title: WT_V-NPC_Sample3

city: Saint Louis

first: Kristen

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

description: Library name: WT V-NPC Sample3

data_processing:
Reads were quality trimmed using cutadapt (v2.4) and quantified using Salmon (v1.10.3) in mapping based mode. Quantifications were summarized to gene level using tximport (v1.32).
Assembly: hg38
Supplementary files format and content: Tab deliminated text file containing estimate gene counts.

source_name: WT

growth_protocol: hPSCs were maintained in StemFlex Media on Vitronectin coated cultureware.

extract_protocol:
RNA was extracted using the the AllPrep DNA/RNA kit (Qiagen)
RNA-seq library preparation was performed using the SMARTer Ultra Low RNA kit (Takara-Clontech) per the manufacturer’s instructions.

value: WT

value: V-NPC

value: Control


title: 68

status: Public on Jan 01 2026

type: SRA

city: East Lansing

first: Tim

last: Zacharewski

state: Michigan

address: 1129 Farm Ln

department: Biochemistry and Molecular Biology, Integrative Toxicological Sciences

country: USA

institute: Michigan State University

description:
Library name: P176_M_68
Adult male mouse dosed every 4 days for 84 days

library_source: transcriptomic

data_processing:
Read quality was assessed using FastQC v0.12.1 and adapter trimming was performed using Trimmomatic v0.39.
Alignment was performed with STAR v2.7.11b. Genome indices were created using Mus_musculus.GRCm39.dna.chromosome.fa and Mus_musculus.GRCm39.104.gtf.
Gene counts were determined using STAR v2.7.3a.
Assembly: mm10 (build 39)
Supplementary files format and content: STAR-aligned counts were transformed with the variance stabilizing transformation method in DESeq2.
Supplementary files format and content: Tab-delimited text files represent the number of aligned PE reads to each gene.

molecule: total RNA

organism: Mus musculus

source_name: Gastrocnemius

extract_protocol:
Frozen muscle (~100 mg) was homogenized in 1 mL of TriZOL with chrome-steel beads using a Mixer Mill 300 (Life Sciences, Carlsbad, CA) for 4 minutes. Following, total RNA was extracted per the manufacturer’s instructions with an additional 5:1 phenol:chloroform extraction step (Sigma Aldrich, St. Louis, MO). RNA purity (260/280 ratio) and concentration (ng/µL) were assessed with a NanoDrop 1000 spectrophotometer. RNA quality was determined using an Agilent 2100 Bioanalyzer. All RNA samples had RNA integrity numbers (RINs) ≥7.
Library preparation was performed using an mRNA-seq Lib Prep Kit for Illumina (RK20302).

treatment_protocol: Mice were orally gavaged with TCDD in sesame oil vehicle every 4 days for 84 days. Half of the mice were exposed to simvastatin in their diet.

tag: strain

value: Charles Rivers Laboratories

tag: Sex

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Tap

tag: name

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

tag: formula

tag: vendor

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

tag: dose

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: WT_V-NPC_Sample4

description: Library name: WT V-NPC Sample4

organism: Homo sapiens

tag: cell line

value: WT

tag: cell type

value: V-NPC

tag: genotype

value: Control


title: 63

description:
Library name: P176_M_63
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604


title: L-1

city: Nanjing

first: can

last: xiong

address: 101 Longmian Avenue, Jiangning District

department: Basic Medical Sciences

country: China

institute: Nanjing Medical University

description:
Library name: L-1
L-1

data_processing:
fastp(v0.23.4)
HISAT2(v2.2.1)
StringTie(v2.2.1)
HTSeq(v0.13.5)
Assembly: hg38

molecule: polyA RNA

source_name: cell

extract_protocol:
RNAprep Pure Tissue Kit(TIANGEN，DP431)
AT4221-U-mRNAseq Library Prep Kit（KAITAI-Bio, AT4221）

tag: tissue

value: cell

value: Cardiomyocyte cell line

tag: treatment

value: Treat the cells with low glucose


title: 62

description:
Library name: P176_M_62
Adult male mouse dosed every 4 days for 84 days

value: Harlan Teklad

value: Yes

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day


title: WT_V-NPC_Sample2

description: Library name: WT V-NPC Sample2

value: WT

value: V-NPC

value: Control


title: cell-free DNA, Preeclampsia pregnancy DNA076200

city: Ghent

first: Bram

last: Van Gaever

address: C. Heymanlsaan 10

country: Belgium

institute: Ghent University

description:
Library name: DNA076200
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

library_source: genomic

data_processing:
Demultiplexing was performed using bcl-convert on standard settings
fastq files were processed with the bismark workflow of the nf-core/methylseq pipeline https://github.com/nf-core/methylseq/
the --rrbs flag was enabled for processing.
further data processing code can be found in the following git repo:https://github.com/bravgaev/ExPECT-analysis
Assembly: hg38
Supplementary files format and content: bismark coverage file

molecule: genomic DNA

source_name: Blood plasma

extract_protocol:
Cell-free DNA (cfDNA) was extracted using the Maxwell RSC LV ccfDNA kit (Promega) according to the manufacturer’s instructions
The cfRRBS protocol was followed as described by De Koker et al.  and adapted by Van Paemel et al. https://doi.org/10.1080/15592294.2020.1790950 the EZ DNA Lightning kit (ZymoResearch) was used.

value: Blood plasma

tag: disease state

value: Preeclampsia

tag: blood tube_type

value: EDTA

tag: patient id

tag: gestational age_(weeks)

tag: sequencing batch


title: cell-free DNA, Healthy pregnancy DNA069828

description:
Library name: DNA069828
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Healthy

value: PAXgene DNA


title: cell-free DNA, Preeclampsia pregnancy DNA076199

description:
Library name: DNA076199
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: WT_V-IN_Sample1

description: Library name: WT V-IN Sample1

value: V-IN


title: WT_V-IN_Sample4

description: Library name: WT V-IN Sample4


title: 1024-GWI-Vehicle, 1024-GWI-Toxicant, 1083-Control-Vehicle, 1083-Control-Toxicant, Mixed FLEX scRNA-seq

city: College Station

first: James

last: Cai

state: TX

address: 4458 TAMU

department: Veterinary Intergrative Biosciences

institute: Texas A&M University

description:
Library name: Pool 26
scRNA-seq of pooled samples from 4 different treatment groups using 10X Chromium Flex RNA protocol

library_source: transcriptomic single cell

data_processing:
Raw reads from FASTQ files were mapped to the human reference genome (GRCh38-2024-A) using CellRanger (version 8.0.1) to generate raw and filtered gene expression matrices.
Assembly: GRCh38-2024-A
Supplementary files format and content: .h5 files containing mapped scRNA-seq count data

source_name: PBMC

growth_protocol: First, the hiPSC colonies were dissociated in ReLeSR (Stem Cell Technologies, Vancouver, BC, Canada, 05872) for 5 min at 37°C. Following this, cells were collected then resuspended in mTeSR Plus with 5x supplement (Stem Cell Technologies, Vancouver, BC, Canada, 100-0276), 10 μM SB-4321542 at 20 ng/ml (Tocris, Bristol, United Kingdom, 1614), 5 μM dorsomorphin (Sigma-Aldrich, cat. no. P5499), and the ROCK inhibitor Y-27632 at 10 μM (Tocris, Bristol, United Kingdom, 1254) on ultra-low adherence plates (Corning, Corning, NY, United States, 3471) for embryoid body (EB) formation. The medium was replaced on day 3 and supplemented with dorsomorphin and SB-4321542. On day 6 the medium was replaced with Neurobasal Differentiation Media (NBM), consisting of Neurobasal-A media (Life Technologies, Carlsbad, CA, United States, cat. no. 10888022) with B27 supplement without vitamin A (Life Technologies, Carlsbad, CA, United States, 12587010) at 2% of the total volume and GlutaMax (Life Technologies, Carlsbad, CA, United States, cat. no. 35050–061) at 1% of the total volume. NBM was supplemented with 20 μg/ml basic fibroblast growth factor (bFGF) (PeproTech, Cranberry, NJ, United States, 100-18B) and 20 μg/ml epidermal growth factor (EGF) (PeproTech, Cranberry, NJ, United States, AF-100-115) from days 6–24. On day 11 the plates were moved to an orbital shaker (Infors HT Celltron, Annapolis Juntion, MD, United States, I69222) at 37°C set at 65 revolutions per minute. From day 26 onward the NBM was supplemented with 20 ng/ml brain-derived neurotrophic factor (BDNF) (PeproTech, Cranberry, NJ, United States, 450-02) and 20 ng/ml neurotrophin 3 (NT3) (PeproTech, Cranberry, NJ, United States, 450-03). The medium was changed every 2–3 days throughout the duration of organoid generation. *Protocol from Yates and Case et al., 2022

