title: PBMCs, Day 0, ATAC individual 43

description: Library name: Ind43d0

value: PBMC

value: monocytes, T and B cells

value: directly before vitamin D3 bolus (1.000 IU/kg) (day 0)


title: PBMCs, Day 1, ATAC individual 42

status: Public on Dec 30 2025

type: SRA

city: Olsztyn

first: Maciej

last: Rybiński

state: Warmian-Masurian Voivodeship

address: Trylińskiego 18

country: Poland

institute: Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences.

description: Library name: Ind42d1

library_source: genomic

data_processing:
ATAC-seq: Paired-end reads were aligned using the STAR aligner. ENCODE-identified blacklisted regions and reads with mapping quality score < 2 were filtered out. Duplicates were identified and marked with samtools markdup. Peak calling done with MACS3 (version 3.0.1) utilizing callpeak function with the parameters --f BAMPE --verbose 3 --shift 0 -g hs -q 0.01 -B. Consensus peak summits matrix generated with DiffBind utilizing dba.count function with summits parameter set to 75.
Assembly: GRCh38.p14
Supplementary files format and content: Cohort_Consensus.csv - Matrix of raw values corresponding to each specific peak summit (rows) across all samples (columns) generated by DiffBind.

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood

extract_protocol:
ATAC-seq: nuclei were isolated from 100,000 PBMCs by incubation in 50 µl lysis buffer (10 mM Tris-HCl, pH 8.0; 10 mM NaCl; 3 mM MgCl₂; 0.1% Tween-20; 0.1% IGEPAL CA-630; 0.01% digitonin). After 3 minutes on ice, 1 ml wash buffer (10 mM Tris-HCl, pH 8.0; 10 mM NaCl; 3 mM MgCl₂; 0.1% Tween-20) was added. Nuclei were pelleted and subjected to transposition using a Tn5 transposase reaction mix (Illumina), supplemented with 0.01% digitonin and 0.1% Tween-20. The transposition reaction was carried out at 37 °C for 30 minutes in a thermomixer. Transposed DNA was purified using the DNA Clean & Concentrator-5 Kit (Zymo Research), followed by PCR amplification, purification, and size selection with SPRISelect beads (Beckman Coulter). Library quality was assessed using an Agilent TapeStation. Indexed libraries were quantified, pooled, and prepared for sequencing.
ATAC-seq  libraries were sequenced paired-end on an Illumina NextSeq500 system (Illumina) at 75 bp read length using standard protocols at the Gene Core facility of the EMBL (Heidelberg, Germany).

treatment_protocol: Peripheral blood samples were obtained from 38 healthy adults enrolled in the VitDPAS trial (ClinicalTrials.gov Identifier: NCT06104111). The study protocol was approved by the Ethics Committee of the Olsztyn Chamber of Doctors (#31/2023/VIII).

tag: tissue

value: peripheral blood

tag: cell line

tag: cell type

tag: treatment

value: 24 h after Vitamin D3 bolus (1.000 IU/kg) (day 1)


title: Cobetia marina sp MM1IDA2H-1 growth at 38°C Replicate 1

city: Valparaíso

first: M.

middle: Alejandro

last: Dinamarca

state: Valparaíso

address: Gran Bretaña 1093

department: Centro de Micro-Bioinnovaci{on

country: Chile

institute: Universidad de Valparaíso

library_source: transcriptomic

data_processing:
Quality control and adapter trimming was performed with bcl-convert (v. 4.2.4; default parameters). Read mapping was performed with HISAT2 (v. 2.2.0; default parameters + ‘--very-sensitive’). Read quantification was performed using Subread`s  featureCounts (v. 2.0.6; default parameters + ‘-Q 20’)  functionality. Read counts were normalized usingedgeR’s (v. 4.0.2) Trimmed Mean of M values (TMM) algorithm, using default parameters. Subsequent values were then converted to counts per million (CPM). Differential expression analysis was performed using edgeR’s (v. 1.14.5) glmQLFTest, with default parameters. The file “All Quantified Genes.tsv” contains the results of the glmQLFTest for all genes in addition to the normalized counts per million. The differentially expressed gene’s normalized counts per million were then used to create a heatmap. The PCA is based on the global expression of all genes. Finally, pathway analysis was performed using limma’s (v. 3.44.3) “kegga” functionality, using default parameters. The genes that were considered Up/Down in this analysis were at Benjamini-Hochberg adjusted p-value < . 05.
Assembly: ASM172048v1r
Supplementary files format and content: The processed file iare in "tsv" format and contain The file “All Quantified Genes.tsv” contains the results of the glmQLFTest for all genes in addition to the normalized counts per million

molecule: total RNA

organism: Cobetia marina

source_name: Bacterial cell

extract_protocol:
For Total RNA extraction, cells were harvested by centrifugation and RNA was extracted using EZNA Total RNA Kit I according to manufacturer´s instructions
Samples were DNAse treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices

value: Bacterial cell

tag: strain


title: PBMCs, Day 1, ATAC individual 45

description: Library name: Ind45d1


title: genomic_DNAmethylation_NP-2_v

type: genomic

city: Boston

first: Maitreyi

last: Mazumdar

state: MA

address: Department of Neurology

country: USA

institute: Boston Children's Hospital & Harvard Medical School

description: Genomic DNA from NP-2_v

hyb_protocol: Bisulfite-converted DNA was processed and hybridized to the bead chips according to the standard Illumina protocol

scan_protocol: HiScan2000 according to the standard Illumina settings

data_processing: minfi preprocessRaw function, betas extracted

label: Cy3 and Cy5

source_name: placenta (chorionic villi)

label_protocol: Standard Illumina protocol

extract_protocol: Qiagen Dneasy blood & tissue kit

value: placenta (chorionic villi)

tag: source

value: Genomic DNA from NP-2_v

tag: status

value: Non-CIUE

tag: Sex

value: Male

value: NO

value: N


title: PBMCs, Day 0, ATAC individual 42

description: Library name: Ind42d0


title: DKAT breast cancer cells, NT, rep2

city: Jerusalem

first: Rami

last: Aqeilan

address: Hadassah medical school

department: Immunology and Cancer Research

country: Israel

institute: Hebrew University

description:
Library name: DKAT_rep2
sBLISS

data_processing:
sBLISS fastq files are initially de-multiplexed using sample barcodes. Quality control is performed with trim galore to eliminate residual adapters, trim reads to a base quality of at least 20, and filter out short reads smaller than 20 bp. Initial and final sample qualities are assessed with fastqc. Quality-processed fastq files are aligned to the GRCh38 assembly with hisat2, then sorted and indexed using samtools. The resulting bam files are de-duplicated with umi-tools, utilizing genomic coordinates and Unique Molecular Identifiers (UMI). Custom Python and R scripts are employed to identify read start positions and convert bam files to bigwig format and BED files for downstream analysis. An additional custom R script is used to discard a blacklist of positions, primarily within centromeres.
BED format Breakome data was associated with genes  using Bedtools V2.26.0. Breaks are counted per gene based on overlapping annotations, GRCh38 gene annotations were downloaded from GENCODE
Assembly: GRCh38
Supplementary files format and content: xlsx file contains raw (non-normalized) break counts per gene per sample

source_name: DKAT

extract_protocol:
sBLISS was conducted as previously described (M Bouwman, B. A. et al. Genome-wide detection of DNA double-strand breaks by in-suspension BLISS. Nat Protoc doi:10.1038/s41596-020-0397-2., Hidmi, O., Oster, S., Shatleh, D., Monin, J. & Aqeilan, R. I. Protocol for mapping physiological DSBs using in-suspension break labeling in situ and sequencing. STAR Protoc 5, (2024).). In summary, 106 cells were fixed in 2% paraformaldehyde in 10% FCS/PBS for 10 minutes at room temperature. The fixation was quenched with 125 mM glycine for 5 minutes at room temperature, followed by another 5 minutes on ice and two washes in ice-cold PBS. Cells were lysed for 60 minutes on ice, and their nuclei were permeabilized for 60 minutes at 37°C. Next, nuclei were rinsed twice with CutSmart Buffer containing 0.1% Triton X-100 (CS/TX100), and double-strand break (DSB) ends were blunted in situ using NEB’s Quick Blunting Kit for 60 minutes at room temperature. The blunted nuclei were then washed twice with 1x CS/TX100 before in situ ligation of the sBLISS adapters to the DSB ends. Adaptor ligation was carried out with T4 DNA Ligase for 20-24 hours at 16°C, with BSA and ATP added. Following ligation, the nuclei underwent two washes with 1x CS/TX100, and genomic DNA was extracted using Proteinase K at 55°C for 14-18 hours. Proteinase K was then heat-inactivated for 10 minutes at 95°C, followed by extraction using Phenol:Chloroform:Isoamyl Alcohol, Chloroform, and ethanol precipitation.
Preparation of sBLISS libraries: The purified DNA was sonicated in 100 μL of ultra-pure water using Covaris M220 for 60 seconds. Sonicated samples were concentrated with AMPure XP beads (Beckman Coulter), and fragment sizes were evaluated using a BioAnalyzer 2100 (Agilent Technologies), targeting a range of 300 bp to 800 bp with a peak around 400-600 bp. The sonicated DNA was then in vitro transcribed using the MEGAscript T7 Kit for 14 hours at 37°C. After RNA purification and ligation of the 3’-Illumina adaptors, the RNA underwent reverse transcription. The final library indexing and amplification step was performed with NEBNext® Ultra™ II Q5® Master Mix.

value: DKAT


title: Cobetia marina sp MM1IDA2H-1 growth at 35°C Replicate 3


title: genomic_DNAmethylation_CHG-1_v

description: Genomic DNA from CHG-1_v

value: Genomic DNA from CHG-1_v

value: CIUE high grade

value: Female

value: YES


title: Cobetia marina sp MM1IDA2H-1 growth at 35°C Replicate 2


title: PBMCs, Day 0, ATAC individual 41

description: Library name: Ind41d0

value: PBMC


title: DKAT breast cancer cells, NT, rep1

description:
Library name: DKAT_rep1
sBLISS


title: genomic_DNAmethylation_CHG-9_v

description: Genomic DNA from CHG-9_v

value: Genomic DNA from CHG-9_v

value: Y


title: PBMCs, Day 1, ATAC individual 41

description: Library name: Ind41d1

value: peripheral blood

value: monocytes, T and B cells


title: Cobetia marina sp MM1IDA2H-1 growth at 35°C Replicate 1

value: Bacterial cell


title: MDAMB231 breast cancer cells, NT, rep3

description:
Library name: MDAMB231_rep3
sBLISS


title: MDAMB231 breast cancer cells, NT, rep2

description:
Library name: MDAMB231_rep2
sBLISS


title: Cobetia marina sp MM1IDA2H-1 growth at 16°C Replicate 3


title: genomic_DNAmethylation_SPLN-7_v

description: Genomic DNA from SPLN-7_v

value: placenta (chorionic villi)

value: Genomic DNA from SPLN-7_v


title: PBMCs, Day 0, ATAC individual 40

description: Library name: Ind40d0

value: directly before vitamin D3 bolus (1.000 IU/kg) (day 0)


title: MDAMB231 breast cancer cells, NT, rep1

description:
Library name: MDAMB231_rep1
sBLISS


title: genomic_DNAmethylation_CHG-10_v

description: Genomic DNA from CHG-10_v

value: Genomic DNA from CHG-10_v

value: Male


title: Cobetia marina sp MM1IDA2H-1 growth at 16°C Replicate 2


title: genomic_DNAmethylation_CLG-8_v

description: Genomic DNA from CLG-8_v

value: Genomic DNA from CLG-8_v

value: CIUE low grade

value: NO


title: non-malignant primary breast cells, BRCA wt7, rep2

description:
Library name: BRCAwt7_rep2
sBLISS

source_name: human mammary epithelial cells (HMECs)

value: human mammary epithelial cells (HMECs)

tag: genotype

value: BRCA WT


title: genomic_DNAmethylation_CHG-19_v

description: Genomic DNA from CHG-19_v

value: Genomic DNA from CHG-19_v

value: CIUE high grade

value: Female

value: N


title: non-malignant primary breast cells, BRCA wt7, rep1

description:
Library name: BRCAwt7_rep1
sBLISS


title: PBMCs, Day 1, ATAC individual 39

description: Library name: Ind39d1

value: peripheral blood

value: PBMC

value: 24 h after Vitamin D3 bolus (1.000 IU/kg) (day 1)


title: Cobetia marina sp MM1IDA2H-1 growth at 16°C Replicate 1

value: Bacterial cell


title: PBMCs, Day 0, ATAC individual 39

description: Library name: Ind39d0

value: monocytes, T and B cells


title: non-malignant primary breast cells, BRCA wt6, rep2

description:
Library name: BRCAwt6_rep2
sBLISS


title: genomic_DNAmethylation_SPLN-12_v

description: Genomic DNA from SPLN-12_v

value: placenta (chorionic villi)

value: Genomic DNA from SPLN-12_v

value: Non-CIUE

value: Y


title: M2 CT

city: Hong Kong

first: Tom

last: Cheung

state: Please Select...

