title: PTB211_batch_1_ROI_10_anno_Alveoli

city: Los Angeles

first: Jonathan

last: Perrie

address: 610 Charles E Young Dr S

department: Bioinformatics

institute: University of California, Los Angeles

description:
Library name: PTB211_batch_1_ROI_10
Alveoli | PTB 21.1 | 10

data_processing:
Analysis began with GeoMx DCC files and followed the pre-processing and normalization steps outlined in the GeoMxWorkflows R vignette.
ROIs were filtered to exclude those detecting less than 5% of total genes from the Whole Transcriptome Atlas. Genes were subsequently filtered to exclude those detected in fewer than 5% of ROIs.
The raw expression matrix was normalized using the 75th percentile normalization.
Assembly: hg38
Supplementary files format and content: DCC files: digital count conversion format per ROI
Supplementary files format and content: geomx_ptb_metadata.csv: ROI attributes after pre-processing
Supplementary files format and content: geomx_ptb_negprobes.csv: negative probe counts
Supplementary files format and content: geomx_ptb_q3_data.csv: quantile normalized counts
Supplementary files format and content: geomx_ptb_raw_data.csv: raw counts
Library strategy: Spatial Transcriptomics

extract_protocol:
Lung FFPE tissue sections were mounted on glass slides, deparaffinized, and rehydrated following the GeoMx DSP manufacturer’s protocol. Slides were hybridized overnight at 37 °C with the GeoMx Human Whole Transcriptome Atlas probe set. Tissue morphology markers were revealed by fluorescent immunostaining to guide the selection of ROIs.
Barcoded oligonucleotide probes were photocleaved from selected ROIs by UV exposure and collected into separate wells. Oligos were uniquely indexed, and paired-end reads were generated by Illumina sequencing, then aligned and quantified using NanoString’s DSP analysis pipeline.

value: Lung

tag: region

value: Alveoli


title: 08_MXZ_Gpm3_gid9

status: Public on Jul 10 2026

type: SRA

city: Mainz

first: Frank

last: Rühle

address: Ackermannweg 4

department: Bioinformatics Core Facility

country: Germany

institute: Institute of Molecular Biology (IMB)

description:
Library name: Sample 8
MXZ-Gpm3-tFT library in gid9∆ background (combinatorial mutagenesis of residues 2 and 3)

library_source: other

data_processing:
Demultiplexed fastq files were checked for raw data quality and potential DNA contamination using FastQC (v0.11.9) and FastQScreen (v0.13) software.
Cutadapt (v4.0) was used to trim adapter sequences and for NextSeq-specific 3’ end quality trimming applying a threshold of 20.
Reads were filtered for a minimum length of 15 nucleotides and a maximum expected number of errors equal to 1 computed from quality values using Cutadapt (v4.0).
Read pairs were assembled using the paired-end read merger PEAR (v0.9.11) to reconstruct amplicon sequences based on a minimum of 10 bases overlap of the paired reads. Unassembled read pairs were discarded.
The variable region and the bin barcode were subsequently extracted from the assembled sequences by applying a design-specific regular expression with the extract command in UMI-Tools (v1.1.2) using flanking common sequences.
Reads were counted for each observed combination of variable region and bin barcode, and were exported as a count matrix in text format. Bin barcodes in order 1 (low stability) to 8 (high stability): TCGTTAAGC, GTCATCGAA, TGGCAACGT, GTGAGGTCT, ACTACCAGG, TGACCACCT, CAGTCACAA, GGACTGTAT
Protein stability indices (PSIs) per sequence variant were calculated from count data either per nucleotide sequence or per translated amino acid sequence as described (PMID 29727619) using the analysis pipeline available at: https://gitlab.rlp.net/imbforge/NGSpipe2go/-/tree/MPSprofiling
Assembly: Not applicable, because no alignment applied
Supplementary files format and content: tab delimited text files (tsv) containing counts of each observed combination of variable region (column ‘sequence’) and bin barcode (column ‘id’).

molecule: other

organism: Saccharomyces cerevisiae

source_name: yeast strain yKEK114 transformed with the desired plasmid variants

growth_protocol: Yeast cells were grown at 30°C in synthetic complete (SC) glucose medium lacking histidine to log-phase and shifted to SC ethanol medium lacking histidine for 24h before sorting.

extract_protocol:
Yeast cells were lysed by mechanical shearing and then the plasmids therein were isolated by column-purification.
The variable regions were PCR-amplified with the incorporation of unique barcode IDs for each stability bin. The PCR products were pooled proportionally according to the number of cells sorted into each bin, and then used as the template for another PCR for adding the sample barcodes and illumina sequencing adaptors.

treatment_protocol: Yeast cells were sorted into 8 stability bins according to the tFT readout. The cells sorted into each bin were separately grown to saturation.

tag: cell type

tag: genotype

value: MATalpha can1delta::STE2pr-SpHIS5 lyp1delta::STE3pr-LEU2 his3delta1 leu2delta0 ura3delta0 leu2delta0::GAL1pr-I-SCEI-natNT2 gid9delta::kanMX6

tag: batch


title: Whole blood DNA methylation, AA CONTROL, 77yo F, 207215830103_R06C01

type: genomic

city: San Francisco

first: Sebastián

last: Cruz-González

state: California

country: USA

institute: UCSF

hyb_protocol: DNA methylation was quantified using the Illumina Infinium MethylationEPIC BeadChip (EPIC v1.0, ~850K CpG sites) according to the manufacturer's standard Infinium HD Assay protocol.

