title: Mouse,PyMT,Tumor,Mental Stress,rep1

first: Pengfei

address: 150 Jimo Road

institute: Shanghai East Hospital, Tongji University School of Medicine

description: Library name: PyMT_Tumor_MS_rep1

data_processing:
Raw reads were quality-controlled, demultiplexed and aligned to the mm10 mouse reference genome and PyMT using Cellranger (version 5.0.0, 10X Genomics). The PyMT gene sequence was retrieved from GeneBank database (accession number AAB59900.1). Cells with less than 250 genes, or greater than 4,000 genes, or over 10% reads aligning to mitochondrial genes, or gene number greater than 0.8 per UMI were filtered. DoubletFinder was employed to identify and remove doublets. SCTransform function in Seurat was applied to identify genes with high variance for normalization, in which mitochondrial mapping percentage was used as a parameter for covariant correction. IntegrateData function in Seurat, jointly integrating Canonical correlation analysis (CCA) and Mutual nearest neighbors (MNN) algorithms, was performed to remove batch effect between samples and then merge together.
1. Raw data processing:    - Base calling: Illumina bcl2fastq v2.20 (--mask-short-adapter-reads=8)    - Demultiplexing: Cell Ranger mkfastq v5.0.0 (10x Genomics)
2. Reference genome alignment:    - Alignment software: Cell Ranger count v5.0.0    - Reference genome: mm10 (GRCm38) + PyMT transgene (GenBank: AAB59900.1)    - Parameters: --include-introns=false --chemistry=auto
3. Quality control:    - Cell filtering criteria:      * Minimum genes/cell: 250      * Maximum genes/cell: 4,000      * Mitochondrial gene cutoff: <10%      * UMI ratio filter: genes/UMI < 0.8    - Doublet removal: DoubletFinder v2.0.3 (expected_doublet_rate=0.05)
4. Normalization & batch correction:    - Normalization method: SCTransform (Seurat v4.3.0)      * Variance stabilization: 3,000 most variable genes      * Covariates: percent.mt (mitochondrial content)    - Integration:      * Method: CCA + MNN (IntegrateData in Seurat)      * Anchors used: 2,000      * Dimensionality: 30 PCs
Assembly: genome build: GRCm38/mm10 ；PyMT transgene (GenBank: AAB59900.1)
Supplementary files format and content: Filtered_Feature_Barcode_Matrix .h5 HDF5; A sparse matrix containing: - Gene expression counts (UMIs) for cells passing QC filters - Rows: Features (genes + PyMT transgene) - Columns: Cell barcodes

source_name: mammary gland tumor

growth_protocol: Animal housing: 12-hour light/dark cycle, 22±1°C, 50-60% humidity, ad libitum access to standard chow and water. Tumor monitoring: Palpation twice weekly from 6 weeks of age

extract_protocol:
Tumor tissues were minced and then digested at 37 °C for 40 min using an enzyme cocktail containing 150 U/mL of Collagenase Ⅳ, 20 U/mL of Dispase and 0.33 U/mL of DNase I, followed by filtering through a 40 μm strainer to obtain the single cell suspension. Acridine orange (AO) and propidium iodide (PI) were used for fluorescence staining of viable cells. Cell sorting was performed using the WOLF® Cell Sorter (NanoCellect).
Sorted single cells were diluted in DMEM/F12 with 10% FBS, and loaded on a Chromium Controller to generate single-cell gel bead emulsions, targeting 20,000-30,000 cells for each tumor tissue (n=2 in the current study). Single-cell 3′ RNA-seq libraries were generated according to the manufacturer’s instructions (Chromium Single Cell 3′ Reagent v2 Chemistry Kit, 10X Genomics, Inc.), followed by a sequencing analysis to reach an average depth of ~ 200,000 reads per cell using Illumina Novaseq 6000 system.

treatment_protocol: Mental stress exposure was administered to mice in the MS group for continuous 2 weeks. The stress stimuli include noise stimulation (80 decibels for 120 min), restraint stimulation (for 120 min), elevated platform stimulation (10 cm diameter, 1.2 m height of a platform for 120 min), shaking stimulation (60 rpm for 120 min), and somatosensory stimulation (tail-clamping for 1 min, repeating 3 times within 10 min). Each mouse received one of these six stimuli unpredictably through random selection on a daily basis.

value: mammary gland tumor

value: mixed cell population

value: MMTV-PyMT transgenic

value: chronic unpredictable stimulation


title: Valid_GSK_RNA-Epi_Control-4.5-1

status: Public on Jul 23 2025

type: SRA

city: Shanghai

first: Jincan

last: He

address: siping road 1239

country: China

institute: Tongji university

description:
Library name: Valid_GSK_RNA-Epi_Control-4.5-1
GSK_E4.5_samples_TPM_matrix.csv

library_source: transcriptomic

data_processing:
Sequencing reads were initially processed to remove adapters, followed by alignment to the annotated mouse transcriptome (UCSC mm10) using Hisat2 (v2.2.1) with the parameters -k 1 --dta --dta-cufflinks --no-unal. The aligned reads were subsequently assembled into transcripts with reference to the UCSC refGene GTF annotation files utilizing Stringtie (v2.2.1). Gene expression levels were quantified in TPM (Transcripts Per Million).
Assembly: mm10
Supplementary files format and content: comma-delimited text files with normalized abundance for every gene and every sample.

molecule: polyA RNA

organism: Mus musculus

source_name: Epi

growth_protocol: Natural mated embryos were dissected from decidua. Peri-implantation stage embryos for 3D in vitro culture were prepared following a previously published protocol (Li et al., Natl Sci Rev. 2023).

extract_protocol:
Approximately 10-100 cells per sample were lysed, and cDNA synthesis was performed directly on the cytoplasmic lysate. Three biological replicates were performed per group. The resulting cDNA was amplified for 17 cycles to generated a full-length cDNA library.
Sequencing libraries were prepared using the KAPA Hyper Prep Kit (KAPA, KK8504, Switzerland) according to the manufacturer’s instructions.

treatment_protocol: Single cells were collected from E3.5 pre-implantation embryos by fist removing zone pellucida with 20mg/ml PE (Pronase E, Sigma). Embryos were then incubated in Ca2+-free CZB medium and gently pipetting with a fire-polished glass tube to obtain single cells. For peri-implantation embryos (E3.5-E5.5), single cells from different lineages (EPI, PE, and EXE) were collected by separating the embryos from decidua either in vivo or from Matrigel in vitro. The embryos were digested with 0.05% TE (Trypsin-EDTA, Gibco, 25300062) to obtain single cells. All cells were washed at least three times with 0.5% BSA-PBS (MP Biomedicals, USA) solution before used.

tag: tissue

value: Epi

tag: treatment

value: Wild type


title: Mouse,PyMT,Tumor,Native Control,rep2

last: Liu

description: Library name: PyMT_Tumor_NC_rep2

library_source: transcriptomic single cell

tag: cell type

tag: genotype

value: untreated

tag: batch


description: Library name: Valid_mESC_ChIP-EpiLC_dTAG_input-EpiLCK27-1

library_source: genomic

data_processing:
Sequencing reads for RNA were initially processed to remove adapters, followed by alignment to the annotated mouse transcriptome (UCSC mm10) using Hisat2 (v2.2.1) with the parameters -k 1 --dta --dta-cufflinks --no-unal. The aligned reads were subsequently assembled into transcripts with reference to the UCSC refGene GTF annotation files utilizing Stringtie (v2.2.1). Gene expression levels were quantified in TPM (Transcripts Per Million).
Sequencing reads for ChIP-seq/CUT&Tag were first processed to remove adapters and aligned to the mouse genome (UCSC mm10) using Bowtie2 (v2.4.4) with the parameters: -t --no-mixed --no-discordant --no-unal. High-confidence mapped reads were retained using sambamba (v1.0.1) with the parameters: -F "mapping_quality >= 20 and not (unmapped or mate_is_unmapped)". Duplicated reads were removed with picard (v3.1.0) MarkDuplicates function. Genome-wide signals were calculated using ‘bamCoverage’ from deepTools (v3.5.4).
Assembly: mm10
Supplementary files format and content: Gene expression quantification in TPM
Supplementary files format and content: ChIP signal bigwig file

molecule: genomic DNA

source_name: EpiLC

growth_protocol: Mouse ESCs were cultured on a plate coated with feeders (feeder condition medium collected from mitomycin C-treated mouse embryonic fibroblasts, RPMI 1640 (Thermo) supplemented with 20% FBS, 1% non-essential amino acid, 1mM sodium pyruvate, 100 μM β-mercaptoethanol and 2mM L-glutamine) in Serum medium supplemented with 1,000μmol/L LIF, 1μmol/L PD0325901 (S1036, Selleck) and 3μmol/L CHIR9902 (S1263, Selleck). Cells were cultured at 37°C and 5% CO2 and passaged 1:3-1:10 every 2 days by triturating the colonies into a single cell suspension using 0.05% trypsin-EDTA (25200056, Thermo Fisher Scientific).

extract_protocol:
RNA-seq: RNA was extracted from ESCs and EB spheroids using TRIzol Reagent (Invitrogen) followed by chloroform extraction. RNA was then precipitated using isopropanol with the addition of 1/10 volume of 3M NaAC and 2μL glycogen to the aqueous phase. After two washes with 75% ethanol, RNA was resuspended in nuclease-free water. CUT&Tag: Cells were bound to ConA beads and incubated with primary antibody overnight, followed by secondary antibody incubation. Tagmentation was performed using pG-Tn5, and DNA was purified using VAHTS beads and amplified by PCR. Libraries were prepared using the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme Biotech, TD904). ULI-NChIP-seq was performed using 200-500 cells/ sample, with two or three biological replicates per group. Isolated cells were washed with PBS/BSA, and the ULI-NChIP procedure was performed as previously described using 1μg of a histone H3K27me3 or H3K4me3 antibody per immunoprecipitation reaction. XChIP-seq: ESCs/sample were used (2 replicates) for ZBTB17 XChIP-seq. Cells were crosslinked (1% formaldehyde), quenched (glycine), lysed, and sonicated (peak power 75, duty factor 20, cycles 200, 10 min). Chromatin was immunoprecipitated using ZBTB17 antibody and protein A/G beads. DNA was eluted, purified, and precipitated. Libraries were prepared using the KAPA Hyper Prep kit. reChIP-seq: ESCs and EPILCs were processed using the same crosslinking, lysis, and sonication steps as the XChIP-seq protocol. Sequential ChIP was performed using the reChIP-IT kit (Active Motif, 53106).
RNA-seq and ChIP-seq: Libraries were prepared using the KAPA Hyper Prep Kit. Sequenced on Illumina Novaseq. CUT&Tag: Libraries were prepared using the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme Biotech, TD904).

treatment_protocol: Mouse naive ESCs were dissociated with 0.05% trypsin-EDTA and suspended as single cells. A total of 50,000-10,000 2i ESC cells per cm2 were plated on cell culture dishes pretreated with 0.1% Fibronectin in Serum medium supplemented with minimal essential medium (MEM) non-essential amino acids solution, L-glutamine solution, 0.1mM β-mercaptoethanol, 12mg/mL bFGF (Peprotech) and 20ng/mL Activin A (R&D Scientific).

tag: cell line

value: EpiLC

value: dTAG


title: Mouse,PyMT,Tumor,Native Control,rep1

description: Library name: PyMT_Tumor_NC_rep1


title: Valid_Zbtb17_RNA-Epi_Control-5.0-55

description:
Library name: Valid_Zbtb17_RNA-Epi_Control-5.0-55
Zbtb17_dTAG_samples_TPM_matrix.csv


title: Valid_Zbtb17_RNA-Epi_Control-5.0-56

description:
Library name: Valid_Zbtb17_RNA-Epi_Control-5.0-56
Zbtb17_dTAG_samples_TPM_matrix.csv


title: Valid_GSK_RNA-Epi_GSKJ4-4.5-1

description:
Library name: Valid_GSK_RNA-Epi_GSKJ4-4.5-1
GSK_E4.5_samples_TPM_matrix.csv

value: GSK treatment


title: Mouse,PyMT,Tumor,Mental Stress,rep2

description: Library name: PyMT_Tumor_MS_rep2


title: AB18628

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: Library name: Sample30

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: metadata_i.txt tab delimited row  for each cell
Supplementary files format and content: ald_onx02_md.txt tab delimited metadata row  for each 384 plate

source_name: mouse skin

extract_protocol:
Dorsal and ventral sides of the mouse ears were manually separated and cut into small pieces and digested in serum-free Dulbecco’s modified Eagle’s medium (DMEM, Sigma-Aldrich) containing Liberase TL (Thermolysin Low) Research Grade (0.25 mg/ml, Roche) for 75 min at 37°C. Digested tissue was smashed and filtered through a 70-µm cell strainer to obtain single-cell suspensions. Afterwards, cells were washed and resuspended in FACS buffer (PBS, 0.5% BSA and 2 mM EDTA) and prepared for flow cytometry surface marker staining and single-cell sort.
3' end mRNA libraries were prepared for sequencing using SPID-seq (Yofe et al, Cancer Discovery 2023)
Library are single end library. R2 contain cell barcode and UMI only.

