title: MDSL Cell line PU.1 knock out Rep2

description:
Library name: MDSL_PU1_KnockOut_rep2
MDSL_SPI1_KO_bulk_Rep2

data_processing:
After demultiplexing with bcl2fastq v2.20 (Illumina, Inc.), raw data quality checks were performed with FastQC v0.11.8. Adapters removal and dynamic trimming of low-quality bases were performed using Trimmomatic v0.39 with parameters “ILLUMINACLIP:adapters.fa:2:30:10, LEADING:30, MAXINFO:50:0.7, MINLEN:40. Paired-end reads were aligned to the UCSC hg38 human genome using STAR v2.7 with parameters “--outSAMtype BAM SortedByCoordinate, --outFilterMultimapNmax 20. Uniquely mapped pairs were selected for downstream analysis using SAMtools v1.9. Alignments quality controls were carried out using Qualimap v2.2.2a. Gene-level quantification was performed using featureCounts of the Rsubread package v1.34 according to Human GRChg38 annotation. Gene-level counts were then processed with the edgeR to perform sample normalization using the ‘relative-log-expression’ (RLE) method.
Assembly: GRCh38 assembly version
Supplementary files format and content: Gene raw count matrix and log-normalized CPM (Counts per Million) matrix are provided in compressed tab-delimited format.

source_name: MDS-L

extract_protocol:
Human bone marrow aspirates were obtained from in accordance with the Italian laws and the policies and practices of the Ethical Committee of Humanitas Research Hospital. Patients were classified following the updated WHO classification of tumors and lymphoid tissues guidelines 1 and stratified by risk of evolution following the IPSS-R parameters. Bone marrow mononuclear cells (BMNCs) were isolated by density gradient separation with Lympholyte®-H Cell Separation Media (Cedarlane corporation, Burlington, USA) according to manufacturer’s instructions, frozen in fetal bovine serum (FBS) (Lonza, Basel, Switzerland) containing 10% DimethylSulfoxide (DMSO) (Sigma Aldrich, St. Louis, Missouri, USA) and cryopreserved in liquid nitrogen. Bone marrow HSPCs were isolated based on CD34+ surface marker using the MACS CD34 microbead kit on autoMACS (Miltenyi Biotech Inc, San Diego, CA). MDS-L cells were kindly provided by Dr. Daniel Starczynowski, Cincinnati Children's Hospital Medical Center and were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated FBS and 1% P/S and 10ng/mL of hrIL-3 (PeproTech, Paisley, UK). Cells were grown at 37°C and 5%CO2 and treated with 3uM DB2115 (Cat. No. HY-124676A Medchem, NJ, USA) for the specified time.   The crRNAs for PU.1 knock-out were designed using Benchling tool (crRNA sequences are listed in Supplemental Methods). Custom designed crRNAs and Alt-R™ CRISPR-Cas9 tracrRNA 20nmol (Cat. No. 1072533, IDT) were mixed in Nuclease-free Duplex Buffer (IDT) at a molar ratio of 1:1, annealed at 95˚C for 5 minutes and cooled down to room temperature (ramp scale -0.1˚C/sec). The annealed sgRNAs were incubated with Cas9 TrueCut V2 (Cat. No. 36499, Thermo Fisher) in a molar ratio of 1:1 at room temperature for 15 minutes before transfection. After complex formation, 1×106 MDS-L cells were resuspended in P3 Buffer and 10.8 µM Electroporation Enhancer and then transfected using P3 primary cell Nucleofector kit (Cat. No. V4XP3024, Lonza) with Amaxa Nucleofector device (Lonza). 48 hours after electroporation, cells were harvested for PU.1 knock-out validation by Western Blot, and for RNA extraction and library preparation.
Libraries for CD34+ mRNA sequencing were prepared by using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara). Libraries for MDS-L mRNA sequencing were prepared by using the Illumina Stranded mRNA Prep (Illumina). All samples were sequenced at an average of 40 million 50-bp pair-end reads with Novaseq 6000.
All RNA-seq data sets were processed in paired-end.

value: MDS-L

value: knock out


title: Human_gonad_8

status: Public on Jan 29 2026

type: SRA

city: Campinas

first: Helena

last: Fabbri-Scallet

state: São Paulo

address: Av. Cândido Rondon, 400

department: Center for Molecular Biology and Genetic Engineering

country: Brazil

institute: State University of Campinas

description: Library name: OT-P3

library_source: transcriptomic

data_processing:
Raw sequencing reads were quality-checked using FastQC.
Adapter sequences and low-quality reads were removed during preprocessing.
Cleaned reads were aligned to the human reference genome using STAR.
Gene-level read counts were generated using STAR ReadsPerGene.
Count matrices were used for downstream differential expression and pathway analyses.
Assembly: GRCh38
Supplementary files format and content: Processed data consist of tab-delimited text files containing gene-level read counts generated with STAR (ReadsPerGene) using Ensembl gene identifiers.

molecule: total RNA

organism: Homo sapiens

source_name: Gonad

extract_protocol:
Total RNA was extracted from FFPE or fresh gonadal tissue using protocols recommended by the library preparation kits, following the manufacturers’ instructions.
RNA sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero (Illumina, San Diego, CA, USA) for the FFPE samples and the SMARTer® Total RNA-Seq Kit v3 (Qiagen, CA, USA) for the RNA obtained from fresh tissue, following the manufacturer's recommendations.

tag: tissue

value: Gonad

tag: cell line

value: 16 months

tag: cell type

tag: genotype

value: Differences of Sex Development


title: Human_gonad_7

description: Library name: OT-P2

value: 2 years


title: MDSL Cell line Control Rep2

city: Milan

first: Serena

last: Ghisletti

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

description:
Library name: MDSL_Scramble_rep2
MDSL_scramble_bulk_Rep2

molecule: polyA RNA

value: control


title: Ped B30 GEX

city: New York

first: Patrick

last: Wilson

state: NY

address: 413 E 69th St

department: Pediatrics

country: USA

institute: Weill Cornell Medicine

description:
Library name: B30 GEX
multi
b30_feature_reference.csv

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger (v7.0.1 and v7.1.0) functions (mkfastq, count, vdj, multi)
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of cell barcode sequences
Supplementary files format and content: features.tsv.gz: list of gene IDs + names
Supplementary files format and content: matrix.mtx.gx: gene expression count data in Market Exchange Format
Supplementary files format and content: consenus.fasta: the consensus sequence of each assembled contig in FASTA format
Supplementary files format and content: filtered_contig_annotations.csv: high-level annotations of each high-confidence contigs from cell associated barcodes

source_name: Peripheral Blood Mononuclear Cell

extract_protocol:
HA-specific B cells (CD19+Probe+) and total CD19+ B cells were sorted and partitioned into nanoliter-scale Gel Bead-In-Emulsions (GEMs) to achieve single cell resolution using the 10x Genomics Chromium Controller and according to the manufacturer’s instruction
The sorted single cells were processed according to 10x Genomics 5’ single cell gene expression (GEX), B cell Immunoglobulin (Ig) enrichment (VDJ), and cell surface feature barcode (ADT) protocol to prepare the libraries for Illumina sequencing.

value: Peripheral Blood Mononuclear Cell

value: B cells

tag: age

tag: treatment

value: H3N2-H1N1 Influenza infection


title: Ped B1 control GEX

description:
Library name: B1 ctrl GEX
count
d1_ctrl_feature_reference.csv


title: Ped Ag30 control GEX

description:
Library name: Ag30 ctrl GEX
count
d30_ctrl_feature_reference.csv


title: Ped Ag1 control VDJ

description:
Library name: Ag1 ctrl VDJ
vdj


title: Human_gonad_4

description: Library name: PGD-P4

value: 25 years


title: Ped Ag30 VDJ

description:
Library name: Ag30 VDJ
vdj


title: Ped B30 ADT

description:
Library name: B30 ADT
multi
b30_feature_reference.csv

library_source: other

molecule: protein


title: Ped Ag1 VDJ

description:
Library name: Ag1 VDJ
vdj


title: Macrophage TGFβ+linezolid rep 2

city: Dusseldorf

first: Alexandru-Emil

last: Matei

address: Merowingerpl. 1A

country: Germany

institute: Heinrich-Heine-University Düsseldorf

description:
Library name: sample 35
TGFL82A002_MKRN240008613-1A_22C2LNLT4_L2

data_processing:
Raw sequencing reads for all samples were assessed for quality using FastQC on the Galaxy platform. This step identified adaptor sequences and low-quality bases. Adaptor sequences and low-quality bases were removed from all samples using Trim Galore on the Galaxy platform with default parameters. Trimmed reads from all samples were aligned to the reference genome GRCm39 or GRCh38.p14 using HISAT2 on the Galaxy platform. Default settings were applied for the alignment, and no samples were removed during this step. Gene-level read counts for all samples were generated using featureCounts on the Galaxy platform. The GTF annotation file from the reference genome GRCm39 or GRCh38.p14 was used for feature quantification.
Assembly: GRCm39 for mice and GRCh38.p14 for human
Supplementary files format and content: Txt file included raw counts for each samples

source_name: macrophage

extract_protocol:
Total RNA was extracted using Nucleospin RNA kits (Macherey-Nagel) according to the manufacturer’s instructions.
Total RNA was sent to Novogene Co., Ltd. (Cambridge, UK) for library preparation and sequencing. The libraries were constructed using Novogene's standard protocols for RNA sequencing. Details of the library construction procedure can be provided by the service provider upon request.

value: macrophage


title: Ped B1 control ADT

description:
Library name: B1 ctrl ADT
count
d1_ctrl_feature_reference.csv


title: MDSL Cell line Control Rep1

description:
Library name: MDSL_Scramble_rep1
MDSL_scramble_bulk_Rep1


title: Ped Ag1 control ADT

description:
Library name: Ag1 ctrl ADT
count
d1_ctrl_feature_reference.csv


title: Macrophage TGFβ+linezolid rep 1

description:
Library name: sample 34
TGFL7MN010_MKRN240008623-1A_22C2LNLT4_L2


title: Macrophage TGFβ rep 3

description:
Library name: sample 33
TGF82A017_MKRN240008617-1A_227Y3HLT4_L3


title: Ped Ag1 ADT

description:
Library name: Ag1 ADT
count
ag1_feature_reference.csv


title: Ped B1 GEX

description:
Library name: B1 GEX
multi


title: MDSL Cell line PU.1 knock out Rep3

description:
Library name: MDSL_PU1_KnockOut_rep3
MDSL_SPI1_KO_bulk_Rep3


title: MDSL Cell line PU.1 knock out Rep1

description:
Library name: MDSL_PU1_KnockOut_rep1
MDSL_SPI1_KO_bulk_Rep1


title: Human_gonad_6

description: Library name: OT-P1


title: Macrophage TGFβ rep 2

description:
Library name: sample 32
TGF82A002_MKRN240008612-1A_227Y3HLT4_L3


title: Ped Ag30 control ADT

description:
Library name: Ag30 ctrl ADT
count
d30_ctrl_feature_reference.csv


title: MDSL Cell line Control Rep3

description:
Library name: MDSL_Scramble_rep3
MDSL_scramble_bulk_Rep3


title: Human_gonad_1

description: Library name: PGD-P1


title: PY CYP7a1-KO 5

city: Melbourne

first: Andrew

last: Cox

state: Victoria

address: 305 Grattan St

country: Australia

institute: PeterMacCallum Cancer Centre

description:
Library name: PY-CYP75_S169_R1_001
Column name in counts file Crispants_RNAseq.txt: PY-CYP75_S169_R1_001

data_processing:
Raw sequencing data were generated on an Illumina NextSeq 2000 platform using single-end 100 bp reads.
Sequencing reads were initially aligned to the zebrafish danRer10 reference genome using Seqliner v2.6 and subsequently re-aligned to the GRCz11 genome assembly.
Gene-level quantification was performed using the Lawson Lab zebrafish transcriptome annotation (version 4.2.1).
Downstream differential expression and pathway analyses were performed using standard bioinformatic workflows as described in the associated manuscript.
Assembly: Danio rerio genome assembly GRCz11
Supplementary files format and content: Processed data files include tab-delimited text files containing gene-level raw read counts and normalised expression values (counts per million, CPM) for each RNA-seq sample.

organism: Danio rerio

source_name: whole zebrafish

growth_protocol: Zebrafish were housed under standard laboratory conditions and collected at 21 days post fertilisation.