scan_protocol: BeadChips were scanned on an Illumina iScan system to generate raw IDAT files.

data_processing:
All quality control and data normalization were performed using the openSeSAMe pipeline from the SeSAMe R package (Zhou et al., 2018). Probes of poor design were removed, as well as probes with detection P-value > 0.05 in more than 5% of samples. Non-CG probes and probes on X, Y, and mitochondrial chromosomes were also removed. Samples with incomplete bisulfite conversion (GCT score > 1.5) and principal component analysis outliers were excluded. Noob normalization was performed with SeSAMe using a nonlinear dye-bias correction.
processed value definition: Beta values representing the ratio of methylated probe intensity to overall intensity (methylated + unmethylated + offset). Values range from 0 (unmethylated) to 1 (fully methylated).

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: whole blood

label_protocol: Bisulfite conversion of genomic DNA was performed prior to hybridization following standard protocols for the Illumina Infinium MethylationEPIC BeadChip array. Samples were randomized across plates and chips to ensure that ancestry, age, and sex were not confounded with each batch.

extract_protocol: Genomic DNA was extracted from whole blood samples at external processing sites associated with each cohort. Standard column-based DNA extraction methods were used according to each site's established protocols.

tag: Sex

value: Female

tag: disease state

value: Healthy control

tag: tissue

value: whole blood

tag: ethnicity

value: AA

tag: cohort

value: REAAADI

tag: age


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I461

city: Tel Aviv

first: Lubna

last: Khair

address: Weizmann 6

country: Israel

institute: Sourasky medical center

description:
Library name: I461_S32
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: JEB; Gene: LAMB3; Mutation: c.1977-1G>A /  c.1977-1G>A; Clinical severity: Mild; Age: 19; Sex: female; Sample ID: I461; Mutation group: 8; Family: r; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000

library_source: genomic

data_processing:
Raw sequencing reads were quality-checked, adapter-trimmed, and aligned to the human reference genome (GRCh38) using Bismark in non-directional mode. CpG methylation calls were extracted using the Bismark methylation extractor. Methylation percentages were calculated as the number of methylated reads divided by the total reads covering each CpG site. Differentially methylated regions (DMRs) and differentially methylated CpGs (DMCs) were identified using the methylKit package in R after standard coverage filtering, removal of extreme coverage outliers, and false discovery rate (FDR) correction (FDR < 0.05).
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data include CpG methylation calls, methylation percentages, differentially methylated CpGs (DMCs), differentially methylated regions (DMRs), and methylKit output files generated from RRBS analysis.

source_name: peripheral blood

extract_protocol:
Genomic DNA was extracted from peripheral blood leukocytes using the Gentra Puregene Blood Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. For samples collected as saliva, genomic DNA was isolated using standard laboratory procedures. DNA concentration and purity were assessed prior to library preparation.
Reduced Representation Bisulfite Sequencing (RRBS) libraries were prepared using the Zymo-Seq RRBS Library Prep Kit (Zymo Research, Irvine, CA, USA). Genomic DNA was quantified using a Qubit 4 fluorometer, digested with MspI, end-repaired, A-tailed, ligated to methylated adapters, and subjected to bisulfite conversion followed by PCR amplification. Library quality and fragment size distribution were assessed using an Agilent TapeStation 4200. Libraries were pooled equimolarly and sequenced on an Illumina NextSeq 2000 platform using paired-end 2 × 51 bp reads.

value: peripheral blood

value: leukocytes


title: DRG_rat_SoyOilDiet_Control_LeftSide2

city: Loma Linda

first: Hoang

middle: Viet

last: Dinh

state: CA

address: 11085 CAMPUS STREET, MTH-105

department: Center for Health Disparities

institute: Loma Linda university

description: Library name: G1_46L

library_source: transcriptomic

data_processing:
Raw FASTQ reads underwent fastp QC (adapter/poly-N/low-quality removal; Q20/Q30/GC calculated). Clean reads were Hisat2-aligned (v2.0.5) to the reference genome (with splice junction database). Gene expression was quantified via featureCounts (v1.5.0-p3) as FPKM
Assembly: ncbi_rattus_norvegicus_gcf_000002265_2_rn_celera
Supplementary files format and content: tab delimited text file includes raw counts for each sample
Supplementary files format and content: cvs file for FPKM values of each sample

molecule: total RNA

organism: Rattus norvegicus

source_name: Dorsal Root Ganglia

growth_protocol: Female Sprague-Dawley rats were housed in ventilated cages with ad libitum access to food and water, under a 12-hour light/dark cycle

extract_protocol:
total mRNA of DRG was isolated using the Qiagen AllPrep kit (cat. no. 80004) for simultaneous mRNA/DNA/protein. RNA integrity was assessed via Bioanalyzer 2100 (Agilent Technologies, CA, USA).
Messenger RNA is purified from total RNA using poly-T magnetic beads, fragmented, and converted to cDNA using random hexamer primers, with second-strand synthesis using dTTP for non-strand-specific libraries or dUTP for strand-specific libraries. Both library types undergo end repair, A-tailing, adapter ligation, size selection, amplification, and purification, followed by quality control using Qubit, real-time PCR, and a bioanalyzer. Libraries are then pooled and sequenced on an Illumina platform to analyze gene expression.