address: Clear Water Bay

country: Hong Kong

institute: HKUST

description:
Library name: Ctrl3
Ctrl3

data_processing:
HISAT2 v2.1.0 was used to map the reads to the reference genome GRCm38, with parameter "--dta" to enable longer anchor length.
The alignment was then assembled by StringTie v1.3.6 with paramter "-e -B" to measure the gene abundance against the gene annotation of GENCODE vM22 .
Assembly: GRCm38
Supplementary files format and content: comma-delimited text file includes raw counts for each Sample
Supplementary files format and content: comma-delimited text file includes TPM values for each Sample

organism: Mus musculus

source_name: skeletal muscle

extract_protocol:
RNA was extracted using NucleoSpin RNA XS kit (Macherey-Nagel). 5ng RNA of each sample was used for library construction
cDNA library was generated according the the SMART-Seq2 protocol. cDNA tagmentation was performed using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501). Circular ssDNA library was generated using MGIEasy Universal Library Coversion Kit (App-A) (MGI, 1000004155)

value: skeletal muscle

value: muscle stem cell

value: Mouse 2 Control morpholino


title: PBMCs, Day 1, ATAC individual 38

description: Library name: Ind38d1


title: genomic_DNAmethylation_SPLN-14_v

description: Genomic DNA from SPLN-14_v

value: Genomic DNA from SPLN-14_v

value: NO


title: PBMCs, Day 0, ATAC individual 38

description: Library name: Ind38d0

value: directly before vitamin D3 bolus (1.000 IU/kg) (day 0)


title: genomic_DNAmethylation_SPLN-11_v

description: Genomic DNA from SPLN-11_v

value: Genomic DNA from SPLN-11_v

value: Male


title: genomic_DNAmethylation_SPLA-10_v

description: Genomic DNA from SPLA-10_v

value: Genomic DNA from SPLA-10_v


title: PBMCs, Day 1, ATAC individual 40

description: Library name: Ind40d1

value: peripheral blood

value: PBMC


title: M1 Numb

description:
Library name: Numb2
Numb2

value: Mouse 1 Numb exon 6 morpholino


title: non-malignant primary breast cells, BRCA wt6, rep1

description:
Library name: BRCAwt6_rep1
sBLISS

value: human mammary epithelial cells (HMECs)

value: BRCA WT


title: non-malignant primary breast cells, BRCA wt5, rep2

description:
Library name: BRCAwt5_rep2
sBLISS


title: PBMCs, Day 0, ATAC individual 37

description: Library name: Ind37d0

value: monocytes, T and B cells


title: non-malignant primary breast cells, BRCA wt5, rep1

description:
Library name: BRCAwt5_rep1
sBLISS


title: Liver from Triple-Knock out pig RBC transfused NHP 4

city: Jeongeup-Si

first: Ju Young

last: Lee

address: 30 Baekhak 1 Gil,

country: South Korea

institute: Korea institute of toxicology

description: Library name: X_3F2

data_processing:
Illumina bcl2fastq (v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adapter sequences and low-quality filtered using bbduk 39.01.
the clean reads were mapped to the reference genome using STAR 2.7.10b.
The quantification of reads was processed using HTSeq-count 2.0.2.
Assembly: T2T-MFA8v1.0
Supplementary files format and content: tab-delimited text files include read count values for each Sample

organism: Macaca fascicularis

source_name: Liver

extract_protocol:
Total RNA was isolated using Maxwell® RSC miRNA from Kits (Promega™ Corporation).
RNA libraries were prepared for sequencing using QuantSeq 3' mRNA-Seq Library Prep Kit FWD (Lexogen) according to the manufacturer’ instructions.

value: Liver

value: Triple-Knock out pig RBC transfused


title: genomic_DNAmethylation_SPLN-15_v

description: Genomic DNA from SPLN-15_v

value: placenta (chorionic villi)

value: Genomic DNA from SPLN-15_v

value: Non-CIUE

value: Y


title: PBMCs, Day 1, ATAC individual 36

description: Library name: Ind36d1

value: 24 h after Vitamin D3 bolus (1.000 IU/kg) (day 1)


title: genomic_DNAmethylation_CHG-6_v

description: Genomic DNA from CHG-6_v

value: Genomic DNA from CHG-6_v

value: CIUE high grade

value: YES

value: N


title: Liver from Triple-Knock out pig RBC transfused NHP 3

description: Library name: X_3F1


title: M2 Numb

description:
Library name: Numb3
Numb3

value: skeletal muscle

value: muscle stem cell

value: Mouse 2 Numb exon 6 morpholino


title: genomic_DNAmethylation_NP-12_v

description: Genomic DNA from NP-12_v

value: Genomic DNA from NP-12_v

value: Female

value: NO


title: non-malignant primary breast cells, BRCA wt4, rep1

description:
Library name: BRCAwt4_rep1
sBLISS

value: human mammary epithelial cells (HMECs)

value: BRCA WT


title: PBMCs, Day 0, ATAC individual 36

description: Library name: Ind36d0

value: peripheral blood

value: PBMC

value: monocytes, T and B cells

value: directly before vitamin D3 bolus (1.000 IU/kg) (day 0)


title: Liver from Triple-Knock out pig RBC transfused NHP 2

description: Library name: X_3M2

value: Liver

value: Triple-Knock out pig RBC transfused


title: Liver from Triple-Knock out pig RBC transfused NHP 1

description: Library name: X_3M1


title: non-malignant primary breast cells, BRCA wt4, rep2

description:
Library name: BRCAwt4_rep2
sBLISS


title: non-malignant primary breast cells, BRCA wt3, rep2

description:
Library name: BRCAwt3_rep2
sBLISS


title: PBMCs, Day 0, ATAC individual 35

description: Library name: Ind35d0


title: genomic_DNAmethylation_CLG-3_v

description: Genomic DNA from CLG-3_v

value: placenta (chorionic villi)

value: Genomic DNA from CLG-3_v

value: CIUE low grade


title: genomic_DNAmethylation_CLG-4_v

description: Genomic DNA from CLG-4_v

value: Genomic DNA from CLG-4_v

value: Male

value: YES

value: N


title: Liver from Non-transfused NHP 3

description: Library name: WT_CON3

value: Non-transfused


title: non-malignant primary breast cells, BRCA wt3, rep1

description:
Library name: BRCAwt3_rep1
sBLISS


title: PBMCs, Day 1, ATAC individual 37

description: Library name: Ind37d1

value: 24 h after Vitamin D3 bolus (1.000 IU/kg) (day 1)


title: M1 CT

description:
Library name: Ctrl2
Ctrl2

value: skeletal muscle

value: muscle stem cell

value: Mouse 1 Control morpholino


title: PBMCs, Day 1, ATAC individual 34

description: Library name: Ind34d1

value: peripheral blood

value: PBMC


title: genomic_DNAmethylation_NP-4_v

description: Genomic DNA from NP-4_v

value: Genomic DNA from NP-4_v

value: Non-CIUE

value: Female

value: NO


title: non-malignant primary breast cells, BRCA wt2, rep2

description:
Library name: BRCAwt2_rep2
sBLISS

value: human mammary epithelial cells (HMECs)

value: BRCA WT


title: Liver from Non-transfused NHP 2

description: Library name: WT_CON2

value: Liver


title: genomic_DNAmethylation_SPLN-10_v

description: Genomic DNA from SPLN-10_v

value: placenta (chorionic villi)

value: Genomic DNA from SPLN-10_v

value: Male


title: non-malignant primary breast cells, BRCA wt2, rep1

description:
Library name: BRCAwt2_rep1
sBLISS


title: PBMCs, Day 0, ATAC individual 34

description: Library name: Ind34d0

value: monocytes, T and B cells

value: directly before vitamin D3 bolus (1.000 IU/kg) (day 0)


title: Liver from Non-transfused NHP 1

description: Library name: WT_CON1

value: Non-transfused


title: genomic_DNAmethylation_SPLN-4_v

description: Genomic DNA from SPLN-4_v

value: Genomic DNA from SPLN-4_v

value: N


title: non-malignant primary breast cells, BRCA wt1, rep3

description:
Library name: BRCAwt1_rep3
sBLISS


title: PBMCs, Day 0, ATAC individual 33

description: Library name: Ind33d0

value: peripheral blood


title: non-malignant primary breast cells, BRCA wt1, rep2

description:
Library name: BRCAwt1_rep2
sBLISS


title: PBMCs, Day 1, ATAC individual 33

description: Library name: Ind33d1

value: PBMC

value: 24 h after Vitamin D3 bolus (1.000 IU/kg) (day 1)


title: genomic_DNAmethylation_SPLA-2_v

description: Genomic DNA from SPLA-2_v

value: Genomic DNA from SPLA-2_v

value: Non-CIUE

value: Y


title: non-malignant primary breast cells, BRCA wt1, rep1

description:
Library name: BRCAwt1_rep1
sBLISS

value: human mammary epithelial cells (HMECs)


title: M_KO_Vh_R3

first: Jennifer

middle: J

last: Schlezinger

address: 715 Albany St

department: Environmental Health

institute: Boston University

description:
Library name: IV5_Liver_32
count_expression_matrix_KO_analytical.txt

data_processing:
Adapter sequences were trimmed from sequencing reads using Cutadapt (v1.15) and sequencing read quality was determined using FastQC (v0.11.5).
Gene expression counts were quantified using featureCounts (v1.6.1).
Gene expression analyses were performed in R (v4.1.0). The following filtering criteria were applied to raw gene expression counts: 1) At least 10 counts per sample, 2) At least 15 counts across all samples 3) At least 1 count in 70% of samples for each genotype/sex group. Log2 counts-per-million reads normalized gene expression were calculated for each sample using the edgeR R package (v3.36.0).
Analyses were run on original, non-batch corrected data following an assessment of batch effects.
Assembly: Reads were mapped to the GRCm39 mouse genome assembly using STAR (v2.5.3)
Supplementary files format and content: count_expression_matrix_hPPARa_analytical.txt is a text file containing count data for each vehicle or PFOA treated mouse expressing human PPARa.
Supplementary files format and content: count_expression_matrix_KO_analytical.txt is a text file containing count data for each vehicle or PFOA treated PPARa knockout (KO) mouse.

source_name: bulk liver tissue

growth_protocol: Male and female PPARa knockout and human PPARa expressing mice were exposed to vehicle or PFOA containing drinking water for 6-7 weeks in conjunction with an American diet.

extract_protocol:
Total RNA was extracted from bulk liver tissue and genomic DNA was removed using the Direct-zol RNA Miniprep Kit. RNA concentration was measured and only samples with RIN>7 were sequenced.
Library construction and RNA sequencing was conducted by BGI Americas on the BGI proprietary platform.

value: bulk liver tissue

value: PPARa knockout

value: Vh

value: M


title: genomic_DNAmethylation_CHG-8_v

description: Genomic DNA from CHG-8_v

value: placenta (chorionic villi)

value: Genomic DNA from CHG-8_v

value: CIUE high grade

value: Female

value: NO


title: PBMCs, Day 1, ATAC individual 31

description: Library name: Ind31d1

value: monocytes, T and B cells


title: PBMCs, Day 1, ATAC individual 35

description: Library name: Ind35d1

value: peripheral blood


title: PBMCs, Day 0, ATAC individual 31

description: Library name: Ind31d0

value: PBMC

value: directly before vitamin D3 bolus (1.000 IU/kg) (day 0)


title: genomic_DNAmethylation_CLG-10_v

description: Genomic DNA from CLG-10_v

value: Genomic DNA from CLG-10_v

value: CIUE low grade

value: Male


title: M_KO_PFOA_R2

description:
Library name: IV5_Liver_27
count_expression_matrix_KO_analytical.txt

value: PFOA


title: non-malignant primary breast cells, BRCA2 mut4, rep2

description:
Library name: BRCA2mut4_rep2
sBLISS

value: human mammary epithelial cells (HMECs)

value: BRCA2 mutant


title: genomic_DNAmethylation_CHG-15_v

description: Genomic DNA from CHG-15_v

value: Genomic DNA from CHG-15_v

value: YES

value: N


title: PBMCs, Day 1, ATAC individual 29

description: Library name: Ind29d1

value: 24 h after Vitamin D3 bolus (1.000 IU/kg) (day 1)


title: non-malignant primary breast cells, BRCA2 mut4, rep1

description:
Library name: BRCA2mut4_rep1
sBLISS


title: F_KO_PFOA_R3

description:
Library name: IV5_Liver_23
count_expression_matrix_KO_analytical.txt

value: bulk liver tissue

value: PPARa knockout

value: F


title: PBMCs, Day 0, ATAC individual 29

description: Library name: Ind29d0

value: monocytes, T and B cells


title: genomic_DNAmethylation_NP-7_v

description: Genomic DNA from NP-7_v

value: placenta (chorionic villi)

value: Genomic DNA from NP-7_v

value: Non-CIUE

value: Female

value: NO


title: PBMCs, Day 1, ATAC individual 28

description: Library name: Ind28d1

value: peripheral blood

value: PBMC


title: genomic_DNAmethylation_SPLN-2_v

description: Genomic DNA from SPLN-2_v

value: Genomic DNA from SPLN-2_v

value: Male


title: F_KO_Vh_R1

description:
Library name: IV5_Liver_33
count_expression_matrix_KO_analytical.txt

value: Vh


title: M_KO_PFOA_R1

description:
Library name: IV5_Liver_21
count_expression_matrix_KO_analytical.txt