extract_protocol:
Whole zebrafish larvae were euthanised in tricaine, pooled into microcentrifuge tubes, snap-frozen in liquid nitrogen, and stored at −80°C. Total RNA was extracted using the Direct-zol RNA Miniprep kit following homogenisation in TRIzol reagent, according to the manufacturer’s instructions. RNA concentration and integrity were assessed using the Agilent TapeStation system.
RNA sequencing libraries were prepared using the Lexogen QuantSeq 3′ mRNA-Seq library preparation protocol according to the manufacturer’s instructions. Libraries were generated from total RNA and are enriched for the 3′ end of polyadenylated transcripts.

treatment_protocol: Zebrafish embryos were injected with CRISPR/Cas9 complexes delivered into the yolk, using guide RNAs targeting SLC45a2 alone or in combination with TGR5 or CYP7a1.

value: whole zebrafish

value: crispr-cas9 gene knockout


title: Fibroblast TGFβ+linezolid rep 1

description:
Library name: sample 28
TGFL169_MKRN240020580-1A_22GV72LT4_L6

source_name: fibroblast

value: fibroblast


title: Ped Ag1 control GEX

description:
Library name: Ag1 ctrl GEX
count
d1_ctrl_feature_reference.csv


title: PY CYP7a1-KO 4

description:
Library name: PY-CYP74_S168_R1_001
Column name in counts file Crispants_RNAseq.txt: PY-CYP74_S168_R1_001


title: Fibroblast TGFβ rep 3

description:
Library name: sample 27
TGF198_MKRN240020571-1A_22C2KLLT4_L2


title: Macrophage TGFβ rep 1

description:
Library name: sample 31
TGF7MN010_MKRN240008622-1A_22C2LNLT4_L2


title: PY CYP7a1-KO 2

description:
Library name: PY-CYP72_S166_R1_001
Column name in counts file Crispants_RNAseq.txt: PY-CYP72_S166_R1_001


title: Fibroblast TGFβ rep 2

description:
Library name: sample 26
TGF172_MKRN240020575-1A_22C2KLLT4_L2


title: Ped Ag1 GEX

description:
Library name: Ag1 GEX
count
ag1_feature_reference.csv


title: Ped Ag30 ADT

description:
Library name: Ag30 ADT
count
ag30_feature_reference.csv


title: PY CYP7a1-KO 1

description:
Library name: PY-CYP71_S165_R1_001
Column name in counts file Crispants_RNAseq.txt: PY-CYP71_S165_R1_001


title: PY CYP7a1-KO 3

description:
Library name: PY-CYP73_S167_R1_001
Column name in counts file Crispants_RNAseq.txt: PY-CYP73_S167_R1_001


title: PY TGR5-KO 1

description:
Library name: PY-TGR51_S159_R1_001
Column name in counts file Crispants_RNAseq.txt: PY-TGR51_S159_R1_001


title: PCSS+linezolid rep 3

description:
Library name: sample 23
Line_185

source_name: Skin

value: Skin


title: PY SLC45a2-KO 5

description:
Library name: PY-SLC5_S158_R1_001
Column name in counts file Crispants_RNAseq.txt: PY-SLC5_S158_R1_001


title: PCSS+linezolid rep 1

description:
Library name: sample 21
Line_407


title: PCSS+linezolid rep 4

description:
Library name: sample 24
Line_32_MKRN240024774-1A_22HH5WLT4_L1


title: PY TGR5-KO 5

description:
Library name: PY-TGR55_S164_R1_001
Column name in counts file Crispants_RNAseq.txt: PY-TGR55_S164_R1_001


title: Macrophage TGFβ+linezolid rep 3

description:
Library name: sample 36
TGFL82A017_MKRN240008618-1A_227Y3HLT4_L3


title: PY TGR5-KO 4

description:
Library name: PY-TGR54_S163_R1_001
Column name in counts file Crispants_RNAseq.txt: PY-TGR54_S163_R1_001


title: PY SLC45a2-KO 2

description:
Library name: PY-SLC2_S155_R1_001
Column name in counts file Crispants_RNAseq.txt: PY-SLC2_S155_R1_001


title: Fibroblast TGFβ rep 1

description:
Library name: sample 25
TGF169_MKRN240020579-1A_22C2KLLT4_L2


title: Fibroblast TGFβ+linezolid rep 3

description:
Library name: sample 30
TGFL198_MKRN240020572-1A_22C2KLLT4_L2


title: PY TGR5-KO 2

description:
Library name: PY-TGR52_S160_R1_001
Column name in counts file Crispants_RNAseq.txt: PY-TGR52_S160_R1_001


title: PCSS+linezolid rep 2

description:
Library name: sample 22
Line_464


title: PCSS rep 1

description:
Library name: sample 17
DMSO_407


title: PY TGR5-KO 3

description:
Library name: PY-TGR53_S161_R1_001
Column name in counts file Crispants_RNAseq.txt: PY-TGR53_S161_R1_001


title: Fibroblast TGFβ+linezolid rep 2

description:
Library name: sample 29
TGFL172_MKRN240020576-1A_22C2KLLT4_L2


title: WT CYP7a1-KO 3

description:
Library name: WT-CYP73_S152_R1_001
Column name in counts file Crispants_RNAseq.txt: WT-CYP73_S152_R1_001


title: PY SLC45a2-KO 3

description:
Library name: PY-SLC3_S156_R1_001
Column name in counts file Crispants_RNAseq.txt: PY-SLC3_S156_R1_001


title: WT CYP7a1-KO 2

description:
Library name: WT-CYP72_S150_R1_001
Column name in counts file Crispants_RNAseq.txt: WT-CYP72_S150_R1_001


title: PY SLC45a2-KO 1

description:
Library name: PY-SLC1_S154_R1_001
Column name in counts file Crispants_RNAseq.txt: PY-SLC1_S154_R1_001


title: PCSS rep 3

description:
Library name: sample 19
DMSO_464


title: PCSS rep 4

description:
Library name: sample 20
DMSO_32_MKRN240024763-1A_22HH7WLT4_L3


title: PY SLC45a2-KO 4

description:
Library name: PY-SLC4_S157_R1_001
Column name in counts file Crispants_RNAseq.txt: PY-SLC4_S157_R1_001


title: MYDGF KO iNeutrophil

city: Madison

first: Anna

last: Huttenlocher

state: WI

address: 1550 Linden Drive

institute: University of Wisconsin School of Medicine and Public Health

description:
Library name: Sample2
10x Genomics

data_processing:
Data was processed with bcl2fastq for the generation of FASTQ files. Raw sequencing reads in the FASTQ files were mapped to GRCh38 human genome by Cell Ranger (v6.1.2, 10x Genomics).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: Bone marrow-derived human iPSCs (hiPSCs) – IISH2i-BM9 (WiCell) – were cultured in mTesR-Plus medium (STEMCELL Technologies) on tissue culture plates coated with Cultrex™ (Biotechne). hiPSCs were first differentiated into hemogenic endothelium in TeSR-E8 medium (STEMCELL Technologies) using ETV2 modified messenger RNA (mmRNA) (TriLink Biotechnologies), TasnIT reagent and mRNA boost (Mirus Bio). Cells were detached using TrypLE Select (Life Technologies) one hour prior to transfection. Lifted cells were then plated onto tissue culture plates coated with human collagen type IV (2.4 µg/mL; Millipore Sigma) in TeSR-E8 medium supplemented with ROCK inhibitor Y-27632 (ROCKi; Tocris). One day after transfection, the medium was modified to StemLineII media (Sigma Aldrich) supplemented with FGF2 (20 ng/mL; PeproTech) and VEGF-165 (20 ng/mL; PeproTech) to induce hemogenic endothelial cell differentiation; this cocktail is known as Media A. After two days media was changed to induce granulocyte-monocyte progenitor differentiation using StemLineII media (Sigma Aldrich) supplemented with FGF2 (20 ng/mL; PeproTech), GMCSF (25 ng/mL; Peprotech), and UM171 (50 nM; Xcess Biosciences); this cocktail is known as Media B. On days 8 to 10 following transfection, suspension cells were collected and plated for terminal neutrophil differentiation on tissue culture treated plates. These cells were cultured using StemSpan SFEM II medium (STEMCELL Technologies) supplemented with ExCyte 0.2% (Merck Millipore), GlutaMAX (1X; Thermo Fisher Scientific), and AM580 (2.5 µM; STEMCELL Technologies) at a density of 1x106 cells/mL; this cocktail is known as Media C. After four days, Media C was refreshed on the suspension cells. iNeutrophils were then collected from the supernatant 7 to 10 days after this media change.

extract_protocol:
2e5 iNeutrophils were collected at day 7 following transfer into Media C, spun down, and resuspended in 200 µL of PBS + 0.04% Bovine Serum Albumin (BSA; Sigma-Aldrich). All cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin–Madison Biotechnology Center (RRID: SCR_017757).
Libraries were constructed according to the Chromium Single Cell 3’ Reagent Kit v3.1 user guide (10x Genomics, Pleasanton, CA). Cell concentration and viability were quantified on the Luna-FX7 (Logos Biosystems, Anyang, South Korea) using acridine orange/propidium iodide stain. Cells were loaded onto a Chromium Single Cell Chip G chip for the single cell partitioning GEM reaction on the Chromium iX platform. Next, GEMs were transferred to emulsion safe strip tubes for reverse transcription and cell/transcript barcoding using an Eppendorf MasterCycler Pro thermocycler (Eppendorf, Hamburg, Germany). Following reverse transcription, GEMs were broken, and pooled single cell cDNA was amplified for 13 cycles, purified using SPRIselect beads (Beckman Coulter, Brea, CA), and quantified on a Bioanalyzer 2100 (Agilent, Santa Clara, CA) using the High Sensitivity DNA kit. A portion of the full-length cDNA was fragmented and used to generate cDNA libraries according to standard 10x Genomics workflow.

value: iPSC-derived neutrophil

value: MYDGF KO


title: Pu1_AML_patient_sample_372

description: Library name: PU1_AML_patient_sample_372

library_source: genomic

data_processing:
Paired-end reads were processed using trimmomatic-v0.39 for base-quality check and adaptor removal.Sequences were mapped onto the human genome using Bowtie-2 with the following settings: -N 1 -p 4 --end-to-end --time -x <genome index> -1 <fastq.gz1> -2 <fastq.gz2> -U <unpaired fastq.gz> --un-conc-gz <unmapped fastq.gz> --al-conc-gz <mapped fastq.gz>. Uniquely mapped reads were retained using samtools view with options -b -q 10 -o <out.bam>. Properly mapped pairs were selected and duplicate reads were then removed using ‘markdup –r’ function from samtools. Peaks were called using Macs-v2  against a reference ChIP input with parameters --format BAMPE and –q 0.01 in either broad or narrow modality for h3k27ac and Pu.1 samples, respectively. Peaks overlapping blacklisted regions (https://github.com/Boyle-Lab/Blacklist/blob/master/lists/hg38-blacklist.v2.bed.gz) was discarded using bedtools_v.2.30. For each sample, a fragment pile-up in ‘read per million’ was generated using Macs2-callpeak’ function with parameters --format BAMPE -B --SPMR. The resulting BedGraph file was then compared to that of the input to generate a signal profile in BigWig format for browser visualization with the Integrative Genomic Viewer.
Assembly: GRCh38 assembly version
Supplementary files format and content: Normalized coverage data are provided in BigWig format.