treatment_protocol: After 1 week of acclimatization, rats were divided randomly into two dietary groups (n=20 each): a control diet (AIN-93G-based) and a fish oil-enriched diet with modified n-3 fatty acid sources. Following 4 weeks of dietary intervention, each group was subdivided by surgical procedure: control/sham, control/chronic constriction injury (CCI), fish oil/sham, and fish oil/CCI. A 3–4 mm incision exposed the left sciatic nerve below the femur, and four loose chromic gut 4.0 ligatures (Ethicon, USA) were tied 1 mm apart proximal to the trifurcation, ensuring minimal nerve compression. Sham rats underwent identical exposure without ligatures. Muscle was sutured, skin closed with stainless steel staples, and rats recovered for 1 week with daily monitoring

value: Dorsal Root Ganglia

value: WT_Soy Oil Diet_Control

tag: treatment

value: Control


title: Whole blood DNA methylation, NHW AD, 79yo F, 207215830114_R02C01

value: Alzheimer's disease

value: NHW


title: d3_142_mix_L_2

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

description: Library name: d3_142_mix_L_2

data_processing:
FASTQ files were preprocessed using the nf-core RNA-seq pipeline (v3.14.0) with default parameters, except for UMI extraction, which was done using the following options: --with_umi --umitools_extract_method "regex" --umitools_bc_pattern2 "^(?P<umi_1>.{8})(?P<discard_1>.{6}).*".
Briefly, paired-end reads were aligned to the human genome (Ensembl release 110) using STAR, and transcript quantification was performed with Salmon.
Assembly: hg38
Supplementary files format and content: count tables (.txt)

source_name: skin

growth_protocol: HDFs were cultured on gelatin-coated plates in complete DMEM (high glucose) supplemented with 10% FBS, 2 mM GlutaMAX, 1 mM sodium pyruvate, and penicillin/streptomycin supplemented with the JAK inhibitor ruxolitinib (10 μM).

extract_protocol:
5000-10000 cells were sorted into RLT lysis buffer. RNA was exracted with the miRNeasy Tissue/Cells Advanced Kit according to manufacturer's protocol.
Libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian kit by Takara.

treatment_protocol: HDFs were trasduced on day -1 and/or transfected with PIB-encoding mRNAs and miRNA mimics on day 0 of reprogramming. Cells were sorted on day 3 or 6 by FACS.

value: skin

value: human dermal fibroblast

value: WT

value: Cells were transfected with mRNAs coding for Pu.1, Irf8, Batf3 (PIB) and miR-142-3p, miR-142-3p-1, miR-142-3p-3 and miR-142-5p-1 mimics on day 0 of reprogramming.

tag: time

value: Cells were collected on day 3 of reprogramming.

tag: sorted cells

value: live (DAPI-) and CD45+


title: CnR_H3K27me3_K27MKO_Day3_Rep1

city: Oxford

first: Alan

last: Jiao

state: MA

address: Old Road Campus Research Building

country: United Kingdom

institute: Ludwig Institute for Cancer Research, Oxford University

data_processing:
Reads were aligned to the human hg38 (target genome) and Saccharomyces cerevisiae sacCer3 (spike-in genome) using Bowtie2 v2.3.5.1, with settings --no-unal --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700
Spike-in-normalized bigwig track files were created using bamCoverage from deepTools v3.3.1, with settings --binSize=20 --smoothLength=60 --normalizeUsing BPM --scaleFactor $scale_factor.
Scale factors were calculated as the ratio of total reads / spike-in reads
Assembly: hg38, sacCer3
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: DIPG-XIII

growth_protocol: DIPG-XIII cells were maintained in tumor stem medium as gliomaspheres in low attachment culture flasks in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
CUT&RUN (Cleavage under targets and release using nuclease). Enriched genomic DNA fragments were extracted using Monarch PCR & DNA Cleanup columns (NEB T1030S).
3-15ng of genomic DNA was used for library construction. Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer's protocol.

treatment_protocol: Differentiation was induced by treatment with DMEM/F-12 medium containing 10% FBS

tag: cell line

value: DIPG-XIII

value: Glioma

value: Serum differentiation

tag: cut&run antibody


title: Whole blood DNA methylation, NHW CONTROL, 69yo F, 207215830118_R04C01

value: Female

value: Healthy control

value: whole blood


title: 07_MXZ_Gpm3_WT

description:
Library name: Sample 7
MXZ-Gpm3-tFT library in wild type background (combinatorial mutagenesis of residues 2 and 3)

source_name: yeast strain yMaM330 transformed with the desired plasmid variants

value: MATalpha can1delta::STE2pr-SpHIS5 lyp1delta::STE3pr-LEU2 his3delta1 leu2delta0 ura3delta0 leu2delta0::GAL1pr-I-SCEI-natNT2