value: PFOA

value: M


title: non-malignant primary breast cells, BRCA2 mut3, rep1

description:
Library name: BRCA2mut3_rep1
sBLISS

value: human mammary epithelial cells (HMECs)

value: BRCA2 mutant


title: non-malignant primary breast cells, BRCA2 mut2, rep2

description:
Library name: BRCA2mut2_rep2
sBLISS


title: M_KO_Vh_R2

description:
Library name: IV5_Liver_14
count_expression_matrix_KO_analytical.txt

value: bulk liver tissue

value: PPARa knockout


title: genomic_DNAmethylation_CHG-3_v

description: Genomic DNA from CHG-3_v

value: Genomic DNA from CHG-3_v

value: CIUE high grade

value: N


title: M_KO_PFOA_R3

description:
Library name: IV5_Liver_29
count_expression_matrix_KO_analytical.txt


title: PBMCs, Day 1, ATAC individual 27

description: Library name: Ind27d1

value: monocytes, T and B cells

value: 24 h after Vitamin D3 bolus (1.000 IU/kg) (day 1)


title: non-malignant primary breast cells, BRCA2 mut2, rep1

description:
Library name: BRCA2mut2_rep1
sBLISS


title: genomic_DNAmethylation_SPLA-14_v

description: Genomic DNA from SPLA-14_v

value: placenta (chorionic villi)

value: Genomic DNA from SPLA-14_v

value: Non-CIUE

value: Female

value: NO

value: Y


title: non-malignant primary breast cells, BRCA2 mut1, rep2

description:
Library name: BRCA2mut1_rep2
sBLISS


title: PBMCs, Day 0, ATAC individual 27

description: Library name: Ind27d0

value: peripheral blood

value: PBMC

value: directly before vitamin D3 bolus (1.000 IU/kg) (day 0)


title: genomic_DNAmethylation_CLG-2_v

description: Genomic DNA from CLG-2_v

value: Genomic DNA from CLG-2_v

value: CIUE low grade

value: Male


title: F_KO_PFOA_R1

description:
Library name: IV5_Liver_10
count_expression_matrix_KO_analytical.txt

value: bulk liver tissue

value: PPARa knockout

value: PFOA

value: F


title: M_KO_Vh_R1

description:
Library name: IV5_Liver_11
count_expression_matrix_KO_analytical.txt

value: Vh

value: M


title: genomic_DNAmethylation_CHG-2_v

description: Genomic DNA from CHG-2_v

value: placenta (chorionic villi)

value: Genomic DNA from CHG-2_v

value: CIUE high grade

value: YES


title: non-malignant primary breast cells, BRCA2 mut1, rep1

description:
Library name: BRCA2mut1_rep1
sBLISS

value: human mammary epithelial cells (HMECs)

value: BRCA2 mutant


title: genomic_DNAmethylation_CLG-12_v

description: Genomic DNA from CLG-12_v

value: Genomic DNA from CLG-12_v

value: NO

value: N


title: M_hPPARa_PFOA_R3

description:
Library name: IV5_Liver_28
count_expression_matrix_hPPARa_analytical.txt

value: human PPARa


title: PBMCs, Day 0, ATAC individual 26

description: Library name: Ind26d0

value: peripheral blood

value: PBMC

value: monocytes, T and B cells

value: directly before vitamin D3 bolus (1.000 IU/kg) (day 0)


title: PBMCs, Day 1, ATAC individual 26

description: Library name: Ind26d1

value: 24 h after Vitamin D3 bolus (1.000 IU/kg) (day 1)


title: F_hPPARa_PFOA_R2

description:
Library name: IV5_Liver_26
count_expression_matrix_hPPARa_analytical.txt

value: bulk liver tissue

value: PFOA

value: F


title: PBMCs, Day 1, ATAC individual 25

description: Library name: Ind25d1


title: non-malignant primary breast cells, BRCA2 mut3, rep2

description:
Library name: BRCA2mut3_rep2
sBLISS


title: PBMCs, Day 0, ATAC individual 28

description: Library name: Ind28d0


title: non-malignant primary breast cells, BRCA1 mut8, rep1

description:
Library name: BRCA1mut8_rep1
sBLISS

value: BRCA1 mutant


title: F_KO_PFOA_R2

description:
Library name: IV5_Liver_22
count_expression_matrix_KO_analytical.txt

value: PPARa knockout


title: F_hPPARa_PFOA_R1

description:
Library name: IV5_Liver_25
count_expression_matrix_hPPARa_analytical.txt


title: PBMCs, Day 0, ATAC individual 25

description: Library name: Ind25d0


title: M_hPPARa_PFOA_R2

description:
Library name: IV5_Liver_20
count_expression_matrix_hPPARa_analytical.txt

value: M


title: non-malignant primary breast cells,BRCA1 mut7, rep2

description:
Library name: BRCA1mut7_rep2
sBLISS

value: human mammary epithelial cells (HMECs)


title: genomic_DNAmethylation_SPLA-7_v

description: Genomic DNA from SPLA-7_v

value: placenta (chorionic villi)

value: Genomic DNA from SPLA-7_v

value: Non-CIUE

value: Male

value: Y


title: PBMCs, Day 1, ATAC individual 24

description: Library name: Ind24d1

value: peripheral blood


title: F_hPPARa_Vh_R3

description:
Library name: IV5_Liver_19
count_expression_matrix_hPPARa_analytical.txt

value: human PPARa

value: Vh


title: genomic_DNAmethylation_SPLA-5_v

description: Genomic DNA from SPLA-5_v

value: Genomic DNA from SPLA-5_v

value: Female

value: NO


title: PBMCs, Day 0, ATAC individual 24

description: Library name: Ind24d0

value: PBMC

value: monocytes, T and B cells

value: directly before vitamin D3 bolus (1.000 IU/kg) (day 0)


title: non-malignant primary breast cells, BRCA1 mut6, rep2

description:
Library name: BRCA1mut6_rep2
sBLISS

value: BRCA1 mutant


title: non-malignant primary breast cells, BRCA1 mut6, rep1

description:
Library name: BRCA1mut6_rep1
sBLISS


title: PBMCs, Day 1, ATAC individual 23

description: Library name: Ind23d1

value: 24 h after Vitamin D3 bolus (1.000 IU/kg) (day 1)


title: M_hPPARa_Vh_R2

description:
Library name: IV5_Liver_15
count_expression_matrix_hPPARa_analytical.txt

value: bulk liver tissue

value: M


title: genomic_DNAmethylation_CLG-1_v

description: Genomic DNA from CLG-1_v

value: placenta (chorionic villi)

value: Genomic DNA from CLG-1_v

value: CIUE low grade


title: non-malignant primary breast cells, BRCA1 mut8, rep2

description:
Library name: BRCA1mut8_rep2
sBLISS

value: human mammary epithelial cells (HMECs)


title: non-malignant primary breast cells, BRCA1 mut5, rep2

description:
Library name: BRCA1mut5_rep2
sBLISS


title: genomic_DNAmethylation_SPLA-6_v

description: Genomic DNA from SPLA-6_v

value: Genomic DNA from SPLA-6_v

value: Non-CIUE

value: Male

value: Y


title: M_hPPARa_PFOA_R1

description:
Library name: IV5_Liver_13
count_expression_matrix_hPPARa_analytical.txt

value: human PPARa

value: PFOA


title: M_hPPARa_Vh_R1

description:
Library name: IV5_Liver_12
count_expression_matrix_hPPARa_analytical.txt

value: Vh


title: PBMCs, Day 1, ATAC individual 22

description: Library name: Ind22d1

value: peripheral blood

value: PBMC

value: monocytes, T and B cells


title: non-malignant primary breast cells, BRCA1 mut5, rep1

description:
Library name: BRCA1mut5_rep1
sBLISS

value: BRCA1 mutant


title: genomic_DNAmethylation_SPLN-8_v

description: Genomic DNA from SPLN-8_v

value: Genomic DNA from SPLN-8_v

value: NO


title: genomic_DNAmethylation_SPLN-6_v

description: Genomic DNA from SPLN-6_v

value: placenta (chorionic villi)

value: Genomic DNA from SPLN-6_v

value: Female

value: N


title: PBMCs, Day 0, ATAC individual 22

description: Library name: Ind22d0

value: directly before vitamin D3 bolus (1.000 IU/kg) (day 0)


title: non-malignant primary breast cells, BRCA1 mut3, rep2

description:
Library name: BRCA1mut3_rep2
sBLISS

value: human mammary epithelial cells (HMECs)


title: 32

city: Jejusi

first: Hyesung

last: Kim

address: Aran 13 gil, 15

department: Convergence Biomedical Science

institute: Jeju National University College of medicine

hyb_protocol: Samples were hybridized to the Infinium MethylationEPIC BeadChip (Illumina) following the manufacturer's protocol. DNA was denatured, amplified, and fragmented before hybridization to the array.

scan_protocol: Arrays were scanned using the Illumina iScan System according to the standard Illumina scanning protocol.

data_processing:
Python package
Avarage value

source_name: Stomach

extract_protocol: Genomic DNA isolation using Purelink Genomic DNA Mini kit (Invitrogen)

value: Stomach

value: Organoid


title: PBMCs, Day 1, ATAC individual 18

description: Library name: Ind18d1

value: 24 h after Vitamin D3 bolus (1.000 IU/kg) (day 1)


title: F_hPPARa_Vh_R1

description:
Library name: IV5_Liver_2
count_expression_matrix_hPPARa_analytical.txt

value: bulk liver tissue

value: human PPARa

value: F


title: OLIG KO 3N_TF day7 (MGI)

city: Hefei

first: lingling

last: zhu

address: JinZhai Road

country: China

institute: University of Science and Technology of China

description:
Library name: olig1/2/3 ko day7
MGISEQ-2000 sequencer
TF_DS_DX_OL_samples.rds

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using DNBelab C Series analysis software (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software) and Cell Ranger software v8.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/8.0) separately for scRNA-data sequenced by MGI process and 10X process.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: hPSCs

growth_protocol: The human hPSCs lines were maintained on feeder-free Matrigel-coated plates. All cultures were grown at 37 °C with 5% CO2 in mTeSR1 medium.

extract_protocol:
Cells were disassociated with Accutase to single cell.
scRNA-seq libraries were prepared using DNBelab C Series Sinlge-Cell Library Prep set (MGI, 1000021082) or 10X Genomic Chromium Single Cell library kit. CUT-TAG (cleavage under targets & release using nuclease) chromatin profiling were performed using Hyperactive® Universal CUT&Tag Assay Kit (vazyme, TD903). ATAC seq were performed using Hyperactive ATAC-Seq Library Prep Kit (vazyme, TD711).

treatment_protocol: Neurogenesis from hPSCs with 3N_TF (NEUROG1, NEUROG2, NEUROD1) overexpression or dual SMAD inhibition

value: hPSCs

value: neurogenesis from hPSCs

value: dox inducible NEUROG1, NEUROG2, NEUROD1 overexpression in OLIG1/OLIG2/OLIG3 knock out hPSCs


title: 31


title: non-malignant primary breast cells, BRCA1 mut7, rep1

description:
Library name: BRCA1mut7_rep1
sBLISS

value: BRCA1 mutant


title: genomic_DNAmethylation_CHG-7_v

description: Genomic DNA from CHG-7_v

value: Genomic DNA from CHG-7_v

value: CIUE high grade

value: Male

value: YES


title: PBMCs, Day 0, ATAC individual 18

description: Library name: Ind18d0

value: peripheral blood

value: PBMC

value: monocytes, T and B cells


title: F_hPPARa_Vh_R2

description:
Library name: IV5_Liver_18
count_expression_matrix_hPPARa_analytical.txt

value: Vh


title: non-malignant primary breast cells, BRCA1 mut2, rep2

description:
Library name: BRCA1mut2_rep2
sBLISS

value: human mammary epithelial cells (HMECs)


title: 30

value: Stomach

value: Organoid


title: non-malignant primary breast cells, BRCA1 mut2, rep1

description:
Library name: BRCA1mut2_rep1
sBLISS


title: PBMCs, Day 1, ATAC individual 17

description: Library name: Ind17d1

value: 24 h after Vitamin D3 bolus (1.000 IU/kg) (day 1)


title: 29


title: OLIG KO 3N_TF day1 (MGI)

description:
Library name: olig1/2/3 ko day1
MGISEQ-2000 sequencer
TF_DS_DX_OL_samples.rds


title: OLIG KO 3N_TF day4 (MGI)

description:
Library name: olig1/2/3 ko day4
MGISEQ-2000 sequencer
TF_DS_DX_OL_samples.rds


title: PBMCs, Day 0, ATAC individual 23

description: Library name: Ind23d0

value: directly before vitamin D3 bolus (1.000 IU/kg) (day 0)


title: PBMCs, Day 0, ATAC individual 17

description: Library name: Ind17d0


title: 28


title: non-malignant primary breast cells, BRCA1 mut1, rep1

description:
Library name: BRCA1mut1_rep1
sBLISS


title: non-malignant primary breast cells, BRCA1 mut1, rep2

description:
Library name: BRCA1mut1_rep2
sBLISS


title: 27


title: PBMCs, Day 1, ATAC individual 16

description: Library name: Ind16d1


title: PBMCs, Day 0, ATAC individual 16

description: Library name: Ind16d0


title: 26


title: 3N_TF dox-day 15 (10X) (male)