molecule: genomic DNA

source_name: Bone marrow-CD34+

extract_protocol:
Human bone marrow aspirates were obtained from in accordance with the Italian laws and the policies and practices of the Ethical Committee of Humanitas Research Hospital. Patients were classified following the updated WHO classification of tumors and lymphoid tissues guidelines 1 and stratified by risk of evolution following the IPSS-R parameters. Bone marrow mononuclear cells (BMNCs) were isolated by density gradient separation with Lympholyte®-H Cell Separation Media (Cedarlane corporation, Burlington, USA) according to manufacturer’s instructions, frozen in fetal bovine serum (FBS) (Lonza, Basel, Switzerland) containing 10% DimethylSulfoxide (DMSO) (Sigma Aldrich, St. Louis, Missouri, USA) and cryopreserved in liquid nitrogen. Bone marrow HSPCs were isolated based on CD34+ surface marker using the MACS CD34 microbead kit on autoMACS (Miltenyi Biotech Inc, San Diego, CA). MDS-L cells were kindly provided by Dr. Daniel Starczynowski, Cincinnati Children's Hospital Medical Center and were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated FBS and 1% P/S and 10ng/mL of hrIL-3 (PeproTech, Paisley, UK). Cell lines were grown at 37°C and 5%CO2 and treated with DB2115 (Cat. No. HY-124676A Medchem, NJ, USA) for the specified time and concentrations
For CD34+ HSPCs and MDS-L cells, H3K27Ac and PU.1 ChIP-seq were carried out fixing 1x10⁵ cells with 1% formaldehyde (cat. no. 252549, Merck, NJ, USA) for 10 min at room temperature followed by quenching with 125 mM Tris-HCl pH 7.6. Fixed samples were lysed using SDS Shearing Buffer D3 (Covaris, MA, USA) supplemented by protease inhibitors to prepare total extracts. Chromatin shearing was performed by sonication using microtube-130 AFA Fiber Strip V2 (Cat no. 520217, Covaris, MA, USA) with Covaris ME220 Focused-Ultrasonicator. For H3K27Ac and PU.1 ChIP-seq, then lysates were diluted with ChIP Buffer (10 mM Tris-HCl pH 7.6, 1 mM EDTA pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate) and incubated overnight at 4°C with protein G Dynabeads (cat. no.10009D, Invitrogen, Paisley, UK) previously coupled with 3 μg of H3K27Ac antibody (cat. no. ab4729, Abcam, Cambridge, UK), or 1.5ug of PU.1 antibody (Cat no. 2258S, Cell Signaling, MA, USA). After immunoprecipitation, beads were recovered using a magnetic stand and washed with RIPA buffer (50 mM HEPES-KOH at pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-deoxycholate). Immunoprecipitated chromatin was eluted and crosslink-reverted overnight at 65°C. DNA was purified with QIAquick PCR purification kit (cat. no. 28106, Qiagen, Hilden, Germany) and then quantified with QuantiFluor (cat. no. E2670, Promega, WI, USA).
DNA libraries were prepared from 0.5ng of DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (Cat no.  NEB E7645S, New England Biolabs GmbH) and Unique Dual Index Primer Pairs (Cat no. NEB E6440S, New England Biolabs GmbH) following producer instructions. The purified DNA libraries were quantified with Quantifluor reagent (cat. no. E2670, Promega, WI, USA) and library quality size was controlled with 4200 TapeStation System (Agilent, CA, USA) using the high-sensitivity assay HD5000 (cat. no. 5067-5592, Agilent, CA, USA).
All ChIPseq data sets were processed in paired-end.

value: Bone marrow-CD34+

tag: disease state

value: AML

tag: chip antibody


title: WT CYP7a1-KO 4

description:
Library name: WT-CYP74_S153_R1_001
Column name in counts file Crispants_RNAseq.txt: WT-CYP74_S153_R1_001


title: PCSS rep 2

description:
Library name: sample 18
EN1_Mut_185


title: WT CYP7a1-KO 1

description:
Library name: WT-CYP71_S149_R1_001
Column name in counts file Crispants_RNAseq.txt: WT-CYP71_S149_R1_001


title: Pu1_AML_patient_sample_317

description: Library name: PU1_AML_patient_sample_317


title: ENDO_D6_Rep1_Seq1

city: Los Angeles

first: Marty

middle: G

last: Yang

state: CA

address: 615 Charles E Young Dr S

department: Biological Chemistry

institute: University of California, Los Angeles

description: Library name: Sample 147

data_processing:
Reads were demultiplexed using lima to produce a .bam file for subreads for each sample.
Circular consensus sequences (CCS) were generated for each sample using ccs to produce a corresponding .bam file per sample.
Alignment was done using pbmm2 on each CCS .bam file to mm10 genome.
Assembly: mm10
Supplementary files format and content: _full.pickle files contain IPD measurements for each base in forward and reverse strands per CCS read. _zmwinfo.pickle files contain additional information per CCS read.
Supplementary files format and content: .bam files contain alignment information (to mm10 genome) and requisite tags for visualization of single-molecule accessibility patterns on IGV (Ml and Mm) from the default t-value used in our NN-HMM (t = 1 / 1,000). Included are additional corresponding tags for t = 31 / 1,000 (Mn and Mo), t = 51 / 1,000 (Mp and Mq), t = 71 / 1,000 (Mr and Ms), and t = 101 / 1,000 (Mt and Mu).

source_name: Cultured hiPSCs

extract_protocol:
Nuclei were isolated by incubating 1e6 cells in 1 mL ice-cold NE1 Buffer (20 mM HEPES, 10 mM KCl, 1 mM MgCl2, 0.1% Triton X-100, 20% glycerol, 1x Protease Inhibitor (Roche 4693132001)) for 5 min on ice. Nuclei were pelleted by centrifuging at 500 g for 5 min at 4C, and rinsed in 1 mL Buffer M (15 mM Tris-HCl pH 8.0, 15 mM NaCl, 60 mM KCl, 0.5 mM spermidine). Nuclei were re-pelleted by centrifuging at 500 g for 5 min at 4C, and were resuspended in 200 µL Buffer M with 1 mM SAM (NEB B9003S) and 10 µL high-concentration EcoGII (custom order from NEB). For footprinting, nuclei were incubated at 37C for a total of 30 min, with 1 µL 32 mM SAM stock spike-in after 15 min to supplement the reaction. Footprinted nuclei were pelleted by centrifuging at 500 g for 5 min at 4C, resuspended in 200 µL Buffer M with 1 mM CaCl2 and 0.02 U MNase (Sigma N3755), and incubated on ice for 30 min for MNase digest. 2 mM EGTA was added to stop the MNase reaction. For purifying DNA, samples were treated with 10 µL RNaseA (ThermoFisher AM2270) for 10 min at 37C, followed by the addition of 2 µL 10% SDS and 2 µL 20 mg/mL Proteinase K (ThermoFisher AM2548) and incubation >2 hr (up to overnight) at 65C. To extract DNA, an equal volume (~250 µL) phenol-chloroform-isoamyl alcohol was added, samples were mixed by brief vortexing, and samples were centrifuged at max speed for 2 min. The aqueous phase was transferred to a fresh tube, and 0.1x volumes 3M NaOAc, 2x volumes ice-cold 100% ethanol, and 1 µL GlycoBlue co-precipitant (Thermo AM9516) were added. Samples were mixed by inverting tubes and incubated overnight at -20C, centrifuged at max speed for 30 min at 4C, washed with 500 µL ice-cold 70% ethanol, air dried, and resuspended in 30 µL Buffer EB. DNA concentrations were measured by Qubit dsDNA High Sensitivity Quantification Kit (ThermoFisher Q32851).
Up to 1 µg DNA was prepared into PacBio SMRT libraries with the SMRTbell Express Template Prep Kit 2.0 / 3.0 per manufacturer’s directions. Briefly, this includes DNA damage repair, end repair, A-tailing, ligation of barcoded SMRTbell adapters, exonuclease clean-up, and 1x AMPure PB bead clean-up. DNA concentrations were measured by Qubit dsDNA High Sensitivity Quantification Kit and fragment size distributions were estimated with the Femto Pulse.

value: Cultured hiPSCs

value: EcoGII


title: ENDO_D6_Rep3_Seq1

description: Library name: Sample 149


title: WT iNeutrophil

description:
Library name: Sample1
10x Genomics

value: WT


title: Pu1_AML_patient_sample_300

description: Library name: PU1_AML_patient_sample_300


title: WT TGR5-KO 1

description:
Library name: WT-TGR51_S145_R1_001
Column name in counts file Crispants_RNAseq.txt: WT-TGR51_S145_R1_001


title: WT TGR5-KO 4

description:
Library name: WT-TGR54_S148_R1_001
Column name in counts file Crispants_RNAseq.txt: WT-TGR54_S148_R1_001


title: WT TGR5-KO 3

description:
Library name: WT-TGR53_S147_R1_001
Column name in counts file Crispants_RNAseq.txt: WT-TGR53_S147_R1_001


title: WT SLC45a2-KO 4

description:
Library name: WT-SLC4_S144_R1_001
Column name in counts file Crispants_RNAseq.txt: WT-SLC4_S144_R1_001


title: Pu1_AML_patient_sample_256

description: Library name: PU1_AML_patient_sample_256


title: Pu1_LR_patient_sample_214

description: Library name: PU1_LR_patient_sample_214

value: LR


title: ENDO_D6_Rep2_Seq1

description: Library name: Sample 148


title: Pu1_AML_patient_sample_286

description: Library name: PU1_AML_patient_sample_286


title: Pu1_LR_patient_sample_197

description: Library name: PU1_LR_patient_sample_197


title: Pu1_LR_patient_sample_162

description: Library name: PU1_LR_patient_sample_162


title: WT SLC45a2-KO 3

description:
Library name: WT-SLC3_S143_R1_001
Column name in counts file Crispants_RNAseq.txt: WT-SLC3_S143_R1_001


title: Ped B30 H1 only GEX

description:
Library name: B30 H1 only GEX
count
b_h1only_feature_reference.csv

value: Peripheral Blood Mononuclear Cell

value: H1N1 Influenza infection


title: ENDO_D0_Rep1_Seq1

description: Library name: Sample 144


title: ENDO_D0_Rep2_Seq1

description: Library name: Sample 145


title: WT SLC45a2-KO 2

description:
Library name: WT-SLC2_S142_R1_001
Column name in counts file Crispants_RNAseq.txt: WT-SLC2_S142_R1_001


title: ENDO_D0_Rep3_Seq1

description: Library name: Sample 146


title: Pu1_LR_patient_sample_138

description: Library name: PU1_LR_patient_sample_138


title: Ped B1 H1 only GEX

description:
Library name: B1 H1 only GEX
count
b_h1only_feature_reference.csv

value: B cells


title: Ped B30 reverse GEX

description:
Library name: B30 rev GEX
count
b_rev_feature_reference.csv

value: H1N1-H3N2 Influenza infection


title: HIPR T2 VDJ

description:
Library name: HIPR T2 VDJ
multi

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger (v7.0.1, v7.1.0, v9.0.0) functions (mkfastq, count, vdj, multi)
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of cell barcode sequences
Supplementary files format and content: features.tsv.gz: list of gene IDs + names
Supplementary files format and content: matrix.mtx.gx: gene expression count data in Market Exchange Format
Supplementary files format and content: consenus.fasta: the consensus sequence of each assembled contig in FASTA format
Supplementary files format and content: filtered_contig_annotations.csv: high-level annotations of each high-confidence contigs from cell associated barcodes

value: 6-12 months

value: Influenza inactivated vaccines


title: Ped B1 reverse ADT

description:
Library name: B1 rev ADT
count
b_rev_feature_reference.csv


title: DRG, contralateral, uninjured

city: St. Louis

first: Valeria

last: Cavalli

state: MO

address: 1 Bookings Dr.

institute: Washington University in St. Louis

description:
Library name: CONTRA
10X Genomics

data_processing:
A digital expression matrix was obtained using the 10X Genomics Cell Ranger pipeline.
Assembly: Mus musculus mm10
Supplementary files format and content: Tab-separated values and matrix files

organism: Mus musculus

source_name: Dorsal root ganglion (L4-L5)

extract_protocol:
Whole DRG’s were dissociated with enzyme mix (Papain, Collagenase) to a single cell suspension, washed in 1X PBS+0.2%BSA solution, passed through a 70-micron cell strainer and FACS sorted using live/dead staining. Sorted cells were loaded on the 10X Chromium system.
single-cell RNA-Seq libraries were prepared using GemCode Single-Cell 3′ Gel Bead and Library Kit (10x Genomics). polyA selection based RNA capture as per the manufacturer's instructions provided by 10X genomics platform. Libraries were prepared as per manufacturer's insturctions provided by 10X genomics platform (https://www.10xgenomics.com/single-cell/).