extract_protocol:
Next GEM Single Cell Fixed RNA Sample Preparation To fix the organoids, we utilized the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10X Genomics, Pleasanton, CA, United States, 1000414). First, to dissociate the samples, the organoids were collected into a 15 mL conical tube with a wide-bore tip. Excess media was carefully removed, and the organoids were gently washed with 2 mL of sterile PBS (Gibco, Waltham, MA, United States, 10010023). Once the organoids were settled, the PBS was replaced with 2mL of prewarmed Accutase (Invitrogen, Carlsbad, California, United States, 00-4555-56) with 20 μL of DNase (Thermo Fisher Scientific, Waltham, MA, United States, EN0521). The tube was placed in the water bath at 37ºC for 2 minutes, flicked to unsettle the organoids, then incubated for an additional 2 minutes. After this period the Accutase was removed, and the organoids were briefly washed with 5 mL of neurobasal media four times. At this point, the organoids were triturated 8-10 times with a 1 mL pipette until the organoids were well dispersed in the solution. The cells were next counted with a hemocytometer (Hausser Scientific, Horsham, PA, United States) and trypan blue (Gibco, Waltham, MA, United States, 15250061). For sample fixation, the organoid samples were then spun down in a swinging-bucket rotor centrifuge (Eppendorf, Hamburg, Germany, 022628113) at 300-400 rcf for 5 minutes at 4 º C. The supernatant was then removed (careful to not disturb the pellet) and 1 mL of room temperature Fixation Buffer (recipe below) and mix five times with a 1 mL pipette then incubate overnight (16 -24 hours) at 4º C. Do not agitate or mix the sample during incubation – fixation time and temperature should be consistent across all sample collection. Following the overnight fixation, centrifuge the sample at 850 rcf for 5 minutes at room temperature then remove the supernatant without disturbing the pellet. Next, add 1 mL of chilled Quenching Buffer (recipe below) to the pellet an mix five time and place on ice. Using a hemocytometer and trypan blue, the cells were then counted to determine cell concentration. The Enhancer (10X Genomics, Pleasanton, CA, United States, PN-20000482) was thawed in a water bath for 10 minutes at 65º C for ten minutes, then briefly vortex and centrifuged. It is important to keep the enhancer warm and confirm there is no precipitate prior to use. To prepare the samples for long term storage and subsequent shipping to Texas A&M for processing, we added 100 μL of the thawed Enhancer (10X Genomics, Pleasanton, CA, United States, PN-20000482) to the fixed sample in the Quenching buffer and mixed in with a pipette. Then, the 275 μL of the 50% glycerol solution was added to the sample and gently mixed. These samples were stored in a -80º C freezer until all samples were collected. Samples can be stored this way for up to six months. Buffer Preparation (prepare fresh) Fixation Buffer -Maintain at room temperature   Nuclease Free Water : 791.9 μL 10X Conc. Fix & Prem Buffer (10X Genomics, 20000517): 100μL -Thaw at room temperature. -Vortex, check for precipitation, and centrifuge briefly   37% Formaldehyde : 108.1μL Total  -  -  1000.0μL  Quenching Buffer -Maintain at 4º C   Nuclease Free Water: 875.0μL 8X Conc. Quench Buffer (10X Genomics, 20000516): 125.0μL -Thaw at room temperature. -Vortex and centrifuge briefly.   Total  -  -  1000.0μL  Storage Buffer for fixed samples (prepare fresh): 50% glycerol solution 1. Mix equal volumes of nuclease free water (Invitrogen, Carlsbad, California, United States, 10977-015) and molecular biology grade 99% glycerol (Thermo Fisher, Waltham, MA, United States, J61059-K2).s 2. Filter the 50% glycerol solution through a 0.2 μm filter (Thermo Fisher, Waltham, MA, United States, 723-2520).
2 pools of 4 samples each were made. Libraries were then tested for quality utilizing an Agilent Bioanalyzer High Sensitivity chip (Agilent, 5067-4626) to determine the average size of the library. Library quantification was performed with the NEBNext Library Quant Kit for Illumina kit (New England Biolabs, E7630L).

treatment_protocol: A total of 2.5 months old organoids were exposed to a GW toxicant regimen adapted from established rodent models (O’Callaghan et al., 2015; Locker et al., 2017) and modified from studies on rat and human two-dimensional neuronal cultures (Rao et al., 2017; Yates et al., 2021) in order to prolong the exposure for cerebral organoids. The toxicant regimen consisted of exposing the organoids to 7 days of 2 μM hydrocortisone (Cortisol) (Sigma-Aldrich, St. Louis, MO, United States, H0888), dissolved in 10% ethanol in ddH2O, followed by 4 days of 2 μM Cortisol plus 200 nM diisopropyl fluorophosphate (DFP) (Sigma-Aldrich, St. Louis, MO, United States, D0879), dissolved in isopropanol, followed by 7 days of washout. *Protocol from Yates and Case et al., 2022

value: PBMC

value: iPSC

value: Neural

value: Mixed

value: Vehicle - 10% ethanol and isopropanol; Toxicant - Cortisol (dissolved in 10% ethanol) and DFP (dissolved in isopropanol)


title: cell-free DNA, Healthy pregnancy DNA069829

description:
Library name: DNA069829
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: WT_V-NPC_Sample1

description: Library name: WT V-NPC Sample1


title: cell-free DNA, Healthy pregnancy DNA069827

description:
Library name: DNA069827
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: WT_V-IN_Sample2

description: Library name: WT V-IN Sample2


title: 61

description:
Library name: P176_M_61
Adult male mouse dosed every 4 days for 84 days

tag: strain

value: Charles Rivers Laboratories

tag: Sex

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: Carbon dioxide euthanasia


title: 165

description:
Library name: P176_M_165
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

tag: bedding

tag: water

value: diet

value: milligram per kilogram per day


title: WT_V-IN_Sample3

description: Library name: WT V-IN Sample3

value: WT

value: V-IN

value: Control


title: WT_iGlut_Sample2

description: Library name: WT iGlut Sample2

value: iGlut


title: WT_D-IN_Sample4

description: Library name: WT D-IN Sample4

value: D-IN


title: WT_iGlut_Sample3

description: Library name: WT iGlut Sample3


title: 144

description:
Library name: P176_M_144
Adult male mouse dosed every 4 days for 84 days

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

tag: name

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

tag: formula

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter


title: 163

description:
Library name: P176_M_163
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

tag: vendor

value: oral gavage

tag: dose

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: cell-free DNA, Healthy pregnancy DNA069825

description:
Library name: DNA069825
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy

value: EDTA


title: WT_D-IN_Sample2

description: Library name: WT D-IN Sample2

tag: cell line

value: WT

tag: cell type

value: D-IN

value: Control


title: _35

description:
Library name: P176_M_35
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter


title: WT_D-IN_Sample3

description: Library name: WT D-IN Sample3

tag: genotype


title: cell-free DNA, Healthy pregnancy DNA069826

description:
Library name: DNA069826
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

tag: tissue

value: Blood plasma

value: Healthy

value: PAXgene DNA


title: R882H_V-NPC_Sample4

description: Library name: R882H V-NPC Sample4

value: V-NPC

value: TBRS R882H


title: WT_iGlut_Sample1

description: Library name: WT iGlut Sample1

value: WT

value: iGlut

value: Control


title: WT_D-IN_Sample1

description: Library name: WT D-IN Sample1

value: D-IN


title: 143

description:
Library name: P176_M_143
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: R882H_V-IN_Sample4

description: Library name: R882H V-IN Sample4

value: V-IN

value: TBRS R882H


title: R882H_V-IN_Sample2

description: Library name: R882H V-IN Sample2


title: cell-free DNA, Healthy pregnancy DNA069823

description:
Library name: DNA069823
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

tag: disease state

value: Healthy

value: EDTA


title: cell-free DNA, Healthy pregnancy DNA069816

description:
Library name: DNA069816
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

tag: blood tube_type

value: PAXgene DNA


title: 142

description:
Library name: P176_M_142
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter


title: cell-free DNA, Healthy pregnancy DNA069817

description:
Library name: DNA069817
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

tag: patient id


title: R882H_iGlut_Sample2

description: Library name: R882H iGlut Sample2

value: iGlut

value: TBRS R882H


title: R882H_iGlut_Sample3

description: Library name: R882H iGlut Sample3


title: cell-free DNA, Healthy pregnancy DNA069815

description:
Library name: DNA069815
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy

tag: gestational age_(weeks)


title: cell-free DNA, Healthy pregnancy DNA069822

description:
Library name: DNA069822
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: EDTA

tag: sequencing batch


title: 140

description:
Library name: P176_M_140
Adult male mouse dosed every 4 days for 84 days

tag: strain

value: Charles Rivers Laboratories

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: R882H_hPSC_Sample3

description: Library name: R882H hPSC Sample3

value: hPSC


title: 135

description:
Library name: P176_M_135
Adult male mouse dosed every 4 days for 84 days

tag: Sex

value: Male

value: day

value: degree celsius

value: percent

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter


title: R882H_V-NPC_Sample3

description: Library name: R882H V-NPC Sample3

value: V-NPC

value: TBRS R882H


title: R882H_V-IN_Sample3

description: Library name: R882H V-IN Sample3

value: V-IN


title: R882H_V-IN_Sample1

description: Library name: R882H V-IN Sample1


title: R882H_V-NPC_Sample2

description: Library name: R882H V-NPC Sample2


title: 137

description:
Library name: P176_M_137
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day


title: 138

description:
Library name: P176_M_138
Adult male mouse dosed every 4 days for 84 days

value: Male

value: day

value: degree celsius

value: percent

tag: water

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard

value: Carbon dioxide euthanasia


title: R882H_V-NPC_Sample1

description: Library name: R882H V-NPC Sample1

value: V-NPC

value: TBRS R882H


title: cell-free DNA, Healthy pregnancy DNA069814

description:
Library name: DNA069814
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy

value: EDTA


title: cell-free DNA, Healthy pregnancy DNA069811

description:
Library name: DNA069811
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: R882H_D-NPC_Sample3

description: Library name: R882H D-NPC Sample3

value: D-NPC


title: cell-free DNA, Healthy pregnancy DNA069812

description:
Library name: DNA069812
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA069808

description:
Library name: DNA069808
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: PAXgene DNA


title: 136

description:
Library name: P176_M_136
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

tag: name

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day


title: R882H_iGlut_Sample1

description: Library name: R882H iGlut Sample1

value: iGlut

value: TBRS R882H


title: R882H_hPSC_Sample2

description: Library name: R882H hPSC Sample2

value: hPSC


title: R882H_D-IN_Sample3

description: Library name: R882H D-IN Sample3

value: D-IN


title: 132

description:
Library name: P176_M_132
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

tag: formula

value: Accustandard

value: Carbon dioxide euthanasia


title: R882H_D-IN_Sample4

description: Library name: R882H D-IN Sample4


title: 134

description:
Library name: P176_M_134
Adult male mouse dosed every 4 days for 84 days