description:
Library name: 3N_TF dox-day 15 (10X) (male)
10x Genomics
Neuron_male.rds

value: hPSCs


title: dox 3N_TF day6 (MGI)

description:
Library name: 3N_TF dox-day6
MGISEQ-2000 sequencer
TF_DS_DX_OL_samples.rds

value: neurogenesis from hPSCs

value: dox inducible NEUROG1, NEUROG2, NEUROD1 overexpression in hPSCs


title: non-malignant primary breast cells, BRCA1 mut3, rep1

description:
Library name: BRCA1mut3_rep1
sBLISS

value: BRCA1 mutant


title: PBMCs, Day 1, ATAC individual 15

description: Library name: Ind15d1


title: PBMCs, Day 0, ATAC individual 15

description: Library name: Ind15d0


title: dox 3N_TF day5 (MGI)

description:
Library name: 3N_TF dox-day5
MGISEQ-2000 sequencer
TF_DS_DX_OL_samples.rds


title: dox 3N_TF day4 (MGI)

description:
Library name: 3N_TF dox-day4
MGISEQ-2000 sequencer
TF_DS_DX_OL_samples.rds


title: 25


title: 3N_TF dox-day 2 (10X) (male)

description:
Library name: 3N_TF dox-day 2 (10X) (male)
10x Genomics
Neuron_male.rds

value: dox inducible NEUROG1, NEUROG2, NEUROD1 overexpression in OLIG1/OLIG2/OLIG3 knock out hPSCs


title: 3N_TF dox-day 7 (10X) (male)

description:
Library name: 3N_TF dox-day 7 (10X) (male)
10x Genomics
Neuron_male.rds


title: 24


title: Dual smad day8 (10X) (male)

description:
Library name: Dual smad day8 (10X) (male)
10x Genomics
Neuron_male.rds


title: PBMCs, Day 1, ATAC individual 13

description: Library name: Ind13d1


title: PBMCs, Day 0, ATAC individual 13

description: Library name: Ind13d0


title: 23


title: 22


title: dox 3N_TF day2 (MGI)

description:
Library name: 3N_TF dox-day2
MGISEQ-2000 sequencer
TF_DS_DX_OL_samples.rds


title: dox 3N_TF day15 (MGI)

description:
Library name: 3N_TF dox-day15
MGISEQ-2000 sequencer
TF_DS_DX_OL_samples.rds


title: dox 3N_TF day3 (MGI)

description:
Library name: 3N_TF dox-day3
MGISEQ-2000 sequencer
TF_DS_DX_OL_samples.rds


title: dox 3N_TF day7 (MGI)

description:
Library name: 3N_TF dox-day7
MGISEQ-2000 sequencer
TF_DS_DX_OL_samples.rds


title: 3N_TF 48h rep2

data_processing:
the raw reads were trimmed with cutadapt and mapped to human genome GRCh38 using hisat2.
the read counts were computed using RSEM.
Counts were further normalized and differentially expressed genes were calculated using DESeq2
Assembly: GRCh38
Supplementary files format and content: file includes raw counts for each Sample


title: PBMCs, Day 1, ATAC individual 12

description: Library name: Ind12d1


title: dox 3N_TF day1 (MGI)

description:
Library name: 3N_TF dox-day1
MGISEQ-2000 sequencer
TF_DS_DX_OL_samples.rds


title: 3N_TF 48h rep1


title: PBMCs, Day 0, ATAC individual 12

description: Library name: Ind12d0


title: 3N_TF 46h rep2


title: 20


title: hPSCs (MGI)

description:
Library name: hPSCs
MGISEQ-2000 sequencer
TF_DS_DX_OL_samples.rds


title: 19


title: 21


title: 3N_TF 46h rep1


title: 3N_TF day25-2 (MGI)

description:
Library name: 3N_TF -neurons day25
MGISEQ-2000 sequencer
TF_and_DS_samples.rds

value: NEUROG1, NEUROG2, NEUROD1 mRNA overexpression in hPSCs


title: PBMCs, Day 1, ATAC individual 11

description: Library name: Ind11d1


title: 18


title: DS day6 (MGI)

description:
Library name: DS day6-7 MIX
MGISEQ-2000 sequencer
TF_and_DS_samples.rds

value: Neurogenesis from hPSCs by dual smad inhibition


title: 3N_TF day4-3 (MGI)

description:
Library name: 3N_TF-neurons day4.5
MGISEQ-2000 sequencer
TF_and_DS_samples.rds


title: 3N_TF 44h rep1


title: PBMCs, Day 1, ATAC individual 10

description: Library name: Ind10d1


title: 17


title: PBMCs, Day 0, ATAC individual 10

description: Library name: Ind10d0


title: 3N_TF 42h rep2


title: 16


title: 3N_TF day4-2 (MGI)

description:
Library name: 3N_TF-neurons day4
MGISEQ-2000 sequencer
TF_and_DS_samples.rds


title: DS day45 (MGI)

description:
Library name: Dual smad day45
MGISEQ-2000 sequencer
TF_and_DS_samples.rds


title: 3N_TF 42h rep1


title: PBMCs, Day 1, ATAC individual 09

description: Library name: Ind09d1


title: 15


title: PBMCs, Day 0, ATAC individual 09

description: Library name: Ind09d0


title: DS day8 (MGI)

description:
Library name: Dual smad day8
MGISEQ-2000 sequencer
TF_and_DS_samples.rds


title: 3N_TF 40h rep2


title: 14


title: PBMCs, Day 1, ATAC individual 08

description: Library name: Ind08d1


title: 13


title: 3N_TF 40h rep1


title: DS day13-2 (MGI)

description:
Library name: Dual smad day13-2
MGISEQ-2000 sequencer
TF_and_DS_samples.rds


title: 3N_TF 44h rep2


title: PBMCs, Day 0, ATAC individual 11

description: Library name: Ind11d0


title: 3N_TF 38h rep1


title: PBMCs, Day 1, ATAC individual 07

description: Library name: Ind07d1


title: 12


title: 11


title: DS day3 (MGI)

description:
Library name: Dual smad day3
MGISEQ-2000 sequencer
TF_and_DS_samples.rds


title: 3N_TF 36h rep2


title: PBMCs, Day 0, ATAC individual 07

description: Library name: Ind07d0


title: DS day13 (MGI)

description:
Library name: Dual smad day13
MGISEQ-2000 sequencer
TF_and_DS_samples.rds


title: 3N_TF 38h rep2


title: DS day30 (MGI)

description:
Library name: Dual smad day30
MGISEQ-2000 sequencer
TF_and_DS_samples.rds


title: PBMCs, Day 0, ATAC individual 08

description: Library name: Ind08d0


title: PBMCs, Day 1, ATAC individual 06

description: Library name: Ind06d1


title: 9


title: 3N_TF 36h rep1


title: 3N_TF day45 (MGI)

description:
Library name: 3N_TF TFs day45
MGISEQ-2000 sequencer
TF_and_DS_samples.rds


title: 3N_TF day38 (MGI)

description:
Library name: 3N_TF TFs day38
MGISEQ-2000 sequencer
TF_and_DS_samples.rds


title: 3N_TF 34h rep2


title: PBMCs, Day 0, ATAC individual 06

description: Library name: Ind06d0


title: PBMCs, Day 1, ATAC individual 05

description: Library name: Ind05d1


title: 7


title: 3N_TF 34h rep1


title: 3N_TF day25-1 (MGI)

description:
Library name: 3N_TF day 25
MGISEQ-2000 sequencer
TF_and_DS_samples.rds


title: 3N_TF 32h rep2


title: 3N_TF day15 (MGI)

description:
Library name: 3N_TF day 15
MGISEQ-2000 sequencer
TF_and_DS_samples.rds


title: PBMCs, Day 1, ATAC individual 04

description: Library name: Ind04d1


title: 6


title: 3N_TF 32h rep1


title: 10


title: 5


title: PBMCs, Day 0, ATAC individual 04

description: Library name: Ind04d0


title: 3N_TF day7  (MGI)

description:
Library name: 3N_TF day  7
MGISEQ-2000 sequencer
TF_and_DS_samples.rds


title: 3N_TF 30h rep2


title: PBMCs, Day 1, ATAC individual 03

description: Library name: Ind03d1


title: 3N_TF day5  (MGI)

description:
Library name: 3N_TF day  5
MGISEQ-2000 sequencer
TF_and_DS_samples.rds


title: 3


title: PBMCs, Day 0, ATAC individual 03

description: Library name: Ind03d0


title: 4


title: 3N_TF day4-1 (MGI)

description:
Library name: 3N_TF day  4
MGISEQ-2000 sequencer
TF_and_DS_samples.rds


title: 3N_TF 28h rep2


title: 8


title: 3N_TF 30h rep1


title: 2


title: 3N_TF day2 (MGI)

description:
Library name: 3N_TF day  2
MGISEQ-2000 sequencer
TF_and_DS_samples.rds


title: PBMCs, Day 0, ATAC individual 05

description: Library name: Ind05d0


title: 3N_TF day0 (MGI)

description:
Library name: 3N_TF day  0
MGISEQ-2000 sequencer
TF_and_DS_samples.rds


title: 3N_TF 28h rep1


title: PBMCs, Day 0, ATAC individual 02

description: Library name: Ind02d0


title: 1


title: BMEL_pIGrhl2_n4

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

country: France

institute: CNRS

data_processing:
RNAseq reads were mapped on mouse genome (mm10) using Hisat2 v.2.2.1
Read counting was performed using the count function of the HTSeq tool (version 0.9.1)using the following parameters: mode = UNION, Stranded = No, Minimum alignment quality = 10, Feature types = Exon, ID attributes = Gene ID (Anders et al. 2015)
Normalization of gene expression data and differential expression analyses were performed in R (R_Core_Team 2023) using the DESeq2 (version 1.40.2) package (Love et al. 2014)
Pre-filtering was applied to remove genes with low counts, i.e. genes with cumulated reads in all samples below 10
Normalized gene expression data were obtained by dividing Rlog normalized gene expression data obtained from DESeq2 by transcript lengths. Transcript lengths had previously been calculated by averaging the lengths of all transcripts associated to a given gene symbol in Ensembl (GRCm39 or GRCh.38.p13) (Cunningham et al. 2022).
Assembly: mm10
Supplementary files format and content: Matrix tab-delimited file includes raw counts for all samples ("FPKM_RNASeq_BMEL_overexpression_Grhl2_MGI_symbol.txt")

source_name: BMEL

growth_protocol: RPMI 1640 Glutamax supplemented with 10% Fetal Bovine Serum, 30 mg/mL IGFII, 50ng/mL mouse EGF, 10 µg/mL bovin insulin and 100 U/mL penicillin-streptomycin. Cells were cultured at 37°C at 5%CO2 on collagen coated dish.

extract_protocol:
RNA were purified using Nucleospin RNA kit from Macherey Nagel according to the manufacturer's instructions and processed for analysis using RNAseq.
RNA seq librairies were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina NR605 following manufacturer's protocols
RNA seq, paired-end, 150bp

treatment_protocol: BMEL cells were transfected with a plasmid coding for GRHL2 fused to a flag tag or a pcDNA vector. RNA were harvested 48h later.

value: BMEL

value: Bipotential mouse embryonic liver cells

tag: plasmid


title: 3N_TF 26h rep2


title: 275, scRNAseq

city: New Haven

first: Ruben

last: De Man

state: CT

address: 333 Cedar St

institute: Yale School of Medicine

description: 10x Genomics

data_processing:
Reads were demultiplexed, aligned, and counted using Cell Ranger (10X Genomics).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
Samples were collected from cryopreserved human lung samples in 10%DMSO. After thawing at 37*C, the tissue was minced into small pieces, incubated for 45min at 37*C with DMEM + Elastase, DNAase, liberase and 1% penicillin+streptomycin+glutamine. Digestion was stopped with fetal bovine tissue ato 10%. The digested tissue was passed on a 100micron mesh and later on centrifuged at 300g for 10 min. Cell pellets were resuspended with MACS medium, and later on the cells were barcoded using the 10x chromium single cell platform.
The samples were processed either with the Chromium X or the Chromium Controller, using the Single cell 5' v2, or Single Cell 5' v2 HT kit. Libraries were sequenced using the Illumina NextSeq 500 system.

value: Lung


title: 3N_TF 26h rep1


title: 3N_TF 24h rep2


title: BMEL_pIGrhl2_n3


title: TC_2

city: Shanghai

first: Xuefeng

last: Wang

address: 320 Yueyang Road

institute: Chinese Academy of Sciences

description: Library name: Sample 8

data_processing:
Raw reads underwent filtration via cutadapt (version 1.11).
Clean reads were aligned to the Mus musculus reference transcripts using Hisat2 (version 2.1.0).
Transcript abundance and expression normalization were calculated as fragments per kilobase of transcript per million mapped reads.
Assembly: Mus musculus reference (GRCm38.p6)
Supplementary files format and content: text files include FPKM values for Sample 1, Sample 2, Sample 3, Sample 4, Sample 5, Sample 6, Sample 7, Sample 8, Sample 9 (CTR_1_FPKM.txt, CTR_2_FPKM.txt, CTR_3_FPKM.txt, NC_1_FPKM.txt, NC_2_FPKM.txt, NC_3_FPKM.txt, TC_1_FPKM.txt, TC_2_FPKM.txt, TC_3_FPKM.txt).