value: Dorsal root ganglion (L4-L5)

tag: strain

value: 8-12 weeks

tag: Sex

value: female

value: uninjured


title: HIPR T2 GEX

description:
Library name: HIPR T2 GEX
multi
hipr_t2_feature_reference.csv


title: WT SLC45a2-KO 1

description:
Library name: WT-SLC1_S141_R1_001
Column name in counts file Crispants_RNAseq.txt: WT-SLC1_S141_R1_001

value: whole zebrafish

value: crispr-cas9 gene knockout


title: Pu1_LR_patient_sample_156

description: Library name: PU1_LR_patient_sample_156

value: Bone marrow-CD34+


title: Ped B30 reverse ADT

description:
Library name: B30 rev ADT
count
b_rev_feature_reference.csv


title: WT TGR5-KO 2

description:
Library name: WT-TGR52_S146_R1_001
Column name in counts file Crispants_RNAseq.txt: WT-TGR52_S146_R1_001


title: DRG, AIH, rep 2

description:
Library name: AIH_n2
10X Genomics

value: acute intermittent hypoxia


title: Ped B30 H1 only ADT

description:
Library name: B30 H1 only ADT
count
b_h1only_feature_reference.csv


title: HIPR T2 ADT

description:
Library name: HIPR T2 ADT
multi


title: Ped B1 H1 only ADT

description:
Library name: B1 H1 only ADT
count
b_h1only_feature_reference.csv


title: Pu1_LR_patient_sample_114

description: Library name: PU1_LR_patient_sample_114


title: RNA library from F2 12 weeks IVF Liver Female 5 [IVF_F2_12wks_Liver_Female_5]

city: Philadelphia

first: Eric

middle: Alejandro

last: Rhon Calderon

state: Pennsylvania

address: 3400 Civic Center Blvd, Bldg 421, Floor 9-175

department: Cell and Developmental Biology

institute: University of Pennsylvania

description: Library name: IVF_F2_12wks_Liver_Female_5

data_processing:
RNA-seq reads were trimmed for quality using Trimmomatic (version 0.32). Illumina TruSeq3-PE primers, leading and trailing low-quality (below quality 3) and N base calls were trimmed, and reads were scanned using a 4-bp sliding window and trimmed when the average quality per base dropped below 15. Reads of at least 30-bp in length following this quality control process were retained and used for subsequent analyses.
The resulting reads were then aligned to mm10 reference genome assembly using STAR (version 2.3.0e), allowing read pairs to align no farther than 2000-bp apart and keeping alignments with a mapping quality score (MAPQ) greater than 1 for genome-wide transcript counting.
FeatureCounts (version 1.5.0) was used to generate a matrix of mapped fragments per RefSeq annotated gene.
Analysis for differential gene expression was performed using DESeq2 with the cutoff of FDR < 0.05. Clustering and heatmaps of differentially expressed genes were generated using heatmaply R package. Chord plots were done using complexheatmap, clusterprofiler and circlize packages in R. WGCNA was done using the WGCNA package for R.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: F2 12 weeks Liver

growth_protocol: All animals were housed in polysulfone cages containing drinking water and chow (Laboratory Irradiated Rodent Diet 5LG4, LabDiet) ad libitum.

extract_protocol:
For tissue: RNA was extracted using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries. For single oocytes and cumulus cells: a modified SMART-seq extraction protocol was used using TCL and BME for cell lysis
For tissue: RNA libraries for RNA-seq were prepared using KAPA Stranded mRNA-Seq Kit (Illumina Platforms) and KAPA Single-Indexed adapter kit following manufacturer's protocols. For single oocytes and cumulus cells: Nextera Library prep and Nextera sequencing indexes (Illumina) were used.

treatment_protocol: E18.5 ovaries, 12 weeks ovaries, 39 weeks ovaries, 12 weeks single oocytes, 39 weeks single oocytes, 12 cumulus cells pools, 39 weeks cumulus cells pools, F2 12 weeks testis, F2 12 weeks male livers, F2 12 weeks ovaries, F2 weeks female livers awere collected, snap frozen in liquid nitrogen and stored at -80C for RNA extraction.

value: F2 12 weeks Liver

value: Female

value: IVF


title: DRG, SNC, injured

description:
Library name: SNC
10X Genomics

value: sciatic nerve crush


title: DRG, AIH, rep 1

description:
Library name: AIH_n1
10X Genomics


title: Pu1_AML_patient_sample_63

description: Library name: PU1_AML_patient_sample_63

value: AML


title: Ped B1 reverse GEX

description:
Library name: B1 rev GEX
count
b_rev_feature_reference.csv

value: Peripheral Blood Mononuclear Cell

value: B cells


title: Pu1_AML_patient_sample_79

description: Library name: PU1_AML_patient_sample_79


title: RNA library from F2 12 weeks IVF Liver Female 7 [IVF_F2_12wks_Liver_Female_7]

description: Library name: IVF_F2_12wks_Liver_Female_7


title: RNA library from F2 12 weeks IVF Liver Female 3 [IVF_F2_12wks_Liver_Female_3]

description: Library name: IVF_F2_12wks_Liver_Female_3


title: Pu1_LR_patient_sample_74

description: Library name: PU1_LR_patient_sample_74

value: LR


title: RNA library from F2 12 weeks IVF Liver Female 4 [IVF_F2_12wks_Liver_Female_4]

description: Library name: IVF_F2_12wks_Liver_Female_4


title: RNA library from F2 12 weeks IVF Liver Female 6 [IVF_F2_12wks_Liver_Female_6]

description: Library name: IVF_F2_12wks_Liver_Female_6


title: Pu1_LR_patient_sample_121

description: Library name: PU1_LR_patient_sample_121


title: SE6_paired.counts

city: Camerino

first: Michele

last: Bellesi

address: Via Gentile III Da Varano

institute: University of Camerino

description:
Library name: Sample 8
raw counts for all samples

data_processing:
All the raw data were analysed using Galaxy Europe_https://usegalaxy.eu
Using FastQC for quality control, Trimmomatic for read trimming
Alignment to the mm39 mouse genome followed by filtering with SAMtools
Gene quantification with featureCounts, differential expression analysis with DESeq2
Functional enrichment analysis using STRING
Assembly: mm39
Supplementary files format and content: Raw read counts for each sample are provided in tab-separated matrix tables
Supplementary files format and content: Normalized read counts for each sample provided as tab-separated matrix tables

source_name: Brain tissue

extract_protocol:
RNA extraction with Qiagen RNeasy Mini Kit_performed by the GENEWIZ Germany GmbH Part of Azenta Life Sciences
Library prepration all completed by GENEWIZ Germany GmbH Part of Azenta Life Sciences

treatment_protocol: 11 days of rocking during the light period

value: Brain tissue

value: Rocking during light period


title: Pu1_LR_patient_sample_55

description: Library name: PU1_LR_patient_sample_55


title: RNA library from F2 12 weeks Natural Liver Female 5 [Natural_F2_12wks_Liver_Female_5]

description: Library name: Natural_F2_12wks_Liver_Female_5

value: Natural


title: RNA library from F2 12 weeks Natural Liver Female 4 [Natural_F2_12wks_Liver_Female_4]

description: Library name: Natural_F2_12wks_Liver_Female_4


title: Mouse heart single cell RNA-seq under NFD or HFD

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

description:
Library name: ParseSublibraries
Parse sublibraries for scRNA samples. NFD sample is for A1 through A6, HFD sample is A7 through A12

data_processing:
Parse split-pipe v1.0.4
Assembly: mm10
Supplementary files format and content: Cell x count matrices

source_name: Whole heart

growth_protocol: Male C57BL/6J mice were housed under standard laboratory conditions with controlled temperature and a 12-hour light/dark cycle.

extract_protocol:
Whole hearts were harvested and enzymatically dissociated into single-cell suspensions according to standard protocols. Cells were filtered to remove debris, counted, and assessed for viability prior to single-cell RNA sequencing library preparation.
Single-cell RNA sequencing libraries were prepared using the Evercode Whole Transcriptome Mini v3 kit (Parse Biosciences) following the manufacturer’s protocol. Cells were barcoded using Parse Biosciences’ combinatorial barcoding strategy, and libraries were amplified and prepared for paired-end sequencing.

treatment_protocol: NFD (normal fat diet, 10% kcal fat, 4 weeks) or HFD (high fat diet, 60% kcal fat, 4 weeks)

value: Whole heart

value: male

value: NFD or HFD


title: RNA library from F2 12 weeks IVF Liver Female 2 [IVF_F2_12wks_Liver_Female_2]

description: Library name: IVF_F2_12wks_Liver_Female_2


title: SE4_paired.counts

description:
Library name: Sample 6
raw counts for all samples


title: CTR5_paired.counts

description:
Library name: Sample 4
raw counts for all samples


title: RNA library from F2 12 weeks Natural Liver Female 1 [Natural_F2_12wks_Liver_Female_1]

description: Library name: Natural_F2_12wks_Liver_Female_1


title: RNA library from F2 12 weeks IVF Liver Female 1 [IVF_F2_12wks_Liver_Female_1]

description: Library name: IVF_F2_12wks_Liver_Female_1


title: Pu1_LR_patient_sample_50

description: Library name: PU1_LR_patient_sample_50


title: RNA library from F2 12 weeks IVF Ovary Female 6 [IVF_F2_12wks_Ovary_Female_6]

description: Library name: IVF_F2_12wks_Ovary_Female_6

source_name: F2 12 weeks Ovary

value: F2 12 weeks Ovary


title: RNA library from F2 12 weeks Natural Liver Female 6 [Natural_F2_12wks_Liver_Female_6]

description: Library name: Natural_F2_12wks_Liver_Female_6


title: Pu1_LR_patient_sample_56

description: Library name: PU1_LR_patient_sample_56

value: Bone marrow-CD34+


title: RNA library from F2 12 weeks Natural Liver Female 3 [Natural_F2_12wks_Liver_Female_3]

description: Library name: Natural_F2_12wks_Liver_Female_3


title: Pu1_AML_patient_sample_44

description: Library name: PU1_AML_patient_sample_44


title: RNA library from F2 12 weeks IVF Ovary Female 3 [IVF_F2_12wks_Ovary_Female_3]

description: Library name: IVF_F2_12wks_Ovary_Female_3


title: Pu1_AML_patient_sample_39

description: Library name: PU1_AML_patient_sample_39


title: CTR2_paired.counts

description:
Library name: Sample 2
raw counts for all samples


title: RNA library from F2 12 weeks IVF Ovary Female 2 [IVF_F2_12wks_Ovary_Female_2]

description: Library name: IVF_F2_12wks_Ovary_Female_2


title: RNA library from F2 12 weeks Natural Liver Female 2 [Natural_F2_12wks_Liver_Female_2]

description: Library name: Natural_F2_12wks_Liver_Female_2


title: SE3_paired.counts

description:
Library name: Sample 5
raw counts for all samples


title: Pu1_AML_patient_sample_38

description: Library name: PU1_AML_patient_sample_38


title: Allogeneic treated vancomycin rep5

description:
Library name: sample 16
Vancomycin5

value: Skin


title: Pu1_LR_patient_sample_54

description: Library name: PU1_LR_patient_sample_54


title: SE5_paired.counts

description:
Library name: Sample 7
raw counts for all samples


title: RNA library from F2 12 weeks IVF Ovary Female 1 [IVF_F2_12wks_Ovary_Female_1]

description: Library name: IVF_F2_12wks_Ovary_Female_1


title: Pu1_AML_patient_sample_42

description: Library name: PU1_AML_patient_sample_42


title: RNA library from F2 12 weeks IVF Ovary Female 4 [IVF_F2_12wks_Ovary_Female_4]

description: Library name: IVF_F2_12wks_Ovary_Female_4


title: Pu1_LR_patient_sample_23

description: Library name: PU1_LR_patient_sample_23


title: rat adrenal gland, Dexamethasone replicate 1

type: RNA

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

description: Adrenal gland from rat receiving Dexamethasone injections at 0, 12, 24 h, decapitated 12 h after last injection

hyb_protocol: Biotin-labelled cDNA fragments (5.5 μg) were hybridized to Affymetrix Rat Gene 1.1 ST Array Strips at 45°C for 20 h.

scan_protocol: After hybridization, array strips were washed and stained using the Fluidics Station of Gene Atlas System (Affymetrix), then scanned using the Imaging Station of Gene Atlas System.

data_processing: Raw CEL files were processed using R (v4.5.1) with Bioconductor packages. Gene expression values were calculated using Robust Multiarray Average (RMA) normalization algorithm implemented in the affy library. Differential expression analysis was performed using limma package with empirical Bayes moderation. DEGs were identified using |fold change| >= 1.8 and adjusted p-value < 0.05 (Benjamini-Hochberg FDR correction).

label: biotin

organism: Rattus norvegicus

source_name: rat adrenal gland

label_protocol: Total RNA (100 ng) underwent two rounds of sense cDNA amplification, biotin labelling, and fragmentation using the GeneChip WT Plus Reagent Kit (Affymetrix) following manufacturer's instructions.

growth_protocol: Adult male Wistar rats (160-200 g) were obtained from the Laboratory Animals Breeding Centre, Poznan University of Medical Sciences. Animals were housed under standard laboratory conditions with a 12:12 h light-dark cycle at 22-24°C, with ad libitum access to standard chow and tap water. Prior to experiments, animals were habituated to human contact and handled with care to mitigate stress.

extract_protocol: Total RNA was extracted from adrenal glands using TRI Reagent (Sigma-Aldrich) followed by purification using NucleoSpin Total RNA Isolation columns (Qiagen). RNA quantity was determined using NanoDrop spectrophotometer. RNA purity was assessed by 260/280 nm ratio (>=1.8 required). RNA integrity was verified using Bioanalyzer 2100 (Agilent), with RIN values ranging from 8.5 to 10 (mean: 9.2).

treatment_protocol: Animals were randomly assigned to four groups (n=3 per group). Control: saline injections at 0, 12, 24 h. Acute ACTH: single ACTH injection (Synacthen, 5 μg/rat). Prolonged ACTH: ACTH injections at 0, 12, 24 h. Dexamethasone: Dexamethasone injections (Dexaven, 5 μg/rat) at 0, 12, 24 h. Control, Prolonged ACTH, and Dexamethasone groups were decapitated 12 h after last injection; Acute ACTH group was decapitated 1 h post-injection.