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

tag: vendor

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma


title: R882H_hPSC_Sample1

description: Library name: R882H hPSC Sample1

value: hPSC

value: TBRS R882H


title: R882H_hPSC_Sample4

description: Library name: R882H hPSC Sample4


title: 133

description:
Library name: P176_M_133
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Harlan Teklad 22/5 Rodent Diet 8604

tag: dose

value: diet

value: milligram per kilogram per day


title: cell-free DNA, Healthy pregnancy DNA069810

description:
Library name: DNA069810
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy

value: PAXgene DNA


title: cell-free DNA, Healthy pregnancy DNA069806

description:
Library name: DNA069806
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: R882H_D-NPC_Sample4

description: Library name: R882H D-NPC Sample4

tag: cell line

value: D-NPC


title: 129

description:
Library name: P176_M_129
Adult male mouse dosed every 4 days for 84 days

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad

value: Yes

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: Carbon dioxide euthanasia


title: P904L_V-IN_Sample2

description: Library name: P904L V-IN Sample2

tag: cell type

value: V-IN

value: TBRS P904L


title: P904L_V-IN_Sample4

description: Library name: P904L V-IN Sample4

tag: genotype


title: P904L_iGlut_Sample2

description: Library name: P904L iGlut Sample2

value: iGlut


title: cell-free DNA, Healthy pregnancy DNA069807

description:
Library name: DNA069807
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

tag: tissue

value: Blood plasma

value: Healthy

value: PAXgene DNA


title: cell-free DNA, Healthy pregnancy DNA069804

description:
Library name: DNA069804
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

tag: disease state

value: EDTA


title: cell-free DNA, Healthy pregnancy DNA069805

description:
Library name: DNA069805
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

tag: blood tube_type


title: R882H_D-NPC_Sample2

description: Library name: R882H D-NPC Sample2

value: D-NPC

value: TBRS R882H


title: cell-free DNA, Healthy pregnancy DNA069802

description:
Library name: DNA069802
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

tag: patient id


title: P904L_V-NPC_Sample1

description: Library name: P904L V-NPC Sample1

value: V-NPC


title: P904L_V-NPC_Sample2

description: Library name: P904L V-NPC Sample2


title: R882H_D-NPC_Sample1

description: Library name: R882H D-NPC Sample1


title: 127

description:
Library name: P176_M_127
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day


title: 131

description:
Library name: P176_M_131
Adult male mouse dosed every 4 days for 84 days

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: Carbon dioxide euthanasia


title: P904L_iGlut_Sample1

description: Library name: P904L iGlut Sample1

value: iGlut

value: TBRS P904L


title: R882H_D-IN_Sample1

description: Library name: R882H D-IN Sample1

value: D-IN

value: TBRS R882H


title: P904L_V-NPC_Sample4

description: Library name: P904L V-NPC Sample4

value: V-NPC


title: 130

description:
Library name: P176_M_130
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes


title: 128

description:
Library name: P176_M_128
Adult male mouse dosed every 4 days for 84 days

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: P904L_V-NPC_Sample3

description: Library name: P904L V-NPC Sample3

value: V-NPC

value: TBRS P904L


title: R882H_D-IN_Sample2

description: Library name: R882H D-IN Sample2

value: D-IN

value: TBRS R882H


title: cell-free DNA, Healthy pregnancy DNA069803

description:
Library name: DNA069803
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy

value: EDTA

tag: gestational age_(weeks)


title: P904L_V-IN_Sample3

description: Library name: P904L V-IN Sample3

value: V-IN


title: P904L_D-IN_Sample1

description: Library name: P904L D-IN Sample1


title: P904L_iGlut_Sample3

description: Library name: P904L iGlut Sample3

value: iGlut


title: P904L_V-IN_Sample1

description: Library name: P904L V-IN Sample1


title: cell-free DNA, Healthy pregnancy DNA069798

description:
Library name: DNA069798
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

tag: sequencing batch


title: 124

description:
Library name: P176_M_124
Adult male mouse dosed every 4 days for 84 days

tag: strain

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter


title: P904L_D-IN_Sample3

description: Library name: P904L D-IN Sample3

value: D-IN

value: TBRS P904L


title: C-WT_V-NPC_Sample4

description: Library name: C-WT V-NPC Sample4

source_name: C-WT

value: C-WT

value: V-NPC

value: Control


title: 121

description:
Library name: P176_M_121
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

tag: Sex

value: Male

value: day

value: degree celsius

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: C-WT_V-NPC_Sample2

description: Library name: C-WT V-NPC Sample2


title: cell-free DNA, Healthy pregnancy DNA069783

description:
Library name: DNA069783
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy

value: EDTA


title: 123

description:
Library name: P176_M_123
Adult male mouse dosed every 4 days for 84 days

value: percent

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter


title: C-WT_V-IN_Sample3

description: Library name: C-WT V-IN Sample3

value: C-WT

value: V-IN

value: Control


title: cell-free DNA, Preeclampsia pregnancy DNA069801

description:
Library name: DNA069801
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Preeclampsia


title: 126

description:
Library name: P176_M_126
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

tag: water

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: cell-free DNA, Preeclampsia pregnancy DNA069800

description:
Library name: DNA069800
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: EDTA


title: P904L_D-IN_Sample2

description: Library name: P904L D-IN Sample2

value: D-IN

value: TBRS P904L


title: cell-free DNA, Healthy pregnancy DNA068988

description:
Library name: DNA068988
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Healthy

value: PAXgene DNA


title: C-WT_iGlut_Sample3

description: Library name: C-WT iGlut Sample3

value: C-WT

value: iGlut

value: Control


title: 122

description:
Library name: P176_M_122
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

tag: name

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter


title: 115

description:
Library name: P176_M_115
Adult male mouse dosed every 4 days for 84 days

value: degree celsius

tag: formula

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: cell-free DNA, Preeclampsia pregnancy DNA069785

description:
Library name: DNA069785
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Preeclampsia

value: EDTA


title: C-WT_iGlut_Sample2

description: Library name: C-WT iGlut Sample2

value: C-WT

value: iGlut

value: Control


title: 119

description:
Library name: P176_M_119
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

tag: vendor

value: Accustandard

value: Room temperature


title: P904L_D-IN_Sample4

description: Library name: P904L D-IN Sample4

value: D-IN

value: TBRS P904L


title: C-WT_hPSC_Sample4

description: Library name: C-WT hPSC Sample4

value: C-WT

value: hPSC


title: C-WT_iGlut_Sample1

description: Library name: C-WT iGlut Sample1

value: iGlut

value: Control


title: C-WT_V-NPC_Sample3

description: Library name: C-WT V-NPC Sample3

value: V-NPC


title: 113

description:
Library name: P176_M_113
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: sesame oil

value: milliliter

value: oral gavage

tag: dose

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: C-WT_hPSC_Sample2

description: Library name: C-WT hPSC Sample2

tag: cell line

value: C-WT

value: hPSC


title: C-WT_hPSC_Sample1

description: Library name: C-WT hPSC Sample1

tag: cell type

value: Control


title: 118

description:
Library name: P176_M_118
Adult male mouse dosed every 4 days for 84 days

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard

value: Room temperature


title: cell-free DNA, Healthy pregnancy DNA068989

description:
Library name: DNA068989
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy

value: PAXgene DNA


title: C-WT_D-NPC_Sample4

description: Library name: C-WT D-NPC Sample4

value: D-NPC

tag: genotype


title: C-WT_V-NPC_Sample1

description: Library name: C-WT V-NPC Sample1

value: V-NPC


title: C-WT_V-IN_Sample2

description: Library name: C-WT V-IN Sample2

value: C-WT

value: V-IN


title: 117

description:
Library name: P176_M_117
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: 112

description:
Library name: P176_M_112
Adult male mouse dosed every 4 days for 84 days

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard

value: Room temperature


title: 111

description:
Library name: P176_M_111
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: sesame oil

value: milliliter


title: 116

description:
Library name: P176_M_116
Adult male mouse dosed every 4 days for 84 days

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day


title: cell-free DNA, Healthy pregnancy DNA068987

description:
Library name: DNA068987
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

tag: tissue

value: Blood plasma

value: Healthy

value: EDTA


title: cell-free DNA, Healthy pregnancy DNA068986

description:
Library name: DNA068986
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

tag: disease state

value: PAXgene DNA


title: 114

description:
Library name: P176_M_114
Adult male mouse dosed every 4 days for 84 days