source_name: pericardium

extract_protocol:
Total RNA of pericudium tissues were extracted with TRIzol reagent (Invitrogen).
The indexed library was sequenced with the Illumina NovaSeq X Plus platform.

treatment_protocol: Balbc female mice were transplanted with or without 4T1 cells through i.v. injection. Fifteen days later, pericudiums were collected from mice and then analyzied by RNA sequencing.

value: pericardium

value: with tumor-induced calcification


title: 273, scRNAseq

description: 10x Genomics


title: TC_3

description: Library name: Sample 9


title: 3N_TF 24h rep1


title: BMEL_pcDNA_n3


title: PBMCs, Day 1, ATAC individual 02

description: Library name: Ind02d1

value: peripheral blood

value: PBMC

value: monocytes, T and B cells


title: TC_1

description: Library name: Sample 7


title: NC_3

description: Library name: Sample 6

value: with natural calcification


title: 3N_TF 22h rep2


title: 491, scRNAseq

description: 10x Genomics


title: 3N_TF 22h rep1


title: BMEL_pcDNA_n2


title: BMEL_pIGrhl2_n2


title: 485, scRNAseq

description: 10x Genomics


title: NC_2

description: Library name: Sample 5


title: 3N_TF 20h rep2


title: NC_1

description: Library name: Sample 4


title: 484, scRNAseq

description: 10x Genomics


title: CTR_3

description: Library name: Sample 3

value: without calcification


title: 3N_TF 20h rep1

value: hPSCs


title: hSTAT2 mouse, Fetal brain, PBS/ZIKV, E12.5 injection, E18.5

city: Piscataway

first: Brian

last: Daniels

state: NJ

address: 604 Allison Road

department: Cell Biology and Neuroscience

institute: Rutgers, The State University of New Jersey

description: Library name: Single-Cell-Sample

data_processing:
scRNA-seq: Data was processed through CellRanger.
Data analysis was performed with Scanpy.
Assembly: GRCm38
Supplementary files format and content: scRNA-seq: Cell Ranger software output files

molecule: nuclear RNA

source_name: Fetal brain

extract_protocol:
For single nuclei, brains were dissociated and fixed following manufacturer's protocols using Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit
Single-nucleus libraries were prepared with 10X Genomics Chromium 3' gene express10X Genomics® Chromium™ Fixed RNA-seq library preparation

treatment_protocol: Pregnant hSTAT2 mice were subcutaneously injected with either PBS or ZIKV-maDakar on embryonic day (E) 12.5. Brains of the offspring were harvested on E18.5.

value: Fetal brain

value: PBS/ZIKV-maDakar


title: BMEL_pcDNA_n1


title: 448, scRNAseq

description: 10x Genomics


title: 3N_TF 18h rep2

value: neurogenesis from hPSCs

value: dox inducible NEUROG1, NEUROG2, NEUROD1 overexpression in hPSCs


title: 501, scRNAseq

description: 10x Genomics


title: BMEL_pcDNA_n4


title: CTR_2

description: Library name: Sample 2


title: ENTPD-8 KO-3

city: New York

first: George

last: Hasko

state: NY

address: 622 West 168th Street

department: Department of Anesthesiology

institute: Columbia University

data_processing:
Trim Galore! (Adapter and quality trimming)
STAR (Aligment to Mus_musculus/Ensembl/GRCm38)
Salmon(Quantification)
Assembly: Mus_musculus/Ensembl/GRCm38
Supplementary files format and content: gene_counts.tsv, tab-delimited file, ENSEMBL Gene Id, Gene Counts for WT1, WT2, WT3,KO1,KO2,KO3 computed by Salmon respectively)

growth_protocol: Mice were bred iand maintained in a specific pathogen-free facility at Charles River

extract_protocol:
RNA was harvested using Rneasy kit (Qiagen)
Poly(A) RNA enrichment was conducted using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB), and the sequencing library was constructed by using the NEBNext Ultra II RNA Library Prep Kit (NEB) (P/N: E7765L, NEB, Ipswich, MA) following the manufacturer’s instructions.

value: Liver

value: ENTPD-8 knockout


title: ENTPD-8 KO-2


title: CTR_1

description: Library name: Sample 1


title: 3N_TF 18h rep1


title: 435, scRNAseq

description: 10x Genomics


title: 416, scRNAseq

description: 10x Genomics


title: 499, scRNAseq

description: 10x Genomics


title: 3N_TF 16h rep2


title: ENTPD-8 WT-3

value: wild type


title: LNCaP.exp1.total.shNUP93_rep1

city: San Antonio

first: Kexin

last: Xu

state: Texas

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

data_processing:
Basecalls were performed using Illumina Casava software.
Reads were aligned to hg19 genome assembly using STAR 2.5.2b. Refseq transcripts were supplied in GTF format file.
featureCounts package was used to count the uniquely mapped reads in union mode.
Differentially expressed genes were detected by DESeq2 with FDR thresold 0.05
Assembly: hg19
Supplementary files format and content: tab-delimited text files include reads counts for each Sample

source_name: LNCaP

growth_protocol: The human prostate adenocarcinoma cell line LNCaP was cultured with RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Cells were grown in a 5% CO2 cell culture incubator at 37 °C. Human cervical carcinoma HeLa cells (ATCC® CCL-2) were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) (Fisher scientific, Corning® 31053-028) supplemented with 10% fetal bovine serum (FBS) (Sigma-Aldrich, F4135) and 1% penicillin-streptomycin (Gibco, 15140-122). Human podocytes were cultured in RPMI-1640 supplemented with 10% FBS, 1% penicillin-streptomycin and 1% Insulin-Transferrin-Selenium (ITS-G) (Gibco, 41400-045) at 33°C with 5% CO2 in a humidified incubator. For the differentiation of podocytes, cells were moved from 33°C to 37°C for 14 days. All cell lines were routinely tested for mycoplasma contamination.

extract_protocol:
Total RNA was extracted by TRIzol™ Reagent (Thermo Fisher, 15596018)
RNA library was prepared by KAPA Stranded mRNA- Seq Kit (96rxn, KK8421), according to the manufacturer’s instructions.

treatment_protocol: LNCaP cells were transduced with control shRNA (shCtrl), shRNA targeting METTL3 (shMETTL3) or shRNA targeting NUP93 (shNUP93) and then overexpressed in NUP93-knockdown cells control vector (empty), wild-type NUP93 (WTR) or A333P mutant (A333PR), which are HA-tagged and contain synonymous mutations rendering resistance to shNUP93. HeLa cells were transduced with shCtrl, shMETTL3 or shNUP93. Podocytes were transduced with control shRNA (shCtrl), shRNA targeting METTL3 (shMETTL3) or shRNA targeting NUP93 (shNUP93) and then overexpressed in NUP93-knockdown cells control vector (empty), wild-type NUP93 (WTR) or R388W mutant (R388WR), which are HA-tagged and contain synonymous mutations rendering resistance to shNUP93.

value: LNCaP

tag: transfection

value: Cells were infected with NUP93 shRNAs


title: BMEL_pIGrhl2_n1

value: BMEL

value: Bipotential mouse embryonic liver cells


title: 3N_TF 16h rep1


title: 475, scRNAseq

description: 10x Genomics

value: Lung


title: 478, scRNAseq

description: 10x Genomics


title: LNCaP.exp1.total.shMETTL3_rep2

value: Cells were infected with METTL3 shRNAs


title: 3N_TF 14h rep2


title: ENTPD-8 WT-2


title: 3N_TF 14h rep1


title: 460, scRNAseq

description: 10x Genomics


title: ENTPD-8 WT-1


title: LNCaP.exp1.total.shNUP93_rep2


title: LNCaP.exp1.total.shMETTL3_rep1


title: 3N_TF 12h rep2


title: 446, scRNAseq

description: 10x Genomics


title: LNCaP.exp1.total.shCtrl_rep2

value: Cells were infected with control shRNAs


title: DSSHA71

city: Nanjing

first: Mingrui

last: Zhao

state: Jiangsu

address: No. 639, Longmian Avenue, Chunhua Street, Nanjing City, Jiangning District, China Pharmaceutical University

institute: China Pharmaceutical University

description: Library name: sample8

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

organism: Mus

source_name: liver tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen.1.3 ug of total RNA was used for the construction of sequencing libraies.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep kit following manufacturer's protocols.

value: liver tissue

value: alcohol, high-fat diet, and DSS


title: DSSHA65

description: Library name: sample7


title: 3N_TF 12h rep1

value: hPSCs


title: LNCaP.exp1.total.shCtrl_rep1


title: 445, scRNAseq

description: 10x Genomics


title: DSSHA45

description: Library name: sample6


title: 3N_TF 10h rep2


title: 429, scRNAseq

description: 10x Genomics


title: ENTPD-8 KO-1


title: DSSHA35

description: Library name: sample5


title: 3N_TF 10h rep1


title: 454, scRNAseq

description: 10x Genomics


title: Podocyte.Total_WT_rep2

source_name: Podocyte

value: Podocyte


title: Podocyte.Total_WT_rep1


title: DSS50

description: Library name: sample4

value: DSS


title: 3N_TF 8h rep2

value: neurogenesis from hPSCs


title: Podocyte.Total_MT_rep2


title: 424, scRNAseq

description: 10x Genomics


title: DSS49

description: Library name: sample3


title: Podocyte.Total_MT_rep1


title: 3N_TF 8h rep1

value: dox inducible NEUROG1, NEUROG2, NEUROD1 overexpression in hPSCs


title: Podocyte.Nuclear_WT_rep2


title: 408, scRNAseq

description: 10x Genomics


title: 399, scRNAseq

description: 10x Genomics


title: 3N_TF 6h rep1


title: DSS15

description: Library name: sample1


title: Podocyte.Nuclear_WT_rep1


title: 398, scRNAseq

description: 10x Genomics


title: 39_mPFC, control IL-1RA, 24h

city: Budapest

first: <Up loaded by Bioinformatics core  facility>

last: <PI shown in the article>

address: Szigony st 43.

country: Hungary

description: Library name: X39

data_processing:
Raw Data Processing  were done with salmon 1.10.2 and  FastQC v0.12.1
Transcriptome quantification was performed using Salmon with a rat transcriptome index (SeqHash: e3e65d03eb7cb31ad8f22dd2d8518d11c118f2f0d5bc09119fe09f7cd02fe9a1) The salmon parameters used for quantification: -l A -1 {seq1} -2 {seq2} --validateMappings -o
Gene-level summarization was carried out using tximport 1.24.0 with type='salmon, using the tx2gene file generated from Rattus_norvegicus.mRatBN7.2.106 gtf file (txi <- tximport(files, type="salmon", tx2gene=tx2gene, ignoreTxVersion = TRUE) The provided txi_counts.txt  file contains the gene level count estimates for every samples.
Statistical Analysis Preparation Genes with minimum of total 10 counts in a group were retained. DESeqDataSet object was generated with DESeqDataSetFromTximport and differential expression analysis were performed with Deseq2 1.36.0
Assembly: Rattus_norvegicus.mRatBN7.2.106
Supplementary files format and content: comma delimited text file includes gene level count estimates derived from salmon and tximport

organism: Rattus norvegicus

source_name: mPFC

growth_protocol: Male and female Wistar rats (Charles River  Laboratories, Germany) from the HUN-REN Institute of Experimental Medicine (HUN-REN IEM, Budapest, Hungary) breeding colony were used. Rats were housed in temperature (24±1 °C) and humidity (50±10 %) controlled rooms under a 12-hour light-dark cycle, with ad libitum chow (Special Diets Services, VR1) and water. Breeding pairs were cohoused for 5 days, and dams were isolated in large cages (1354G, Eurostandard IV, Tecniplast, Italy) for the remainder of pregnancy. Litters were culled to 8-10 pups per litter on postnatal day 0 (P0) to minimise maternal care variations. Pups were individually marked on P3 with a green paw tattoo (Micro-Tattooing System, Harvard Apparatus, USA; Ketchum Animal Tattoo Ink Paste, Canada) for identification.

extract_protocol:
After deep anesthesia and decapitation, brains were dissected into coronal blocks, and bilateral medial prefrontal cortices were microdissected (N= 8-10 animals/ treatment group). Total RNA was isolated using the RNeasy Lipid Tissue Mini Kit (Qiagen), followed by DNase treatment.
Total RNA was isolated using the RNeasy Lipid Tissue Mini Kit (Qiagen), followed by DNase treatment. RNA quality was assessed with an Agilent TapeStation (Agilent  Technologies, USA), showing RIN values above 9.5. Libraries were prepared using the Illumina Stranded mRNA Prep kit (Illumina, Inc., USA, #20040534) and sequenced on an Illumina NextSeq 2000.