value: mouse skin

tag: mouse id

tag: gating

value: DC

value: ALD


title: AB18629

description: Library name: Sample31

value: all


title: AB18627

description: Library name: Sample29


title: AB18626

description: Library name: Sample28


title: AB18623

description: Library name: Sample25


title: AB18624

description: Library name: Sample26


title: AB18622

description: Library name: Sample24


title: AB18621

description: Library name: Sample23

value: UT


title: AB18636

description: Library name: Sample38

value: ALD-ONX


title: AB18638

description: Library name: Sample40


title: AB18635

description: Library name: Sample37


title: AB18648

description: Library name: Sample50


title: AB18642

description: Library name: Sample44


title: AB18649

description: Library name: Sample51


title: AB18646

description: Library name: Sample48


title: AB18645

description: Library name: Sample47


title: AB18634

description: Library name: Sample36


title: AB18641

description: Library name: Sample43


title: AB18647

description: Library name: Sample49


title: AB18632

description: Library name: Sample34


title: AB18631

description: Library name: Sample33


title: AB18640

description: Library name: Sample42


title: AB18637

description: Library name: Sample39


title: AB18650

description: Library name: Sample52


title: AB18643

description: Library name: Sample45


title: AB18644

description: Library name: Sample46


title: AB18633

description: Library name: Sample35


title: AB18639

description: Library name: Sample41


title: AB18630

description: Library name: Sample32


title: AB18619

description: Library name: Sample21


title: AB18620

description: Library name: Sample22


title: AB18617

description: Library name: Sample19


title: AB18615

description: Library name: Sample17


title: AB18616

description: Library name: Sample18


title: AB18614

description: Library name: Sample16


title: AB18613

description: Library name: Sample15


title: AB18607

description: Library name: Sample9


title: AB18606

description: Library name: Sample8


title: AB18611

description: Library name: Sample13


title: NR1364Li

city: Kansas City

first: Andrew

middle: Joseph

last: Price

state: MO

address: 1000 E. 50th Street

department: Computational Biology

country: USA

institute: Stowers Institute for Medical Research

description:
Library name: L74141
LightOnset_WT_Male_Liver_rep1
instrument model: G4

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl-convert 3.10.5
Reads were aligned to UCSC genome GRCm39 with STAR aligner (version 2.7.10b ), using Ens_110 gene models
TPM values were generated using RSEM (version v1.3.1 )
Assembly: GRCm39 (Ens110 gene model)
Supplementary files format and content: Raw counts
Supplementary files format and content: Raw counts

source_name: liver

extract_protocol:
TRIzol extraction followed by DNaseI treatment and RNA column cleanup
mRNAseq libraries were generated from 500 ng of high-quality total RNA, as assessed using the Bioanalyzer (Agilent), according to the manufacturer’s directions using a 5-fold dilution of the universal adaptor and 9 cycles of PCR per the respective masses with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760L), the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L), and the NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) (NEB, E6440S) and purified using the SPRIselect bead-based reagent (Beckman Coulter, B23318).

value: liver

value: Wild Type

tag: Sex

value: male

tag: mouse earcode


title: NR1360Li

description:
Library name: L74137
LightOnset_Mut_Female_Liver_rep2
instrument model: G4

value: Mutant

value: female


title: AB18604

description: Library name: Sample6


title: NR1380Li

description:
Library name: L74144
LightOnset_Mut_Female_Liver_rep2
instrument model: G4


title: AB18612

description: Library name: Sample14


title: NR1362Li

description:
Library name: L74139
LightOnset_Mut_Male_Liver_rep2
instrument model: G4


title: NR1361Li

description:
Library name: L74138
LightOnset_Mut_Male_Liver_rep1
instrument model: G4


title: AB18609

description: Library name: Sample11


title: AB18601

description: Library name: Sample3


title: AB18605

description: Library name: Sample7


title: AB18610

description: Library name: Sample12


title: AB18625

description: Library name: Sample27


title: AB18603

description: Library name: Sample5


title: AB18599

description: Library name: Sample1


title: NR1366Li

description:
Library name: L74143
LightOnset_WT_Male_Liver_rep3
instrument model: G4


title: NR1337Li

description:
Library name: L74135
LightOnset_WT_Female_Liver_rep2
instrument model: G4


title: NR1355Li

description:
Library name: L74136
LightOnset_Mut_Female_Liver_rep1
instrument model: G4


title: AB18618

description: Library name: Sample20


title: NR1336Li

description:
Library name: L74134
LightOnset_WT_Female_Liver_rep1
instrument model: G4


title: NR1380Br

description:
Library name: L74133
LightOnset_Mut_Female_Brain_rep2
instrument model: G4

source_name: brain

value: brain


title: NR1366Br

description:
Library name: L74132
LightOnset_WT_Male_Brain_rep3
instrument model: G4


title: AB18600

description: Library name: Sample2


title: AB18608

description: Library name: Sample10


title: NR1365Br

description:
Library name: L74131
LightOnset_WT_Male_Brain_rep2
instrument model: G4


title: NR1364Br

description:
Library name: L74130
LightOnset_WT_Male_Brain_rep1
instrument model: G4


title: NR1360Br

description:
Library name: L74126
LightOnset_Mut_Female_Brain_rep1
instrument model: G4


title: NR1363Br

description:
Library name: L74129
LightOnset_Mut_Male_Brain_rep3
instrument model: G4


title: NR1337Br

description:
Library name: L74124
LightOnset_WT_Female_Brain_rep2
instrument model: G4


title: NR1304Li

description:
Library name: L73743
DarkOnset_Mut_Male_Liver_rep2
instrument model: G4


title: NR1303Li

description:
Library name: L73742
DarkOnset_Mut_Male_Liver_rep1
instrument model: G4


title: NR1361Br

description:
Library name: L74127
LightOnset_Mut_Male_Brain_rep1
instrument model: G4


title: NR1362Br

description:
Library name: L74128
LightOnset_Mut_Male_Brain_rep2
instrument model: G4


title: NR1299Li

description:
Library name: L73738
DarkOnset_WT_Male_Liver_rep3
instrument model: G4


title: NR1301Li

description:
Library name: L73740
DarkOnset_Mut_Female_Liver_rep1
instrument model: G4


title: NR1296Li

description:
Library name: L73735
DarkOnset_WT_Female_Liver_rep2
instrument model: G4


title: NR1336Br

description:
Library name: L74123
LightOnset_WT_Female_Brain_rep1
instrument model: G4


title: NR1306Li

description:
Library name: L73744
DarkOnset_Mut_Male_Liver_rep3
instrument model: G4


title: NR1297Li

description:
Library name: L73736
DarkOnset_WT_Male_Liver_rep1
instrument model: G4


title: NR1302Li

description:
Library name: L73741
DarkOnset_Mut_Female_Liver_rep2
instrument model: G4


title: NR1298Li

description:
Library name: L73737
DarkOnset_WT_Male_Liver_rep2
instrument model: G4


title: CD4 Tconv Spinal cord day 50 CSP

city: Toulouse

first: Ilan

last: Fijalkow

address: CHU Purpan – BP 3028 – 31024 Toulouse Cedex, 3, Toulouse

country: France

institute: Infinity-Toulouse Institute for Infectious and Inflammatory Diseases

description:
Library name: SC50-CSP
CSP library

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v6.1.1 and  aligned against a mouse reference genome (mm10-2020-A).
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files
Library strategy: CITE-seq

molecule: total RNA

source_name: Spinal Cord

extract_protocol:
EAE was induced in Foxp3-Cre-YFP mice brain (from which meninges were removed) and spinal cord were collected 14 days and 50 days after EAE immunization and enzymatically digested. Cells were then incubated with fluorochrome-labeled antibodies and antibodies for CITE-seq analysis of CD69, P2RX7 and CXCR6 protein expression all from BioLegend. Antigen-experienced (CD44+, Foxp3-YFP-) TCRβ+ CD11b- conventional CD4+ T cells were then sorted by flow cytometry from both spinal cord and brain from day 14 and day 50 EAE mice.
Between 1000 and 16000  viable cells per sample were encapsulated into droplets using Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 with Feature Barcoding technology for Cell Surface Protein, according to manufacturer’s protocol (10X Genomics CG000206 Rev D user guide), with adjustments to fit TotalSeq-A antibodies.

value: Spinal Cord

value: CD4 T cells

value: EAE day 50


title: CD4 Tconv Brain day 50 CSP

description:
Library name: BR50-CSP
CSP library

source_name: Brain

value: Brain


title: CD4 Tconv Spinal cord day 14 CSP

description:
Library name: SC14-CSP
CSP library

value: EAE day 14


title: NR1300Li

description:
Library name: L73739
DarkOnset_WT_Male_Liver_rep4
instrument model: G4