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard

value: Room temperature

value: Carbon dioxide euthanasia


title: C-WT_V-IN_Sample1

description: Library name: C-WT V-IN Sample1

value: C-WT

value: V-IN

value: Control


title: C-WT_D-IN_Sample4

description: Library name: C-WT D-IN Sample4

value: D-IN


title: 109

description:
Library name: P176_M_109
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day


title: cell-free DNA, Healthy pregnancy DNA068981

description:
Library name: DNA068981
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy

tag: blood tube_type

value: EDTA


title: C-WT_V-IN_Sample4

description: Library name: C-WT V-IN Sample4

value: C-WT

value: V-IN

value: Control


title: cell-free DNA, Healthy pregnancy DNA068985

description:
Library name: DNA068985
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: PAXgene DNA

tag: patient id


title: cell-free DNA, Healthy pregnancy DNA068984

description:
Library name: DNA068984
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

tag: gestational age_(weeks)


title: C-WT_D-NPC_Sample1

description: Library name: C-WT D-NPC Sample1

value: D-NPC


title: C-WT_D-NPC_Sample3

description: Library name: C-WT D-NPC Sample3


title: C-WT_D-NPC_Sample2

description: Library name: C-WT D-NPC Sample2


title: cell-free DNA, Healthy pregnancy DNA068979

description:
Library name: DNA068979
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

tag: sequencing batch


title: WT V-NPC Sample3

description: Library name: WT V-NPC Sample3

data_processing:
Raw reads were processed using AIAP (v1.1) for trimming, alignment, bigWig generation and peak calling
Assembly: hg38
Supplementary files format and content: bigWig density file
Supplementary files format and content: broadPeak file containing output from MACS2 peakcalling
Library strategy: CUT&Tag

extract_protocol:
Genomic DNA was processed using CUT&Tag (Epicypher) and isolated using phenol-chloroform follow by the NucleoSpin® Gel and PCR Clean-Up kit (Macherey-Nagel).
Libraries were generated by PCR with unique dual-end indexes and were pooled at equimolar concentrations.

value: WT

value: V-NPC

tag: antibody


title: cell-free DNA, Healthy pregnancy DNA068980

description:
Library name: DNA068980
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: WT V-NPC Sample4

description: Library name: WT V-NPC Sample4


title: Pancreatic islets, KO, rep2

city: Neuherberg

first: Alina

middle: Agnes

last: Walth-Hummel

address: Ingolstädter Landstrasse 1

country: Germany

institute: Helmholtz Munich

description: Library name: bTBL_R_2

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software,.
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes.
Differential expression analysis between two groups (four biological replicates per condition) was performed using DESeq2 R package. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR).
Assembly: mm10
Supplementary files format and content: tab-delimited file includes raw counts for each samples

source_name: pancreatic islets

extract_protocol:
RNA was isolated using the RNeasy Plus Kit for RNA isolation (Qiagen, Cat# 74134). 1 µg of total RNA were used for library preparation
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

treatment_protocol: Isolated pancreatic islets were immediately lysed in 500 µl TRIzol and stored at -80°C until further processing

value: pancreatic islets

tag: age

value: 5 weeks


title: C-WT_D-IN_Sample3

description: Library name: C-WT D-IN Sample3

value: D-IN


title: cell-free DNA, Healthy pregnancy DNA068982

description:
Library name: DNA068982
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Pancreatic islets, KO, rep4

description: Library name: bTBL_R_4


title: WT V-NPC Sample2

description: Library name: WT V-NPC Sample2


title: cell-free DNA, Healthy pregnancy DNA068977

description:
Library name: DNA068977
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: C-WT_D-IN_Sample2

description: Library name: C-WT D-IN Sample2


title: Pancreatic islets, KO, rep3

description: Library name: bTBL_R_3


title: Pancreatic islets, Control, rep4

description: Library name: Ctr_4

value: wildtype


title: R882H V-NPC Sample2

description: Library name: R882H V-NPC Sample2

value: TBRS R882H


title: cell-free DNA, Healthy pregnancy DNA068976

description:
Library name: DNA068976
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: WT V-NPC Sample1

description: Library name: WT V-NPC Sample1


title: R882H V-NPC Sample1

description: Library name: R882H V-NPC Sample1


title: C-WT_D-IN_Sample1

description: Library name: C-WT D-IN Sample1


title: Pancreatic islets, KO, rep1

description: Library name: bTBL_R_1


title: R882H V-NPC Sample4

description: Library name: R882H V-NPC Sample4


title: Pancreatic islets, Control, rep2

description: Library name: Ctr_2


title: C-WT_hPSC_Sample3

description: Library name: C-WT hPSC Sample3

value: hPSC


title: R882H V-NPC Sample3

description: Library name: R882H V-NPC Sample3


title: P904L V-NPC Sample1

description: Library name: P904L V-NPC Sample1

value: TBRS P904L


title: P904L V-NPC Sample2

description: Library name: P904L V-NPC Sample2


title: cell-free DNA, Healthy pregnancy DNA068974

description:
Library name: DNA068974
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma


title: P904L V-NPC Sample4

description: Library name: P904L V-NPC Sample4


title: C-WT V-NPC Sample2

description: Library name: C-WT V-NPC Sample2


title: left ventricular, cre46

city: Shanghai

first: Zhihong

last: Sun

email: sunzh0819@gmail.com, sszh0819@163.com

address: Second Ruijin Road

institute: Ruijin hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data. At the same time,Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were performed based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using star v2.7.10b and paired-end clean reads were mapped to the reference genome. featureCounts (v2.0.3)was used to count the read numbers mapped to each gene. And then TPM was calculated, which expected number of Transcripts Per Kilobase of exon model per Million mapped reads,considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels. Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.40.2). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 were set as the threshold for significantly differential expression. Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R（4.6.2）, in which gene length bias was corrected. GO terms with corrected P-value less than 0.05 were considered as significantly enriched GO functions of gene set. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular level information, especially large-scale molecular datasets generated by genome Sequencing and other high-through put experimental technologies(http://www.genome.jp/kegg/). We used clusterProfilerR to test the statistical enrichment of differential expression genes in KEGG pathways. GATK v4.2.6.1 software was used to perform SNP calling and SnpEff software was used for Variablesite annotation. Alternative Splicing is an important mechanism in post-transcriptional regulation. rMATS(4.1.2) software was used for AS events analysis. A fusion gene is a hybrid gene formed from two previously independent genes. It can occur as a result of translocation, interstitial deletion, or chromosomal inversion.We used STAR-Fusion v1.11.0 software for analysis and detection of fusion genes. PPI analysis of differentially expressed genes PPI analysis of differentially expressed genes was based on the STRING database, which known and predicted Protein-Protein Interactions. WGCNA (Weighted correlation network analysis) is a systematic biological method used to describe the gene association modes among different samples. it can be used to identify gene sets that are highly synergistic changed, and identify candidate biomarkers or therapeutic targets based on the coherence of gene sets and the correlation between gene sets and phenotypes. The R package WGCNA is a set of functions used to calculate various weighted association analysis, which can be used for network construction, gene screening, gene cluster identification, topological feature calculation, data simulation and visualization. WGCNA is suitable for multi-sample data. Generally, more than 15 samples are required. One input file is sample information, that is, a matrix describing the traits of the sample: the traits used for association analysis must be numeric; If it is a regional or categorical variable, it needs to be converted to a 0-1matrix. The other is gene expression data. For transcriptome sequencing ,FPKM can be used as gene expression data. Gene Set Enrichment Analysis (GSEA) is a computational approach to determine if a pre-defined Gene Set can show a significant consistent difference between two biological states. The genes were ranked according to the degree of differential expression in the two samples, and then the predefined Gene Set were tested to see if they were enriched at the top or bottom of the list. Gene set enrichment analysis can include subtle expression changes. We used clusterProfiler R (4.22) to perform GSEA analysis on the GO and KEGG datasets of this species.
Assembly: mm8
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: left ventricular

extract_protocol:
Left ventricular were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) were used with 1ug tissue. A total of 1 μg total RNA per sample was used as input material for the mRNA library preparation. Most of Eukaryote 'mRNA have polyA tails, which are enriched by Oligo (dT) magnetic beads. Then, the obtained mRNA was randomly interrupted by bivalent cations, and the first strand of cDNA was synthesized in the 1st Strand Enzymes Reverse transcriptase system using the segmented mRNA as the template and the random oligonucleotide as the primer, and the second strand of cDNA was synthesized using the 2nd Strand Enzymes and dNTPs. Purified double-stranded cDNA undergoes end repair, A-tailing, and ligation with sequencing adapters. cDNA with an insert size of approximately 200-300 bp is screened. PCR amplification is performed and the PCR product is purified again, ultimately obtaining a library.And then, library quality was assessed on the Agilent 4200 TapeStation. After passing the library inspection, the library preparations were sequenced on a NovaSeq 6000 platform (CHI BIOTECH CO.,LTD) and 150 bp stand-specific paired-end reads were generated.
RNA libraries were prepared for sequensing using standard illumia protocols

value: left ventricular


title: cell-free DNA, Healthy pregnancy DNA068970

description:
Library name: DNA068970
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Healthy

value: EDTA


title: cell-free DNA, Healthy pregnancy DNA068973

description:
Library name: DNA068973
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: C-WT V-NPC Sample1

description: Library name: C-WT V-NPC Sample1

value: C-WT


title: cell-free DNA, Healthy pregnancy DNA068969

description:
Library name: DNA068969
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: WT D-NPC Sample4

description: Library name: WT D-NPC Sample4

value: Control


title: WT D-NPC Sample3

description: Library name: WT D-NPC Sample3


title: Pancreatic islets, Control, rep3

description: Library name: Ctr_3


title: left ventricular, cre36


title: cell-free DNA, Healthy pregnancy DNA068972

description:
Library name: DNA068972
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: WT D-NPC Sample1

description: Library name: WT D-NPC Sample1


title: C-WT V-NPC Sample4

description: Library name: C-WT V-NPC Sample4


title: cell-free DNA, Healthy pregnancy DNA068967

description:
Library name: DNA068967
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA068971

description:
Library name: DNA068971
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: PAXgene DNA


title: P904L V-NPC Sample3

description: Library name: P904L V-NPC Sample3


title: C-WT V-NPC Sample3

description: Library name: C-WT V-NPC Sample3


title: left ventricular, cki38

value: control


title: P904L D-NPC Sample1

description: Library name: P904L D-NPC Sample1

value: D-NPC


title: cell-free DNA, Healthy pregnancy DNA068968

description:
Library name: DNA068968
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Pancreatic islets, Control, rep1

description: Library name: Ctr_1


title: cell-free DNA, Healthy pregnancy DNA068964

description:
Library name: DNA068964
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA068963