value: adrenal gland

value: Dexamethasone 5 μg/rat at 0, 12, 24 h

tag: time point


title: Allogeneic treated vancomycin rep4

description:
Library name: sample 15
Vancomycin4


title: RNA library from F2 12 weeks Natural Ovary Female 5 [Natural_F2_12wks_Ovary_Female_5]

description: Library name: Natural_F2_12wks_Ovary_Female_5

value: Female


title: rat adrenal gland, Dexamethasone replicate 2


title: RNA library from F2 12 weeks Natural Ovary Female 4 [Natural_F2_12wks_Ovary_Female_4]

description: Library name: Natural_F2_12wks_Ovary_Female_4


title: CTR4_paired.counts

description:
Library name: Sample 3
raw counts for all samples


title: rat adrenal gland, Prolonged ACTH replicate 2

description: Adrenal gland from rat receiving ACTH injections at 0, 12, 24 h, decapitated 12 h after last injection

value: ACTH 5 μg/rat at 0, 12, 24 h


title: RNA library from F2 12 weeks IVF Ovary Female 5 [IVF_F2_12wks_Ovary_Female_5]

description: Library name: IVF_F2_12wks_Ovary_Female_5

value: IVF


title: Allogeneic treated vancomycin rep1

description:
Library name: sample 12
Vancomycin1


title: Allogeneic treated vancomycin rep2

description:
Library name: sample 13
Vancomycin2


title: RNA library from F2 12 weeks Natural Ovary Female 3 [Natural_F2_12wks_Ovary_Female_3]

description: Library name: Natural_F2_12wks_Ovary_Female_3


title: RNA library from F2 12 weeks Natural Ovary Female 2 [Natural_F2_12wks_Ovary_Female_2]

description: Library name: Natural_F2_12wks_Ovary_Female_2


title: rat adrenal gland, Dexamethasone replicate 3


title: Allogeneic treated linezolid rep3

description:
Library name: sample 10
linezolid5


title: rat adrenal gland, Acute ACTH replicate 1

description: Adrenal gland from rat receiving single ACTH injection (Synacthen, 5 μg/rat), decapitated 1 h post-injection

value: ACTH 5 μg/rat single injection

value: 1 h


title: Allogeneic treated vancomycin rep3

description:
Library name: sample 14
Vancomycin3


title: rat adrenal gland, Acute ACTH replicate 3


title: MDSL Cell line DB2115-treated 20h RNA-seq Rep4

description: Library name: MDSL_INH_20h_rep4

data_processing:
After demultiplexing with bcl2fastq v2.20 (Illumina, Inc.), raw data quality checks were performed with FastQC v0.11.8. Adapters removal and dynamic trimming of low-quality bases were performed using Trimmomatic v0.39 with parameters “ILLUMINACLIP:adapters.fa:2:30:10, LEADING:30, MAXINFO:50:0.7, MINLEN:40. Paired-end reads were aligned to the UCSC hg38 human genome using STAR v2.7 22 with parameters “--outSAMtype BAM SortedByCoordinate, --outFilterMultimapNmax 20. Uniquely mapped pairs were selected for downstream analysis using SAMtools v1.9. Alignments quality controls were carried out using Qualimap v2.2.2a 23. Gene-level quantification was performed using featureCounts of the Rsubread package v1.34 according to Human GRChg38 annotation. Gene-level counts were then processed with the edgeR  R-package 24 to perform sample normalization using the ‘relative-log-expression’ (RLE) method.
Assembly: GRCh38 assembly version
Supplementary files format and content: Gene raw count matrix and log-normalized CPM (Counts per Million) matrix are provided in compressed tab-delimited format.

extract_protocol:
Human bone marrow aspirates were obtained from in accordance with the Italian laws and the policies and practices of the Ethical Committee of Humanitas Research Hospital. Patients were classified following the updated WHO classification of tumors and lymphoid tissues guidelines 1 and stratified by risk of evolution following the IPSS-R parameters. Bone marrow mononuclear cells (BMNCs) were isolated by density gradient separation with Lympholyte®-H Cell Separation Media (Cedarlane corporation, Burlington, USA) according to manufacturer’s instructions, frozen in fetal bovine serum (FBS) (Lonza, Basel, Switzerland) containing 10% DimethylSulfoxide (DMSO) (Sigma Aldrich, St. Louis, Missouri, USA) and cryopreserved in liquid nitrogen. Bone marrow HSPCs were isolated based on CD34+ surface marker using the MACS CD34 microbead kit on autoMACS (Miltenyi Biotech Inc, San Diego, CA). MDS-L cells were kindly provided by Dr. Daniel Starczynowski, Cincinnati Children's Hospital Medical Center and were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated FBS and 1% P/S and 10ng/mL of hrIL-3 (PeproTech, Paisley, UK). Cells were grown at 37°C and 5%CO2 and treated with 3uM DB2115 (Cat. No. HY-124676A Medchem, NJ, USA) for the specified time.
Libraries for CD34+ mRNA sequencing were prepared by using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara). Libraries for MDS-L mRNA sequencing were prepared by using the Illumina Stranded mRNA Prep (Illumina). All samples were sequenced at an average of 40 million 50-bp pair-end reads with Novaseq 6000.
All RNA-seq data sets were processed in paired-end.

value: MDS-L

value: DB2115-treated 20h


title: CTR1_paired.counts

description:
Library name: Sample 1
raw counts for all samples

value: Brain tissue


title: Allogeneic treated linezolid rep4

description:
Library name: sample 11
linezolid6


title: RNA library from F2 12 weeks Natural Ovary Female 1 [Natural_F2_12wks_Ovary_Female_1]

description: Library name: Natural_F2_12wks_Ovary_Female_1

value: Natural


title: MDSL Cell line DB2115-treated 20h RNA-seq Rep3

description: Library name: MDSL_INH_20h_rep3


title: MDSL Cell line DB2115-treated 20h RNA-seq Rep1

description: Library name: MDSL_INH_20h_rep1


title: RNA library from F2 12 weeks IVF Liver Male 7 [IVF_F2_12wks_Liver_Male_7]

description: Library name: IVF_F2_12wks_Liver_Male_7

value: F2 12 weeks Liver

value: Male


title: Allogeneic treated linezolid rep2

description:
Library name: sample 9
linezolid2


title: rat adrenal gland, Prolonged ACTH replicate 1


title: rat adrenal gland, Acute ACTH replicate 2


title: rat adrenal gland, Prolonged ACTH replicate 3


title: RNA library from F2 12 weeks IVF Liver Male 6 [IVF_F2_12wks_Liver_Male_6]

description: Library name: IVF_F2_12wks_Liver_Male_6


title: Pu1_LR_patient_sample_5

description: Library name: PU1_LR_patient_sample_5

value: LR


title: MDSL Cell line DB2115-treated 20h RNA-seq Rep2

description: Library name: MDSL_INH_20h_rep2


title: Allogeneic rep 3

description:
Library name: sample 7
Allogeneic3


title: RNA library from F2 12 weeks IVF Liver Male 5 [IVF_F2_12wks_Liver_Male_5]

description: Library name: IVF_F2_12wks_Liver_Male_5


title: RNA library from F2 12 weeks IVF Liver Male 4 [IVF_F2_12wks_Liver_Male_4]

description: Library name: IVF_F2_12wks_Liver_Male_4


title: MDSL Cell line DB2115-treated 8h RNA-seq Rep4

description: Library name: MDSL_INH_8h_rep4

value: DB2115-treated 8h


title: MDSL Cell line DB2115-treated 8h RNA-seq Rep3

description: Library name: MDSL_INH_8h_rep3


title: ARDS, LLL1, Visium HD

city: Chicago

first: Yuanqing

last: Yan

state: IL

address: 303 E Superior Street

institute: Northwestern University

description:
Library name: 8_ARDS-LLL-1
10x Genomics

data_processing:
For scRNAseq, Raw scRNA-seq reads were demultiplexed with CellRanger (v7.1.0) and mapped to the human genome (HG38). Ambient RNA was removed using SoupX, and doublets were filtered with scDblFinder. Additional quality filtering with Seurat excluded cells that had <200 or >7,500 unique features, <400 or >40,000 total RNA counts, or >10% mitochondrial content.  For Visium HD, images were aligned with Loupe Browser (V8.0.0), and Space Ranger (10X Genomics; V3.1.0) was used for genome mapping (HG38). Bin2cell aggregated 2 μm bins to reconstruct single-cell-like profiles based on H&E morphology and gene expression, using 0.5 μm per pixel resolution. Scanpy was employed for downstream analysis; cells with <100 or >40,000 features or >20% mitochondrial content were excluded
Assembly: HG38
Supplementary files format and content: HDF5 of processed data
Library strategy: Spatial Transcriptomics

source_name: Lung

extract_protocol:
Snap-frozen lung samples were obtained for scRNA-seq and formalin-fixed, paraffin-embedded specimens were used for Visium HD spatial transcriptomics.
For scRNAseq, library was performed according to 10X Genomics Chromium Single Cell Flex Gene Expression Assay and sequenced on a HiSeq 4000. For Visium HD, the samples were sectioned at 5 μm and processed at the Northwestern University NUSeq Core according to the manufacturer’s protocol (Visium HD v1).

value: Lung


title: MDSL Cell line DB2115-treated 8h RNA-seq Rep2

description: Library name: MDSL_INH_8h_rep2


title: rat adrenal gland, Control replicate 3

description: Adrenal gland from control rat, saline injections at 0, 12, 24 h, decapitated 12 h after last injection

value: saline control


title: Allogeneic treated linezolid rep1

description:
Library name: sample 8
linezolid1

value: Skin


title: RNA library from F2 12 weeks IVF Liver Male 1 [IVF_F2_12wks_Liver_Male_1]

description: Library name: IVF_F2_12wks_Liver_Male_1


title: ARDS, LUL, Visium HD

description:
Library name: 7_ARDS-LUL
10x Genomics


title: RNA library from F2 12 weeks IVF Liver Male 2 [IVF_F2_12wks_Liver_Male_2]

description: Library name: IVF_F2_12wks_Liver_Male_2


title: rat adrenal gland, Control replicate 2

value: adrenal gland


title: MDSL Cell line Untreated RNA-seq Rep4

description: Library name: MDSL_UT_rep4

value: Untreated


title: Pu1_LR_patient_sample_22

description: Library name: PU1_LR_patient_sample_22

value: Bone marrow-CD34+


title: MDSL Cell line Untreated RNA-seq Rep3

description: Library name: MDSL_UT_rep3


title: ARDS, RLL1, Visium HD

description:
Library name: 4_ARDS-RLL1
10x Genomics


title: rat adrenal gland, Control replicate 1


title: ARDS, RLL2, Visium HD

description:
Library name: 6_ARDS-RLL-2
10x Genomics


title: MDSL Cell line DB2115-treated 8h RNA-seq Rep1

description: Library name: MDSL_INH_8h_rep1


title: Allogeneic rep 2

description:
Library name: sample 6
Allogeneic2


title: Allogeneic rep 1

description:
Library name: sample 5
Allogeneic1


title: ARDS, LLL2, Visium HD

description:
Library name: 10_ARDS-LLL-2
10x Genomics


title: RNA library from F2 12 weeks IVF Liver Male 3 [IVF_F2_12wks_Liver_Male_3]

description: Library name: IVF_F2_12wks_Liver_Male_3

value: IVF


title: MDSL Cell line DB2115-treated 12h Rep2

description: Library name: MDSL_INH_12h_Rep2

data_processing:
Paired-end reads were processed using trimmomatic-v0.39 for base-quality check and adaptor removal.Sequences were mapped onto the human genome using Bowtie-2 with the following settings: -N 1 -p 4 --end-to-end --time -x <genome index> -1 <fastq.gz1> -2 <fastq.gz2> -U <unpaired fastq.gz> --un-conc-gz <unmapped fastq.gz> --al-conc-gz <mapped fastq.gz>. Uniquely mapped reads were retained using samtools view with options -b -q 10 -o <out.bam>. Properly mapped pairs were selected and duplicate reads were then removed using ‘markdup –r’ function from samtools. Peaks were called using Macs-v2  against a reference ChIP input with parameters --format BAMPE –broad –broad--cutoff 0.01. Peaks overlapping blacklisted regions (https://github.com/Boyle-Lab/Blacklist/blob/master/lists/hg38-blacklist.v2.bed.gz) was discarded using bedtools_v.2.30. For each sample, a fragment pile-up in ‘read per million’ was generated using Macs2-callpeak’ function with parameters --format BAMPE -B --SPMR. The resulting BedGraph file was then compared to that of the input to generate a signal profile in BigWig format for browser visualization with the Integrative Genomic Viewer.
Assembly: GRCh38 assembly version
Supplementary files format and content: Normalized coverage data are provided in BigWig format.