treatment_protocol: The approach for the PA insult was based on the seminal work of Pospelov et al., which established key methodological and physiological foundations for this model and was further modified to suit our study purposes. At P7, male and female pups were separated dams, weighted, and randomly assigned to treatment chambers (30x15x20 cm) with perforated plexiglass dividers for individual isolation during PA and recovery. Chambers were placed in an isothermal water bath (35.6 °C; WNB 45, Memmert, Germany). Based on pilot experiments, the pups were kept for 45 minutes to equilibrate their core temperature to normothermia (37.0-37.5 °C). Thereafter, treatment chambers were filled with a PA-inducing gas mixture (4% O2 and 20% CO2 in N2; Messer Hungarogáz Ltd, Hungary), with continuous O2 and CO2 concentration monitoring (TR250Z Oxygen Sensor, K-33 BLG Sensor, CO2Meter Inc., USA). After 15 minutes of exposure to the PA-inducing gas mixture, the chambers were opened and ventilated to restore normoxia. The pups were allowed to recover from the insult for 45 minutes before returning to dams. PA resulted in 25-30% mortality, with no sex differences. No further mortality occurred among pups. Control pups were separated from dams for the same duration in one of the chambers filled with room air throughout the experiment (Fig. 1A). Animals were semi-randomly assigned to experimental groups within litters, using alternation to avoid litter effects and ensure balanced group sizes. To assess and influence inflammation-related mechanisms in the transmission of PA-caused effects, animals were treated with subcutaneous IL-1 receptor antagonist (IL-1RA, Kineret, Swedish Orphan Biovitrum AB) at a dose of 100 mg/kg. A volume of 10 μl/g IL-1RA dissolved in sterile 0.1% bovine serum albumin (BSA) was diluted in phosphate-buffered saline (PBS) and administered at 1 and 20 hours after the PA insult to influence the primary and secondary phase of PA-induced energy failure.

value: mPFC

value: bulk

value: control IL-1RA

tag: batch


title: 3N_TF 4h rep2


title: Podocyte.Nuclear_MT_rep2


title: 38_mPFC, PA IL-1RA, 24h

institute: HUN-REN Institute of Experimental Medicine

description: Library name: X38

value: wild type

value: PA IL-1RA


title: 396, scRNAseq

description: 10x Genomics


title: 3N_TF 4h rep1


title: LNCaP.exp1.NC.shNUP93_rep2

value: LNCaP

value: Cells were infected with NUP93 shRNAs


title: 37_mPFC, control IL-1RA, 24h

description: Library name: X37


title: 383, scRNAseq

description: 10x Genomics

value: Lung


title: 3N_TF 2h rep2


title: 3N_TF 2h rep1


title: 415, scRNAseq

description: 10x Genomics


title: 376, scRNAseq

description: 10x Genomics


title: 36_mPFC, control vehicle, 24h

description: Library name: X36

value: control vehicle


title: 3N_TF 0h rep2


title: 371, scRNAseq

description: 10x Genomics


title: 3N_TF 6h rep2


title: LNCaP.exp1.NC.shNUP93_rep1


title: DSS48

description: Library name: sample2


title: LNCaP.exp1.NC.shMETTL3_rep2

value: Cells were infected with METTL3 shRNAs


title: 368, scRNAseq

description: 10x Genomics


title: LNCaP.exp1.NC.shMETTL3_rep1


title: 3N_TF 0h rep1


title: Flag_Input

description: Library name: Flag_Input

data_processing:
Reads were aligned to mouse genome assembly GRCh38 by Bowtie2 (V 2.5.4) by internal automatically mapping pipeline.
Narrow peaks for each sample were called by MACS2 (V 2.2.9.1), with default parameters using Input as control.
RPM was applied to the normalized read counts to generate bigwig tracks
Assembly: GRCh38
Supplementary files format and content: bw file the software processed by bedGraphToBigWig for IGV display peak
Library strategy: CUT&Tag

extract_protocol:
Cells were disassociated with Accutase to single cell.
CUT-TAG (cleavage under targets & release using nuclease) chromatin profiling were performed using Hyperactive® Universal CUT&Tag Assay Kit (vazyme, TD903).] Antibody against Flag was used at 1:100 for 100,000 cells. DNA was collected for paired-end sequencing. The chromatin immunoprecipitation (ChIP) protocol for OLIG2 was adapted as below. Briefly, cells were crosslinked with 1% formaldehyde for 10 min at room temperature and then treated with 0.2 M glycine to inactive the formaldehyde. Cells were then lysed to obtain chromatin extracts, which were sonicated to obtain DNA fragments with an average size of 300-500 bp. The resulting chromatin extracts were immunoprecipitated by OLIG2 antibody (Sigama, AB9610) immobilized on Protein-G beads.

treatment_protocol: Neurogenesis from hPSCs with 3N_TF (NEUROG1, NEUROG2, NEUROD1) overexpression.


title: 367, scRNAseq

description: 10x Genomics


title: 34_mPFC, control vehicle, 24h

description: Library name: X34


title: Podocyte.Nuclear_MT_rep1


title: 33_mPFC, control IL-1RA, 24h

description: Library name: X33


title: LNCaP.exp1.NC.shCtrl_rep2

value: Cells were infected with control shRNAs


title: 356, scRNAseq

description: 10x Genomics


title: OLIG2

description: Library name: OLIG2

data_processing:
Reads were aligned to mouse genome assembly GRCh38 by Bowtie2 (V 2.5.4) by internal automatically mapping pipeline.
Narrow peaks for each sample were called by MACS2 (V 2.2.9.1), with default parameters using Input as control.
RPM was applied to the normalized read counts to generate bigwig tracks
Assembly: GRCh38
Supplementary files format and content: bw file the software processed by bedGraphToBigWig for IGV display peak

tag: chip antibody

value: OLIG2 antibody (Sigama, AB9610)


title: 32_mPFC, control IL-1RA, 24h

description: Library name: X32


title: 338, scRNAseq

description: 10x Genomics


title: Flag-MSC

description: Library name: Flag-MSC

value: hPSCs

value: Mouse monoclonal anti-FLAG (Sigama, F1804;)


title: LNCaP.TT_shNUP93_vector_rep2


title: 30_mPFC, PA IL-1RA, 24h

description: Library name: X30


title: 35_mPFC, PA vehicle, 24h

description: Library name: X35

value: PA vehicle


title: LNCaP.TT_shNUP93_vector_rep1


title: OLIG2_Input

description: Library name: OLIG2_Input

value: neurogenesis from hPSCs


title: 29_mPFC, PA vehicle, 24h

description: Library name: X29


title: LNCaP.exp1.NC.shCtrl_rep1


title: 302, scRNAseq

description: 10x Genomics


title: LNCaP.TT_shNUP93_WT_rep2

value: Cells were infected with NUP93 shRNAs and shRNA-resistant wild type NUP93


title: 28_mPFC, PA vehicle, 24h

description: Library name: X28

value: mPFC


title: Flag-NEUROG2

description: Library name: Flag-NEUROG2

value: dox inducible NEUROG1, NEUROG2, NEUROD1 overexpression in hPSCs


title: 330, scRNAseq

description: 10x Genomics


title: Lymphatic Malformation Endothelial Cell Line-12

city: Little Rock

first: Ravi

middle: W.

last: Sun

state: Arkansas

address: 4301 W Markham St

department: Department of Otolaryngology - Head and Neck Surgery

institute: University of Arkansas for Medical Sciences

data_processing:
Read trimming, mapping, and quantification of gene level counts were performed by Qiagen's Genomic Services via the CLC Genomics Server 21.0.4. Raw reads were trimmed of 3'-adaptors, low-quality bases, and ambiguous nucleotides. Trimmed reads were then mapped to mouse ribosomal RNA (rRNA) repetitive unit. Reads that did not map to rRNA were aligned to the Human GRCh38 genome and gene level counts quantified via Ensembl 97 GRCh38 annotation.
After removing genes located on chromosomes X and Y a proportion based  counts-per-million (CPM) filter was applied to remove low abundant genes. Criteria for Retention required genes to have a minimum of 1 CPM in at least 75% of the samples in one or more groups. The filtered counts were TMM normalized and converted to logCPM values using edgeR's (version 3.38.1) calcNormFactors() and limma's (version 3.52.2) voomWithQualityWeights() with sample quality weights functions, respectively. Linear modeling, and moderated t-statistics with robust empirical Bayes smoothing were performed using the limma's LmFit(), and eBayes() functions. Genes with an absolute fold-change > 2 and a FDR adjustedp-value < 0.05 were considered significant.
Assembly: Ensembl 97; GRCh38.p12; GCA 000001405.27
Supplementary files format and content: tab-delimited text file containing raw gene level counts for each sample.

source_name: endothelial cells isolated from surgically removed LM tissue

growth_protocol: LM tissue and cystic fluid were collected from patients undergoing surgical resections. LM-ECs were isolated from LM tissue and cystic fluid as previously described [36]. HDLEC C-12216 cell lines (n = 3, isolated from different patients) were purchased from PromoCell (PromoCell, Germany). All cells were cultured in EBM-2 medium (Lonza Group Ltd, Switzerland) supplemented with growth factors, 20% fetal bovine serum (R&D Systems, Inc. Minneapolis, MN), and 1% antibiotic-antimycotic (ThermoFisher Scientific, Waltham, MA) on fibronectin-coated plates and maintained at 37°C in a 5% CO2 humidified chamber.

extract_protocol:
RNA was extracted from each sample using Qiagen's RNeasy Plus Mini Kit. RNA was eluted in 50μl.
Qiagen's QIAseq Stranded mRNA Select Kit with FastSelect rRNA depletion was used to prepare the cDNA libraries. Briefly, mRNA enriched from 500ng starting material was enzymatically fragmented and converted to single stranded cDNA via reverse transcription. Second strand synthesis was then performed to created double-straned cDNA. This was followed by fragment end repair, 3' adenylation, and ligation of 3' and 5' sequencing adapters to allow multiplexing and attachment to the sequencing flow cell. Next, the adapted libraries were PCR amplified (13 cycles) and purified by bead-based cleanup. Library concentrations were normalized to equal concentration, pooled, and sequenced on a NextSeq instrument using a high output flow cell (2 x 75 PE; 2 x 8) according to the manufacture's protocol.

tag: patient id

value: lymphatic malformation endothelial cells (LM-EC)

tag: disease state

value: Lymphatic Malformation

tag: cystic structure

value: Mixed

tag: location

value: L Neck

tag: mutation

value: Male

tag: age


title: Lymphatic Malformation Endothelial Cell Line-8

tag: cell line

value: endothelial cells isolated from surgically removed LM tissue

tag: cell type


title: LNCaP.TT_shNUP93_WT_rep1

value: LNCaP


title: 27_mPFC, control vehicle, 24h

description: Library name: X27

tag: tissue

value: bulk

value: wild type

tag: treatment

value: control vehicle


title: LNCaP.TT_shNUP93_A333P_rep2

value: Cells were infected with NUP93 shRNAs and shRNA-resistant NUP93 A333P mutant


title: Flag-NEUROD1 (3N_TF)

description: Library name: Flag-NEUROD1 (3N_TF)

value: hPSCs

value: Mouse monoclonal anti-FLAG (Sigama, F1804;)


title: Lymphatic Malformation Endothelial Cell Line-7

value: Macrocystic

value: Female


title: Flag-NEUROG2 (3N_TF)

description: Library name: Flag-NEUROG2 (3N_TF)

value: neurogenesis from hPSCs


title: LNCaP.TT_shNUP93_A333P_rep1


title: 26_mPFC, PA IL-1RA, 24h

description: Library name: X26

value: mPFC

value: PA IL-1RA


title: 31_mPFC, control vehicle, 24h

description: Library name: X31


title: Flag-NEUROG1 (3N_TF)

description: Library name: Flag-NEUROG1 (3N_TF)

value: dox inducible NEUROG1, NEUROG2, NEUROD1 overexpression in hPSCs


title: LNCaP.TT_shCtrl_vector_rep2

value: Cells were infected with control shRNAs


title: 25_mPFC, PA vehicle, 24h

description: Library name: X25

value: PA vehicle


title: Lymphatic Malformation Endothelial Cell Line-5

value: lymphatic malformation endothelial cells (LM-EC)

value: Lymphatic Malformation

value: L Neck

value: Unknown

value: Male


title: Flag-NEUROD2

description: Library name: Flag-NEUROD2

value: dox inducible NEUROG2 overexpression in hPSCs


title: 24_mPFC, control IL-1RA, 24h

description: Library name: X24

value: bulk

value: wild type

value: control IL-1RA


title: LNCaP.TT_shCtrl_vector_rep1

value: LNCaP


title: Lymphatic Malformation Endothelial Cell Line-4

value: endothelial cells isolated from surgically removed LM tissue

value: Macrocystic


title: hPSCs-2

description:
Library name: hPSCs-2
Illumina

data_processing:
Reads were aligned to mouse genome assembly GRCh38 by Bowtie2 (V 2.5.4) by internal automatically mapping pipeline.
Narrow peaks for each sample were called by MACS2 (V 2.2.9.1), with default parameters using Input as control.
Assembly: GRCh38
Supplementary files format and content: Narrow peaks for each sample were called by MACS2 (V 2.2.9.1)

value: hPSCs

value: neurogenesis from hPSCs


title: hPSCs-1

description:
Library name: hPSCs-1
Illumina

value: dox inducible NEUROG1, NEUROG2, NEUROD1 overexpression in hPSCs


title: LNCaP.NC_shNUP93_vector_rep2

value: Cells were infected with NUP93 shRNAs


title: 3N_TF day2-2

description:
Library name: 3N_TF day2-2
Illumina


title: 22_mPFC, control vehicle, 24h

description: Library name: X22

value: mPFC

value: control vehicle


title: Lymphatic Malformation Endothelial Cell Line-2

value: lymphatic malformation endothelial cells (LM-EC)