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I460

description:
Library name: I460_S31
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: JEB; Gene: LAMB3; Mutation: c.1977-1G>A /  c.1977-1G>A; Clinical severity: Moderate; Age: 38; Sex: male; Sample ID: I460; Mutation group: 8; Family: r; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000

value: peripheral blood

value: leukocytes


title: Whole blood DNA methylation, NHW CONTROL, 68yo F, 207215830126_R07C01


title: CnR_H3K27me3_DKO_Wk10_Rep1

value: ASCL1-KO; K27M-KO


title: 06_MXZ_Phm8_gid11

description:
Library name: Sample 6
MXZ-Phm8-tFT library in gid11∆ background (combinatorial mutagenesis of residues 2 and 3)

source_name: yeast strain yKEK092 transformed with the desired plasmid variants

value: MATalpha can1delta::STE2pr-SpHIS5 lyp1delta::STE3pr-LEU2 his3delta1 leu2delta0 ura3delta0 leu2delta0::GAL1pr-I-SCEI-natNT2 gid11delta::kanMX6


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I89

description:
Library name: I89_S30
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT5; Mutation: c.464T>C, p.L155P; Clinical severity: Mild; Age: 58; Sex: female; Sample ID: I89; Mutation group: 7; Family: q; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000


title: HEK293T_siHDAC1_sRNA_1

city: Urbana

first: Ruiying

last: Cheng

state: IL

address: B520 Chemical & Life Sciences Laboratory

department: School of Molecular & Cellular Biology

institute: The University of Illinois Urbana-Champaign

description: Library name: siHDAC1_sRNA_1

data_processing:
Small RNA sequencing (sRNA-seq) reads were processed using a standardized pipeline. Raw single-end reads were trimmed with Trim_Galore to remove adapter sequences and low-quality bases, and read quality was assessed using FastQC. Trimmed reads were aligned to the custom THP1_active_PolIIIgenes_100exp index using Bowtie2/2.3.5.1, and resulting SAM files were converted, sorted, and indexed as BAM files using SAMtools/1.9-IGB-gcc-4.9.4. Genome-normalized coverage tracks were generated using deepTools/3.2.1.  Reads counts at RNA central noncoding genes (gene body +- 50bp) were obtained with BEDTools/2.28.0 (coverage function, -counts mode).
Assembly: GRCh38.109
Supplementary files format and content: Bigwig

extract_protocol:
small RNA seq: Total steady-state small RNA was purified from equal numbers (~2 million cells per small RNA-seq experiment) of HEK293T cells treated with siRNA using the mirVana™ PARIS™ RNA and Native Protein Purification Kit (Catalog# AM1556, Invitrogen) according to manufacturer's protocol for sRNA enrichment . The small RNA were treated with Antartic Phosphatase and PNK and libraries were constructed with the NEBNext Small RNA Sample Prep kit (NEB).
Samples are quantified using Bioanalyzer and sequenced with Nova X 25B paired-reads 300-cycle on the NovaSeq X Plus platform


title: CnR_H3K27me3_DKO_Day3_Rep1


title: Whole blood DNA methylation, NHW CONTROL, 69yo F, 207228480032_R06C01

value: NHW


title: Whole blood DNA methylation, NHW CONTROL, 65yo F, 207096540063_R05C01


title: 05_MXZ_Phm8_gid9

description:
Library name: Sample 5
MXZ-Phm8-tFT library in gid9∆ background (combinatorial mutagenesis of residues 2 and 3)

value: yeast strain yKEK114 transformed with the desired plasmid variants

value: MATalpha can1delta::STE2pr-SpHIS5 lyp1delta::STE3pr-LEU2 his3delta1 leu2delta0 ura3delta0 leu2delta0::GAL1pr-I-SCEI-natNT2 gid9delta::kanMX6


title: HEK293T_siCon_sRNA_3

description: Library name: siCon_sRNA_3

value: control siRNA


title: d3_SCR_L_2

description: Library name: d3_SCR_L_2

value: skin

value: human dermal fibroblast

value: WT

value: Cells were transfected with mRNAs coding for Pu.1, Irf8, Batf3 (PIB) and a scrambled miRNA mimic on day 0 of reprogramming.

value: Cells were collected on day 3 of reprogramming.


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I88

description:
Library name: I88_S29
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT5; Mutation: c.464T>C, p.L155P; Clinical severity: Severe; Age: 32; Sex: female; Sample ID: I88; Mutation group: 7; Family: q; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000


title: CnR_H3K27me3_Control_Sph_Wk10_Rep1

value: DIPG-XIII

value: Glioma

value: Serum differentiation


title: CnT_H3K27me3_Control_Sph_Wk10_Rep2

data_processing:
*library strategy: CUT&TAG-Direct
Reads were aligned to the human hg38 (target genome) and E. coli K-12 MG1655 (spike-in genome) using Bowtie2 v2.3.5.1, with settings --no-unal --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700
Spike-in-normalized bigwig track files were created using bamCoverage from deepTools v3.3.1, with settings --binSize=20 --smoothLength=60 --normalizeUsing BPM --scaleFactor $scale_factor.
Scale factors were calculated as the ratio of total reads / spike-in reads
Assembly: hg38, E. coli K-12 (MG1655)
Supplementary files format and content: bigWig

extract_protocol:
CUT&TAG-Direct was performed with anti-H3K27me3 (CST 9733). Tagmented genomic DNA was extracted using 1%SDS/Proteinase K
Released, tagmented DNA from ~50,000 starting cells was amplified using non-hot-start polymerase (NEB M0541S) using the following program: 58oC, 5 mins; 72oC, 5mins; 98oC 30s; (98oC 10s, 63oC 30s) x 12 cycles total, 72oC, 1min.