title: CD4 Tconv Brain day 14 CSP

description:
Library name: BR14-CSP
CSP library


title: CD4 Tconv Spinal cord day 50 RNA

description:
Library name: SC50-RNA
GEX library


title: CD4 Tconv Spinal cord day 14 RNA

description:
Library name: SC14-RNA
GEX library


title: CD4 Tconv Brain day 50 RNA

description:
Library name: BR50-RNA
GEX library

value: EAE  day 50


title: snRNA-Seq of CeA tissue from Mouse 8

city: Portland

first: Justin

last: Anderson

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Behavorial Neuroscience

institute: Oregon Health & Science University

description: Library name: HS_8_GEX

data_processing:
Raw sequencing data for both the ATAC and RNA were demultiplexed, aligned to the GRCm39 mouse genome (Ensembl Mouse 111; GRCm39 GCA_000001635.9), and both mRNA molecules and ATAC peaks were counted with the cell ranger arc pipeline (10x Genomics, v 2.0.2). RNA transcripts were assigned to cell and molecule of origin using barcode sequences from the bead primers.
Alignment: Raw sequencing data for both the ATAC and RNA were demultiplexed, aligned to the GRCm39 mouse genome (Ensembl Mouse 111; GRCm39 GCA_000001635.9), and both mRNA molecules and ATAC peaks were counted with the cell ranger arc pipeline (10x Genomics, v 2.0.2). RNA transcripts were assigned to cell and molecule of origin using barcode sequences from the bead primers.
Droplet Filtering: Raw RNA and ATAC libraries for each sample were imported individually in RStudio using R version 4.4.2 as Seurat  objects (v5.1.0). 8.4M droplets (~524k per sample) with nonzero UMI and genes were sequenced. As the primary focus for this manuscript was mRNA, we discarded the ATAC data at this point for the sake of brevity. The ATAC data will be analyzed at a later date, along with additional whole genome sequencing data. Distributions of unique molecular identifiers (UMI; counts) and uniquely mapped genes (features) were examined, and a lower bound of 250 UMI was used to separate empty droplets from nuclei-containing droplets, resulting in 100,174 remaining. These distributions were observed to be bimodal, showing two populations of droplets with one group containing an average of ~1,000 distinct genes (~2,000 UMI) and the other group containing an average of ~4,000 distinct genes (~10,000 UMI). Samples were examined individually to determine cutoffs to eliminate high and low tails for counts and features for the raw, unnormalized data. A full annotation of snRNA-Seq samples is available in the manuscript, but the mean low feature cut off was ~600 unique genes (~1,200 counts), and the mean high feature cut off was ~6,700 unique genes (~28,000 counts). Next, any droplets meeting the following criteria were dropped: (1) more than 0.5% mitochondrial RNA; (2) more than 10% of total counts belonging to a single gene; (3) low complexity (ratio of features to counts of greater than 0.85). After filtering, 69,318 droplets (hereafter referred to as cells) remained, with ~47k having ~4,000 distinct genes, and ~22k having ~1,000 distinct genes.
Gene Filtering: After filtering for low-quality and empty droplets, a total of 33,589 genes had non-zero counts. As all downstream analysis will focus on a relatively low number (thousands) of highly variable genes, we wish to filter out low expressing genes for the sake of computational and memory efficiency. We drop any genes which have a count of 2 in less than 10 individual cells from further analysis. We additionally follow Hochgerner et al. and drop the following immediate early genes and sex-genes (Btg2, Jun, Egr4, Fosb, Junb, Gadd45g, Fos, Arc, Nr4a1, Npas4, Coq10b, Tns1, Per2, Ptgs2, Rnd3, Tnfaip6, Srxn1, Tiparp, Ccnl1, Mcl1, Dnajb5, Nr4a3, Fosl2, Nptx2, Rasl11a, Mest, Sertad1, Egr2, Midn, Gadd45b, Dusp6, Irs2, Plat, Ier2, Rrad, Tpbg, Csrnp1, Peli1, Per1, Kdm6b, Inhba, Plk2, Ifrd1, Baz1a, Trib1, Pim3, Lrrk2, Dusp1, Cdkn1a, Pim1, Sik1, Frat2, Dusp5, Xist, Tsix, Eif2s3y, Ddx3y, Uty and Kdm5d) from further consideration, leaving 14,533 for downstream analysis
Normalizing and Integration: Samples were individually normalized using the SCTransform function in Seurat, which uses analytical Pearson residuals for transformation and is known to perform particularly well for clustering and marker gene selection in the presence of rare cell populations. All samples were then merged into a single Seurat object, and count corrections were computed to normalize depth across all samples (in contrast to the commonly used cellranger aggregate pipeline, which randomly downsamples to normalize sequencing depth across libraries). No differences were observed in cluster composition in regard to genotype, sample, sex, or sequencing lane, and so no integration or batch-correction was performed.
Clustering: For each stage of the clustering the following steps were taken. First, principal components were calculated, then used to generate a UMAP (for visualization), to calculate k-nearest neighbors and construct a shared nearest neighbor graph. Next, the Leiden algorithm is then used to identify clusters across 12 distinct resolutions, and a final resolution is chosen via visual inspection of the UMAP as well as dendrograms (constructed using Euclidean distance of normalized gene expression). In general, a resolution which included spatially isolated clusters and was the first resolution to split a major cluster into parts was preferred. In all cases a resolution between 0.25 and 0.8 was used. Markers are then identified using the Presto package for Wilcoxon differential expression, where significant markers (FDR < 0.05) were ranked (equally weighted) by their: (1) log-fold change, (2) AUROC metric and (3) relative abundance (log-fold change of the precent cells expressing the gene). Fischer and Gillis  found using multiple datasets from the BICCN that AUROC and log-fold change could be used for rapid identification of ideal markers and that 50-200 was ideal for enrichment testing. Here we also included relative abundance as an additional module characterizing and attempt to use between 50-100 markers for enrichment testing. Markers were used to manually annotate clusters, identify and remove doublet clusters and low-quality/noisy clusters. Clusters are always ordered according to their relative total cell count (e.g. Inh_1 has more cell than Inh_2). Clusters are additionally ordered using unsupervised hierarchical clustering on the Euclidean distance of the highly variant genes to aid visualization and to allow for the identification of clusters which have little differences in their expression patterns and may be combined. This hierarchical clustering also allowed for identification of markers between bifurcations of the associated dendrogram; a positive marker in this context means expression in at least 50% of cells on that side, and a log-fold change of 2 (400% expression), while a negative marker means expression in lower than 5% of cells and a log-fold change of -2 (25% expression). In general, a positive marker on one side is a negative marker on the other, but the opposite is not always true.
Coarse Clustering: We first conducted a course clustering as above using all 69,318 cells, and identified clusters using a majority vote of known markers in their aggregate expression as either inhibitory neurons (expressing Gad1 or Gad2) or excitatory neurons (expressing Slc17a7 (Vglu1) or Slc17a6 (Vglu2)). All remaining clusters were considered non-neuronal. At this point two samples were excluded from further analysis, one for having abnormal high proportion of non-neuronal cells (more than 50%) and another for having twice as many excitatory neurons as inhibitory neurons. Dropping these two samples resulted in a final count of 53,839 cells. Next, markers were identified which distinguish the inhibitory neurons from all other clusters, the excitatory neurons from all other clusters, and the non-neuronal clusters from the neuronal clusters. Manual annotation and literature review yielded the following markers for major cell types: Inhibitory (Gad1, Gad2, Dlx6os1, Slc32a1); Excitatory (Slc17a7, Slc17a6, Nrn1); Astrocyte (Gja1, S1pr1, Fgfr3, Gli2, Ntsr2); Microglia (Cx3cr1, Ikzf1, C1qa, C1qb, C1qc); Oligodendrocyte (Mal, Mog, Mag, Prr5l, Plp1); Oligodendrocyte Precursor Cells (Pdgfra, Cspg4, Olig1, Olig2, C1ql1); Immature Neurons (Tmem72, Oxt2os1, Mecom, Oxt2, Folr1); Endothelial (Vtn, Cldn5, Pdgfrb, Flt1, Acta2, Ly6c1). These were used to classify, clusters in aggregate, and cells, individually, to identify cells to include in finer clustering as above via majority vote. Potential doublet clusters and cells were identified following the methodology of Hochgerner et al., where the expression of the identified cell type markers is compared to all other types, and if the worst ratio is less than 2 than it is considered to be a potential doublet. At the cell level this is likely to include many false positives, as cells where the key markers were excluded from amplification by random chance will also be identified. However, Yao et al. noted that cells which were missing key markers correlated strongly with other low-quality cell metrics, and we will remove these cells to maximize the quality of cells used in fine clustering. In total, 7,620 (~14%) cells were identified as potentially low quality in this manner and excluded. Note, the bimodal distribution of UMI and genes noted in Section 4.4.2 appeared to correspond roughly to neuronal (which had mean counts of ~12,000 and ~4,000 genes) and non-neuronal (mean counts of ~2,000 and ~1,000 genes) cell populations.
Fine Clustering: Cells identified as either inhibitory neurons, excitatory neurons or non-neuronal were clustered separately as above to identify sub-populations and to maximize power and specificity when identifying markers which distinguish each sub-type from its main class. For example, we are most interested in what most distinguishes a given inhibitory neuronal subtype from other inhibitory neurons, rather than all other cell types in the CeA. As before, we drop any genes which have a count of 2 in less than 10 individual cells from further analysis. We additionally drop any cluster which has fewer than an average of 10 cells per sample. A count of cells identified in each cluster after fine clustering (of inhibitory, excitatory and non-neuronal populations) is available for each animal in associated manuscript.
Assembly: GRCm39
Supplementary files format and content: XXX_gex_molecule_info.h5 and XXX_raw_feature_bc_matrix.h5: Output from 'cellRanger-arc count' for a single sample, with no filtering applied.
Supplementary files format and content: cellRanger_Aggr_Unfiltered_barcodes.tsv.gz, cellRanger_Aggr_Unfiltered_features.tsv.gz, cellRanger_Aggr_Unfiltered_matrix.mtx.gz: Output from 'cellranger-arg aggr" for all samples, with no filtering applied.

extract_protocol:
Brain tissue was obtained from experimentally naïve, non-ethanol exposed, S5 HP and LP mice. Mice were 60-70 days of age at the time of tissue harvesting (mean ± SEM = 63 ± 2 days). Mice group-housed by sex (2-4 per cage) were moved to a procedure room at 1000 h and allowed to acclimate for one hour; brains were obtained at 1100 - 1300 h. Mice were euthanized via cervical dislocation immediately followed by decapitation. Brains were removed using RNase-free tools, immediately frozen on dry ice, placed in RNase/DNase free polypropylene tubes and stored at -80°C until dissected. Frozen brains were dissected using anatomical landmarks from Franklin and Paxinos [85]. The CeA was obtained bilaterally, using RNase free tools, an aluminum dissection stage, and micropunches fashioned from blunt-cut 27 gauge needles. The frozen brain was placed ventral side up on the dissection stage and cut using a razor blade just anterior to the posterior boundary of the hypothalamus at bregma -0.82 mm. A second cut posterior to the first was then made at bregma -1.46 mm to obtain a 0.6 mm slice. The CeA was removed from this slice using the forked end of the external capsule, the lateral globus pallidus, and the internal capsule as landmarks. The bilateral CeA punches for each animal were placed in RNase and DNase free microcentrifuge tubes and stored at -80°C until RNA was extracted.
snRNA-Seq libraries were generated from 16 S5 generation mice (n=4/line/sex). Flash-frozen CeA was dissociated into individual nuclei following manufacturer’s instructions (protocol CG000366, 10X Genomics). Nuclei were filtered through a 40-70 mm mesh filter and centrifuged in a 29-50% OptiPrep gradient (Sigma-Aldrich) to separate intact nuclei from debris. Cells were inspected in a counting chamber for intact, bright, nongranular cell morphologies, indicating high viability and successful debris removal. ~ 10,000 single nuclei were captured for each sample in a single channel on the 10X Chromium controller, and snRNA/ATAC-Seq libraries (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression) were generated following the manufacturer’s instructions (10X Genomics). Libraries were sequenced to an average depth of 20,000-25,000 read pairs per nucleus (RNA-Seq and ATAC-Seq, respectively), in a NovaSeq6000 at the MPSSR according to 10X Genomics’ specifications. All samples were processed and sequenced at the same time to avoid batch effects. Before filtering and clustering, we captured a total of 87,570 cells with a median of 4,890 UMI counts per cell and 2,320 genes per cell.

value: HP

value: Naïve

tag: library type

value: mRNA


title: CD4 Tconv Brain day 14 RNA

description:
Library name: BR14-RNA
GEX library

value: EAE  day 14


title: snRNA-Seq of CeA tissue from Mouse 7

description: Library name: HS_7_GEX

value: LP


title: snRNA-Seq of CeA tissue from Mouse 4

description: Library name: HS_4_GEX


title: snRNA-Seq of CeA tissue from Mouse 3

description: Library name: HS_3_GEX


title: snRNA-Seq of CeA tissue from Mouse 15

description: Library name: HS_15_GEX


title: snRNA-Seq of CeA tissue from Mouse 2

description: Library name: HS_2_GEX


title: snRNA-Seq of CeA tissue from Mouse 9

description: Library name: HS_9_GEX


title: snRNA-Seq of CeA tissue from Mouse 6

description: Library name: HS_6_GEX


title: snRNA-Seq of CeA tissue from Mouse 14

description: Library name: HS_14_GEX


title: snRNA-Seq of CeA tissue from Mouse 13

description: Library name: HS_13_GEX


title: snRNA-Seq of CeA tissue from Mouse 16

description: Library name: HS_16_GEX


title: snRNA-Seq of CeA tissue from Mouse 12

description: Library name: HS_12_GEX


title: snRNA-Seq of CeA tissue from Mouse 5

description: Library name: HS_5_GEX


title: snRNA-Seq of CeA tissue from Mouse 11

description: Library name: HS_11_GEX


title: snRNA-Seq of CeA tissue from Mouse 10

description: Library name: HS_10_GEX


title: snRNA-Seq of CeA tissue from Mouse 1

description: Library name: HS_1_GEX


title: snATAC-Seq of CeA tissue from Mouse 8

description: Library name: HS_8_ATAC

library_source: genomic single cell

value: ATAC


title: snATAC-Seq of CeA tissue from Mouse 7

description: Library name: HS_7_ATAC


title: snATAC-Seq of CeA tissue from Mouse 6

description: Library name: HS_6_ATAC


title: snATAC-Seq of CeA tissue from Mouse 4

description: Library name: HS_4_ATAC


title: snATAC-Seq of CeA tissue from Mouse 16

description: Library name: HS_16_ATAC


title: snATAC-Seq of CeA tissue from Mouse 3

description: Library name: HS_3_ATAC


title: snATAC-Seq of CeA tissue from Mouse 14

description: Library name: HS_14_ATAC


title: snATAC-Seq of CeA tissue from Mouse 5

description: Library name: HS_5_ATAC


title: snATAC-Seq of CeA tissue from Mouse 13

description: Library name: HS_13_ATAC


title: snATAC-Seq of CeA tissue from Mouse 2

description: Library name: HS_2_ATAC


title: snATAC-Seq of CeA tissue from Mouse 11

description: Library name: HS_11_ATAC


title: snATAC-Seq of CeA tissue from Mouse 10

description: Library name: HS_10_ATAC


title: NR1301Br

description:
Library name: L73729
DarkOnset_Mut_Female_Brain_rep1
instrument model: G4


title: NR1296Br

description:
Library name: L73724
DarkOnset_WT_Female_Brain_rep2
instrument model: G4

value: Wild Type


title: NR1295Li

description:
Library name: L73734
DarkOnset_WT_Female_Liver_rep1
instrument model: G4

value: liver


title: NR1302Br

description:
Library name: L73730
DarkOnset_Mut_Female_Brain_rep2
instrument model: G4

value: Mutant


title: NR1297Br

description:
Library name: L73725
DarkOnset_WT_Male_Brain_rep1
instrument model: G4

value: male


title: NR1306Br

description:
Library name: L73733
DarkOnset_Mut_Male_Brain_rep3
instrument model: G4