value: Lymphatic Malformation

value: R Neck

value: Female

value: 10 months


title: 21_mPFC, control vehicle, 24h

description: Library name: X21

value: bulk


title: Lymphatic Malformation Endothelial Cell Line-1


title: LNCaP.NC_shNUP93_vector_rep1


title: 3N_TF day2-1

description:
Library name: 3N_TF day2-1
Illumina


title: LNCaP.NC_shNUP93_WT_rep2

value: Cells were infected with NUP93 shRNAs and shRNA-resistant wild type NUP93


title: 20_mPFC, control vehicle, 24h

description: Library name: X20

value: wild type


title: 3N_TF day1-2

description:
Library name: 3N_TF day1-2
Illumina


title: LNCaP.NC_shNUP93_WT_rep1

value: LNCaP


title: Lymphatic Malformation Endothelial Cell Line-6

value: endothelial cells isolated from surgically removed LM tissue

value: Mixed

value: L Cervicofacial


title: Control Human Dermal Lymphatic Endothelial Cell Line-3

source_name: C-12216 (source: PromoCell; Lot#: 466Z006.3)

value: human dermal lymphatic endothelial cells (HDLEC)

value: Control

value: Male


title: 3N_TF day1-1

description:
Library name: 3N_TF day1-1
Illumina

value: hPSCs

value: neurogenesis from hPSCs

value: dox inducible NEUROG1, NEUROG2, NEUROD1 overexpression in hPSCs


title: LNCaP.NC_shNUP93_A333P_rep2

value: Cells were infected with NUP93 shRNAs and shRNA-resistant NUP93 A333P mutant


title: Control Human Dermal Lymphatic Endothelial Cell Line-2

source_name: C-12216 (source: PromoCell; Lot#: 467Z001.2)


title: WT_4

city: BeiJing

first: Yue

last: Zhang

address: North Lishi Road

institute: Fuwai Hospital, Chinese Academy of Medical Sciences

description: Library name: Sample8

data_processing:
The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated. The index of the reference genome was built using Hisat2 v2.0.5. and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Assembly: ncbi_sus_scrofa_gcf_000003025_6_sscrofa11_1

organism: Sus scrofa

source_name: heart

extract_protocol:
Total RNA was extracted from right ventricular tissue of PKP+/- and WT pig using RNeasy Mini Kit.). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated. The index of the reference genome was built using Hisat2 v2.0.5. and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: heart

value: cardiomyocytes


title: 18_mPFC, control IL-1RA, 24h

description: Library name: X18

value: mPFC

value: control IL-1RA


title: LNCaP.NC_shNUP93_A333P_rep1


title: Control Human Dermal Lymphatic Endothelial Cell Line-1

source_name: C-12216 (source: PromoCell; Lot#: 439Z007.2)


title: Lymphatic Malformation Endothelial Cell Line-3

value: lymphatic malformation endothelial cells (LM-EC)

value: Lymphatic Malformation

value: L Neck

value: Unknown

value: Female

value: 4 months


title: WT_3

description: Library name: Sample7


title: 17_mPFC, control vehicle, 24h

description: Library name: X17

value: bulk

value: wild type

value: control vehicle


title: 23_mPFC, PA vehicle, 24h

description: Library name: X23

value: PA vehicle


title: LNCaP.NC_shCtrl_vector_rep2

value: LNCaP

value: Cells were infected with control shRNAs


title: Ube2i d/d, pooled

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

description: Library name: Ube2i_dd

data_processing:
Clean reads were mapped to mouse genome (UCSC mm10) by using HISAT v2.2.1
Mapped reads were assembled by using Cufflinks v2.2.1
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample

source_name: whole uterus

extract_protocol:
TRIzol reagent (Invitrogen) was used to extract total RNAs according to manufacturers’ instructions.
RNA-seq libraries were created by using the TruSeq RNA sample preparation kit (Illumina).

treatment_protocol: Female mice were sacrificed on PND21.

value: whole uterus


title: 16_mPFC, PA IL-1RA, 24h

description: Library name: X16

value: PA IL-1RA


title: WT_2

description: Library name: Sample6

value: heart

value: cardiomyocytes


title: 14_mPFC, PA vehicle, 24h

description: Library name: X14

value: mPFC


title: 12_mPFC, PA vehicle, 24h

description: Library name: X12


title: PKP2_4

description: Library name: Sample4


title: Hela.shNUP93_rep1

source_name: Hela

value: Hela

value: Cells were infected with NUP93 shRNAs


title: PKP2_3

description: Library name: Sample3


title: Hela.shNUP93_rep2


title: 19_mPFC, PA IL-1RA, 24h

description: Library name: X19


title: PKP2_2

description: Library name: Sample2


title: Hela.shMETTL3_rep2

value: Cells were infected with METTL3 shRNAs


title: Small oocytes in culture with external pressure replicate 1

city: Suita

first: Katsuhiko

last: Hayashi

state: Osaka

address: 2-2 Yamadaoka

department: Graduate School of Medicine

country: Japan

institute: The University of Osaka

description:
Library name: Small oocytes in culture_Rep1
Nagamatsu_3

data_processing:
Sequencing was performed on a NovaSeqX Plus (Illumina) to generate 151-bp single-end reads according to the manufacturer’s instructions. Adaptor sequences, low-quality bases and reads (q score < 20) were removed using fastp (v0.20.0). Cleaned reads were aligned to the mouse reference genome (GRCm38) using STAR (v2.7.7a). Gene counts and TPM (transcripts per million) values were then calculated using RSEM.
The gene count matrix is provided in “all_gene_count_matrix.xlsx.” The samples used in this analysis are shown in the columns labeled Nagamatsu_3 and Nagamatsu_4. The remaining 21 columns correspond to data generated through the same process as our previous dataset, GSE128305.
Assembly: GRCm38
Supplementary files format and content: Nagamatsu_all_gene_count_matrix.xlsx

source_name: Oocytes

extract_protocol:
Poly(A)+ RNA were extracted using the Dynabeads mRNA DIRECT Micro Kit (Invitrogen).
Libraries were made for directional RNA-seq library construction using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB). cDNAs were enriched by 12-cycle PCR.

value: Oocytes

value: external pressure (33.3 kPa)


title: 10_mPFC, PA IL-1RA, 24h

description: Library name: X10


title: Hela.shMETTL3_rep1


title: 11_mPFC, PA vehicle, 24h

description: Library name: X11


title: Vehicle RELA Tumor RNA replicate 1

city: Seattle

first: Mehlam

middle: M

last: Saifudeen

state: WA

address: 1100 Fairview Ave North

department: Human Biology

institute: Fred Hutchinson Cancer Center

description:
Library name: Vehicle RELA Tumor RNA 1
Column Name in RELA_Tumor_raw_all_counts.csv: 914 Vehicle RELA Tumor RNA Duplicate 1

data_processing:
Raw RNA-seq reads were aligned to the hg38 reference genome using STAR v2.7.7a with two-pass mode and gene-level quantification enabled (--quantMode GeneCounts). BAM files were sorted and indexed using SAMtools. Gene expression counts were obtained using featureCounts (Subread package) with GENCODE v40 GTF, allowing multimapping reads (-M) and paired-end assignment (-p). The resulting raw gene count matrix was used for downstream analysis.
Assembly: mm10_149
Supplementary files format and content: comma separated file includes raw counts for each sample

source_name: Brain tumor

extract_protocol:
Total cellular RNA was extracted using the GenCatch Total RNA Mini Prep Kit (Epoch Life Science, Missouri City, TX, USA) following the manufacturer’s protocol. The extracted RNA was assessed for quality and quantity using a NanoDrop spectrophotometer (Thermo Fisher Scientific) and Qubit Fluorometer (Invitrogen). RNA integrity was verified using an Agilent Bioanalyzer or TapeStation. 1 μg of total RNA was used for downstream applications, including library preparation.
RNA libraries for RNA sequencing were prepared using Novogene and following the Illumina manufacturer’s protocol.

value: Brain tumor

value: Tissue

value: ZFTA-RELAfusion

value: Vehicle


title: Hela.shCtrl_rep2


title: 9_mPFC, control IL-1RA, 24h

description: Library name: X9

value: bulk

value: wild type

value: control IL-1RA


title: PKP2_1

description: Library name: Sample1


title: LNCaP.NC_shCtrl_vector_rep1

value: Cells were infected with control shRNAs


title: Vehicle RELA Naive RNA replicate 2

description:
Library name: Vehicle RELA Naive RNA 2
Column Name in RELA_Tumor_raw_all_counts.csv: 915 Vehicle RELA Naive RNA Duplicate 2

source_name: Naive Brain tissue

value: Naive Brain tissue


title: dNCM_MEPC_plate120 (dog)

city: Utrecht

first: Frank

last: Riemers

address: Uppsalalaan 8

country: Netherlands

institute: Utrecht University

description: Library name: S120

data_processing:
Mapping was performed against the canine reference genome (ROS_Cfam_1.0)
Counts were assigned to of human or canine origin, based on the HLA signal the wells containing human cells were identified and removed from the dog data., whereas for the human data these wells were selected and kept.
Analysis was peformed in Seurat 5.3.0.
This study involved the sequencing of canine and human cells. Both were collected and sequenced on the same plate. Therefore, they have identical fastq files.
Assembly: ROS_Cfam_1.0
Supplementary files format and content: Tab separated matrix, barcode and features

organism: Canis lupus familiaris

source_name: Nucleus pulposus

extract_protocol:
Two-step enzymatic digestion, using the enzymes pronase (Roche, #11459643001) and collagenase type II (Worthington, #443E23628)
Single cell Sequencing was peformed at Single Cell Discoveries (Utrecht, the Netherlands) according to the SORT-seq protocol, an adapted version of the CEL-seq2 protocol.

value: Nucleus pulposus

value: Nucleus pulposus cells

value: dNCM+hMEPCs


title: 8_mPFC, PA IL-1RA, 24h

description: Library name: X8

value: mPFC

value: PA IL-1RA


title: Vehicle RELA Naive RNA replicate 1

description:
Library name: Vehicle RELA Naive RNA 1
Column Name in RELA_Tumor_raw_all_counts.csv: 914 Vehicle RELA Naive RNA Duplicate 1


title: 7_mPFC, control IL-1RA, 24h

description: Library name: X7


title: WT_1

description: Library name: Sample5

value: heart

value: cardiomyocytes


title: dNCM_MEPC_plate119 (dog)

description: Library name: S119


title: Ube2i f/f, pooled

description: Library name: Ube2i_ff

value: whole uterus


title: Podocyte_m6A_rep2

data_processing:
Basecalls performed using Illuminal CASAVA software.
Cutadapt was used to remove the first 9 bases and N’s on both ends of reads. Reads with minimum of 25 bases were kept. Reads were aligned to human genome (hg19) using STAR. Duplicated reads were marked and removed by Picard. The bam files were transformed into bed12 format by bedtools, and then shifted to 200nt by a custom script and transformed back to bed6 format. Macs2 bdgopt sub-command was used to normalize each sample to a 10 million total reads.
MeTDiff was used to call m6A enriched peaks by combining both replicates with default parameters.
Assembly: hg19
Supplementary files format and content: bigWig file

growth_protocol: Human podocytes were cultured in RPMI-1640 supplemented with 10% FBS, 1% penicillin-streptomycin and 1% Insulin-Transferrin-Selenium (ITS-G) (Gibco, 41400-045) at 33°C with 5% CO2 in a humidified incubator. For the differentiation of podocytes, cells were moved from 33°C to 37°C for 14 days.

extract_protocol:
Total RNA was extracted by TRIzol™ Reagent (Thermo Fisher, 15596018)
RNA library was prepared by SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara-Clontech, 634413), according to the manufacturer’s instructions.

value: Podocyte


title: Hela.shCtrl_rep1

value: Hela


title: Small oocytes in culture with external pressure replicate 2

description:
Library name: Small oocytes in culture_Rep2
Nagamatsu_4

value: Oocytes

value: external pressure (33.3 kPa)


title: MRX 2843 RELA Tumor RNA replicate 2

description:
Library name: MRX 2843 RELA Tumor RNA 2
Column Name in RELA_Tumor_raw_all_counts.csv: 909 MRX 2843 RELA Tumor RNA Duplicate 2

value: Brain tumor

value: Tissue

value: ZFTA-RELAfusion

value: 5 days treatment of 50 mg/kg of MRX-2843


title: dNCM_MEPC_plate118 (dog)

description: Library name: S118


title: 4_mPFC, control IL-1RA, 24h

description: Library name: X4

value: bulk

value: wild type

value: control IL-1RA


title: Podocyte_m6A_rep1


title: dNCM_MEPC_plate117 (dog)

description: Library name: S117

value: Nucleus pulposus

value: Nucleus pulposus cells

value: dNCM+hMEPCs


title: Vehicle RELA Tumor RNA replicate 2

description:
Library name: Vehicle RELA Tumor RNA 2
Column Name in RELA_Tumor_raw_all_counts.csv: 914 Vehicle RELA Tumor RNA Duplicate 2

value: Vehicle


title: 3_mPFC, PA IL-1RA, 24h

description: Library name: X3

value: mPFC

value: PA IL-1RA


title: MRX 2843 Naive RELA RNA replicate 2

description:
Library name: MRX 2843 Naive RELA RNA 2
Column Name in RELA_Tumor_raw_all_counts.csv: 909 MRX 2843 Naive RELA RNA Duplicate 2

value: Naive Brain tissue


title: 2_mPFC, PA vehicle, 24h

description: Library name: X2

value: PA vehicle


title: Deg_control_plate110 (dog)

description: Library name: S110


title: Podocyte_input_rep1

value: Podocyte


title: Deg_control_plate109 (dog)

description: Library name: S109


title: sc_dox free_mouse-3

status: Public on Dec 29 2025

city: Dallas

first: Leijie

last: Li

address: 5323 Harry Hines Blvd.