tag: cut&tag antibody


title: Whole blood DNA methylation, NHW CONTROL, 79yo M, 207096540017_R08C01

value: Male

value: Healthy control

value: whole blood


title: hct116.AIT-ULONT-run1

city: Singapore

first: XIAORAN

last: CHAI

address: 8 College Rd, Singapore 169857

country: Singapore

institute: Duke-NUS Medical School

description: Library name: hct116.AIT-ULONT-run1

data_processing:
For HiFi sequenicng and Revio sequencing, consensus HiFi reads were generated on-instrument using the default CCS function.
For Nanopore sequencing, base calling was performed using dorado-0.9.5 with “super accurate” mode.
Assembly: CHM13-v2.0
Supplementary files format and content: tab-delimited text file includes telomere/subtelomere length and number of TRF1/TRF2 binding sites on each read.

extract_protocol:
Genomic DNA from cultured cells was extracted using the Gentra Puregene Genomic DNA Purification Kit (Qiagen)
For HiFi and Revio sequencing, SMRTBELL EXPRESS TEMPLATE PREP KIT 2.0 was used. For Nanopore sequencing, Ligation Sequencing Kit V14 was used.

value: human colorectal carcinoma cell line


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I718

description:
Library name: I718_S28
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT5; Mutation: c.464T>C, p.L155P; Clinical severity: Severe; Age: 27; Sex: male; Sample ID: I718; Mutation group: 7; Family: q; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000

value: peripheral blood

value: leukocytes


title: CnR_H3K27me3_Control_Day3_Rep1


title: Whole blood DNA methylation, NHW CONTROL, 69yo M, 207215820076_R02C01

value: NHW


title: 04_MXZ_Phm8_WT

description:
Library name: Sample 4
MXZ-Phm8-tFT library in wild type background (combinatorial mutagenesis of residues 2 and 3)

value: yeast strain yMaM330 transformed with the desired plasmid variants

value: MATalpha can1delta::STE2pr-SpHIS5 lyp1delta::STE3pr-LEU2 his3delta1 leu2delta0 ura3delta0 leu2delta0::GAL1pr-I-SCEI-natNT2


title: CnT_H3K27me3_Control_Sph_Wk10_Rep1


title: 03_MXZ_Phm8_gid11

description:
Library name: Sample 3
MXZ-Phm8-tFT library in gid11∆ background (combinatorial mutagenesis of residues 2 and 3)

value: yeast strain yKEK092 transformed with the desired plasmid variants

value: MATalpha can1delta::STE2pr-SpHIS5 lyp1delta::STE3pr-LEU2 his3delta1 leu2delta0 ura3delta0 leu2delta0::GAL1pr-I-SCEI-natNT2 gid11delta::kanMX6


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient EB5702002

description:
Library name: EB5702002_S27
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT5; Mutation: c.1427G>A, p.Gly476Asp; Sample ID: EB5702002; Mutation group: 6; Family: p; Used in differential analysis: no; Exclusion reason: group_not_tested(missing_severity). Instrument model: Illumina NextSeq 2000

value: KRT5 c.1427G>A, p.Gly476Asp


title: Whole blood DNA methylation, NHW CONTROL, 80yo M, 207219770143_R08C01


title: CnT_H3K27me3_Control_Day3_Rep2

value: WT


title: 02_MXZ_Phm8_gid9

description:
Library name: Sample 2
MXZ-Phm8-tFT library in gid9∆ background (combinatorial mutagenesis of residues 2 and 3)

value: yeast strain yKEK114 transformed with the desired plasmid variants

value: MATalpha can1delta::STE2pr-SpHIS5 lyp1delta::STE3pr-LEU2 his3delta1 leu2delta0 ura3delta0 leu2delta0::GAL1pr-I-SCEI-natNT2 gid9delta::kanMX6


title: CnR_H3K27me3_Control_Adh_Wk10_Rep1

value: DIPG-XIII

value: Glioma


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient EB5701001

description:
Library name: EB5701001_S26
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT5; Mutation: c.1427G>A, p.Gly476Asp; Sample ID: EB5701001; Mutation group: 6; Family: p; Used in differential analysis: no; Exclusion reason: group_not_tested(missing_severity). Instrument model: Illumina NextSeq 2000


title: CnR_H3K27me3_ASCL1KO_Wk10_Rep1

value: Serum differentiation


title: Whole blood DNA methylation, NHW CONTROL, 68yo F, 207215820077_R03C01

value: Female

value: Healthy control


title: 01_MXZ_Phm8_WT

description:
Library name: Sample 1
MXZ-Phm8-tFT library in wild type background (combinatorial mutagenesis of residues 2 and 3)


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I847

description:
Library name: I847_S25
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT5; Mutation: c.1427G>A, p.Gly476Asp; Clinical severity: Severe; Age: 12; Sex: male; Sample ID: I847; Mutation group: 6; Family: o; Used in differential analysis: no; Exclusion reason: group_not_tested(missing_severity). Instrument model: Illumina NextSeq 2000


title: Whole blood DNA methylation, NHW CONTROL, 74yo F, 207215820097_R08C01

value: whole blood


title: u218-3

city: Riverside

first: Zachery

last: Wolfe

address: Boyce Hall 1463

department: Biochemistry

institute: University of California, Riverside

description: Library name: Sample 15

data_processing:
.fastqs reconstructed from .bam files using bamtofastq (bedtools)
HTSeq
DESeq
Assembly: caenorhabditis_elegans.PRJNA13758.WBPS18.canonical_geneset.gtf
Supplementary files format and content: Normalized counts from DESeq2. Counts are averaged between replicates within the same treatment type