extract_protocol:
Human bone marrow aspirates were obtained from in accordance with the Italian laws and the policies and practices of the Ethical Committee of Humanitas Research Hospital. Patients were classified following the updated WHO classification of tumors and lymphoid tissues guidelines 1 and stratified by risk of evolution following the IPSS-R parameters. Bone marrow mononuclear cells (BMNCs) were isolated by density gradient separation with Lympholyte®-H Cell Separation Media (Cedarlane corporation, Burlington, USA) according to manufacturer’s instructions, frozen in fetal bovine serum (FBS) (Lonza, Basel, Switzerland) containing 10% DimethylSulfoxide (DMSO) (Sigma Aldrich, St. Louis, Missouri, USA) and cryopreserved in liquid nitrogen.
Bone marrow HSPCs were isolated based on CD34+ surface marker using the MACS CD34 microbead kit on autoMACS (Miltenyi Biotech Inc, San Diego, CA). MDS-L cells were kindly provided by Dr. Daniel Starczynowski, Cincinnati Children's Hospital Medical Center and were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated FBS and 1% P/S and 10ng/mL of hrIL-3 (PeproTech, Paisley, UK). Cell lines were grown at 37°C and 5%CO2 and treated with DB2115 (Cat. No. HY-124676A Medchem, NJ, USA) for the specified time and concentrations
For CD34+ HSPCs and MDS-L cells, H3K27Ac and PU.1 ChIP-seq were carried out fixing 1x10⁵ cells with 1% formaldehyde (cat. no. 252549, Merck, NJ, USA) for 10 min at room temperature followed by quenching with 125 mM Tris-HCl pH 7.6. Fixed samples were lysed using SDS Shearing Buffer D3 (Covaris, MA, USA) supplemented by protease inhibitors to prepare total extracts. Chromatin shearing was performed by sonication using microtube-130 AFA Fiber Strip V2 (Cat no. 520217, Covaris, MA, USA) with Covaris ME220 Focused-Ultrasonicator. For H3K27Ac and PU.1 ChIP-seq, then lysates were diluted with ChIP Buffer (10 mM Tris-HCl pH 7.6, 1 mM EDTA pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate) and incubated overnight at 4°C with protein G Dynabeads (cat. no.10009D, Invitrogen, Paisley, UK) previously coupled with 3 μg of H3K27Ac antibody (cat. no. ab4729, Abcam, Cambridge, UK), or 1.5ug of PU.1 antibody (Cat no. 2258S, Cell Signaling, MA, USA). After immunoprecipitation, beads were recovered using a magnetic stand and washed with RIPA buffer (50 mM HEPES-KOH at pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-deoxycholate). Immunoprecipitated chromatin was eluted and crosslink-reverted overnight at 65°C. DNA was purified with QIAquick PCR purification kit (cat. no. 28106, Qiagen, Hilden, Germany) and then quantified with QuantiFluor (cat. no. E2670, Promega, WI, USA).
DNA libraries were prepared from 0.5ng of DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (Cat no.  NEB E7645S, New England Biolabs GmbH) and Unique Dual Index Primer Pairs (Cat no. NEB E6440S, New England Biolabs GmbH) following producer instructions. The purified DNA libraries were quantified with Quantifluor reagent (cat. no. E2670, Promega, WI, USA) and library quality size was controlled with 4200 TapeStation System (Agilent, CA, USA) using the high-sensitivity assay HD5000 (cat. no. 5067-5592, Agilent, CA, USA).
All ChIPseq data sets were processed in paired-end.


title: ARDS, RML, Visium HD

description:
Library name: 3_ARDS-RML
10x Genomics


title: RNA library from F2 12 weeks Natural Liver Male 7 [Natural_F2_12wks_Liver_Male_7]

description: Library name: Natural_F2_12wks_Liver_Male_7


title: Syngeneic rep 4

description:
Library name: sample 4
Syngeneic4


title: Microglia cells,MCMV Infected PLX5622 treated, 6 months

first: Jessica

last: McCord

state: PA

institute: Thomas Jefferson University

description:
Library name: PLX
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger softwar v9.0.1
Assembly: Mouse mm10
Supplementary files format and content: matrix files

source_name: Retina

extract_protocol:
Newborn Balb/c mice were infected with 200 PFU K181 <24 hours after birth. Control mice were injected with 20ul PBS control. At 2 months of age PLX group was given PLX5622 in chow for 7 days. At 6 months of age, retinal tissue was collected and microglia (CD45 int CD11b+) were sorted by FACS.
Library was performed accoriding to the manufacter's instructions ( Next GEM Single Cell 3’ Reagent Kits v3.1 protocol, 10x Genomics). Briefly, microglia cells were resuspended in master mix and loaded with partitioning oil and gel beads into the chip to mak GEM (gel bead-in-emulsion). The poly-A RNA from the cell lysate in the GEMs were retrotranscripted to cDNA. The barcoded cDNA was cleaned by Silane DynaBeads, aplified by PCR and the appropriate size fragmet was selected with SPRIselect for subsequent library contruction.

treatment_protocol: MCMV infection and PLX5622 treatment

value: Retina

value: Microglia

value: Balb/c

value: MCMV infection and PLX5622 7days at 2months


title: Microglia cells,MCMV Infected, untreated, 6 months

description:
Library name: INF
10x Genomics

value: MCMV infection


title: MDSL Cell line DB2115-treated 1h Rep2

description: Library name: MDSL_INH_1h_Rep2

source_name: MDS-L

value: MDS-L


title: Control, Visium HD

description:
Library name: 1_CT01_LUL3
10x Genomics

value: Unknown


title: Covid, Visium HD

description:
Library name: 5_COVID_TX1_LLL1
10x Genomics


title: RNA library from F2 12 weeks Natural Liver Male 2 [Natural_F2_12wks_Liver_Male_2]

description: Library name: Natural_F2_12wks_Liver_Male_2

value: F2 12 weeks Liver

value: Male

value: Natural


title: Syngeneic rep 3

description:
Library name: sample 3
Syngeneic3


title: MDSL Cell line Untreated RNA-seq Rep2

description: Library name: MDSL_UT_rep2


title: Syngeneic rep 2

description:
Library name: sample 2
Syngeneic2


title: ARDS, RUL, Visium HD

description:
Library name: 2_ARDS-RUL
10x Genomics

value: Lung


title: WT RAW264.7 cells, 1 µg/mL LPS plus 0.5 mM CTM, 24 h, rep2

city: Yokohama

first: Xian-Yang

last: Qin

address: 1-7-22 Suehiro, Tsurumi

department: RIKEN Center for Integrative Medical Sciences

country: Japan

institute: Institute of Physical and Chemical Research

description:
Library name: Sample13
Column name in TPM_RAW_RNA_seq.csv: CTM2

data_processing:
Raw sequencing reads were processed using Salmon.
Assembly: UCSC mm10 (GRCm38)
Supplementary files format and content: csv files include TPM values for each Sample

extract_protocol:
RNA was extracted using a FastGene RNA Basic Kit (NIPPON Genetics).
RNA-seq libraries were prepared using a TruSeq Stranded mRNA Library Prep Kit (Illumina)

value: macrophage-like cell line

value: WT

value: LPS plus CTM

tag: rna extraction_date


title: Control, RML, scRNAseq

description:
Library name: Control_RML
10x Genomics

data_processing:
For scRNAseq, Raw scRNA-seq reads were demultiplexed with CellRanger (v7.1.0) and mapped to the human genome (HG38). Ambient RNA was removed using SoupX, and doublets were filtered with scDblFinder. Additional quality filtering with Seurat excluded cells that had <200 or >7,500 unique features, <400 or >40,000 total RNA counts, or >10% mitochondrial content.  For Visium HD, images were aligned with Loupe Browser (V8.0.0), and Space Ranger (10X Genomics; V3.1.0) was used for genome mapping (HG38). Bin2cell aggregated 2 μm bins to reconstruct single-cell-like profiles based on H&E morphology and gene expression, using 0.5 μm per pixel resolution. Scanpy was employed for downstream analysis; cells with <100 or >40,000 features or >20% mitochondrial content were excluded
Assembly: HG38
Supplementary files format and content: HDF5 of processed data


title: RNA library from F2 12 weeks Natural Liver Male 5 [Natural_F2_12wks_Liver_Male_5]

description: Library name: Natural_F2_12wks_Liver_Male_5


title: RNA library from F2 12 weeks Natural Liver Male 6 [Natural_F2_12wks_Liver_Male_6]

description: Library name: Natural_F2_12wks_Liver_Male_6


title: Syngeneic rep 1

description:
Library name: sample 1
Syngeneic1

data_processing:
Raw sequencing reads for all samples were assessed for quality using FastQC on the Galaxy platform. This step identified adaptor sequences and low-quality bases. Adaptor sequences and low-quality bases were removed from all samples using Trim Galore on the Galaxy platform with default parameters. Trimmed reads from all samples were aligned to the reference genome GRCm39 or GRCh38.p14 using HISAT2 on the Galaxy platform. Default settings were applied for the alignment, and no samples were removed during this step. Gene-level read counts for all samples were generated using featureCounts on the Galaxy platform. The GTF annotation file from the reference genome GRCm39 or GRCh38.p14 was used for feature quantification.
Assembly: GRCm39 for mice and GRCh38.p14 for human
Supplementary files format and content: Txt file included raw counts for each samples

value: Skin


title: RNA library from F2 12 weeks Natural Liver Male 4 [Natural_F2_12wks_Liver_Male_4]

description: Library name: Natural_F2_12wks_Liver_Male_4


title: RNA library from F2 12 weeks Natural Liver Male 3 [Natural_F2_12wks_Liver_Male_3]

description: Library name: Natural_F2_12wks_Liver_Male_3


title: WT RAW264.7 cells, 1 µg/mL LPS plus 0.5 mM CTM, 24 h, rep1

description:
Library name: Sample12
Column name in TPM_RAW_RNA_seq.csv: CTM1


title: RNA library from F2 12 weeks IVF Testis Male 6 [IVF_F2_12wks_Testis_Male_6]

description: Library name: IVF_F2_12wks_Testis_Male_6

source_name: F2 12 weeks Testis

value: F2 12 weeks Testis


title: MDSL Cell line Untreated RNA-seq Rep1

description: Library name: MDSL_UT_rep1

value: Untreated


title: RNA library from F2 12 weeks Natural Liver Male 1 [Natural_F2_12wks_Liver_Male_1]

description: Library name: Natural_F2_12wks_Liver_Male_1


title: WT RAW264.7 cells, 1 µg/mL LPS, 24 h, rep2

description:
Library name: Sample11
Column name in TPM_RAW_RNA_seq.csv: LPS2

value: LPS


title: Control, RUL, scRNAseq

description:
Library name: Control_RUL
10x Genomics


title: RNA library from F2 12 weeks IVF Testis Male 4 [IVF_F2_12wks_Testis_Male_4]

description: Library name: IVF_F2_12wks_Testis_Male_4

value: IVF


title: MDSL Cell line Untreated Rep2

description: Library name: MDSL_UT_Rep2


title: MDSL Cell line Untreated Rep1

description: Library name: MDSL_UT_Rep1


title: Microglia cells,Control uninfected untreated, 6 months

description:
Library name: CTR
10x Genomics

value: Retina

value: Microglia

value: Balb/c


title: MDSL Cell line DB2115-treated 1h Rep1

description: Library name: MDSL_INH_1h_Rep1

value: MDS-L


title: Control, RLL2, scRNAseq

description:
Library name: Control_RLL2
10x Genomics

value: Unknown


title: RNA-seq AID-DIvA U2OS knockout-untreated-rep2

city: Heidelberg

first: Ali

last: Bakr

address: Im Neuenheimer Feld 280

department: Cancer Epigenomics

institute: Deutsches Krebsforschungszentrum

description: Library name: RNA-seq knockout-untreated-rep2

data_processing:
Data was processed by the Omics IT and Data Management Core Facility (DKFZ, Heidelberg), using the Roddy RNA-seq Workflow. Default parameters were used unless mentioned otherwise. Sequences were aligned to the human reference genome (hg19/GRCh37) by applying the software STAR (22). Gene counts were generated with featureCounts (23) and the gene annotation v.29 lift 37.
Assembly: hg19/GRCh37
Supplementary files format and content: *.tsv file with raw and normalised reads for each transcript

source_name: bone

extract_protocol:
RNA extraction was performed as described previously (see references in the paper)
Sequencing libraries were prepared by the Genomics and Proteomics Core Facility (DKFZ, Heidelberg) from total RNA using the Illumina TrueSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions. Samples were sequenced in a paired-end setting (100 bp) on an Illumina NovaSeq 6000 machine for sequencing.