department: Molecular Biology

institute: UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER

description: Library name: m7_3

data_processing:
Trim Galore (Version 0.6.10) was utilized for quality control with quality score higher than Q30 and length larger than 20pb. Hisat2 (Version 2.1.0) and StringTie (Version 2.1.7) were used for sequence BLAST, assembly, and quantification. The GRCh38 and GRCm39 were downloaded from Ensembl database as the reference genomes for human and mouse, respectively. DESeq2 (Version 1.38.3) was applied to normalize gene expression in order to reduce the influence of batch effects and outlier genes in downstream analyses.
Assembly: GRCh38 and GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Mouse EpiSCs

growth_protocol: Mouse EpiSCs derived from the C57BL/6 strain (B6 mEpiSCs) were cultured in NBFR medium atop a MEF feeder layer. Primed H9 human ESCs were maintained in mTeSR Plus medium on Matrigel-coated dishes during routine passaging and transfection, with 10 mM ROCKi for 24 hours after each passage.Cultured cells were treated with TrypLE for 3 minutes at 37℃ to detach them from the plate, then counted using a hemocytometer and passage into new plates at different dilution ratios depending on the cell line.

extract_protocol:
PSCs from different species were seeded onto MEF-coated plates either cultured separately or mixed at different ratios for co-cultures in NBFR medium. The seeding ratio and density were empirically tested and decided based on cell growth rate. For 4-days-co-culture assays between human-mouse, cells were seeded at a 4:1 ratio at a density of 1.25 × 10-4 cells cm−2. At each of the indicated time points, cell concentration was manually counted and calculated, and the percentages of each cell line were determined using FACS Calibur system (BD Bioscience). Total cell numbers (tN) for each species in co-cultures or separate cultures were determined by multiplying total cell volume (V) with cell concentration (CC) and percentage (P). tN = V × CC × P. Cell density (cells cm−2) was calculated by dividing the total cell number by the surface area.
by Novogene

value: Mouse EpiSCs


title: 1_mPFC, control vehicle, 24h

description: Library name: X1

value: control vehicle


title: sc_dox free_mouse-1

description: Library name: m7_1


title: sc_dox free_mouse-2

description: Library name: m7_2


title: sc_dox_mouse-3

description: Library name: m6_3


title: sc_dox_mouse-2

description: Library name: m6_2


title: cc_dox free_mouse-2

description: Library name: m4_2


title: cc_dox free_mouse-3

description: Library name: m4_3


title: sc_dox_mouse-1

description: Library name: m6_1


title: cc_dox free_mouse-1

description: Library name: m4_1


title: MRX 2843 RELA Tumor RNA replicate 1

description:
Library name: MRX 2843 RELA Tumor RNA 1
Column Name in RELA_Tumor_raw_all_counts.csv: 909 MRX 2843 RELA Tumor RNA Duplicate 1

value: Brain tumor

value: Tissue


title: cc_dox_mouse-3

description: Library name: m2_3


title: BSC, stimulated with haptoglobin (400 µM) for 24 h, rep12

city: Zürich

first: Raphael

middle: Matthias

last: Buzzi

address: Rämistrasse 100

department: Division of Internal Medicine

country: Switzerland

institute: Universitätsspital and University of Zurich

description: Library name: E2_90_24_Hp400_M3

data_processing:
equence reads were processed using the FeatureCountsApp workflow. Reads were aligned to the Mus musculus GRCm39 reference genome in antisense strand mode, with a minimum mapping quality of 10, allowing multi-overlaps and counting multi-hits. FeatureCounts was run at the gene level with transcript type restricted to protein-coding, using paired-end or single-end mode as appropriate.
Assembly: GRCm39
Supplementary files format and content: Each processed data file contains normalized gene expression counts from RNA-seq experiments, with rows corresponding to gene identifiers and columns providing expression values for each gene in a given sample. The files are tab-delimited and are suitable for downstream analysis such as differential expression or pathway enrichment. All files use consistent formatting to facilitate direct comparison across experimental groups.

source_name: brain

growth_protocol: Coronal BSCs were prepared essentially as described by Stoppini et al. (1991) with minor adaptations.(Stoppini et al. 1991; Michler-Stuke et al. 1984; Sünwoldt et al. 2017; Voss et al. 2020) Briefly, deeply anesthetized mice were transcardially perfused with ice-cold phosphate-buffered saline (PBS, Gibco 17502048). Brains were removed, glued to the vibratome stage, and sectioned coronally (150 μm; speed 4, frequency 10) into Hibernate‑A at 4°C (<15 min). Two slices were placed on each PTFE insert (0.4 μm, Millicell) in 6‑well plates containing 1.1 mL plating medium (Neurobasal‑A + 20 % heat‑inactivated horse serum + antibiotic‑antimycotic). Cultures were kept at 37 °C, 5 % CO₂. On day 4, medium was replaced with serum‑free growth medium (Neurobasal‑A supplemented with N‑2, B‑27 Plus, G‑5, and antibiotics). Experiments were performed on day 7 or, for longer cultivation, after a half‑medium change.

extract_protocol:
Lexogen SPLIT kit
Illumina Truseq mRNA

treatment_protocol: On day 7, slices were treated for 24–48 hours with 200 μM Hb or heme-albumin, with or without stoichiometric Hp or Hpx.

value: brain

value: brain slice cultur

tag: strain


title: cc_dox_mouse-2

description: Library name: m2_2


title: cc_dox_mouse-1

description: Library name: m2_1


title: BSC, stimulated with haptoglobin (400 µM) for 24 h, rep11

description: Library name: E2_89_24_Hp400_M2


title: BSC, stimulated with haptoglobin (400 µM) for 24 h, rep10

description: Library name: E2_88_24_Hp400_M1


title: BSC, stimulated with haptoglobin (400 µM) for 24 h, rep8

description: Library name: E2_86_24_Hp400_F2


title: BSC, stimulated with haptoglobin (400 µM) for 24 h, rep7

description: Library name: E2_85_24_Hp400_F1


title: BSC, stimulated with haptoglobin (400 µM) for 24 h, rep9

description: Library name: E2_87_24_Hp400_F3


title: BSC, stimulated with haptoglobin (400 µM) for 48 h, rep9

description: Library name: E2_80_48_Hp400_F1


title: MRX 2843 Naive RELA RNA replicate 1

description:
Library name: MRX 2843 Naive RELA RNA 1
Column Name in RELA_Tumor_raw_all_counts.csv: 909 MRX 2843 Naive RELA RNA Duplicate 1

value: ZFTA-RELAfusion

value: 5 days treatment of 50 mg/kg of MRX-2843


title: Podocyte_input_rep2


title: BSC, stimulated with hemoglobin-haptoglobin (400 µM) for 24 h, rep10

description: Library name: E2_83_24_HbHpx400_M2


title: BSC, stimulated with haptoglobin (400 µM) for 48 h, rep11

description: Library name: E2_84_48_Hp400_F3


title: BSC, stimulated with haptoglobin (400 µM) for 48 h, rep8

description: Library name: E2_78_48_Hp400_M3


title: BSC, stimulated with hemoglobin-haptoglobin (400 µM) for 24 h, rep9

description: Library name: E2_77_24_HbHpx400_F2


title: BSC, stimulated with haptoglobin (400 µM) for 48 h, rep10

description: Library name: E2_82_48_Hp400_F2


title: BSC, control (0 µM, 24 h), rep11

description: Library name: E2_7_24_ctrl_M2


title: BSC, stimulated with haptoglobin (400 µM) for 48 h, rep7

description: Library name: E2_76_48_Hp400_M2


title: BSC, stimulated with hemoglobin-haptoglobin (400 µM) for 48 h, rep9

description: Library name: E2_66_48_HbHpx400_M2


title: BSC, stimulated with hemoglobin-haptoglobin (400 µM) for 48 h, rep10

description: Library name: E2_72_48_HbHpx400_F2


title: BSC, stimulated with hemoglobin-haptoglobin complex (400 µM) for 24 h, rep3

description: Library name: E2_65_24_HbHp400_F3


title: BSC, stimulated with hemoglobin-haptoglobin complex (400 µM) for 24 h, rep4

description: Library name: E2_71_24_HbHp400_M3


title: BSC, stimulated with haptoglobin (400 µM) for 48 h, rep6

description: Library name: E2_74_48_Hp400_M1


title: BSC, stimulated with hemoglobin-haptoglobin complex (400 µM) for 24 h, rep2

description: Library name: E2_63_24_HbHp400_F2


title: BSC, stimulated with hemoglobin-haptoglobin complex (400 µM) for 48 h, rep5

description: Library name: E2_62_48_HbHp400_F2


title: BSC, stimulated with hemoglobin-haptoglobin (400 µM) for 48 h, rep8

description: Library name: E2_64_48_HbHpx400_M1


title: BSC, stimulated with hemoglobin-haptoglobin complex (400 µM) for 24 h

description: Library name: E2_61_24_HbHp400_F1


title: BSC, stimulated with hemoglobin-haptoglobin complex (200 µM) for 24 h, rep8

description: Library name: E2_57_24_HbHp200_M4


title: BSC, stimulated with hemoglobin-haptoglobin complex (400 µM) for 48 h, rep4

description: Library name: E2_60_48_HbHp400_F1


title: BSC, stimulated with hemoglobin-haptoglobin complex (400 µM) for 48 h, rep3

description: Library name: E2_58_48_HbHp400_M4


title: BSC, stimulated with hemoglobin-haptoglobin complex (200 µM) for 24 h, rep7

description: Library name: E2_55_24_HbHp200_M3


title: BSC, stimulated with hemoglobin-haptoglobin complex (200 µM) for 24 h, rep5

description: Library name: E2_51_24_HbHp200_M1


title: BSC, stimulated with hemoglobin-haptoglobin complex (400 µM) for 48 h, rep2

description: Library name: E2_56_48_HbHp400_M3


title: BSC, stimulated with hemoglobin-haptoglobin complex (200 µM) for 24 h, rep6

description: Library name: E2_53_24_HbHp200_M2


title: BSC, stimulated with hemoglobin-haptoglobin complex (200 µM) for 48 h, rep8

description: Library name: E2_50_48_HbHp200_F4


title: BSC, stimulated with hemoglobin-haptoglobin complex (400 µM) for 48 h

description: Library name: E2_52_48_HbHp400_M1


title: BSC, stimulated with hemoglobin-haptoglobin complex (200 µM) for 24 h, rep4

description: Library name: E2_49_24_HbHp200_F4


title: BSC, stimulated with hemoglobin-haptoglobin complex (200 µM) for 24 h, rep2

description: Library name: E2_45_24_HbHp200_F2


title: BSC, stimulated with hemoglobin-haptoglobin complex (200 µM) for 48 h, rep5

description: Library name: E2_44_48_HbHp200_F1


title: BSC, stimulated with hemoglobin-haptoglobin complex (200 µM) for 48 h, rep6

description: Library name: E2_46_48_HbHp200_F2


title: BSC, stimulated with hemoglobin-haptoglobin complex (200 µM) for 48 h, rep7

description: Library name: E2_48_48_HbHp200_F3


title: BSC, stimulated with hemoglobin-haptoglobin complex (200 µM) for 24 h

description: Library name: E2_43_24_HbHp200_F1


title: BSC, stimulated with hemoglobin-haptoglobin complex (200 µM) for 24 h, rep3

description: Library name: E2_47_24_HbHp200_F3


title: BSC, stimulated with hemoglobin-haptoglobin complex (200 µM) for 48 h, rep3

description: Library name: E2_40_48_HbHp200_M3


title: BSC, stimulated with hemoglobin-haptoglobin complex (200 µM) for 48 h, rep2

description: Library name: E2_38_48_HbHp200_M2


title: BSC, stimulated with hemoglobin-haptoglobin (400 µM) for 24 h, rep8

description: Library name: E2_75_24_HbHpx400_F3


title: BSC, control (0 µM, 48 h), rep9

description: Library name: E2_2_48_ctrl_M1


title: BSC, stimulated with haptoglobin (400 µM) for 48 h, rep5

description: Library name: E1_84_48_Hp400_M5


title: BSC, stimulated with hemoglobin (400 µM) for 48 h, rep10

description: Library name: E2_28_48_Hb400_M4


title: BSC, stimulated with haptoglobin (400 µM) for 48 h, rep4

description: Library name: E1_79_48_Hp400_M1


title: BSC, stimulated with hemoglobin-haptoglobin complex (200 µM) for 48 h

description: Library name: E2_36_48_HbHp200_M1


title: BSC, stimulated with hemoglobin-haptoglobin (400 µM) for 48 h, rep6

description: Library name: E1_75_48_Hpx400_M2


title: BSC, stimulated with hemoglobin-haptoglobin (400 µM) for 48 h, rep5

description: Library name: E1_70_48_Hpx400_M2