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole-animal

extract_protocol: RNA extraction via NEBNext polyA kit

value: whole-animal

tag: strain

value: u218 KO


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I710

description:
Library name: I710_S24
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT5; Mutation: c.1427G>A, p.Gly476Asp; Clinical severity: Mild; Age: 44; Sex: male; Sample ID: I710; Mutation group: 6; Family: o; Used in differential analysis: no; Exclusion reason: group_not_tested(missing_severity). Instrument model: Illumina NextSeq 2000

value: peripheral blood

value: leukocytes


title: Whole blood DNA methylation, NHW CONTROL, 69yo F, 207215830103_R07C01

value: NHW


title: CnR_H3K27M_K27MKO_TSM_rep2


title: CnR_H3K27M_K27MKO_TSM_rep1


title: u218-1

description: Library name: Sample 13


title: Whole blood DNA methylation, NHW CONTROL, 68yo M, 207215830114_R04C01

value: Male


title: CnR_H3K27M_Control_TSM_rep2


title: u74-3

description: Library name: Sample 12

value: u74 KO


title: CnR_H3K27M_Control_TSM_rep1


title: u74-2

description: Library name: Sample 11


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient EB44-02002

description:
Library name: EB44_02002_S20
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT5; Mutation: c.596A>G, p.Lys199Arg; Sample ID: EB44-02002; Mutation group: 5; Family: l; Used in differential analysis: no; Exclusion reason: group_not_tested(missing_severity). Instrument model: Illumina NextSeq 2000

value: KRT5 c.596A>G, p.Lys199Arg


title: Whole blood DNA methylation, NHW CONTROL, 70yo F, 207215820131_R08C01


title: CnR_BRG1_K27MKO_Day3_Rep2


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient EB44- 01001

description:
Library name: EB44_01001_S19
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT5; Mutation: c.596A>G, p.Lys199Arg; Clinical severity: Mild; Sample ID: EB44- 01001; Mutation group: 5; Family: l; Used in differential analysis: no; Exclusion reason: group_not_tested(missing_severity). Instrument model: Illumina NextSeq 2000


title: Whole blood DNA methylation, NHW CONTROL, 70yo M, 207219630122_R02C01


title: MEC8-3

description: Library name: Sample 9


title: CnR_BRG1_K27MKO_Day3_Rep1


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I2209

description:
Library name: I2209_S18
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT5; Mutation: c.932T>C, p.Leu311Pro; Clinical severity: Mild; Age: 45; Sex: male; Sample ID: I2209; Mutation group: 4; Family: k; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000

value: KRT5 c.932T>C, p.Leu311Pro


title: CnR_BRG1_DKO_Day3_Rep3

value: ASCL1-KO; K27M-KO


title: MEC8-2

description: Library name: Sample 8


title: Whole blood DNA methylation, NHW CONTROL, 69yo F, 207215830027_R07C01


title: Whole blood DNA methylation, NHW CONTROL, 72yo M, 207215820047_R08C01


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I2208

description:
Library name: I2208_S17
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT5; Mutation: c.932T>C, p.Leu311Pro; Clinical severity: Mild; Age: 9; Sex: female; Sample ID: I2208; Mutation group: 4; Family: k; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000


title: MEC8-1

description: Library name: Sample 7


title: CnR_BRG1_DKO_Day3_Rep1


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I2207

description:
Library name: I2207_S16
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT5; Mutation: c.932T>C, p.Leu311Pro; Clinical severity: Mild; Age: 12; Sex: male; Sample ID: I2207; Mutation group: 4; Family: k; Used in differential analysis: no; Exclusion reason: excluded_low_coverage. Instrument model: Illumina NextSeq 2000


title: Whole blood DNA methylation, NHW CONTROL, 78yo F, 207097650075_R08C01


title: CnR_BRG1_Control_Day3_Rep3

value: WT


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I1567

description:
Library name: I1567_S15
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT5; Mutation: c.932T>C, p.Leu311Pro; Clinical severity: Moderate; Age: 15; Sex: male; Sample ID: I1567; Mutation group: 4; Family: j; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000


title: Whole blood DNA methylation, NHW CONTROL, 67yo M, 207215820013_R02C01


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I2039

description:
Library name: I2039_S14
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT5; Mutation: c.932T>C, p.Leu311Pro; Clinical severity: Mild; Age: 13; Sex: female; Sample ID: I2039; Mutation group: 4; Family: j; Used in differential analysis: no; Exclusion reason: excluded_low_coverage. Instrument model: Illumina NextSeq 2000


title: N2-5

description: Library name: Sample 5


title: CnR_BRG1_Control_Day3_Rep2

value: DIPG-XIII


title: N2-4

description: Library name: Sample 4


title: N2-6

description: Library name: Sample 6


title: Whole blood DNA methylation, NHW CONTROL, 79yo M, 207215830018_R08C01


title: N2-3

description: Library name: Sample 3


title: Whole blood DNA methylation, NHW CONTROL, 70yo M, 207215830057_R01C01


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient EB1501001

description:
Library name: EB1501001_S12
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT5; Mutation: c.932T>C, p.Leu311Pro; Clinical severity: Mild; Age: 45; Sex: female; Sample ID: EB1501001; Mutation group: 4; Family: j; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient EB1502002