value: bone

value: AID-DIvA U2OS

value: osteosarcoma

value: mocetinostat-treated


title: RNA library from F2 12 weeks IVF Testis Male 5 [IVF_F2_12wks_Testis_Male_5]

description: Library name: IVF_F2_12wks_Testis_Male_5

value: Male


title: WT RAW264.7 cells, PBS, 24 h, rep2

description:
Library name: Sample9
Column name in TPM_RAW_RNA_seq.csv: PBS2

value: macrophage-like cell line

value: WT

value: PBS


title: Control, LLL2, scRNAseq

description:
Library name: Control_LLL2
10x Genomics

value: Lung


title: RNA library from F2 12 weeks IVF Testis Male 3 [IVF_F2_12wks_Testis_Male_3]

description: Library name: IVF_F2_12wks_Testis_Male_3

value: F2 12 weeks Testis


title: WT RAW264.7 cells, 1 µg/mL LPS, 24 h, rep1

description:
Library name: Sample10
Column name in TPM_RAW_RNA_seq.csv: LPS1

value: LPS


title: Control, LUL, scRNAseq

description:
Library name: Control_LUL
10x Genomics


title: MDSL Cell line DB2115-treated 12h Rep1

description: Library name: MDSL_INH_12h_Rep1


title: RNA-seq AID-DIvA U2OS knockout-untreated-rep1

description: Library name: RNA-seq knockout-untreated-rep1


title: WT RAW264.7 cells, PBS, 24 h, rep1

description:
Library name: Sample8
Column name in TPM_RAW_RNA_seq.csv: PBS1


title: Control, RLL1, scRNAseq

description:
Library name: Control_RLL1
10x Genomics


title: RNA-seq AID-DIvA U2OS knockout-untreated-rep3

description: Library name: RNA-seq knockout-untreated-rep3


title: Control, LLL1, scRNAseq

description:
Library name: Control_LLL1
10x Genomics


title: RNA library from F2 12 weeks IVF Testis Male 2 [IVF_F2_12wks_Testis_Male_2]

description: Library name: IVF_F2_12wks_Testis_Male_2

value: IVF


title: RNA library from F2 12 weeks IVF Testis Male 1 [IVF_F2_12wks_Testis_Male_1]

description: Library name: IVF_F2_12wks_Testis_Male_1


title: RNA library from F2 12 weeks Natural Testis Male 6 [Natural_F2_12wks_Testis_Male_6]

description: Library name: Natural_F2_12wks_Testis_Male_6

value: Natural


title: Cell-free DNA Day 6, DNMT1i, Recovery

city: Berlin

first: Anja

last: Hess

email: ahess@molgen.mpg.de, anja.hess@mail.de

address: Ihnestrasse 63-67

institute: Max-Planck-Institut für molekulare Genetik

description:
Library name: cfDNA_D6_DNMT1i_Recovery
Cell-free DNA

data_processing:
Adapter trimming/QC: Raw reads were processed with cutadapt (version 2.4; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read.
Alignment/ Methylation calling: reads were aligned to mm10 with BSMAP (version 2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Duplicates were removed using the ‘MarkDuplicates’ command from GATK (version 4.1.4.1; --VALIDATION_STRINGENCY=LENIENT –REMOVE_DUPLICATES=true). Methylation rates were called using mcall from the MOABS package (version 1.3.2; default parameters).
Final filtering: All analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.
Assembly: mm10
Supplementary files format and content: CpG.bed - bedgraph files with methylation calls
Supplementary files format and content: filtered.bed - bedgraph files with methylation calls, coverage 10-150X, autosomes only
Supplementary files format and content: filtered.bw - bigwig files of filteres bedgraph methylation call files for IGV exploration
Supplementary files format and content: H5AD - AnnData matrix of methylation calls
Supplementary files format and content: TSV - methylation call table

molecule: other

growth_protocol: KH2 mESCs were cultured on 0.2% gelatin in knockout DMEM medium (Gibco, 10829018) with 15% FBS, 1% penicillin/streptomycin (ThermoFisher Scientific, 15140122), 1% glutamine (ThermoFisher Scientific, 35050038), 1% non-essential amino acids (NEAA, Gibco), 0.055 mM β-mercaptoethanol (Gibco, 11140-035) and leukemia inhibitory factor (LIF, generated in house) and split with TrypLE (Gibco, 12604-021).

extract_protocol:
Supernatants were treated with Proteinase K (Jena, 845-CH-0010030, stock concentration 22 mg/mL) for 1 hour or overnight at 37°C at 8.3 µl per 100 µl medium, and purified with the DNA Clean & Concentrator Kit (Zymo, D4004) mixing SN with DNA binding buffer at ratio 1:5. Genomic DNA was isolated with the PureLink Genomic DNA kit (Invitrogen,  K182001) according to manufacturer’s instructions.
gDNA, but not cfDNA, was fragmented using a Covaris S2 system (intensity:10, duty cycle: 5%, cycles per burst: 200, duration: 90 seconds), cleaned up with the DNA Clean and Concentrator-5 kit (Zymo, D4004), quantified and quality-controlled on a TapeStation device as described above, and 100 ng of sheared reference genomic DNA and 48 ng of cell-free DNA were bisulfite converted using the EZ DNA Methylation-Gold kit (Zymo, D5005), eluting in lowEDTA TE buffer, pH 8.0 (IDT11-05-01-13). WGBS libraries were prepared with the xGen™ Methyl-Seq DNA Library Prep Kit (IDT, 10009824), at 8 indexing PCR cycles with the xGEN UDIPrimer Plate 2, 8nt (IDT, 10009816), and sequenced as 150-bp paired-end reads on an Illumina NovaSeq 6000 system.

treatment_protocol: Feeder-depleted KH2 mESCs were treated with 2.5µM DNMT1-Inhibitor GSK-3484862 (MedChem, HY-135146) for four days, followed by a two-day recovery period. Cells treated with equal volume of DMSO served as a negative control. Each day, cells were washed with DPBS(-/-) one hour before cfDNA collection, and cfDNA and matched genomic DNA were collected from the same well.

value: embryonic stem cell

value: wildtype

tag: batch


title: Cell-free DNA Day 5, DNMT1i, Recovery

description:
Library name: cfDNA_D5_DNMT1i_Recovery
Cell-free DNA


title: RNA-seq AID-DIvA U2OS knockout-hdaci-treated-recovery-rep2

description: Library name: RNA-seq knockout-hdaci-treated-recovery-rep2

value: untreated


title: RNA-seq AID-DIvA U2OS knockout-hdaci-treated-recovery-rep3

description: Library name: RNA-seq knockout-hdaci-treated-recovery-rep3


title: RNA library from F2 12 weeks Natural Testis Male 5 [Natural_F2_12wks_Testis_Male_5]

description: Library name: Natural_F2_12wks_Testis_Male_5


title: Cell-free DNA Day 4, DNMT1i

description:
Library name: cfDNA_D4_DNMT1i
Cell-free DNA

value: DNMT1-i, 2.5µM


title: RNA library from F2 12 weeks Natural Testis Male 4 [Natural_F2_12wks_Testis_Male_4]

description: Library name: Natural_F2_12wks_Testis_Male_4


title: Cell-free DNA Day 3, DNMT1i

description:
Library name: cfDNA_D3_DNMT1i
Cell-free DNA


title: ARDS, RML, scRNAseq

description:
Library name: ARDS_RML
10x Genomics


title: ARDS, RLL2, scRNAseq

description:
Library name: ARDS_RLL2
10x Genomics


title: RNA-seq AID-DIvA U2OS control-untreated-rep3

description: Library name: RNA-seq control-untreated-rep3

value: bone

value: wt


title: RNA-seq AID-DIvA U2OS knockout-hdaci-treated-recovery-rep1

description: Library name: RNA-seq knockout-hdaci-treated-recovery-rep1

value: AID-DIvA U2OS

value: osteosarcoma


title: ARDS, LUL, scRNAseq

description:
Library name: ARDS_LUL
10x Genomics


title: RNA-seq AID-DIvA U2OS control-untreated-rep1

description: Library name: RNA-seq control-untreated-rep1

value: mocetinostat-treated


title: ARDS, LLL2, scRNAseq

description:
Library name: ARDS_LLL2
10x Genomics


title: RNA-seq AID-DIvA U2OS control-untreated-rep2

description: Library name: RNA-seq control-untreated-rep2


title: RNA library from F2 12 weeks Natural Testis Male 1 [Natural_F2_12wks_Testis_Male_1]

description: Library name: Natural_F2_12wks_Testis_Male_1

value: Male


title: Cell-free DNA Day 1, DNMT1i

description:
Library name: cfDNA_D1_DNMT1i
Cell-free DNA


title: ARDS, RUL, scRNAseq

description:
Library name: ARDS_RUL
10x Genomics


title: RNA library from E18.5 IVF female placenta 5 [IVF_F2_E185_placenta_Female_5]

description: Library name: IVF_F2_E185_placenta_Female_5

source_name: F2 E185 Placenta

value: F2 E185 Placenta

value: Female


title: RNA library from F2 12 weeks Natural Testis Male 2 [Natural_F2_12wks_Testis_Male_2]

description: Library name: Natural_F2_12wks_Testis_Male_2


title: Cell-free DNA Day 0

description:
Library name: cfDNA_D0
Cell-free DNA


title: stiripentol 5

city: Köln

first: Cyrielle

middle: Louise

last: Bouchez

address: Lübecker strasse 5

institute: Uniklinik Köln

description: Library name: sample 10

data_processing:
Transfering gene counts to CPM using GENAVi
GSEA using VolcaNoiseR
Assembly: mm10
Supplementary files format and content: comma seperated value (.csv); comma as seperator.xlsx-file

source_name: lung origine

growth_protocol: The cell lines were cultured under conditions of 5% CO2 and 37°C. The cell culture media RPMI medium 1640 (Thermo Fisher Scientific Inc., USA) was supplemented with 10% FBS (PAN-Biotech, Aidenbach, Germany)

extract_protocol:
RNA was harvested using the RNeasy Mini Kit (Qiagen N.v., Netherlands) according to manufacturer’s instruction.
RNA libraries for RNASeq are generated using TruSeq total RNA. 1µg of total RNAwas used for library preparation.

treatment_protocol: Stiripentol or DMSO are cultivated 48hours

value: lung origine


title: ARDS, RLL1, scRNAseq

description:
Library name: ARDS_RLL1
10x Genomics

value: Lung


title: RNA-seq AID-DIvA U2OS control-hdaci-treated-recovery-rep3

description: Library name: RNA-seq control-hdaci-treated-recovery-rep3


title: RNA-seq AID-DIvA U2OS control-hdaci-treated-recovery-rep2

description: Library name: RNA-seq control-hdaci-treated-recovery-rep2


title: RNA-seq AID-DIvA U2OS control-hdaci-treated-recovery-rep1

description: Library name: RNA-seq control-hdaci-treated-recovery-rep1


title: stiripentol 3

description: Library name: sample 8


title: ARDS, LLL1, scRNAseq

description:
Library name: ARDS_LLL1
10x Genomics


title: Cell-free DNA Day 2, DNMT1i

description:
Library name: cfDNA_D2_DNMT1i
Cell-free DNA


title: RNA library from E18.5 IVF female placenta 3 [IVF_F2_E185_placenta_Female_3]

description: Library name: IVF_F2_E185_placenta_Female_3


title: RNA library from F2 12 weeks Natural Testis Male 3 [Natural_F2_12wks_Testis_Male_3]

description: Library name: Natural_F2_12wks_Testis_Male_3

value: F2 12 weeks Testis


title: RNA library from E18.5 IVF female placenta 4 [IVF_F2_E185_placenta_Female_4]

description: Library name: IVF_F2_E185_placenta_Female_4

value: IVF


title: AML_patient_sample_371

first: Serena

last: Ghisletti

institute: European Institute of Oncology

description: Library name: sample_371

growth_protocol: Human bone marrow aspirates were obtained from in accordance with the Italian laws and the policies and practices of the Ethical Committee of Humanitas Research Hospital. Patients were classified following the updated WHO classification of tumors and lymphoid tissues guidelines 1 and stratified by risk of evolution following the IPSS-R parameters. Bone marrow mononuclear cells (BMNCs) were isolated by density gradient separation with Lympholyte®-H Cell Separation Media (Cedarlane corporation, Burlington, USA) according to manufacturer’s instructions, frozen in fetal bovine serum (FBS) (Lonza, Basel, Switzerland) containing 10% DimethylSulfoxide (DMSO) (Sigma Aldrich, St. Louis, Missouri, USA) and cryopreserved in liquid nitrogen. Bone marrow HSPCs were isolated based on CD34+ surface marker using the MACS CD34 microbead kit on autoMACS (Miltenyi Biotech Inc, San Diego, CA).