value: brain


title: NR1298Br

description:
Library name: L73726
DarkOnset_WT_Male_Brain_rep2
instrument model: G4


title: NR1303Br

description:
Library name: L73731
DarkOnset_Mut_Male_Brain_rep1
instrument model: G4


title: NR1304Br

description:
Library name: L73732
DarkOnset_Mut_Male_Brain_rep2
instrument model: G4


title: NR1300Br

description:
Library name: L73728
DarkOnset_WT_Male_Brain_rep4
instrument model: G4


title: snATAC-Seq of CeA tissue from Mouse 12

description: Library name: HS_12_ATAC


title: snATAC-Seq of CeA tissue from Mouse 15

description: Library name: HS_15_ATAC


title: NR1299Br

description:
Library name: L73727
DarkOnset_WT_Male_Brain_rep3
instrument model: G4


title: NR1295Br

description:
Library name: L73723
DarkOnset_WT_Female_Brain_rep1
instrument model: G4

value: female


title: snATAC-Seq of CeA tissue from Mouse 9

description: Library name: HS_9_ATAC


title: snATAC-Seq of CeA tissue from Mouse 1

description: Library name: HS_1_ATAC


title: Germ-free C57BL/6 mice, control group

city: Seoul

first: IlSeok

last: Choi

address: 50, Yonsei-ro, Seodaemun-gu

department: Biotechnology

country: South Korea

institute: Yonsei University

description:
Library name: GF mice validation control group
10X Genomics 5'

data_processing:
Sequencing reads were aligned to the mouse reference genome (GRCm39) using Cell Ranger software (v9.0.0).
Assembly: GRCm39
Assembly: Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Supplementary files format and content: CellRanger output .h5 file containing filtered gene by cell count data

source_name: normal colon tissue

growth_protocol: Six-week-old female germ-free (GF) mice with a C57BL/6 background were used in all experiments. Ten mice were randomly divided into two groups (5 mice per group) including control group and Fn group. All animal experiments were conducted in accordance with the Public Health Service Policy on Humane Care and Use of Laboratory Animals and approved by the IACUC (2022-0286) of the Department of Laboratory Animal Resources of Yonsei University College of Medicine, accredited by AAALAC International (#001071). GF mice were housed in individually ventilated caging (IVC) systems under controlled temperature (22–23°C) and light (12 h light/12 h dark) conditions. Food and water were sterile and provided to mice and were available ad libitum.

extract_protocol:
All colon tissues, from proximal to distal, were cut open longitudinally and washed in ice-cold PBS twice. The colon tissues were then immersed in ice-cold RPMI-1640 media and processed for tissue dissociation. Cecum was isolated from the gastrointestinal tract by performing a horizontal dissection at the junction between the cecum and the ileum, and between the cecum and proximal region of colon. The weight of the cecum in each group was measured. Dissected colon tissues from PBS control (n=5) and Fn-treated (n=5) GF mice were pooled for each group. Colon tissues were cut into approximately 5 mm pieces and washed three times with ice-cold PBS. The tissue fragments were pre-digested twice for 20 min in Hanks' Balanced Salt Solution (HBSS, Gibco, USA) without Ca2+ and Mg2+ containing 5 mM EDTA, 5% fetal bovine serum (FBS), 1 mM DTT at 37°C using a rotator mixer (Miltenyi Biotec, USA). The fragments were further transferred into a C-tube (Cat# 130-096-334, Miltenyi Biotec, USA) containing HBSS with Ca2+ and Mg2+ (Gibco, USA) and an enzyme mix (enzyme D, enzyme R, enzyme A) prepared from the mouse Lamina Propria Dissociation Kit (Cat# 130-097-410, Miltenyi Biotec, USA). The mixture was churned by gentleMACS Octo Dissociator (Cat# 130-134-029, Miltenyi Biotec, USA) with heaters for 30 min at 37°C. After incubation, ice-cold PB buffer (PBS containing 0.5% bovine serum albumin) was added to the C-tubes and the samples were passed through the 100 μm strainer. The samples were centrifugated at 300 x g for 10 min at 4°C and the pellet was resuspended in ice-cold PB buffer. The samples were filtered through a 70 μm strainer, and rinsed once with ice-cold PB buffer.
Viable cells were subsequently purified using the Dead Cell Removal Kit (Cat# 130-090-101, Miltenyi Biotec). Single-cell suspensions were processed using 10X Chromium Next GEM Single Cell 5’ RNA library v2 and 10X Chromium Next GEM Single Cell VDJ library v2 kit.

treatment_protocol: GF mice were fasted for 2 hours prior to oral gavage. Fn group received an oral administration of 1 × 10⁹ colony-forming units (CFU) in 200 µL of PBS, while the control group received an equivalent volume of PBS alone, three times per week for 5 weeks. The body weight of each mouse was measured three times weekly until the point of sacrifice. At the end of the experiment, the GF mice were sacrificed, and colon tissues were collected from control (n=5) and Fn (n=5) groups.

value: normal colon tissue

tag: fusobacterium positivity

value: NEG

tag: age

value: 6 weeks

tag: host strain


title: CeA Sample From Mouse 211

description: Library name: S211

data_processing:
Sequences raw files were imported into PARC's Prime‐Seq, LabKey Server‐based system (Nelson EK, Piehler B, Eckels J, et al. LabKey server: an open source platform for scientific data integration, analysis and collaboration. BMC Bioinformatics. 2011;12(1):71.)
Quality control of the sequences was verified through FastQC (Andrews, 2010).
Illumina adapters were removed and 3' read ends were trimmed using Trimmomatic (Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114‐2120)
Reads were aligned to the Mus Musculus reference genome (Ensemble_Mouse_GRCm39_GCA_000001635.9) using the STAR aligner (v. 2.7.3a) allowing for maximum of 3 mismatches and only unique alignments.
Per‐sample gene count tables were generated by STAR using Ensembl gene annotations (Mus_musculus.GRCm39.105) and were merged to form a single gene count matrix.
Genes with either: (1) less than 1 count-per-million across samples, or (2) above 120,000 counts in a single sample were removed from further analysis.
Seven samples were dropped from further analysis (three for being potentially mis-gendered, one as a PCA outlier, and three for having an inter-sample-correlation three standard deviations away from the median)
Differentially expressed genes, differentially variable genes and differentially wired genes were identified using the limma+voom pipeline, f-test and changes in correlation, respectively.
Assembly: Ensembl Mouse 105; GRCm39 GCA_000001635.9
Supplementary files format and content: HPLP_STAR_Counts.csv, STAR alignment counts for all 200 samples and 55,414 aligned genes and gene-like features
Supplementary files format and content: HPLP_Normalized_Counts.csv, limma+voom TMM  normalized counts for 193 samples and 16,198 genes

extract_protocol:
Brain tissue was obtained from experimentally naïve, non-ethanol exposed, S5 HP and LP mice. Mice were 60-70 days of age at the time of tissue harvesting (mean ± SEM = 63 ± 2 days). Mice group-housed by sex (2-4 per cage) were moved to a procedure room at 1000 h and allowed to acclimate for one hour; brains were obtained at 1100 - 1300 h. Mice were euthanized via cervical dislocation immediately followed by decapitation. Brains were removed using RNase-free tools, immediately frozen on dry ice, placed in RNase/DNase free polypropylene tubes and stored at -80°C until dissected. Frozen brains were dissected using anatomical landmarks from Franklin and Paxinos [85]. The CeA was obtained bilaterally, using RNase free tools, an aluminum dissection stage, and micropunches fashioned from blunt-cut 27 gauge needles. The frozen brain was placed ventral side up on the dissection stage and cut using a razor blade just anterior to the posterior boundary of the hypothalamus at bregma -0.82 mm. A second cut posterior to the first was then made at bregma -1.46 mm to obtain a 0.6 mm slice. The CeA was removed from this slice using the forked end of the external capsule, the lateral globus pallidus, and the internal capsule as landmarks. The bilateral CeA punches for each animal were placed in RNase and DNase free microcentrifuge tubes and stored at -80°C until RNA was extracted.
Frozen tissue samples were transferred to the Gene Profiling Shared Resource at Oregon Health & Science University for total RNA isolation, using QIAsymphony RNA extraction methods for fatty tissue (QIAsymphony RNA Handbook, November 2020; Qiagen, Redwood City, CA, USA). Quality of the RNA was assessed by UV absorption (NanoDrop 8000) and all CeA samples had an average 260/280 ratio of 2.3, indicating high sample purity. RNA Integrity Number scores were obtained using a Bioanalyzer assay and ranged from 9.1 – 10.0, consistent with high quality RNA. Samples were transferred to the Massively Parallel Sequencing Shared Resource (MPSSR) for RNA-Seq data collection. The total number of samples was 200; 47-52 per lineper sex. The MPSSR completed library formation and sequencing according to Illumina’s specifications. Stranded libraries (polyA+) were prepared using the TruSeq Stranded mRNA kit (Illumina, San Diego CA, USA) and were multiplexed in five batches of 40 on an Illumina NovaSeq 6000, yielding approximately 20 million paired-end reads per sample. Batches were balanced for sex and line.

value: Brain

tag: region

value: CeA

tag: animal id


title: CeA Sample From Mouse 212

description: Library name: S212

value: HP


title: CeA Sample From Mouse 209

description: Library name: S209

value: Naïve


title: CeA Sample From Mouse 205

description: Library name: S205


title: CeA Sample From Mouse 204

description: Library name: S204


title: CeA Sample From Mouse 207

description: Library name: S207


title: CeA Sample From Mouse 208

description: Library name: S208


title: CeA Sample From Mouse 203

description: Library name: S203


title: CeA Sample From Mouse 202

description: Library name: S202


title: CeA Sample From Mouse 201

description: Library name: S201


title: CeA Sample From Mouse 197

description: Library name: S197


title: CeA Sample From Mouse 196

description: Library name: S196


title: CeA Sample From Mouse 195

description: Library name: S195


title: CeA Sample From Mouse 189

description: Library name: S189


title: CeA Sample From Mouse 191

description: Library name: S191


title: CeA Sample From Mouse 186

description: Library name: S186


title: AB18602

description: Library name: Sample4

value: mouse skin

value: DC

value: ALD-ONX


title: CeA Sample From Mouse 184

description: Library name: S184


title: NR1365Li

description:
Library name: L74142
LightOnset_WT_Male_Liver_rep2
instrument model: G4


