 years

value: Male


title: DGF_005

value: Patient 5 DGF 005

value: 52 years


title: WT-Py-rep 3

value: ERT2cre+, Traf3+/+


title: P300_E13.5Ngn3L_1

description: CUT&RUN

value: fetal pancreas


title: E13_5_Ngn3_KO_1_18_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: DGF_004

value: Patient 4 DGF 004

value: 33 years

value: Female


title: P300_E13.5Ngn3H_2

description: CUT&RUN


title: DGF_003

description:
raw data file: slide1.tar
CosMx 6000 human gene panel

value: Patient 3 DGF 003

value: 45 years


title: WT-Py-rep 2

value: spleen

value: PbTII TFH cells


title: wild-type vehicle ovay 1

value: Ovary

value: Jcl:SD wild-type


title: E13_5_Ngn3_KO_1_17_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: P300_E13.5Ngn3H_1

description: CUT&RUN


title: WT-Py-rep 1

value: tamoxifen, P.yoelii  infection

value: day 8 post-infection


title: E13_5_Ngn3_KO_1_16_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: DGF_002

value: Patient 2 DGF 002

value: kidney

value: Delay graft function allograft

value: 51 years


title: Ngn3_E13.5Ngn3L_2

description: CUT&RUN


title: E13_5_Ngn3_KO_1_20_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: KO-LCMVarm-rep3

value: SMARTA TFH cells

value: ERT2cre+, Traf3fl/fl

value: tamoxifen, LCMV armstrong infection


title: E13_5_Ngn3_KO_1_15_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv

value: fetal pancreas


title: DGF_001

description:
raw data file: slide2.tar
CosMx 6000 human gene panel

value: Patient 1 DGF 001

value: 33 years

value: Female


title: E13_5_Ngn3_KO_1_1_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: E13_5_Ngn3_KO_1_14_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: IGF_008

source_name: Immediate graft function allograft

value: Patient 8 IGF 008

value: Immediate graft function allograft

value: 37 years


title: E13_5_Ngn3_KO_1_19_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: KO-Py-rep1

value: spleen

value: PbTII TFH cells


title: Ngn3_E13.5Ngn3H_2

description: CUT&RUN


title: KO-LCMVarm-rep2

value: day 8 post-infection


title: E13_5_Ngn3_KO_1_13_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Ngn3_E13.5Ngn3H_1

description: CUT&RUN


title: IGF_009

value: Patient 9 IGF 009

value: 50 years


title: IGF_010

value: Patient 10 IGF 010

value: kidney


title: E13_5_Ngn3_KO_1_12_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: WT-LCMVarm-rep 3

value: SMARTA TFH cells

value: ERT2cre+, Traf3+/+


title: Adult_cortex, HET, rep2, Hi-C

description: Library name: Sample 4

data_processing:
Raw FASTQ reads were mapped to the mouse reference genome assembly (GRCm38/mm10) using the HiC-Pro pipeline. The resulting allValidPairs files were converted to the hic format files using the hicpro2juicebox script from the HiC-Pro toolkit, enabling analysis with Juicer tools. Subsequently, the hic format was converted to cooler format using hic2cool (v0.8.3). To ensure accuracy, the contact matrix was normalized to a contact depth of 100 million based on cis-interactions using the Knight-Ruiz (KR) method. The Hi-C contact maps for targeted genomic regions were generated using the fancplot module in FAN-C toolkits, and the differential contact heatmaps were constructed using Seaborn, a Python library. At a 100-Kb resolution, the Hi-C cis-Eigenvector 1 values and Pearson’s correlation matrix were calculated utilizing the Juicer software. Subsequently, the resulting cis-Eigenvector 1 values were converted into the bedGraph format for visualization in the UCSC genome browser. Scatterplots with a heat density were depicted using the R package ggpointdensity (v0.1.0).
Assembly: GRCm38
Supplementary files format and content: The mcool files detail signals of DNA-DNA interactions.