description:
Library name: DNA068963
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: C-WT D-NPC Sample2

description: Library name: C-WT D-NPC Sample2


title: R882H D-NPC Sample4

description: Library name: R882H D-NPC Sample4


title: left ventricular, cre40


title: R882H D-NPC Sample3

description: Library name: R882H D-NPC Sample3


title: cell-free DNA, Preeclampsia pregnancy DNA068956

description:
Library name: DNA068956
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Preeclampsia


title: IgG Neg Ctrl Input sample, primary rat DRG neuorns, bio rep 4

city: Boston

first: Rosalind

middle: A

last: Segal

state: MA

address: 360 Longwood Ave, LC6301

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description:
Library name: IgG-INPUT-4
column name in raw_counts_allRIPSamples.txt: IgG-INPUT-4

data_processing:
Illumina Bcl2fastq v2.18
Sequences were aligned to rat reference genome with STAR_(v2.5)
Raw gene counts were generated from STAR output
Assembly: USCS rn6
Supplementary files format and content: tab delimited text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: primary rat DRG neurons

growth_protocol: Timed pregnant Sprague-Dawley rats were purchased from Charles River for primary DRG neuron isolation. Embryos from timed pregnant Sprague-Dawley rats (aged E15) were used for primary cell culture isolation. All embryos, presumably of both sexes, were used. DRGs were dissected, dissociated, and plated in Matrigel (1:45; Thermo Fisher Scientific)-coated p35 dishes. DRG cultures were maintained in NeuroBasal medium supplemented with 2% B27, 1% Glutamax, 1% penicillin and streptomycin, 0.08% glucose, 1–100 ng/ml nerve growth factor (NGF)/brain-derived neurotrophic factor (BDNF; PeproTech), and 0.5 µM Cytarabine (AraC). Cultures were maintained in incubators at 37°C with 7.5% CO2 for 5 days.

extract_protocol:
RNA Immunoprecipitation was performed according to the EZ- Magna RIP RNA-Binding Protein Immunoprecipitation (Millipore Sigma) protocol. In brief, on Day 5 of primary DRG neuron cell culture, cells were washed with ice-cold PBS and lysed at -80 °C overnight in Complete Lysis Buffer. Lysates were spun down to pellet cellular debris and the supernatant added to Protein A/G Beads conjugated with 5μg of primary anti-SFPQ (Abcam, #ab38148), anti-SRSF10 (MBL, #50304712), or anti-rabbit IgG (EZ-Magna Kit). Lysate-bead mixtures were incubated at 4 °C overnight with end-to-end rotation. Protein-RNA complexes were eluted from beads in a Proteinase K Buffer for 30 mins at 55 °C. RNA was further purified using phenol:chloroform:isoamyl alcohol procedure followed by absolute ethanol and salt RNA precipitation.
Libraries were prepared with Takara SmartSeq v4 full length cDNA synthesis using oligo dT priming & 5’ template switching enzyme.

treatment_protocol: RNA Immunoprecipitation was performed with SFPQ, SRSF10, and control IgG antibodies according to the Z- Magna RIP RNA-Binding Protein Immunoprecipitation (Millipore Sigma).

value: primary rat DRG neurons

tag: treatment

value: IgG Neg Ctrl Input


title: P904L D-NPC Sample2

description: Library name: P904L D-NPC Sample2


title: cell-free DNA, Healthy pregnancy DNA068966

description:
Library name: DNA068966
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA068962

description:
Library name: DNA068962
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: R882H D-NPC Sample2

description: Library name: R882H D-NPC Sample2


title: left ventricular, cki44


title: cell-free DNA, Preeclampsia pregnancy DNA068955

description:
Library name: DNA068955
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA068965

description:
Library name: DNA068965
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: left ventricular, cki41


title: IgG Neg Ctrl Input sample, primary rat DRG neuorns, bio rep 2

description:
Library name: IgG-INPUT-2
column name in raw_counts_allRIPSamples.txt: IgG-INPUT-2


title: IgG Neg Ctrl Input sample, primary rat DRG neuorns, bio rep 1

description:
Library name: IgG-INPUT-1
column name in raw_counts_allRIPSamples.txt: IgG-INPUT-1


title: P904L D-NPC Sample4

description: Library name: P904L D-NPC Sample4


title: cell-free DNA, Preeclampsia pregnancy DNA068954

description:
Library name: DNA068954
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: R882H D-NPC Sample1

description: Library name: R882H D-NPC Sample1


title: WT D-NPC Sample2

description: Library name: WT D-NPC Sample2

value: WT


title: P904L D-NPC Sample3

description: Library name: P904L D-NPC Sample3


title: APP-2-C1-HTO

city: Heidelberg

first: Julius

last: Michel

address: Im Neueunheimer Feld 280

department: Neuroimmunology and brain tumor immunology

description: 14 months, M1+M2 Wt, HTO

library_source: other

data_processing:
final libraries was paired-end sequenced (26 and 92 bp) on one Illumina NovaSeq 6000 S2 lane
Assembly: mm10
Supplementary files format and content: CellRanger output files: mRNA_barcodes.tsv.gz, mRNA_features.tsv.gz, mRNA_matrix.tsv.gz
Supplementary files format and content: CellRanger output files: HTO_barcodes.tsv.gz, HTO_features.tsv.gz, HTO_matrix.tsv.gz
Supplementary files format and content: CellRanger output files: VDJ_filtered_contig_annotations.csv, VDJ_clonotypes.csv
Library strategy: CITE-Seq

molecule: protein

source_name: brain

extract_protocol:
APP23tg/APP23wt mice were sacrificed using Ketamin/Rompun overdose intraperitoneally, brains were isolated respectively, followed by 50 ug/ml Liberase (Sigma) digestion at 37ºC for 8 min and mashing through a 100 and 70 µm strainer (Miltenyi) to generate a single cell suspension. Subsequently, Myelin removal was performed using a 30% continuous Percoll (GE Healthcare) gradient and centrifugation at 2700 rpm.
library preparation were carried out on the Chromium platform (10x Genomics) with the Single Cell 5ʹ reagent v2 kit (10x Genomics) according to the manufacturer’s protocol

value: brain

tag: library type

value: HTO

value: CD45+ immune cells

value: B6, wildtype littermates


title: APP-2-C2-HTO

description: 14 months, M3+M4 Wt, HTO


title: IgG Neg Ctrl IP sample, primary rat DRG neuorns, bio rep 1

description:
Library name: IgG-IP-1
column name in raw_counts_allRIPSamples.txt: IgG-IP-1

value: IgG Neg Ctrl IP


title: APP-1-A2-HTO

description: 24 months, M3+M4 APP23-tg, HTO

value: B6, D2-TgN[Thy-APPSWE]-23- tg


title: C-WT D-NPC Sample1

description: Library name: C-WT D-NPC Sample1


title: IgG Neg Ctrl IP sample, primary rat DRG neuorns, bio rep 2

description:
Library name: IgG-IP-2
column name in raw_counts_allRIPSamples.txt: IgG-IP-2


title: APP-2-A2-HTO

description: 14 months, M3+M4 APP23-tg, HTO


title: APP-1-A1-HTO

description: 24 months, M1+M2 APP23-tg, HTO


title: APP-2-A1-HTO

description: 14 months, M1+M2 APP23-tg, HTO


title: C-WT D-NPC Sample3

description: Library name: C-WT D-NPC Sample3


title: SRSF10 Input sample, primary rat DRG neurons, bio rep 1

description:
Library name: SRSF10-INPUT-1
column name in raw_counts_allRIPSamples.txt: SRSF10-INPUT-1

value: SRSF10 Input


title: C-WT D-NPC Sample4

description: Library name: C-WT D-NPC Sample4


title: SRSF10 Input sample, primary rat DRG neurons, bio rep 3

description:
Library name: SRSF10-INPUT-3
column name in raw_counts_allRIPSamples.txt: SRSF10-INPUT-3


title: IgG Neg Ctrl Input sample, primary rat DRG neuorns, bio rep 3

description:
Library name: IgG-INPUT-3
column name in raw_counts_allRIPSamples.txt: IgG-INPUT-3


title: APP-2-C1-VDJ

description: 14 months, M1+M2 Wt, VDJ

molecule: other

value: VDJ


title: APP-2-A2-VDJ

description: 14 months, M3+M4 APP23-tg, VDJ


title: SRSF10 IP sample, primary rat DRG neurons, bio rep 2

description:
Library name: SRSF10-IP-2
column name in raw_counts_allRIPSamples.txt: SRSF10-IP-2

value: SRSF10 IP


title: cell-free DNA, Healthy pregnancy DNA060418

description:
Library name: DNA060418
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy

value: EDTA


title: SFPQ Input sample, primary rat DRG neurons, bio rep 3

description:
Library name: SFPQ-INPUT-3
column name in raw_counts_allRIPSamples.txt: SFPQ-INPUT-3

value: SFPQ Input


title: SFPQ Input sample, primary rat DRG neurons, bio rep 4

description:
Library name: SFPQ-INPUT-4
column name in raw_counts_allRIPSamples.txt: SFPQ-INPUT-4


title: cell-free DNA, Healthy pregnancy DNA060417

description:
Library name: DNA060417
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: IgG Neg Ctrl IP sample, primary rat DRG neuorns, bio rep 4

description:
Library name: IgG-IP-4
column name in raw_counts_allRIPSamples.txt: IgG-IP-4


title: APP-2-C2-VDJ

description: 14 months, M3+M4 Wt, VDJ


title: APP-1-C2-HTO

description: 24 months, M3+M4 Wt, HTO


title: APP-1-C2-VDJ

description: 24 months, M3+M4 Wt, VDJ


title: cell-free DNA, Healthy pregnancy DNA060416

description:
Library name: DNA060416
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: APP-1-C1-VDJ