title: CeA Sample From Mouse 190

description: Library name: S190

value: LP


title: CeA Sample From Mouse 177

description: Library name: S177


title: CeA Sample From Mouse 180

description: Library name: S180


title: CeA Sample From Mouse 181

description: Library name: S181


title: CeA Sample From Mouse 198

description: Library name: S198


title: CeA Sample From Mouse 174

description: Library name: S174


title: CeA Sample From Mouse 200

description: Library name: S200


title: CeA Sample From Mouse 167

description: Library name: S167


title: CeA Sample From Mouse 166

description: Library name: S166


title: CeA Sample From Mouse 199

description: Library name: S199


title: CeA Sample From Mouse 194

description: Library name: S194


title: CeA Sample From Mouse 164

description: Library name: S164


title: CeA Sample From Mouse 162

description: Library name: S162


title: CeA Sample From Mouse 161

description: Library name: S161


title: CeA Sample From Mouse 188

description: Library name: S188


title: CeA Sample From Mouse 193

description: Library name: S193


title: CeA Sample From Mouse 187

description: Library name: S187


title: CeA Sample From Mouse 192

description: Library name: S192


title: CeA Sample From Mouse 159

description: Library name: S159


title: CeA Sample From Mouse 155

description: Library name: S155


title: CeA Sample From Mouse 185

description: Library name: S185


title: CeA Sample From Mouse 206

description: Library name: S206


title: CeA Sample From Mouse 210

description: Library name: S210


title: CeA Sample From Mouse 182

description: Library name: S182


title: CeA Sample From Mouse 183

description: Library name: S183


title: CeA Sample From Mouse 152

description: Library name: S152


title: CeA Sample From Mouse 149

description: Library name: S149


title: CeA Sample From Mouse 151

description: Library name: S151


title: CeA Sample From Mouse 147

description: Library name: S147


title: CeA Sample From Mouse 154

description: Library name: S154


title: CeA Sample From Mouse 179

description: Library name: S179


title: CeA Sample From Mouse 178

description: Library name: S178


title: CeA Sample From Mouse 176

description: Library name: S176


title: CeA Sample From Mouse 153

description: Library name: S153


title: CeA Sample From Mouse 146

description: Library name: S146


title: CeA Sample From Mouse 144

description: Library name: S144


title: CeA Sample From Mouse 172

description: Library name: S172


title: CeA Sample From Mouse 173

description: Library name: S173


title: CeA Sample From Mouse 175

description: Library name: S175


title: CeA Sample From Mouse 170

description: Library name: S170


title: CeA Sample From Mouse 168

description: Library name: S168


title: CeA Sample From Mouse 165

description: Library name: S165


title: CeA Sample From Mouse 140

description: Library name: S140


title: CeA Sample From Mouse 138

description: Library name: S138


title: CeA Sample From Mouse 163

description: Library name: S163


title: CeA Sample From Mouse 136

description: Library name: S136


title: CeA Sample From Mouse 160

description: Library name: S160


title: CeA Sample From Mouse 157

description: Library name: S157


title: CeA Sample From Mouse 158

description: Library name: S158


title: CeA Sample From Mouse 132

description: Library name: S132


title: CeA Sample From Mouse 156

description: Library name: S156


title: CeA Sample From Mouse 150

description: Library name: S150


title: CeA Sample From Mouse 145

description: Library name: S145


title: CeA Sample From Mouse 148

description: Library name: S148


title: CeA Sample From Mouse 169

description: Library name: S169


title: CeA Sample From Mouse 143

description: Library name: S143


title: CeA Sample From Mouse 142

description: Library name: S142


title: CeA Sample From Mouse 125

description: Library name: S125


title: CeA Sample From Mouse 139

description: Library name: S139


title: CeA Sample From Mouse 141

description: Library name: S141


title: CeA Sample From Mouse 123

description: Library name: S123


title: CeA Sample From Mouse 134

description: Library name: S134


title: CeA Sample From Mouse 137

description: Library name: S137


title: CeA Sample From Mouse 135

description: Library name: S135


title: CeA Sample From Mouse 120

description: Library name: S120


title: CeA Sample From Mouse 131

description: Library name: S131


title: CeA Sample From Mouse 130

description: Library name: S130


title: CeA Sample From Mouse 129

description: Library name: S129


title: CeA Sample From Mouse 128

description: Library name: S128


title: CeA Sample From Mouse 126

description: Library name: S126


title: CeA Sample From Mouse 127

description: Library name: S127


title: CeA Sample From Mouse 118

description: Library name: S118


title: CeA Sample From Mouse 117

description: Library name: S117


title: CeA Sample From Mouse 122

description: Library name: S122


title: CeA Sample From Mouse 116

description: Library name: S116


title: CeA Sample From Mouse 133

description: Library name: S133


title: CeA Sample From Mouse 121

description: Library name: S121


title: CeA Sample From Mouse 108

description: Library name: S108


title: CeA Sample From Mouse 119

description: Library name: S119


title: CeA Sample From Mouse 106

description: Library name: S106


title: CeA Sample From Mouse 112

description: Library name: S112


title: CeA Sample From Mouse 114

description: Library name: S114


title: CeA Sample From Mouse 109

description: Library name: S109


title: CeA Sample From Mouse 105

description: Library name: S105


title: CeA Sample From Mouse 111

description: Library name: S111


title: CeA Sample From Mouse 107

description: Library name: S107


title: CeA Sample From Mouse 115

description: Library name: S115


title: CeA Sample From Mouse 100

description: Library name: S100


title: CeA Sample From Mouse 102

description: Library name: S102


title: CeA Sample From Mouse 110

description: Library name: S110


title: CeA Sample From Mouse 99

description: Library name: S99


title: CeA Sample From Mouse 101

description: Library name: S101


title: CeA Sample From Mouse 97

description: Library name: S97


title: CeA Sample From Mouse 91

description: Library name: S91


title: CeA Sample From Mouse 95

description: Library name: S95


title: CeA Sample From Mouse 93

description: Library name: S93


title: CeA Sample From Mouse 96

description: Library name: S96


title: CeA Sample From Mouse 94

description: Library name: S94


title: CeA Sample From Mouse 92

description: Library name: S92


title: CeA Sample From Mouse 90

description: Library name: S90


title: CeA Sample From Mouse 89

description: Library name: S89


title: CeA Sample From Mouse 87

description: Library name: S87


title: CeA Sample From Mouse 88

description: Library name: S88


title: CeA Sample From Mouse 86

description: Library name: S86


title: CeA Sample From Mouse 83

description: Library name: S83


title: CeA Sample From Mouse 82

description: Library name: S82


title: CeA Sample From Mouse 85

description: Library name: S85


title: CeA Sample From Mouse 80

description: Library name: S80


title: CeA Sample From Mouse 81

description: Library name: S81


title: CeA Sample From Mouse 75

description: Library name: S75


title: CeA Sample From Mouse 76

description: Library name: S76


title: CeA Sample From Mouse 74

description: Library name: S74


title: CeA Sample From Mouse 124

description: Library name: S124


title: CeA Sample From Mouse 73

description: Library name: S73


title: CeA Sample From Mouse 72

description: Library name: S72


title: CeA Sample From Mouse 71

description: Library name: S71


title: CeA Sample From Mouse 70

description: Library name: S70


title: CeA Sample From Mouse 66

description: Library name: S66


title: CeA Sample From Mouse 67

description: Library name: S67


title: CeA Sample From Mouse 64

description: Library name: S64


title: CeA Sample From Mouse 65

description: Library name: S65


title: CeA Sample From Mouse 84

description: Library name: S84


title: CeA Sample From Mouse 79

description: Library name: S79


title: CeA Sample From Mouse 62

description: Library name: S62


title: CeA Sample From Mouse 69

description: Library name: S69


title: CeA Sample From Mouse 78

description: Library name: S78


title: CeA Sample From Mouse 58

description: Library name: S58


title: CeA Sample From Mouse 61

description: Library name: S61


title: CeA Sample From Mouse 57

description: Library name: S57


title: CeA Sample From Mouse 60

description: Library name: S60


title: CeA Sample From Mouse 59

description: Library name: S59


title: CeA Sample From Mouse 55

description: Library name: S55


title: CeA Sample From Mouse 53

description: Library name: S53


title: CeA Sample From Mouse 54

description: Library name: S54


title: CeA Sample From Mouse 49

description: Library name: S49


title: CeA Sample From Mouse 51

description: Library name: S51


title: CeA Sample From Mouse 50

description: Library name: S50


title: CeA Sample From Mouse 63

description: Library name: S63


title: CeA Sample From Mouse 48

description: Library name: S48


title: CeA Sample From Mouse 77

description: Library name: S77


title: CeA Sample From Mouse 45

description: Library name: S45


title: CeA Sample From Mouse 46

description: Library name: S46


title: CeA Sample From Mouse 44

description: Library name: S44


title: CeA Sample From Mouse 43

description: Library name: S43


title: CeA Sample From Mouse 42

description: Library name: S42


title: CeA Sample From Mouse 41

description: Library name: S41


title: CeA Sample From Mouse 36

description: Library name: S36


title: CeA Sample From Mouse 38

description: Library name: S38


title: CeA Sample From Mouse 35

description: Library name: S35


title: CeA Sample From Mouse 40

description: Library name: S40


title: CeA Sample From Mouse 68

description: Library name: S68


title: CeA Sample From Mouse 103

description: Library name: S103


title: CeA Sample From Mouse 34

description: Library name: S34


title: CeA Sample From Mouse 52

description: Library name: S52


title: CeA Sample From Mouse 33

description: Library name: S33


title: CeA Sample From Mouse 32

description: Library name: S32


title: CeA Sample From Mouse 30

description: Library name: S30


title: CeA Sample From Mouse 28

description: Library name: S28


title: CeA Sample From Mouse 47

description: Library name: S47


title: CeA Sample From Mouse 25

description: Library name: S25


title: CeA Sample From Mouse 24

description: Library name: S24


title: CeA Sample From Mouse 23

description: Library name: S23


title: CeA Sample From Mouse 37

description: Library name: S37


title: CeA Sample From Mouse 27

description: Library name: S27


title: CeA Sample From Mouse 19

description: Library name: S19


title: CeA Sample From Mouse 56

description: Library name: S56


title: CeA Sample From Mouse 12

description: Library name: S12


title: CeA Sample From Mouse 20

description: Library name: S20


title: CeA Sample From Mouse 16

description: Library name: S16


title: CeA Sample From Mouse 7

description: Library name: S7


title: CeA Sample From Mouse 8

description: Library name: S8


title: CeA Sample From Mouse 31

description: Library name: S31


title: CeA Sample From Mouse 4

description: Library name: S4


title: CeA Sample From Mouse 29

description: Library name: S29


title: CeA Sample From Mouse 3

description: Library name: S3


title: Mouse,wild type, TAC2

city: xian

first: Run

middle: jing

last: Li

address: huangchengxi street

institute: xian jiaotong University

description: Library name: TAC2

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the mus musculus（ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/） reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: FPKM values for each Sample

source_name: Left ventricle

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: Left ventricle

value: wild type

value: TAC surgery


title: Mouse,wild type, TAC3

description: Library name: TAC3


title: Mouse,wild type, TAC1

description: Library name: TAC1


title: Mouse,wild type, Sham3

description: Library name: Sham3

value: Sham


title: CeA Sample From Mouse 26

description: Library name: S26

value: male


title: Mouse,wild type, Sham1

description: Library name: Sham1


title: Mouse,wild type, Sham2

description: Library name: Sham2


title: Mettl3_CKO_b

city: Guangzhou

first: SHUYI

last: CHEN

state: Guangdong

address: 54 S. Xianlie Rd

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center, SYSU

description: Library name: Mettl3-CKO_b

data_processing:
Basecalls performed using CASAVA
clean reads were aligned to the mouse reference genome (mm10) using Hisat2
featureCounts was used to count the reads numbers mapped to each genes
Assembly: mm10
Supplementary files format and content: read counts for each genes were given in the processed data files

source_name: lens

extract_protocol:
RNAs were extracted using TRIzol reagent
NEBNext UltraTM RNA library Prep Kit for Illumina following manufacturer's protocol

value: lens

value: Mettl3 CKO


title: Mettl3_CKO_a

description: Library name: Mettl3-CKO_a


title: CeA Sample From Mouse 11

description: Library name: S11

value: female


title: CeA Sample From Mouse 15

description: Library name: S15


title: CeA Sample From Mouse 171

description: Library name: S171


title: Control_b

description: Library name: Ctrl_b

value: control


title: Control_a

description: Library name: Ctrl_a


title: Lens_m6Aseq_IP

description: Library name: Lens_m6Aseq_IP

data_processing:
raw data was processed to remove adaptor and low quanlity reads using trimmomatic and get clean reads
clean reads were aligned to the mouse reference genome (mm10) using Bowtie2
peak calling was performed using MACS2  peak finding algorithm.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: m6A-Seq

extract_protocol:
RNAs were extracted using TRIzol reagent
poly(A)-RNA was purified using Dynabeads mRNA DIRECT purification kit (Thermo Fisher), and was then immunoprecipitated against an m6A antibody (Synaptic Systems) bound to Protein G Dynabeads (Thermo Fisher), eluted by competition with free m6A (Sigma). The precipitated RNAs were reverse transcribed, amplified, tagmented and indexed using Smart-Seq2 protocol.

tag: antibody

value: m6A antibody (Synaptic Systems)


title: OCT4 ChIP-seq, mESC-Pou5F1-lin-del, Clone7

city: Edinburgh

first: Abdenour

last: Soufi

address: 5 Little France Drive

department: School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

description: Library name: OCT4-ChIP_mESC-Pou5F1-lin-del_CL7

data_processing:
The ChIP-seq pair-end reads were mapped to the human genome assembly MGSCv37 (mm9) using Bowtie (version 2.3.4.1) and very sensitive parameters.
Duplicated reads were then removed using MarkDuplicates from the Picard toolkit.
Reads mapping to the backlisted regions as determined by Encyclopaedia of DNA Elements (ENCODE) were discarded.
The sequencing coverage and the insert size distribution were measured from the resulting bam files using Qualimap (version 2.2.1).
The peaks of OCT4 wild-type and mutants showing significant enrichment over input DNA were called using MACS2 (version 2.1.1.20160309), and a fragment size of 200 bp and were controlled to a q-value (minimum FDR) cut-off of 0.01. The peaks that overlapped with the ENCODE blacklist were removed.
Assembly: MGSCv37 (mm9)
Supplementary files format and content: The aligned ChIP-seq reads were normalised for sequencing coverage to 1x genome depth (reads per genome coverage, RPGC) using the bamCoverage tool from DeepTools and a bin size of 10 bp and extendReads parameters.

source_name: embryonic

growth_protocol: Mouse embryonic stem cells were cultured in GMEM medium supplemented with 10% FCS, 1 mM sodium pyruvate (#11360-039; Gibco), 1 mM glutamine (#25030-024; Gibco), Non-Essential Amino Acids (#11140050; Gibco), and 50 µM 2-mercaptoethanol (#11528926; Gibco), supplemented with 100U/ml LIF and grown at 37°C and 5% CO2.