description:
Library name: EB1502002_S13
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT5; Mutation: c.932T>C, p.Leu311Pro; Clinical severity: Mild; Age: 76; Sex: female; Sample ID: EB1502002; Mutation group: 4; Family: j; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000


title: Whole blood DNA methylation, NHW CONTROL, 71yo M, 207215830103_R03C01


title: CnR_BRG1_ASCL1KO_Day3_Rep3

value: Glioma


title: CnR_BRG1_Control_Day3_Rep1

value: Serum differentiation


title: Whole blood DNA methylation, NHW CONTROL, 79yo F, 207215820075_R03C01

value: Female


title: CnR_H3K27me3_ASCL1KO_Day3_Rep1


title: N2-2

description: Library name: Sample 2


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient EB1504001

description:
Library name: EB1504001_S11
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT5; Mutation: c.932T>C, p.Leu311Pro; Clinical severity: Moderate; Age: 18; Sex: female; Sample ID: EB1504001; Mutation group: 4; Family: j; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000


title: CnR_BRG1_ASCL1KO_Day3_Rep2


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I192

description:
Library name: I192_S23
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT5; Mutation: c.596A>G, p.Lys199Arg; Clinical severity: Moderate; Age: 46; Sex: female; Sample ID: I192; Mutation group: 5; Family: n; Used in differential analysis: no; Exclusion reason: group_not_tested(missing_severity). Instrument model: Illumina NextSeq 2000


title: u218-2

description: Library name: Sample 14


title: Whole blood DNA methylation, AA CONTROL, 66yo F, 207215820055_R05C01

value: Healthy control

value: AA

value: REAAADI


title: N2-1

description: Library name: Sample 1

value: whole-animal


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I1805

description:
Library name: I1805_S10
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT14; Mutation: c.373C>T, p.Arg125Cys; Clinical severity: Severe; Age: 5; Sex: male; Sample ID: I1805; Mutation group: 3; Family: i; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000

value: peripheral blood

value: KRT14 c.373C>T, p.Arg125Cys


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I1743

description:
Library name: I1743_S22
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT5; Mutation: c.596A>G, p.Lys199Arg; Clinical severity: Mild; Sample ID: I1743; Mutation group: 5; Family: m; Used in differential analysis: no; Exclusion reason: group_not_tested(missing_severity). Instrument model: Illumina NextSeq 2000

value: leukocytes


title: CnR_BRG1_ASCL1KO_Day3_Rep1


title: Whole blood DNA methylation, NHW CONTROL, 68yo F, 207228480014_R04C01

value: whole blood

value: NHW


title: Whole blood DNA methylation, NHW CONTROL, 87yo M, 207215820045_R06C01

value: Male


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I1741

description:
Library name: I1741_S21
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT5; Mutation: c.596A>G, p.Lys199Arg; Clinical severity: Moderate; Age: 23; Sex: female; Sample ID: I1741; Mutation group: 5; Family: m; Used in differential analysis: no; Exclusion reason: group_not_tested(missing_severity). Instrument model: Illumina NextSeq 2000

value: KRT5 c.596A>G, p.Lys199Arg


title: Whole blood DNA methylation, AA CONTROL, 81yo M, 207215820121_R05C01


title: CD4_d0957

city: Stanford

first: Laura

last: Amaya

address: 269 Campus Drive

institute: Stanford University

description: Library name: CD4_d0957

data_processing:
Adapters were trimmed using cutadapt, and reads were mapped to the hg38 genome using bowtie2 with a maximum fragment length of 2000bp. Filtering criteria included non-mitochondrial reads, mapq > 20, and properly paired reads. Duplicates were removed using Picard tools. Peak calling was performed using macs2 with specific parameters (--shift -75 --extsize 150 --nomodel --call-summits --nolambda -p 0.01 -B –SPMR) on Tn5 insertion sites.
ChrAccR (https://github.com/GreenleafLab/ChrAccR) was utilized for differential accessibility analysis between sorted T cell populations.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Blood

growth_protocol: Tr1 and non-Tr1 cells were isolated from T-allo10 cell products, and Teff isolated from T-allo cell products at day 10 of culture by FACS. CD4+ T cells, CD4+ T cells were isolated using FACS from cryopreserved PBMC from the first cohort of patients with hematological malignancies infused with 1 x 106 T-allo10 cells/kg a day before their unmanipulated allo-HSCT (ClinicalTrials.gov ID: NCT03198234) at day 35, 90 and 300 post-treatment (n = 3), and four healthy donors.