description: 24 months, M1+M2 Wt, VDJ


title: cell-free DNA, Preeclampsia pregnancy DNA068953

description:
Library name: DNA068953
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Preeclampsia


title: APP-1-A2-VDJ

description: 24 months, M3+M4 APP23-tg, VDJ


title: IgG Neg Ctrl IP sample, primary rat DRG neuorns, bio rep 3

description:
Library name: IgG-IP-3
column name in raw_counts_allRIPSamples.txt: IgG-IP-3

value: primary rat DRG neurons


title: APP-1-C1-HTO

description: 24 months, M1+M2 Wt, HTO


title: cell-free DNA, Healthy pregnancy DNA060408

description:
Library name: DNA060408
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: APP-1-A1-VDJ

description: 24 months, M1+M2 APP23-tg, VDJ


title: cell-free DNA, Healthy pregnancy DNA060421

description:
Library name: DNA060421
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: SRSF10 IP sample, primary rat DRG neurons, bio rep 3

description:
Library name: SRSF10-IP-3
column name in raw_counts_allRIPSamples.txt: SRSF10-IP-3


title: cell-free DNA, Healthy pregnancy DNA060422

description:
Library name: DNA060422
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: KO_rep1

type: RNA

city: Shimotsuke

first: Taka-aki

last: Koshimizu

state: Tochigi

department: Pharmaclogy

country: Japan

institute: Jichi medical university

description: Gene expression data from adrenal glands at 2 months of age

hyb_protocol: see manufacturer's web site

scan_protocol: see manufacturer's web site

data_processing: R/Bioconductor, gcRMA

label: biotin

source_name: V1aKO mouse adrenal gland

label_protocol: see manufacturer's web site

extract_protocol: Microarray experiments were performed as previously described (Tamaki et al., 2013). Briefly, total RNA from the adrenal gland was isolated using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA, USA) and mRNA was isolated using an Oligotex mRNA Kit (QIAGEN, Hilden, Germany). The quality of mRNA was evaluated using an Agilent 2001 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), which calculates the RNA integrity number. mRNA samples (1 mg) with RNA integrity number values from 8.0 to 9.0 were further subjected to the labeling procedure with a One-Cycle Target Labeling Assay kit (Thermo Fisher Scientific) according to the manufacturer?s instructions. Labeled DNA was hybridized onto the GeneChip? Mouse Genome 430 2.0 Array (Thermo Fisher Scientific), and data were collected using a GeneChip? Scanner 3000. The resultant CEL files were analyzed using the gcRMA package (Wu et al., 2021) in Bioconductor 3.14 software (Huber et al., 2015).

tag: gender

value: male


title: APP-2-C2-GEX

description: 14 months, M3+M4 Wt, GEX

value: mRNA


title: SRSF10 IP sample, primary rat DRG neurons, bio rep 4

description:
Library name: SRSF10-IP-4
column name in raw_counts_allRIPSamples.txt: SRSF10-IP-4


title: cell-free DNA, Healthy pregnancy DNA060396

description:
Library name: DNA060396
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: SRSF10 IP sample, primary rat DRG neurons, bio rep 1

description:
Library name: SRSF10-IP-1
column name in raw_counts_allRIPSamples.txt: SRSF10-IP-1


title: SRSF10 Input sample, primary rat DRG neurons, bio rep 4

description:
Library name: SRSF10-INPUT-4
column name in raw_counts_allRIPSamples.txt: SRSF10-INPUT-4


title: 4-5

city: Tianjin

first: Jing

last: Yan

address: 154 Anshan Road in Heping District

institute: Tianjin Medical University General Hospital

description: Library name: sample 29

data_processing:
RNA sequencing: The data obtained from sequencing are raw data. Subsequently, quality is performed on the raw reads to determine whether the sequencing data are suitable for downstream analysis. Then, filtered clean reads are aligned to the reference sequence. Following alignment, the distribution and coverage of reads on the reference sequence are analyzed to assess whether the alignment results pass the second QC (QC of alignment). If the criteria are met, further analyses are conducted, including: Gene expression quantification, alternative splicing analysis, novel transcript prediction, SNP detection, gene structure optimization. From the gene expression results, differentially expressed genes (DEGs) between samples are identified. Based on these DEGs, Gene Ontology (GO) functional enrichment analysis and KEGG pathway enrichment analysis are performed to determine significant biological functions and pathways. 16s rRNA sequencing: Greengenes database was used to perform taxonomic assignment. Microbiome bioinformatics was mainly performed with QIIME 2 2019.4, including the composition of gut microbiota, alpha and beta diversity index analysis. R and Linear discriminant analysis Effect Size (LEfSe) were used to analyze different species and principal components.
Assembly: RNA sequencing: Reference genome: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.26; 16s rRNA sequencing: Greengenes Release 13.8; Primers: 341F: 5’-ACTCCTACGGGRSGCAGCAG-3’, 806R: 5’-GGACTACVVGGGTATCTAATC-3’
Supplementary files format and content: group.fpkm DSS vs DSS+KS.xls; DSS_vs_DK.Differential_allgene.results.xls; otu_table_genus.xls
Library strategy: 16S rRNA-seq

source_name: feces

extract_protocol:
For RNA sequencing, after extracting total RNA from the samples, eukaryotic mRNA was enriched using magnetic beads coated with Oligo(dT). For 16s rRNA sequencing, Total fecal bacterial DNA was extracted using a QIAamp® Fast DNA Stool Mini Kit (QIAamp, Germany).
For RNA sequencing, the mRNA was fragmented into short pieces by adding fragmentation buffer. Using the fragmented mRNA as a template, the first strand of cDNA was synthesized with random hexamer primers. Subsequently, the second cDNA strand was synthesized by adding buffer, dNTPs, RNase H, and DNA polymerase I. The double-stranded cDNA then underwent end repair, poly(A) tailing, and sequencing adapter ligation. The product was purified and size-selected using magnetic beads. Finally, PCR amplification was performed to generate the sequencing library. 16s rRNA sequencing: The 16S rRNA gene sequencing procedure was carried out by the Bioyigene Biotechnology Co. Ltd (Wuhan, China) using an Illumina HiSeq platform. We used the Thermo Scientific NanoDrop 2000 UV microspectrophotometer and 1.2 % agarose gel electrophoresis for quality control. Specific primers (341F: 5’-ACTCCTACGGGRSGCAGCAG-3’, 806R: 5’-GGACTACVVGGGTATCTAATC-3’) were prepared for PCR amplification using TransStart® FastPfu high fidelity DNA polymerase, and product purification was finished by Vazyme VAHTSTM DNA Clean Beads. First, the sequencing library was constructed and underwent quality inspection. Next, the libraries were sequenced using Illumina Novaseq. The library sequences were quality filtered, trimmed, denoised, and merged, and then the chimeric sequences were identified and removed to analyze the abundance, diversity and composition of the gut microbiota.

value: feces

tag: strain

tag: Sex

value: female

value: WT

value: DSS plus 7-ketositosterol

tag: time

value: Day 21


title: 4-4

description: Library name: sample 28


title: APP-2-A2-GEX

description: 14 months, M3+M4 APP23-tg, GEX

value: brain

value: CD45+ immune cells

value: B6, D2-TgN[Thy-APPSWE]-23- tg


title: cell-free DNA, Healthy pregnancy DNA060419

description:
Library name: DNA060419
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: APP-2-A1-VDJ

description: 14 months, M1+M2 APP23-tg, VDJ

value: VDJ


title: SRSF10 Input sample, primary rat DRG neurons, bio rep 2

description:
Library name: SRSF10-INPUT-2
column name in raw_counts_allRIPSamples.txt: SRSF10-INPUT-2

value: SRSF10 Input


title: cell-free DNA, Healthy pregnancy DNA060420

description:
Library name: DNA060420
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy

value: PAXgene DNA


title: WT_rep1

source_name: wild type mouse adrenal gland


title: cell-free DNA, Healthy pregnancy DNA060415

description:
Library name: DNA060415
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: EDTA


title: APP-2-A1-GEX

description: 14 months, M1+M2 APP23-tg, GEX


title: SFPQ IP sample, primary rat DRG neurons, bio rep 3

description:
Library name: SFPQ-IP-3
column name in raw_counts_allRIPSamples.txt: SFPQ-IP-3

value: primary rat DRG neurons

value: SFPQ IP


title: SFPQ IP sample, primary rat DRG neurons, bio rep 4

description:
Library name: SFPQ-IP-4
column name in raw_counts_allRIPSamples.txt: SFPQ-IP-4


title: SFPQ IP sample, primary rat DRG neurons, bio rep 2

description:
Library name: SFPQ-IP-2
column name in raw_counts_allRIPSamples.txt: SFPQ-IP-2


title: 4-1

description: Library name: sample 25


title: SFPQ Input sample, primary rat DRG neurons, bio rep 1

description:
Library name: SFPQ-INPUT-1
column name in raw_counts_allRIPSamples.txt: SFPQ-INPUT-1

value: SFPQ Input


title: APP-1-C2-GEX

description: 24 months, M3+M4 Wt, GEX

value: mRNA

value: B6, wildtype littermates


title: SFPQ Input sample, primary rat DRG neurons, bio rep 2

description:
Library name: SFPQ-INPUT-2
column name in raw_counts_allRIPSamples.txt: SFPQ-INPUT-2


title: 3-5

description: Library name: sample 23

value: feces

value: female

value: WT

value: DSS


title: WT_rep2

value: male


title: 3-4

description: Library name: sample 22

value: Day 21


title: APP-1-C1-GEX

description: 24 months, M1+M2 Wt, GEX

value: brain

value: CD45+ immune cells


title: cell-free DNA, Healthy pregnancy DNA060407

description:
Library name: DNA060407
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma


title: KO_rep2


title: SFPQ IP sample, primary rat DRG neurons, bio rep 1

description:
Library name: SFPQ-IP-1
column name in raw_counts_allRIPSamples.txt: SFPQ-IP-1


title: 4-6

description: Library name: sample 30

value: DSS plus 7-ketositosterol


title: 4-2

description: Library name: sample 26


title: 4-3

description: Library name: sample 27


title: APP-1-A1-GEX

description: 24 months, M1+M2 APP23-tg, GEX

value: B6, D2-TgN[Thy-APPSWE]-23- tg


title: APP-2-C1-GEX

description: 14 months, M1+M2 Wt, GEX


title: 3-6

description: Library name: sample 24


title: 2-2

description: Library name: sample 14


title: cell-free DNA, Preeclampsia pregnancy DNA060388

description:
Library name: DNA060388
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Preeclampsia

value: PAXgene DNA


title: cell-free DNA, Healthy pregnancy DNA060395

description:
Library name: DNA060395
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Healthy

value: EDTA


title: 2-1

description: Library name: sample 13


title: APP-1-A2-GEX

description: 24 months, M3+M4 APP23-tg, GEX

value: mRNA


title: EFNA3-2

city: xiamen

first: feng

last: deyi

state: xiamen

address: Xiamen University

institute: xiamen university

data_processing:
trim-galore;subjunc and featurecount
Assembly: mm39
Supplementary files format and content: Norm.csv

source_name: mammary

growth_protocol: Luminal  cells were purified by folw cytometry and cultured in DMEM/F12 supplemented with 5% FBS, 10 ng/mL EGF (Novoprotein, C029), 20 ng/mL FGF2 (GenScript, Z03116), 4 µg/mL heparin, 5 µM Y-27632, 1% L-Ala-Gln, and 1% P/S.

extract_protocol:
Total RNA was extracted using either the Micro RNA extraction kit(Magen, R4125).
RNA libraries for RNA-seq were prepared using the Illumina® Stranded mRNA Prep, Ligation kit (San Diego, CA)  according to the manufacturer’s protocols

treatment_protocol: Luminal cells were serum-starved for 12 hours, followed by incubation with 1 µg/ml EFNA3 protein in serum-free medium for 24 hours prior to RNA extraction.

value: mammary

value: mammary epithelial cells

value: 1µg/ml EFNA3


title: 2-3

description: Library name: sample 15

value: feces

value: female

value: WT


title: cell-free DNA, Preeclampsia pregnancy DNA060386

description:
Library name: DNA060386
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA060385

description:
Library name: DNA060385
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA060380

description:
Library name: DNA060380
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA060384

description:
Library name: DNA060384
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: 1-6

description: Library name: sample 12

value: control

value: Day 21


title: EFNA3-1


title: 1-4

description: Library name: sample 10


title: 1-1

description: Library name: sample 7


title: 2-5

description: Library name: sample 17


title: Control-1

value: 0µg/ml EFNA3


title: Control-2


title: Control-3


title: 3-2

description: Library name: sample 20

value: DSS


title: 3-3

description: Library name: sample 21


title: BL-55h-3

data_processing:
trim-galore;subjunc and featurecount
Assembly: mm39
Supplementary files format and content: counts.txt

growth_protocol: Luminal and basal cells were purified by folw cytometry and generated mammary aggregates of three types: luminal-only (Lu), basal-only (Ba), and mixed luminal-basal aggregates (Balu)

treatment_protocol: Heparin sulfate beads (100-150 µm in diameter) were pre-soaked in 10 µL of 100 µg/mL FGF10 . After Matrigel (80%) solidification on the culture dish, beads and mammary organoids were positioned ~100 µm apart using a tungsten needle, followed by the addition of 1 mL basal medium (DMEM/F12 supplemented with 1% P/S, 1% L-Ala-Gln, and 1% ITS.

tag: cell subtype

value: mixed luminal-basal aggregates (Balu)

value: after migrating for 56 hours under the induction of FGF10 beads


title: EFNA3-3

tag: cell type


title: HTGTS_Chr8_70Mb_APH03_ATRi_replicate_1

first: Pei-Chi

last: Wei

state: Baden-Württemberg

address: Im Neuenheim Feld 280

department: Structural and functional genomics

institute: German Cancer Research Center

data_processing:
LAM-HTGTS: a sigularity package https://github.com/brainbreaks/HTGTS
Repli-seq: a sindularity pacakge https://github.com/brainbreaks/HighRes_RepliSeq
GRO-seq:as described in Wei et al., 2016 Cell (https://doi.org/10.1016/j.cell.2015.12.039)
Assembly: mm10
Supplementary files format and content: tlx files contain LAM-HTGTS bait and prey junction, sequneces, start, end, and direction (Strand).
Supplementary files format and content: Bedgraph: display of continuous-valued data in track format
Library strategy: LAM-HTGTS

source_name: ESC-NPC

growth_protocol: The Xrcc4/p53-deficient mouse embryonic stem cells were cultured in DMEM medium supplemented with 15% ESC-grade fetal bovine serum, 20mM HEPES, non-essential amino acids, 100 U/ml Pen/Strep and glutamine mixture, 0.1mM beta-mercaptoethanol and 1000 U/mL ESGRO recombinant mouse leukemia inhibitory factor (LIF) on a monolayer of confluent irradiated mouse fibroblasts. The CAST x 129 hybrid mouse ES cells were cultured in 2i medium (50% DMEM/F12, 50% NeuralBasal, 0.5X N2 supplement, 0.5X B27 supplement, BSA, 10 mM PD03259010, 10 mM CHIR99021, 200 mM Glutamine, 11.9M Monothioglycerol, and 1x10^6 U/ml LIF). To induce mouse neural progenitor cells, Xrcc4/p53-deficient mouse ES cells were plated on laminine/poly-L-ornithine-coated plates and cultured in N2B27 medium (50% DMEM/F12, 50% NeuralBasal, 1% modified N2 supplement, 2% B27 supplement without RA, 1X Glutamax) for seven days. Cells were then passaged to laminin-coated plates and culture in NBBG medium (NeralBasalA, 2% B27 supplement without RA, 0.5 mM Glutamax, 10ng/ml human EGF, 10ng/ml mouse FGFb) for another five to six days. Neural progenitor cells were then collected for nucleofection, DRIP-seq, or Repli-seq experiments.

extract_protocol:
Genomic DNA for HTGTS: cells were lyzed in proteinase K digestion buffer, and genomic DNA were extraced with a standard phenol/chlorofomr protocol. RNA were removed by treating samples with RNAseA prior phenol/chlroform extraction. Genomic DNA for two fraction Repli-seq: cells were lyzed in proteinase K digestion buffer, and genomic DNA were extraced with a standard phenol/chlorofomr protocol. Nascent RNA for GRO-seq: nuclei were lysed in TriZol reagents. RNA were extraced as manufacture instruction.
We follow the published protocol, as indicated below, to construct the libraries. GRO-seq:https://www.sciencedirect.com/science/article/pii/S0092867415017031?via%3Dihub Repli-seq: https://pubmed.ncbi.nlm.nih.gov/29599440/ HTGTS: https://www.nature.com/articles/nprot.2016.043

treatment_protocol: Cells were treated with indicated concentration of aphidicolin or the veichle control DMSO for the indicated period.

tag: cell line

value: ESC-NPC

value: Neural progenitor cells

tag: genotype

value: Aphidicolin 0.3 uM 96h; ATRi 5 nM 96h


title: 2-4

description: Library name: sample 16

tag: tissue


title: K Bulk RNA-seq rep1

city: Guangzhou

first: Hui

last: Zheng

state: Guangdong

address: No.190 Kaiyuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
Fastq files were generated from illumina BCL raw data using bcl2fastq scripts;
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Mapped read counts were calculated using RSEM(1.2.22) with parameters(-p 8 --estimated-rspd --no-bam-output).
Assembly: mm10
Supplementary files format and content: Comma separated values files include counts for each Sample

source_name: Mouse embryonic fibroblasts reprgramming cells

growth_protocol: Cells were maintained in iCD1 reprogramming medium.

extract_protocol:
Cells were lysised by Trizol and total RNAs were extracted by chloroform-isopropanol method.
Libraries for RNA-seq were prepared using VAHTS mRNA-seq V2 Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: MEF cells were infected with different TF combinations.

value: Over expression KLF4


title: 3-1

description: Library name: sample 19


title: cell-free DNA, Healthy pregnancy DNA060382

description:
Library name: DNA060382
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

tag: disease state

value: Healthy

tag: blood tube_type

value: EDTA


title: cell-free DNA, Healthy pregnancy DNA060383

description:
Library name: DNA060383
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

tag: patient id

tag: gestational age_(weeks)


title: S Bulk RNA-seq rep1

value: Mouse embryonic fibroblasts reprgramming cells

value: Over expression SOX2


title: 2-6

description: Library name: sample 18

value: feces

value: female


title: cell-free DNA, Preeclampsia pregnancy DNA038618

description:
Library name: DNA038618
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Preeclampsia

value: PAXgene DNA

tag: sequencing batch


title: 1-3

description: Library name: sample 9

value: WT

value: control

value: Day 21


title: O Bulk RNA-seq rep2

value: Over expression OCT4


title: 1-5

description: Library name: sample 11


title: cell-free DNA, Healthy pregnancy DNA060378

description:
Library name: DNA060378
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Lu-55h-2

value: mammary

value: mammary epithelial cells

value: luminal-only (Lu)

value: after migrating for 56 hours under the induction of FGF10 beads


title: cell-free DNA, Preeclampsia pregnancy DNA060381

description:
Library name: DNA060381
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma


title: HTGTS_Chr8_70Mb_APH03_no_ATRi_replicate_2

value: ESC-NPC

value: Neural progenitor cells

value: Aphidicolin 0.3 uM 96h


title: cell-free DNA, Preeclampsia pregnancy DNA060376

description:
Library name: DNA060376
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: EDTA


title: cell-free DNA, Preeclampsia pregnancy DNA038622

description:
Library name: DNA038622
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Saos2/LentiCas9-dPML#2 + sgPAXIP1

city: New york

first: Jihye

last: Paik

state: NY

address: 1300 York Ave.