extract_protocol:
Cells were washed 3X with PBS at RT on 15 cm dishes. After final wash, 15mL of PBS/MgCl2 was added to each plate and 120ul of fresh DSG (0.25M stock prepared by adding 613L DMSO to 50mg of DSG) were added to each plate to get a final concentration of 2mM. Plates were incubated at RT for 45min in a horizontal shaker with constant moving followed by 3X washes of PBS. After the last wash, 20 mL of PBS were added to each plate followed by adding 3mL of Formaldehyde crosslinking buffer (50mM HEPES-KOH, pH7.5, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 11% formaldehyde). Crosslinking was blocked by adding 1.65 mL of 2.5M Glycine and incubating for 5 minutes at room temperature. Cells were harvested using a silicon scraper and centrifuged for 5 minutes at 1,350 rcf at 4C. Cell pellets were then re-suspended in 10ml Lysis Buffer 1 (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40 Substitute, 0.25% Triton X100 and cOmplete Ultra Protease Inhibitor rotated for 10 minutes at 4C. Cells were disrupted using a tight 7mL dounce homogeniser with 80 strokes on ice. Nuclei were collected by centrifugation at 1350rcf for 5 minutes at 4C. The nuclei were washed in 10ml Lysis Buffer 2 (10mM Tris-HCl pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA and cOmplete Ultra Protease Inhibitor) for 10 minutes a rotator at room temperature. The nuclei were collected by centrifugation and resuspended in Lysis Buffer 3 (10mM Tris-HCl pH8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine and cOmplete Ultra Protease Inhibitor). Samples were sonicated for 140 min in 10 minutes intervals using a Covaris M220 sonicator. To solubilise chromatin following sonication, 100ul of 10% Triton X-100 was added per 1ml of sonicated chromatin. Before ChIP, 50ul of sonicated chromatin were collected to confirm optimum DNA fragmentation (~ 200 bp) was achieved by agarose gel electrophoresis. Three ChIPs were performed for each ChIP-seq sample (OCT4 WT and mutants). Dyna G Magnetic Beads were transferred to a Prechilled LoBind tube and washed 3X with 1ml of Blocking buffer (0.5 BSA in PBS). Beads were resuspended in 800 ul of Blocking buffer and incubated with 10ug of OCT4 antibody per ChIP and incubated for 6 hr (minimum) on a rotating platform at 4C. Beads were washed 3X in 1ml of blocking solution and resuspended in 100ul Lysis buffer 3. Sonicated chromatin (40 ug) were added to each ChIP and volume was top up to 900 ul with Lysis buffer 3 buffer containing protease inhibitors. ChIPs were incubated overnight in a rotating platform at 4C. To reduce background the ChIP reactions were transferred to fresh pre-chill LoBind tube. Beads were washed 4X with cold RIPA-wash buffer (50 mM Hepes-KOH pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) using magnetic rack. Beads were washed once with TE+NaCl (10mM Tris-HCl pH 8, 1mM EDTA pH 8 and 50mM NaCl), followed by a spin at 300 x g for 3 minutes at 4C and to remove any residual TE buffer. Bound chromatin fragments were eluted by addin 210 ul elution buffer to the beads and incubated at 65C for 30 minutes shaking at 1200rpm. Tubes were centrifuged at 16,000 x g for 1 minute at room temperature and 200ul of supernatant was transferred to a new tube. In parallel, 50ul of sonicated chromatin from the INPUT after sonication was thawed before adding 150ul of ChIP elution buffer. ChIPs and input were reverse cross-linked by incubating at 65C overnight (shake 700rpm). An equal volume (200ul) of TE (10mM Tris-HCl pH8, 1mM EDTA) was added and incubated with 0.2mg/mL RNAse A for 2 hours at 37C. Proteins were then digested by incubating with 0.2mg/mL Proteinase K for 2 hours at 55C. To extract DNA, 400ul Phenol:chloroform:isoamyl alcohol were added to the samples to separate phases by spinning the sample at top speed for 5 min. The aqueous layer was transferred to a new tube containing 16ul of 5M NaCl (200 mM final concentration) and 1.5ul of 20 g/L glycogen (30 g total). DNA precipitation was performed by adding 0.8ml of cold 100% EtOH and incubated for 180 min at least at -20C. Tubes were centrifuged 20,000 x g for 10 minutes at 4C to pellet DNA. Supernatants were carefully decanted without disturbing the DNA pellet, which was further washed with 500ul of 80% EtOH and spining at 20,000 x g for 10 minutes at 4C. Supernatants were removed by pipetting and pellets were allowed to dry for 5 min. Each pellet was resuspended in 20ul MiniPrep Elution buffer (10mM Tris-HCl pH8.5, Qiagen) using a P20 pipette. DNA was quantified by Qubit 2.0 using the HS dsDNA quantification kit.
ChIP-seq DNA libraries were prepared using 20-50ng ChIP-DNA prepared by pooling equal volumes of 3X ChIP replicates for each OCT4 (WT and mutant) using the NEBNext Ultra II Library Preparation Kit with Dual Index Primers. Size selection for DNA fragments of approximately 200bp was carried out using SpeedBeads, which comprise magnetic carboxylate modified particles. PCR amplification during library preparation was limited such that samples underwent 10 cycles of PCR amplification. Libraries were quantified using a Qubit 2.0 device with a high sensitivity dsDNA kit and fragment size was determined using an Agilent 2200 Tapestation with D1000 HS reagents. The DNA libraries were then pooled by mixing an equal concentration of each ChIP DNA library. The concentration of the ChIP DNA library pool was determined by an Agilent 2200 Tapestation with D1000 HS reagents.

tag: tissue

value: embryonic

value: mouse embryonic stem cells

value: Pou5F1lin-del mutant


title: OCT4 ChIP-seq, mESC-Pou5F1-lin-del, Clone1

description: Library name: OCT4-ChIP_mESC-Pou5F1-lin-del_CL1


title: WC2w_1

city: Nagoya

first: Eri

last: Wada

state: Aichi

address: Furo-cho, Chikusa-ku

department: Research Institute of Environmental Medicine

country: Japan

institute: Nagoya University

description: Library name: Sample7

data_processing:
Raw reads were filtered to remove reads containing adapters or reads of low quality. Clean reads were mapped to the reference genome (GRCm38/mm10) using the HISAT2 software.
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Raw reads filtering is as follows: 1. Remove reads with adapter contamination, 2. Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%), and 3. Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.(Yan et al, 2011)
Perform alignments with HISAT2 to the reference. HISAT2(Mortazavi et al., 2008) uses a graph-based alignment and has succeeded HISAT and TOPHAT2.
Gene expression level is calculated by the number of mapped reads.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample
Supplementary files format and content: tab-delimited txt file includes FPKM values for each sample

source_name: Epididymal adipose tissue

extract_protocol:
Total RNA was purified using RNeasy MiniElute Cleanup Kit (QIAGEN, Hilden, Germany).
RNA libraries for RNA-seq were prepared by Novogene following Novogene's standard protocols.

treatment_protocol: We fed high-fat diet (HFD) to eight-week-old male C57BL/6J mice for 8 weeks (pre weight loss; preWL), followed by standard diet for 2 weeks (WL1w, WL2w) for weight loss

value: Epididymal adipose tissue

value: WT

tag: treatment

value: Weight loss 2 weeks 1


title: WC2w_3

description: Library name: Sample9

value: Weight loss 2 weeks 3


title: WC2w_2

description: Library name: Sample8

value: Weight loss 2 weeks 2


title: preWC_1

description: Library name: Sample1

value: Pre weight loss 1


title: WC1w_1

description: Library name: Sample4

value: Weight loss a week 1


title: preWC_2

description: Library name: Sample2

value: Pre weight loss 2


title: WC1w_3

description: Library name: Sample6

value: Weight loss a week 3


title: preWC_3

description: Library name: Sample3

value: Pre weight loss 3


title: Rep3-DMSO-2d

city: Ulm

first: Alexey

last: Ushmorov

address: Albert-Einstein-Allee 11

department: Institute of Physiological Chemistry

country: Germany

institute: Ulm University

description:
Library name: DMSO-3-2d
DMSO2d_3.bam

data_processing:
Raw sequence reads were mapped to the mm10 reference mouse genome using STAR v2.7.11b. Transcripts were quantified with Salmon v1.1.1 and differentially expressed genes were calculated using DESeq2 v.1.44.0. Genes with an adjusted p-value < 0.05 and log2(Fold Change) >1.5 were considered as significantly differentially expressed.
Assembly: mm10
Supplementary files format and content: RNA-Seq_Processed.xlsx

source_name: Bone marrow

growth_protocol: IMDM + 20% FBS + beta-mercaptoethanol + glutamate + Pen/Strep, 37°C, 5% CO2

extract_protocol:
Quiagen Rneasy
Novogene library preparation from cDNA for Illumina

treatment_protocol: 200 nM 4OHT or equivalent EtOH, 70 nM AS184 or equivalent DMSO treatment for 24h or 48 hours

value: Bone marrow

value: DMSO


title: Rep3-AS18-2d

description:
Library name: AS184-3-2d
AS182d_3.bam


title: Rep2-AS18-2d

description:
Library name: AS184-2-2d
AS182d_2.bam


title: Rep2-DMSO-2d

description:
Library name: DMSO-2-2d
DMSO2d_2.bam


title: Rep1-DMSO-2d

description:
Library name: DMSO-1-2d
DMSO2d_1.bam


title: Rep2-DMSO-1d

description:
Library name: DMSO-2-1d
DMSO1d_2.bam


title: Lens_m6Aseq_input

description: Library name: Lens_m6Aseq_input

value: lens

value: wild type


title: OCT4 ChIP-seq, mESC-Pou5F1-lin-del, Clone3

description: Library name: OCT4-ChIP_mESC-Pou5F1-lin-del_CL3

value: embryonic

tag: cell type


title: Rep2-AS18-1d

description:
Library name: AS184-2-1d
AS181d_2.bam


title: Rep1-DMSO-1d

description:
Library name: DMSO-1-1d
DMSO1d_1.bam


title: Rep1-AS18-1d

description:
Library name: AS184-1-1d
AS181d_1.bam


title: Rep3-AS18-1d

description:
Library name: AS184-3-1d
AS181d_3.bam


title: Rep3-CreMinus-2d

description:
Library name: EtOH-3-2d
CM2d_3.bam

value: EtOH


title: WC1w_2

description: Library name: Sample5

tag: genotype

value: Weight loss a week 2


title: Rep3-CrePlus-2d

description:
Library name: 4OHT-3-2d
CP2d_3.bam


title: Rep2-CreMinus-2d

description:
Library name: EtOH-2-2d
CM2d_2.bam


title: Rep2-CrePlus-2d

description:
Library name: 4OHT-2-2d
CP2d_2.bam


title: Rep3-CreMinus-1d

description:
Library name: EtOH3-1d
CM1d_3.bam


title: Rep1-CreMinus-2d

description:
Library name: EtOH-1-2d
CM2d_1.bam


title: Rep2-CrePlus-1d

description:
Library name: 4OHT-2-1d
CP1d_2.bam


title: Rep3-CrePlus-1d

description:
Library name: 4OHT-3-1d
CP1d_3.bam


title: Rep1-CrePlus-2d

description:
Library name: 4OHT-1-2d
CP2d_1.bam


title: Rep2-CreMinus-1d

description:
Library name: EtOH-2-1d
CM1d_2.bam


title: Rep1-CreMinus-1d

description:
Library name: EtOH1-1d
CM1d_1.bam


title: Rep1-AS18-2d

description:
Library name: AS184-1-2d
AS182d_1.bam


title: Rep1-CrePlus-1d

description:
Library name: 4OHT-1-1d
CP1d_1.bam


title: Rep3-DMSO-1d

description:
Library name: DMSO-3-1d
DMSO1d_3.bam


title: Sox4KO MPEC RNA-seq replicate 2

first: Zhonghui

last: Tang

address: No. 74 Zhongshan Second Road, Guangzhou

institute: Sun Yat-sen University

data_processing:
RNA-seq reads were filtered by removing reads containing adapter and low quality.
The mouse reference genome (GRCm38/mm10) was indexed using Hisat2, and paired-end reads were mapped to the mm10 reference genome using Hista2 with the default parameters.
HTSeq was employed to quantify the read counts for each gene in the mm10 genome assembly.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files includes row counts for each Sample

source_name: Lymphocytes

extract_protocol:
RNA-seq extraction were done by SMART-Seq V4 as instruction
RNA-seq libraries were constructed by SMART-Seq V4, then assessed by lllumina NovaSeq 6000