extract_protocol:
Briefly, cortical tissues were dissected out using fine forceps and immediately transferred to a dish containing ice-cold NeuroBasal medium. The tissues were then torn into pieces using fine forceps and transferred to an Eppendorf tube containing 0.25% trypsin-EDTA. The sample was incubated at 37°C for 15 min with continuous shaking at 300 rpm. The trypsin digestion of tissues was quenched by the addition of 10% FBS in the PBS buffer. After filtering the dissociated tissues into a single-cell suspension, the volume was adjusted to 5 ml using 10% FBS in the PBS for crosslinking.
In situ Hi-C experiments were carried out following the previous protocol with minor modifications. Briefly, after single-cell isolation from the cortical tissues, one million cells were cross-linked with 1% formaldehyde (Thermo Scientific 28906) at room temperature for 10 min with slow rotations. The crosslinked cells were washed twice with 1 × PBS (Gibco 70011044) and lysed twice with 250 ml of ice-cold lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% NP-40) for 10 min at 4°C to obtain nuclei. Subsequently, the nuclei were permeabilized in 50 ml of 0.05% SDS at 62°C for 10 min, then quenched by the addition of Triton X-100, and digested with 100 U of MboI (NEB R0147L) in a total volume of 250 ml overnight at 37°C with shaking at 900 rpm. After heat inactivating MboI at 62°C for 20 min, the digested DNA ends were filled in and labeled by adding a mixture that included DNA Polymerase I, Large (Klenow) Fragment (NEB M0210S), biotin-14-dATP (Thermo 19524016), as well as dCTP, dTTP, and dGTP (NEB N0446S). The reaction was then incubated at 37°C for 1 h. After labeling the ends of restriction fragments, the digested nuclei were proximally ligated with 2 ml of T4 DNA ligase (NEB M0202S) at room temperature for 4 h. The ligated chromatin was digested using 4 ml of 20 mg/ml proteinase K (Invitrogen AM2546) at 55°C for 4 h and then reverse crosslinked overnight at 68 °C overnight. The DNA was purified through phenol-chloroform extraction followed by ethanol precipitation as described above. After precipitation, the DNA was dissolved in 130 ml of 10 mM Tris-HCl pH 8.0. Sonication of the DNA was carried out using a Bioruptor system at high intensity levels. The process consisted of 15 cycles, each comprising 30-sec sonication followed by 30-sec interval. DNA fragments of 300–500 bp were selected using AMPure XP beads (Beckman A63881) and subsequently captured using streptavidin beads (Thermo 11206D) to enrich the biotin-labeled DNA fragments. The biotin-DNA on the beads was stringently washed twice with 2-min of vortices at 55°C. The purified DNA was used as a template for library preparation as described above. The library was then subjected to sequencing on the MGI-T7 platform via the PE150 sequencing strategy.

value: Brain

value: Cortical neuron

value: Neuron

value: Heterozygous

value: CTCF ADA mutation


title: KO-LCMVarm-rep1

value: ERT2cre+, Traf3fl/fl

value: tamoxifen, LCMV armstrong infection


title: E13_5_Ngn3_KO_1_11_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv

value: fetal pancreas


title: IGF_007

value: Patient 7 IGF 007

value: Immediate graft function allograft

value: 31 years

value: Male


title: WT-LCMVarm-rep 2

value: spleen

value: day 8 post-infection


title: Adult_cortex, HET, rep1, Hi-C

description: Library name: Sample 3


title: WT-LCMVarm-rep 1


title: IGF_006

value: Patient 6 IGF 006

value: kidney

value: 55 years


title: E13_5_Ngn3_KO_1_10_190906

description:
Smartseq2 scRNA-seq
sm2_Ngn3KO.rc.csv


title: Adult_cortex, WT, rep2, Hi-C

description: Library name: Sample 2

value: Brain

value: Wild type

value: No treatment


title: IGF_005

value: Patient 5 IGF 005

value: 36 years

value: Female


title: ATAC_E15.5WT_1

description: Bulk cell ATAC-seq


title: Adult_cortex, WT, rep1, Hi-C

description: Library name: Sample 1

value: Cortical neuron

value: Neuron