value: Bone marrow-CD34+

value: AML


title: AML_patient_sample_370

description: Library name: sample_370


title: stiripentol 1

description: Library name: sample 6


title: gDNA Day 3, DNMT1i

description:
Library name: gDNA_Day3_DNMT1i
gDNA

value: embryonic stem cell

value: wildtype


title: gDNA Day 3, DMSO control

description:
Library name: gDNA_Day3_DMSO-Control
gDNA

value: DMSO


title: RNA library from E18.5 Natural female placenta 5 [Natural_F2_E185_placenta_Female_5]

description: Library name: Natural_F2_E185_placenta_Female_5

value: Natural


title: AML_patient_sample_372

description: Library name: sample_372


title: gDNA Day 6, DNMT1i, Recovery

description:
Library name: gDNA_Day6_DNMT1i_Recovery
gDNA


title: gDNA Day 5, DNMT1i, Recovery

description:
Library name: gDNA_Day5_DNMT1i_Recovery
gDNA


title: stiripentol 2

description: Library name: sample 7


title: AML_patient_sample_369

description: Library name: sample_369


title: RNA library from E18.5 IVF female placenta 2 [IVF_F2_E185_placenta_Female_2]

description: Library name: IVF_F2_E185_placenta_Female_2


title: gDNA Day 2, DNMT1i

description:
Library name: gDNA_Day2_DNMT1i
gDNA

value: DNMT1-i, 2.5µM


title: stiripentol 4

description: Library name: sample 9


title: RNA library from E18.5 IVF female placenta 1 [IVF_F2_E185_placenta_Female_1]

description: Library name: IVF_F2_E185_placenta_Female_1


title: gDNA Day 4, DNMT1i

description:
Library name: gDNA_Day4_DNMT1i
gDNA


title: AML_patient_sample_368

description: Library name: sample_368


title: AML_patient_sample_365

description: Library name: sample_365


title: AML_patient_sample_364

description: Library name: sample_364


title: Keratinocyte from SN supressed-68 mouse

city: Hangzhou

first: Zhang

middle: Zhou

last: melanoma

state: China

address: 西湖大学医学院

country: China

institute: Westlake University

description:
raw_counts.txt
IFE68

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastp v0.12.4.
The clean sequenced reads were mapped to mm10 whole genome using hisat2 v2.2.1.
HISAT2 alignments were used to generate genomic features using featureCounts v2.0.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include readcount values for each sample

source_name: Epidermis of back skin

extract_protocol:
RNA samples were purified using RNeasy Plus Micro Kit (Qiagen 74034)
RNA-seq libraries were generated using Single Cell Full Length mRNA-Amplification Kit (Vazyme N712) and TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme TD503)

value: Epidermis of back skin

value: Keratinocyte

value: DBHCre; R26-LSL-Gi-DREADD

value: CNO


title: RNA library from E18.5 Natural female placenta 1 [Natural_F2_E185_placenta_Female_1]

description: Library name: Natural_F2_E185_placenta_Female_1

value: F2 E185 Placenta


title: RNA library from E18.5 Natural female placenta 4 [Natural_F2_E185_placenta_Female_4]

description: Library name: Natural_F2_E185_placenta_Female_4

value: Female


title: WGBS_KD_2_28dpi

first: Jaime

last: Diaz-Larrosa

state: Baden Württemberg

address: INF 580

department: Epigenetics

institute: DKFZ

description:
Library name: WGBS_Sample4
Column name: KD_2_avg_meth_ratio

data_processing:
Data were processed adapting the pipeline of Gatzmann et al, 2018 filtering out those cytosines with < 10X coverage and keeping those annotated genes with at least 10 CpGs.
Mapped cytosines were uniquely annotated to display methylation values using tabix and annotated to all transcript variants regardless of the overlapping using the intersect argument of bedtools (v2.24.0)
Assembly: pvir_genome_ncbi_v1.0
Supplementary files format and content: Tab separated average methlation values per gene and corresponding Gene IDs

organism: Procambarus virginalis

source_name: Hemolymph

extract_protocol:
Samples were digested using proteinase K (Invitrogen, #AM2546) and RNAse A (Sigma-Aldrich, #R6513). gDNA was precipitated using isopropanol and its quality assessed on a 2,200 TapeStation (Agilent). EZ DNA Methylation-Gold kit (Zymo Research, #D5006) was used for bisulfite conversion.
Library amplification was performed using KAPA HIFI HotStart ReadyMix (Roche, #07958935001).

value: Hemolymph

value: Hemocytes

value: Dnmt1 Knockdown

value: dsDnmt1 injection


title: control 3

description: Library name: sample 3

value: lung origine


title: control 5

description: Library name: sample 5


title: control 4

description: Library name: sample 4


title: gDNA Day 1, DNMT1i

description:
Library name: gDNA_Day1_DNMT1i
gDNA


title: AML_patient_sample_366

city: Milan

address: Via Adamello 16

description: Library name: sample_366

source_name: Bone marrow-CD34+

value: Bone marrow-CD34+

value: AML


title: control 2

description: Library name: sample 2


title: RNA library from E18.5 Natural female placenta 3 [Natural_F2_E185_placenta_Female_3]

description: Library name: Natural_F2_E185_placenta_Female_3


title: RNA library from E18.5 IVF male placenta 5 [IVF_F2_E185_placenta_Male_5]

description: Library name: IVF_F2_E185_placenta_Male_5

value: Male

value: IVF


title: RNA library from E18.5 Natural female placenta 2 [Natural_F2_E185_placenta_Female_2]

description: Library name: Natural_F2_E185_placenta_Female_2

value: Natural


title: Keratinocyte from SN supressed-18 mouse

description:
raw_counts.txt
IFE18


title: AML_patient_sample_367

description: Library name: sample_367


title: gDNA Day 0

description:
Library name: gDNA_Day0
gDNA

value: embryonic stem cell

value: wildtype


title: RNA library from E18.5 IVF male placenta 3 [IVF_F2_E185_placenta_Male_3]

description: Library name: IVF_F2_E185_placenta_Male_3


title: control 1

description: Library name: sample 1


title: AML_patient_sample_361

description: Library name: sample_361


title: Keratinocyte from SN supressed-69 mouse

description:
raw_counts.txt
IFE69

value: Epidermis of back skin

value: Keratinocyte


title: RNA library from E18.5 IVF male placenta 6 [IVF_F2_E185_placenta_Male_6]

description: Library name: IVF_F2_E185_placenta_Male_6


title: RNA library from E18.5 IVF male placenta 4 [IVF_F2_E185_placenta_Male_4]

description: Library name: IVF_F2_E185_placenta_Male_4


title: WGBS_Control_1_28dpi

description:
Library name: WGBS_Sample1
Column name: Control_1_avg_meth_ratio

value: Control

value: dsGFP injection


title: AML_patient_sample_359

description: Library name: sample_359


title: AML_patient_sample_363

description: Library name: sample_363


title: Keratinocyte from control-23 mouse

description:
raw_counts.txt
IFE23

value: CNO


title: Keratinocyte from control-15 mouse

description:
raw_counts.txt
IFE15


title: WGBS_KD_1_28dpi

description:
Library name: WGBS_Sample3
Column name: KD_1_avg_meth_ratio

value: Hemolymph


title: AML_patient_sample_362

description: Library name: sample_362


title: AML_patient_sample_360

description: Library name: sample_360


title: RNA library from E18.5 IVF male placenta 2 [IVF_F2_E185_placenta_Male_2]

description: Library name: IVF_F2_E185_placenta_Male_2

value: F2 E185 Placenta


title: WGBS_Control_2_28dpi

description:
Library name: WGBS_Sample2
Column name: Control_2_avg_meth_ratio

value: Hemocytes


title: 18-month WT male mouse thyroid-3

city: Shanghai

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

source_name: thyroid

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: thyroid

value: wild type


title: atxr5;atxr5;atxr6hyp;atxr6c-1_input rep2

city: Beijing

first: Xiaoyi

last: Li

address: west beichen

department: Chinese Academy of Sciences

institute: Institute of Genetics and Developmental Biology

description: Library name: atxr5;atxr5;atxr6hyp;atxr6c-1_input_rep2

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1
Reads were mapped to the Arabidopsis (TAIR10) genome with Botiew2 version 2.4.2
Duplicate reads were filtered using Picard version 2.24.0 MarkDuplicates (https://github.com/broadinstitute/picard)
H3K36me3 peaks in WT Col were called using MACS2 version 2.1.2 with default parameters. Only peaks identified in both biological replicates were retained
For data visualization, data from two biological replicates were merged, and bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp
Assembly: TAIR10
Supplementary files format and content: bigwig

organism: Arabidopsis thaliana

source_name: leaves of 3-week-old Arabidopsis plants

growth_protocol: Plants were grown under long day conditions (16h light/8h dark) at 22°C

extract_protocol:
Materials were ground with liquid nitrogen into fine powder and fixed with 1% formaldehyde.To profile H3K36me3, nuclei were extracted and mononucleosomes were generated with micrococcal nuclease (MNase)(Sigma, N5386) digestion. Immunoprecipitation was conducted with  anti-H3K36me3 (Abcam, ab9050). After antibody incubation, Protein A Dynabeads (Life technologies, 10002D) were added to collect the immunocomplexes, followed by elution, reverse cross-linking and DNA purification.
Immunoprecipitated DNA were subjected to library preparation with the VAHTS universal DNA library prep kit for Illumina (Vazyme, ND607-02) according to the manufacturer’s instruction

treatment_protocol: ChIP-seq was performed using leaves from 3-week-old Arabidopsis plants

value: leaves of 3-week-old Arabidopsis plants


title: RNA library from E18.5 IVF male placenta 1 [IVF_F2_E185_placenta_Male_1]

description: Library name: IVF_F2_E185_placenta_Male_1

data_processing:
RNA-seq reads were trimmed for quality using Trimmomatic (version 0.32). Illumina TruSeq3-PE primers, leading and trailing low-quality (below quality 3) and N base calls were trimmed, and reads were scanned using a 4-bp sliding window and trimmed when the average quality per base dropped below 15. Reads of at least 30-bp in length following this quality control process were retained and used for subsequent analyses.
The resulting reads were then aligned to mm10 reference genome assembly using STAR (version 2.3.0e), allowing read pairs to align no farther than 2000-bp apart and keeping alignments with a mapping quality score (MAPQ) greater than 1 for genome-wide transcript counting.
FeatureCounts (version 1.5.0) was used to generate a matrix of mapped fragments per RefSeq annotated gene.
Analysis for differential gene expression was performed using DESeq2 with the cutoff of FDR < 0.05. Clustering and heatmaps of differentially expressed genes were generated using heatmaply R package. Chord plots were done using complexheatmap, clusterprofiler and circlize packages in R. WGCNA was done using the WGCNA package for R.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample


title: AML_patient_sample_358

description: Library name: sample_358

value: Bone marrow-CD34+

value: AML


title: AML_patient_sample_357

description: Library name: sample_357


title: Keratinocyte from control-22 mouse

description:
raw_counts.txt
IFE22


title: 18-month WT male mouse thyroid-1


title: 18-month WT male mouse thyroid-2


title: Col_input rep1

description: Library name: Col_input_rep1

value: WT


title: RNA library from E18.5 Natural male placenta 2 [Natural_F2_E185_placenta_Male_2]

description: Library name: Natural_F2_E185_placenta_Male_2

value: Male

value: Natural


title: AML_patient_sample_355

description: Library name: sample_355


title: atxr5;atxr5;atxr6hyp;atxr6c-1_input rep1

description: Library name: atxr5;atxr5;atxr6hyp;atxr6c-1_input_rep1


title: RNA library from E18.5 Natural male placenta 4 [Natural_F2_E185_placenta_Male_4]

description: Library name: Natural_F2_E185_placenta_Male_4


title: 2-month WT male mouse thyroid-6


title: AML_patient_sample_354

description: Library name: sample_354


title: AML_patient_sample_356

description: Library name: sample_356


title: RNA library from E18.5 Natural male placenta 3 [Natural_F2_E185_placenta_Male_3]

description: Library name: Natural_F2_E185_placenta_Male_3


title: RNA library from E18.5 Natural male placenta 5 [Natural_F2_E185_placenta_Male_5]

description: Library name: Natural_F2_E185_placenta_Male_5