value: Lymphocytes


title: Sox4WT MPEC RNA-seq replicate 1

value: WT


title: Sox4WT MPEC RNA-seq replicate 2


title: Sox4KO MPEC RNA-seq replicate 1


title: NR1265Li

description:
L67220
LightOnset_WT_Female_Liver_rep4
LightOnset_counts.csv

value: liver

tag: time point

value: LightOnset

value: Wild Type

value: female


title: NR1267Li

description:
L67222
LightOnset_WT_Male_Liver_rep2
LightOnset_counts.csv

value: male


title: NR1266Li

description:
L67221
LightOnset_WT_Male_Liver_rep1
LightOnset_counts.csv


title: NR1260Li

description:
L67219
LightOnset_WT_Female_Liver_rep3
LightOnset_counts.csv


title: NR1259Li

description:
L67218
LightOnset_WT_Female_Liver_rep2
LightOnset_counts.csv


title: NR1257Li

description:
L67216
LightOnset_Mut_Male_Liver_rep3
LightOnset_counts.csv

value: Mutant


title: NR1256Li

description:
L67215
LightOnset_Mut_Male_Liver_rep2
LightOnset_counts.csv


title: NR1258Li

description:
L67217
LightOnset_WT_Female_Liver_rep1
LightOnset_counts.csv


title: CeA Sample From Mouse 113

description: Library name: S113

value: Brain

value: CeA

value: LP

value: Naïve

tag: batch


title: NR1255Li

description:
L67214
LightOnset_Mut_Female_Liver_rep3
LightOnset_counts.csv


title: NR1254Li

description:
L67213
LightOnset_Mut_Male_Liver_rep1
LightOnset_counts.csv


title: NR1253Li

description:
L67212
LightOnset_Mut_Female_Liver_rep2
LightOnset_counts.csv


title: NR1252Li

description:
L67211
LightOnset_Mut_Female_Liver_rep1
LightOnset_counts.csv


title: CeA Sample From Mouse 98

description: Library name: S98

value: HP


title: NR1267Br

description:
L67210
LightOnset_WT_Male_Brain_rep2
LightOnset_counts.csv

value: brain


title: NR1260Br

description:
L67207
LightOnset_WT_Female_Brain_rep3
LightOnset_counts.csv


title: NR1259Br

description:
L67206
LightOnset_WT_Female_Brain_rep2
LightOnset_counts.csv


title: NR1265Br

description:
L67208
LightOnset_WT_Female_Brain_rep4
LightOnset_counts.csv


title: CeA Sample From Mouse 104

description: Library name: S104


title: NR1258Br

description:
L67205
LightOnset_WT_Female_Brain_rep1
LightOnset_counts.csv


title: NR1257Br

description:
L67204
LightOnset_Mut_Male_Brain_rep3
LightOnset_counts.csv


title: NR1252Br

description:
L67199
LightOnset_Mut_Female_Brain_rep1
LightOnset_counts.csv


title: NR1253Br

description:
L67200
LightOnset_Mut_Female_Brain_rep2
LightOnset_counts.csv


title: NR1244Li

description:
L66918
DarkOnset_Mut_Female_Liver_rep2
DarkOnset_counts.csv

value: DarkOnset


title: NR1246Li

description:
L66920
DarkOnset_Mut_Male_Liver_rep1
DarkOnset_counts.csv


title: NR1241Li

description:
L66915
DarkOnset_WT_Male_Liver_rep2
DarkOnset_counts.csv


title: NR1247Li

description:
L66921
DarkOnset_Mut_Male_Liver_rep2
DarkOnset_counts.csv


title: NR1254Br

description:
L67201
LightOnset_Mut_Male_Brain_rep1
LightOnset_counts.csv


title: NR1242Li

description:
L66916
DarkOnset_WT_Male_Liver_rep3
DarkOnset_counts.csv


title: NR1255Br

description:
L67202
LightOnset_Mut_Female_Brain_rep3
LightOnset_counts.csv


title: NR1243Li

description:
L66917
DarkOnset_Mut_Female_Liver_rep1
DarkOnset_counts.csv


title: NR1245Li

description:
L66919
DarkOnset_Mut_Female_Liver_rep3
DarkOnset_counts.csv


title: NR1237Li

description:
L66912
DarkOnset_WT_Female_Liver_rep2
DarkOnset_counts.csv


title: NR1256Br

description:
L67203
LightOnset_Mut_Male_Brain_rep2
LightOnset_counts.csv


title: NR1240Li

description:
L66914
DarkOnset_WT_Male_Liver_rep1
DarkOnset_counts.csv


title: NR1236Li

description:
L66911
DarkOnset_WT_Female_Liver_rep1
DarkOnset_counts.csv


title: NR1238Li

description:
L66913
DarkOnset_WT_Female_Liver_rep3
DarkOnset_counts.csv


title: NR1248Br

description:
L66910
DarkOnset_Mut_Male_Brain_rep2
DarkOnset_counts.csv


title: NR1247Br

description:
L66909
DarkOnset_Mut_Male_Brain_rep1
DarkOnset_counts.csv


title: NR1245Br

description:
L66907
DarkOnset_Mut_Female_Brain_rep2
DarkOnset_counts.csv


title: NR1241Br

description:
L66903
DarkOnset_WT_Male_Brain_rep1
DarkOnset_counts.csv


title: NR1242Br

description:
L66904
DarkOnset_WT_Male_Brain_rep2
DarkOnset_counts.csv


title: NR1244Br

description:
L66906
DarkOnset_Mut_Female_Brain_rep1
DarkOnset_counts.csv


title: NR1238Br

description:
L66901
DarkOnset_WT_Female_Brain_rep2
DarkOnset_counts.csv


title: NR1237Br

description:
L66900
DarkOnset_WT_Female_Brain_rep1
DarkOnset_counts.csv


title: NR1266Br

description:
L67209
LightOnset_WT_Male_Brain_rep1
LightOnset_counts.csv


title: SC10_4 - NOS3Data_NOS3Data (570)

city: STONY BROOK

first: chelsea

last: estrada

state: NY

address: Nicolls Road

institute: STONY BROOK MEDICINE

description: CCTAGACC ATCTCTGT TAGCTCTA GGAGAGAG

data_processing:
Illumina software used for basecalling.
CellRanger used for raw processing
Seurat R-package used for further analysis
Assembly: mm10
Supplementary files format and content: A xlsx spreadsheet containing normalized expression of genes based on cluster and group
Supplementary files format and content: Normalized Expression Matrix.csv

molecule: nuclear RNA

source_name: Kidney Cortex

extract_protocol:
Kidneys were perfused with HBSS and stored in RNALater at -80C. A 2 mm3 section of tissue was rinsed briefly with PBS and minced before adding 1 mL of lysis buffer containing 20 mM Tris-HCl (pH 8), 320 mM sucrose, 5 mM CaCl2, 3 mM MgAc2,  0.1 mM EDTA, and 0.1% TritonX-100. The tissue was initially dissociated by pipetting up and down ~10X with a p-1000 tip and then being passed through a 25G syringe ~10X. The tissue was incubated on ice for 10 minutes and then passed through a 30 µm CellTrics filter. Nuclei were pelleted by centrifugation (5 min, 500g, 4°C) and washed with PBS after removal of supernatant. Nuclei were pelleted again and resuspended in 1 mL of PBS containing 0.04% BSA and RNAse inhibitor (0.2u/µL) before counting by hemocytometer.  Nuclei were then diluted and prepared using the 10X Chromium System according to the manufacturer’s instructions (10X Genomics).
RNA libraries were prepared for sequencing using standard 10X Genomics and Illumina protocols

value: Kidney Cortex


title: SC10_3 - K4KDData_K4KDData (KD2)

description: CCACTTAT AACTGGCG TTGGCATA GGTAACGC


title: SC10_2 - WTData_WTData (WT5)

description: TCTCAGTG GAGACTAT CGCTTAGC ATAGGCCA


title: WT_ChIP-PrE_H3K4me3-4.5-2

data_processing:
Sequencing reads were first processed to remove adapters and aligned to the mouse genome (UCSC mm10) using Bowtie2 (v2.4.4) with the parameters: -t --no-mixed --no-discordant --no-unal. High-confidence mapped reads were retained using sambamba (v1.0.1) with the parameters: -F "mapping_quality >= 20 and not (unmapped or mate_is_unmapped)". Duplicated reads were removed with picard (v3.1.0) MarkDuplicates function. Genome-wide signals were calculated using ‘bamCoverage’ from deepTools (v3.5.4) with the parameters: --effectiveGenomeSize 2652783500 --extendReads 250 --binSize 20 --normalizeUsing RPKM.
Assembly: mm10
Supplementary files format and content: ChIP signal bigwig file

source_name: PrE

growth_protocol: Natural mated embryos were dissected from decidua. Peri-implantation stage embryos for 3D in vitro culture were prepared following a previously published protocol (Li et al., Natl Sci Rev.2023).

extract_protocol:
Approximately 200-500 cells per sample were harvested, washed, and lysed before MNase digestion. After adding MNase stop solution, the supernatant containing fragmented chromatin is collected. Meanwhile, the target protein antibody is first incubated with Dynabeads Protein A/G (Life Technologies) for 4 hours at 4℃. Then, the supernatant is added to the antibody-beads mixture and incubated overnight 4℃. The complex is washed, and bound DNA is eluted using ChIP elution buffer. DNA purification is performed using phenol chloroform extraction and ethanol precipitation.
Sequencing libraries were prepared using the KAPA Hyper Prep Kit (KAPA, KK8504, Switzerland) according to the manufacturer’s instructions.

value: PrE

value: Wild type

tag: developmental stage


title: WT_ChIP-PrE_H3K27me3-5.5-2


title: WT_ChIP-VE_H3K4me3-5.5-1

source_name: VE

value: VE


title: SC10_1 - DKOData_DKOData (650)

description: GCGCAGAA ATCTTACC TATGGTGT CGAACCTG


title: WT_ChIP-Epi_input-5.5-1

source_name: Epi

value: Epi


title: WT_ChIP-Epi_input-4.5-1


title: WT_ChIP-Epi_input-4.75-1


title: WT_ChIP-PrE_input-4.5-1


title: WT_ChIP-VE_input-5.5-1


title: WT_ChIP-PrE_H3K4me3-4.5-1


title: WT_ChIP-Epi_input-5.0-1


title: WT_ChIP-PrE_H3K27me3-4.5-1


title: WT_ChIP-Epi_input-5.25-1


title: WT_ChIP-Epi_H3K4me3-5.5-2


title: WT_ChIP-PrE_H3K27me3-5.5-1


title: WT_ChIP-Epi_H3K4me3-5.25-2


title: WT_ChIP-Epi_H3K4me3-5.0-2


title: WT_ChIP-Epi_H3K4me3-5.5-1


title: WT_ChIP-Epi_H3K4me3-5.25-1


title: WT_ChIP-Epi_H3K4me3-4.75-2


title: WT_ChIP-Epi_H3K4me3-5.0-1


title: WT_ChIP-Epi_H3K4me3-4.5-1


title: WT_ChIP-Epi_H3K4me3-4.5-2


title: WT_ChIP-Epi_H3K4me3-4.75-1


title: WT_ChIP-VE_H3K4me3-5.5-2


title: WT_ChIP-Epi_H3K27me3-5.5-2


title: WT_ChIP-PrE_H3K27me3-4.5-2


title: WT_ChIP-Epi_H3K27me3-5.5-1


title: WT_ChIP-Epi_H3K27me3-5.0-2


title: WT_ChIP-Epi_H3K27me3-5.25-2


title: Valid_Zbtb17_ChIP-Epi_Zbtb17KO_input-5.0-1

description: Valid_Zbtb17_ChIP-Epi_Zbtb17KO_input-5.0.bw

value: Zbtb17 KO


title: WT_ChIP-Epi_H3K27me3-4.5-1


title: WT_ChIP-Epi_H3K27me3-4.75-1


title: WT_Pol2-VE_Pol2-5.5-CUT&Tag 1

data_processing:
Sequencing reads were first processed to remove adapters and aligned to the mouse genome (UCSC mm10) using Bowtie2 (v2.4.4) with the parameters: -t --no-mixed --no-discordant --no-unal. High-confidence mapped reads were retained using sambamba (v1.0.1) with the parameters: -F "mapping_quality >= 20 and not (unmapped or mate_is_unmapped)". Duplicated reads were removed with picard (v3.1.0) MarkDuplicates function. Genome-wide signals were calculated using ‘bamCoverage’ from deepTools (v3.5.4) with the parameters: --effectiveGenomeSize 2652783500 --extendReads 250 --binSize 20 --normalizeUsing RPKM.
Assembly: mm10
Supplementary files format and content: ChIP signal bigwig file
Library strategy: CUT&Tag