department: Pathology

institute: Weill Cornell Medical College

description:
Library name: DPM24DP
PML KO + PAXIP KO

data_processing:
Illumina bcl2fastq2 v2.17 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the UCSC hg38reference genome using tophat v2.0.11.
Transcript abundances was estimated with Salmon. Salmon outputs normalized expression values, including TPM (Transcripts Per Million) and FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Assembly: hg38
Supplementary files format and content: .tsv tab limited text file contains raw count

source_name: bone

growth_protocol: cell were grown in 10% FBS, 1% PenStrep, in DMEM media

extract_protocol:
Total RNA was extracted with NuceloSpin RNA extraction kit (MN#740955.250) followed by manufacturer's instructions. Briefly, the brains were lysed with 350 uL of lysis buffer (RA) and cleaned with Nucleospin filter. Added the 70% EtOH to bound RNA to RNA column. After digest genomic DNA with DNase, the columns were washed with provided wash solutions and eluted RNA with 30 uL of RNase free water. The RNA concentrations were determined with NanoDrop.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone

value: osteosarcoma

value: PML PAXIP1 double null

tag: batch

value: single


title: cell-free DNA, Healthy pregnancy DNA060377

description:
Library name: DNA060377
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Healthy


title: Saos2/LentiCas9-dPML#2

description:
Library name: DPM24C
PML KO

value: PML null


title: Saos2/LentiCas9-dPML#1 + sgPAXIP1

description:
Library name: DPM8DP
PML KO + PAXIP KO


title: HTGTS_Chr8_70Mb_APH03_ATRi_replicate_3

tag: treatment

value: Aphidicolin 0.3 uM 96h; ATRi 5 nM 96h


title: 1-2

description: Library name: sample 8

value: feces

value: female

value: WT

value: control

value: Day 21


title: Lu-55h-1

value: mammary

value: mammary epithelial cells

value: luminal-only (Lu)

value: after migrating for 56 hours under the induction of FGF10 beads


title: HTGTS_Chr8_70Mb_APH03_ATRi_replicate_2

value: ESC-NPC

value: Neural progenitor cells


title: cell-free DNA, Preeclampsia pregnancy DNA038621

description:
Library name: DNA038621
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Preeclampsia

value: EDTA


title: HTGTS_Chr8_70Mb_APH03_no_ATRi_replicate_1

value: Aphidicolin 0.3 uM 96h


title: BL-55h-2

value: mixed luminal-basal aggregates (Balu)


title: S Bulk RNA-seq rep2

value: Mouse embryonic fibroblasts reprgramming cells

value: Over expression SOX2


title: K Bulk RNA-seq rep2

value: Over expression KLF4


title: BL-55h-1

value: WT


title: Lu-55h-3


title: cell-free DNA, Preeclampsia pregnancy DNA038620

description:
Library name: DNA038620
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: PTEN MUT 4

first: David

last: Chen

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana Farber Cancer Institute

description: Library name: NU02673

data_processing:
Standard Python-based Scanpy workflows for quality control filtering, data normalization, detection of highly variable genes, and downstream analyses were conducted. Cells with less than 200 gene feature counts and greater than 10% mitchondrial RNA content were excluded. Genes with less than 3 cells with non-zero feature counts were excluded. Counts were normalization to a factor of 10,000 and log-scaled. Principal component analysis (PCA) of the first 50 components was conducted on the normalized data using the top 6000 variable features. Nearest neighbors distance matrix was generated using the first 50 PCA components and nearest10 cell neighbors. Cells were visualized using the UMAP non-linear dimension reduction.
Assembly: Human GRCh38
Supplementary files format and content: H5 File of Cell ID and Raw FeatureCounts

source_name: Blood

extract_protocol:
Human samples were obtained from the Nervous System Tumor Bank at Northwestern University. In brief, patients diagnosed with GBM underwent surgery for tumor resection following standard clinical practices. After the tumor was removed, an adequate amount of tissue was sent to pathology for clinical diagnosis. During the surgery, a maximum of 60 mL of peripheral blood was collected while the patient was under anesthesia. Blood was drawn by the anesthesiologist from an arterial line, central venous line, or a peripheral IV, all of which were part of routine anesthesia care.  The peripheral blood was then centrifuged using a Ficoll gradient to separate the peripheral blood leukocytes and plasma, which were collected and frozen separately. Before analysis, the peripheral blood mononuclear cells (PBMCs) were retrieved from liquid nitrogen and thawed in a 37°C water bath. The cells were washed with phosphate-buffered saline (PBS) and subjected to the EasySep™ Dead Cell Removal (Annexin V) Kit (STEMCELL, #7899), following the manufacturer’s protocol. The viable cells were then sent to the NUSeq Core at Northwestern University for scRNA-seq analysis.
The scRNA-seq library was prepared by Northwestern University NUseq facility core with NIH Grant (1S10OD025120). To ensure the quality of library, the number and viability of human GBM patients' PBMCs were stained with AO/PI Staining Solution and analyzed by Nexcelom Cellometer Auto2000 cell viability analyzer. PBMCs were loaded into the Chromium Controller (10X Genomics, PN-120223) on a Chromium Next GEM Chip K (10X Genomics, PN-1000127), and processed to generate single cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol. The cDNA and library were generated using the Chromium Next GEM Single Cell 5’ Reagent Kits v2 (10X Genomics, PN-1000283) according to the manufacturer’s manual.

value: Blood

value: PBMC

value: Mixed


title: Saos2/LentiCas9 #1 + sgPAXIP1

description:
Library name: SAO1DP
PAXIP1 KO

value: bone

value: osteosarcoma

value: PAXIP1 null

value: single


title: Ba-55h-2

value: mammary

value: mammary epithelial cells

value: basal-only (Ba)

value: after migrating for 56 hours under the induction of FGF10 beads


title: cell-free DNA, Healthy pregnancy DNA038605

description:
Library name: DNA038605
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy

value: EDTA


title: cell-free DNA, Healthy pregnancy DNA038606

description:
Library name: DNA038606
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Saseq_DF2_cKO_5hr_1

city: Daejeon

first: Ki-Jun

last: Yoon

address: 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
Illumina Real Time Analysis (RTA3) is used for base calling and blc2fastq is used for fastq file conversion.
Cutadapt (v3.5) is used for adapter trimming.
The expression level was calculated by the RSEM (v1.3.3) and STAR (v2.7.10b) with default parameters.
do rsem-calculate-expression --star -p 8  --star-gzipped-read-file --paired-end $i"_1.fastq.gz" $i"_2.fastq.gz"
Assembly: mm10
Supplementary files format and content: tab-seperated text file include TPM and FPKM values

source_name: DIV6 Mouse Primary Neuron

growth_protocol: Mouse primary neurons were isolated from the P0 forebrain. Neurons were cultured in Neurobasal medium supplemented with B-27, GlutaMAX, penicillin-streptomycin, and gentamycin on poly-D-lysine-coated 6-well plates.

extract_protocol:
Primary neurons were collected in TRIzol (Invitrogen) and stored at -80°C overnight. Total RNA was isolated from each sample, and further RNA cleanup was performed using the RNeasy Mini Kit (Qiagen). The Dynabeads mRNA DIRECT Purification Kit (Invitrogen) was used to isolate mRNA from the samples.
The NEBNext Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs) was used, and the recommended protocol was followed to generate the library.

treatment_protocol: At DIV7, Actinomycin D was added at a 5 µM concentration, and neurons were collected at two time points (0 and 5 hours) after washing with DPBS.

value: DIV6 Mouse Primary Neuron

value: Nestin-Cre Ythdf2 cKO

value: ActD 5hr treatment


title: cell-free DNA, Healthy pregnancy DNA038604

description:
Library name: DNA038604
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: PAXgene DNA


title: PTEN WT 3

description: Library name: NU01920

value: Blood

value: PBMC


title: Saos2/LentiCas9-dPML#1

description:
Library name: DPM8C
PML KO

value: bone

value: PML null


title: cell-free DNA, Preeclampsia pregnancy DNA038609

description:
Library name: DNA038609
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Preeclampsia


title: O Bulk RNA-seq rep1

value: Mouse embryonic fibroblasts reprgramming cells

value: Over expression OCT4


title: PTEN WT 2

description: Library name: NU03446

value: Mixed


title: cell-free DNA, Preeclampsia pregnancy DNA038617

description:
Library name: DNA038617
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA038602

description:
Library name: DNA038602
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Saos2/LentiCas9 #2 + sgPAXIP1

description:
Library name: SB4DP
PAXIP1 KO

value: osteosarcoma

value: PAXIP1 null

value: single


title: Ba-55h-3

value: mammary

value: mammary epithelial cells

value: basal-only (Ba)

value: WT

value: after migrating for 56 hours under the induction of FGF10 beads


title: cell-free DNA, Healthy pregnancy DNA038601

description:
Library name: DNA038601
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy

value: EDTA


title: Ba-55h-1


title: cell-free DNA, Preeclampsia pregnancy DNA038607

description:
Library name: DNA038607
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Saos2/LentiCas9 #1 + sgRosa

description:
Library name: SAO1C
sgRosa expressing control

value: bone

value: control