extract_protocol:
Cut&Tag was performed as previously described using the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme Biotech, TD904). Briefly, cells were bound to 10μL of pre-washed ConA beads in a 200μL low-binding tube and incubated overnight at 4°C with 50 μL of antibody buffer containing 0.5μg of the target antibody. After two washes with dig-wash buffer, cells were incubated with 50μL of dig-wash buffer containing 0.5μg of a secondary antibody for 1 hour at room temperature. Following two additional washes with 200μL of dig-wash buffer, tagmentation was performed by adding 1μL of pG-Tn5 in 100μL of dig-300 buffer and incubating for 1 hour at room temperature. After two final washes with 200μL of dig-wash buffer, tagmentation buffer was added, and samples were incubated at 37°C for 1 hour. The reaction was stopped by adding 10% SDS, and tagmented DNA fragments were purified using VAHTS beads. Following purification, libraries were amplified by PCR.
Sequencing libraries were prepared continue using the Hyperactive In-Situ ChIP Library Prep Kit (Vazyme Biotech, TD904). The index used for library preparation were from the TruePrep index Kit V2 for Illumina (Vazyme Biotech, TD202)

value: wild type


title: WT_ChIP-Epi_H3K27me3-5.25-1


title: WT_ChIP-Epi_H3K27me3-4.5-2


title: Valid_Zbtb17_ChIP-Epi_Zbtb17KO_H3K4me3-5.0-2

description: Valid_Zbtb17_ChIP-Epi_Zbtb17KO_H3K4me3-5.0.bw


title: Valid_Zbtb17_ChIP-Epi_Zbtb17KO_H3K27me3-5.0-2

description: Valid_Zbtb17_ChIP-Epi_Zbtb17KO_H3K27me3-5.0.bw


title: Valid_Zbtb17_ChIP-Epi_Zbtb17KO_H3K4me3-5.0-1


title: WT_Pol2-PrE_Pol2-4.5-CUT&Tag 1


title: CeA Sample From Mouse 39

description: Library name: S39


title: WT_ChIP-Epi_H3K27me3-5.0-1


title: WT_Pol2-Epi_Pol2-4.5-CUT&Tag 1


title: WT_Pol2-Epi_Pol2-5.0-CUT&Tag 1


title: Valid_Tfap2c_CT-Epi_WT_H3K27me3-5.0-CUT&Tag 2


title: Valid_Otx2_CT-Epi_WT_H3K27me3-5.0-CUT&Tag 2


title: Valid_Tfap2c_CT-Epi_WT_H3K27me3-5.0-CUT&Tag 1


title: Valid_Zbtb17_ChIP-Epi_Zbtb17KO_H3K27me3-5.0-1


title: Valid_Tfap2c_CT-Epi_Tfap2c_H3K27me3-5.0-CUT&Tag 2

description: Valid_Tfap2c_CT-Epi_Tfap2c_H3K27me3-5.0.bw

value: Tfap2c KO


title: Valid_Tfap2c_CT-Epi_Tfap2c_H3K27me3-5.0-CUT&Tag 1


title: Valid_Otx2_CT-Epi_Otx2_H3K27me3-5.0-CUT&Tag 1

value: Otx2 KO


title: Valid_Otx2_CT-Epi_WT_H3K27me3-5.0-CUT&Tag 1


title: Valid_Otx2_CT-Epi_Otx2_H3K27me3-5.0-CUT&Tag 2


title: WT_ChIP-Epi_H3K27me3-4.75-2


title: Valid_GSK_CT-Epi_WT_H3K27me3-5.0-CUT&Tag 1


title: Valid_GSK_CT-Epi_WT_H3K27me3-5.0-CUT&Tag 2


title: WT_Pol2-ICM_Pol2-3.5-CUT&Tag 1

source_name: ICM

value: ICM


title: Valid_GSK_CT-Epi_Gsk_H3K27me3-5.0-CUT&Tag 2

value: GSK treatment


title: WT_Pol2-Epi_Pol2-5.5-CUT&Tag 2


title: Valid_EB_CT-EB_ZbKO_H3K4me3-d3-CUT&Tag 2

source_name: EB

value: EB


title: Valid_EB_CT-EB_ZbKO_H3K4me3-d3-CUT&Tag 1


title: Valid_EB_CT-EB_ZbKO_Eed-d3-CUT&Tag 2


title: Valid_EB_CT-EB_ZbKO_H3K27me3-d3-CUT&Tag 1


title: Valid_EB_CT-EB_ZbHA_H3K4me3-d3-CUT&Tag 1


title: Valid_EB_CT-EB_ZbKO_Eed-d3-CUT&Tag 1


title: Valid_EB_CT-EB_ZbHA_H3K4me3-d3-CUT&Tag 2


title: Valid_EB_CT-EB_ZbKO_H3K27me3-d3-CUT&Tag 2


title: Valid_EB_CT-EB_ZbHA_H3K27me3-d3-CUT&Tag 2


title: Valid_EB_CT-EB_ZbHA_Eed-d3-CUT&Tag 2


title: Valid_EB_CT-EB_ZbHA_Eed-d3-CUT&Tag 1


title: Valid_TFs_RNA_batch9-Epi_Wt1-5.0-2

data_processing:
Sequencing reads were initially processed to remove adapters, followed by alignment to the annotated mouse transcriptome (UCSC mm10) using Hisat2 (v2.2.1) with the parameters -k 1 --dta --dta-cufflinks --no-unal. The aligned reads were subsequently assembled into transcripts with reference to the UCSC refGene GTF annotation files utilizing Stringtie (v2.2.1). Gene expression levels were quantified in TPM (Transcripts Per Million).
Assembly: mm10
Supplementary files format and content: comma-delimited text files with normalized abundance for every gene and every sample.

extract_protocol:
Approximately 10-100 cells per sample were lysed, and cDNA synthesis was performed directly on the cytoplasmic lysate. Three biological replicates were performed per group. The resulting cDNA was amplified for 17 cycles to generated a full-length cDNA library.
Sequencing libraries were prepared using the KAPA Hyper Prep Kit (KAPA, KK8504, Switzerland) according to the manufacturer’s instructions.

value: Wt1 KO


title: Valid_TFs_RNA_batch9-Epi_Zfp281-5.0-3

value: Zfp281 KO


title: Valid_TFs_RNA_batch9-Epi_Sox4-5.0-3

value: Sox4 KO


title: Valid_TFs_RNA_batch9-Epi_Zfp281-5.0-1


title: Valid_TFs_RNA_batch9-Epi_Zfp281-5.0-2


title: Valid_TFs_RNA_batch9-Epi_Wt1-5.0-3


title: Valid_TFs_RNA_batch9-Epi_Sox4-5.0-2


title: Valid_TFs_RNA_batch9-Epi_Wt1-5.0-1


title: Valid_TFs_RNA_batch9-Epi_Smad2-5.0-3

value: Smad2 KO


title: Valid_TFs_RNA_batch9-Epi_Smad2-5.0-2


title: Valid_TFs_RNA_batch9-Epi_Sox4-5.0-1


title: Valid_TFs_RNA_batch9-Epi_Ovol2-5.0-3

value: Ovol2 KO


title: Valid_GSK_CT-Epi_Gsk_H3K27me3-5.0-CUT&Tag 1


title: Valid_TFs_RNA_batch9-Epi_Smad2-5.0-1


title: Valid_TFs_RNA_batch9-Epi_Ovol2-5.0-2


title: Valid_EB_CT-EB_ZbHA_H3K27me3-d3-CUT&Tag 1


title: Valid_TFs_RNA_batch9-Epi_Ovol2-5.0-1


title: Valid_TFs_RNA_batch9-Epi_Control-5.0-3


title: Valid_TFs_RNA_batch9-Epi_Control-5.0-1


title: Valid_TFs_RNA_batch9-Epi_Control-5.0-2


title: Valid_TFs_RNA_batch8-Epi_Control-6.0-3


title: Valid_TFs_RNA_batch8-Epi_Control-6.0-2


title: Valid_TFs_RNA_batch8-Epi_Control-6.0-1


title: Valid_TFs_RNA_batch8-Epi_Bend3-6.0-1

value: Bend3 KO


title: Valid_TFs_RNA_batch8-Epi_Bend3-6.0-3


title: Valid_TFs_RNA_batch7-Epi_Control-5.0-2


title: Valid_TFs_RNA_batch7-Epi_Control-5.0-1


title: Valid_TFs_RNA_batch8-Epi_Bend3-6.0-2


title: Valid_TFs_RNA_batch7-Epi_Bend3-5.0-3


title: Valid_TFs_RNA_batch6-Epi_Zbtb17-5.0-2


title: Valid_TFs_RNA_batch7-Epi_Bend3-5.0-2


title: Valid_TFs_RNA_batch6-Epi_Control-5.0-3


title: Valid_TFs_RNA_batch6-Epi_Zbtb17-5.0-3


title: Valid_TFs_RNA_batch7-Epi_Bend3-5.0-1


title: Valid_TFs_RNA_batch6-Epi_Control-5.0-2


title: Valid_TFs_RNA_batch6-Epi_Zbtb17-5.0-1


title: Valid_TFs_RNA_batch5-Epi_Zfp57-5.0-3

value: Zfp57 KO


title: Valid_TFs_RNA_batch6-Epi_Control-5.0-1

value: Wild type


title: Valid_TFs_RNA_batch5-Epi_Zfp57-5.0-1


title: Valid_TFs_RNA_batch5-Epi_Kdm6b-5.0-3

value: Kdm6b KO


title: Valid_TFs_RNA_batch5-Epi_Zfp57-5.0-2

value: Epi


title: Valid_TFs_RNA_batch5-Epi_Kdm6b-5.0-2


title: Valid_TFs_RNA_batch5-Epi_Ezh2-5.0-3

value: Ezh2 KO


title: Valid_TFs_RNA_batch5-Epi_Kdm6b-5.0-1


title: Valid_TFs_RNA_batch5-Epi_Ezh2-5.0-1


title: Valid_TFs_RNA_batch5-Epi_Ezh2-5.0-2


title: Valid_TFs_RNA_batch5-Epi_Control-5.0-2


title: Valid_TFs_RNA_batch4-Epi_Tfap2c-5.0-3


title: Valid_TFs_RNA_batch5-Epi_Control-5.0-3


title: Valid_TFs_RNA_batch5-Epi_Control-5.0-1


title: Valid_TFs_RNA_batch4-Epi_Tfap2c-5.0-2


title: Valid_TFs_RNA_batch4-Epi_Otx2-5.0-3


title: Valid_TFs_RNA_batch4-Epi_Myc-5.0-3

value: Myc KO


title: Valid_TFs_RNA_batch4-Epi_Otx2-5.0-1


title: Valid_TFs_RNA_batch4-Epi_Myc-5.0-1


title: Valid_TFs_RNA_batch4-Epi_Otx2-5.0-2


title: Valid_TFs_RNA_batch4-Epi_Myc-5.0-2


title: Valid_TFs_RNA_batch4-Epi_Kdm6a-5.0-3

value: Kdm6a KO


title: Valid_TFs_RNA_batch4-Epi_Control-5.0-3


title: Valid_TFs_RNA_batch3-Epi_Rnf2-5.0-3

value: Rnf2 KO


title: Valid_TFs_RNA_batch3-Epi_Jarid2-5.0-3

value: Jarid2 KO


title: Valid_TFs_RNA_batch3-Epi_Rnf2-5.0-1


title: Valid_TFs_RNA_batch4-Epi_Control-5.0-2


title: Valid_TFs_RNA_batch3-Epi_Control-5.0-1


title: Valid_TFs_RNA_batch3-Epi_Control-5.0-3


title: Valid_TFs_RNA_batch3-Epi_Jarid2-5.0-1


title: Valid_TFs_RNA_batch3-Epi_Jarid2-5.0-2


title: Valid_TFs_RNA_batch4-Epi_Tfap2c-5.0-1

value: Tfap2c KO


title: Valid_TFs_RNA_batch3-Epi_Cbx7-5.0-3

value: Cbx7 KO


title: Valid_TFs_RNA_batch3-Epi_Cbx7-5.0-1


title: Valid_TFs_RNA_batch3-Epi_Cbx7-5.0-2


title: Valid_TFs_RNA_batch3-Epi_Cbx2-5.0-3

value: Cbx2 KO


title: Valid_TFs_RNA_batch3-Epi_Cbx2-5.0-2


title: Valid_TFs_RNA_batch3-Epi_Cbx2-5.0-1


title: Valid_TFs_RNA_batch3-Epi_Atrx-5.0-3

value: Atrx KO


title: Valid_TFs_RNA_batch4-Epi_Control-5.0-1


title: Valid_TFs_RNA_batch4-Epi_Kdm6a-5.0-2


title: Valid_TFs_RNA_batch3-Epi_Rnf2-5.0-2