extract_protocol:
DNA was tagmented and libraries prepared following the OMNI-ATAC protocol
DNA was tagmented and libraries prepared following the OMNI-ATAC protocol

value: Blood

value: Healthy

value: No treatment

value: TimeNA


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient EB6501001/I224

description:
Library name: EB6501001_S9
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT14; Mutation: c.373C>T, p.Arg125Cys; Clinical severity: Moderate; Age: 46; Sex: female; Sample ID: EB6501001/I224; Mutation group: 3; Family: h; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000


title: CnR_ASCL1_K27MKO_Wk10_Rep2

value: DIPG-XIII

value: Glioma

value: Serum differentiation

value: ASCL1 (Abcam, ab74065)


title: Whole blood DNA methylation, NHW AD, 81yo M, 207228480014_R05C01

value: Alzheimer's disease


title: CD4_d0008

description: Library name: CD4_d0008


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient EB5001001

description:
Library name: EB5001001_S8
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT14; Mutation: c.373C>T, p.Arg125Cys; Clinical severity: Mild; Sample ID: EB5001001; Mutation group: 3; Family: g; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000


title: Whole blood DNA methylation, AA CONTROL, 65yo F, 207215830118_R08C01

value: Female

value: Healthy control

value: AA

value: REAAADI


title: CnR_ASCL1_K27MKO_TSM_Rep3


title: u74-1

description: Library name: Sample 10

value: whole-animal

value: u74 KO


title: CD4_d0143

description: Library name: CD4_d0143


title: CnR_ASCL1_K27MKO_TSM_Rep2


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I240

description:
Library name: I240_S4
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT14; Mutation: c.374G>A, p.Arg125His; Clinical severity: Mild; Age: 14; Sex: female; Sample ID: I240; Mutation group: 2; Family: c; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000

value: peripheral blood

value: leukocytes

value: KRT14 c.374G>A, p.Arg125His


title: Whole blood DNA methylation, AA CONTROL, 72yo F, 207219770143_R05C01

value: whole blood


title: CD4_d0587

description: Library name: CD4_d0587

value: Blood

value: Healthy

value: No treatment


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I242

description:
Library name: I242_S3
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT14; Mutation: c.374G>A, p.Arg125His; Clinical severity: Mild; Age: 29; Sex: female; Sample ID: I242; Mutation group: 2; Family: c; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000


title: CnR_ASCL1_K27MKO_TSM_Rep1

value: DIPG-XIII

value: Glioma


title: Whole blood DNA methylation, AA CONTROL, 67yo F, 207219770143_R01C01


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient EB61

description:
Library name: EB61_S2
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT14; Mutation: c.356T>C, p.Met119Thr; Clinical severity: Mild; Age: 27; Sex: female; Sample ID: EB61; Mutation group: 1; Family: b; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000

value: KRT14 c.356T>C, p.Met119Thr


title: CD4_d4147

description: Library name: CD4_d4147

value: TimeNA


title: Whole blood DNA methylation, AA AD, 88yo F, 207215830065_R05C01

value: Female

value: Alzheimer's disease


title: DN_d0957

description: Library name: DN_d0957

value: DN


title: CnR_ASCL1_Control_TSM_Rep2

value: WT

value: Serum differentiation

value: ASCL1 (Abcam, ab74065)


title: Whole blood DNA methylation, HISPANIC CONTROL, 82yo F, 207215820132_R07C01

value: Healthy control

value: HISPANIC

value: PRADI


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I2180

description:
Library name: I2180_S1
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: EBS; Gene: KRT14; Mutation: c.356T>C, p.Met119Thr; Clinical severity: Severe; Age: 20; Sex: female; Sample ID: I2180; Mutation group: 1; Family: a; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000

value: peripheral blood

value: leukocytes


title: CnR_ASCL1_Control_TSM_Rep3


title: DN_d0008

description: Library name: DN_d0008

value: Blood

value: Healthy


title: SAM non-converted 4

city: Pozzuoli

first: Davide

last: Cacchiarelli

state: Napoli

address: via campi flegrei,34

country: Italy

institute: TIGEM

description:
Library name: SAM non-converted 4
amplicon

data_processing:
Illumina NovaSeq base call (BCL) files were converted into FASTQ files through bcl2fastq. Sequence reads were hard trimmed at the extremities to remove non- variable regions using cutadapt43 (v. 4.4). Trimmed reads were aligned to the reference P63 sequence using bwa44 (v.0.7.17) with default parameters.
The evaluation and quantification of mutations in P63 sequence was achieved with the gatk45 (v. 4.3.0) module AnalyzeSaturationMutagenesis with the parameter –min-q set to 15.
Assembly: hg38
Supplementary files format and content: tab-separated count matrix files

source_name: BJ-T converted to iKCs

growth_protocol: BJ-T cells were grown in DMEM/F12 (Euroclone # ECM0095) supplemented with 10% FBS (Euroclone #ECS0186L), 1x Glutamax (Thermo #35050061), 1xNEAA (Thermo #11140035), 1x 2-Mercapto-ethanol (Thermo #21985023)

extract_protocol:
Genomic DNA was extracted with phenol/Chlorophorm procedure
Amplicon generation with oligos containing illumina adaptors

treatment_protocol: Two days after transduction, the cells were split and plated at 20% confluency, and the medium was supplemented with 10 ug/ml blasticidin (Thermo #A1113903), for four days. After antibiotic selection, the medium was changed to 50% fibroblast medium + 50% keratinocyte medium (Lonza, KGM-Gold BulletKit #192060) and supplemented with 1x Revitacell (Thermo #A2644501). After two days, the medium was switched to 100% keratinocyte medium supplemented with 1x Revitacell. The medium was changed every two days until day 14

value: BJ-T converted to iKCs

value: iKCs conversion


title: Whole blood DNA methylation, AA CONTROL, 81yo F, 207219630047_R05C01

value: whole blood

value: AA

value: REAAADI


title: CnR_ASCL1_Control_TSM_Rep1

value: DIPG-XIII

value: Glioma


title: Whole blood DNA methylation, AA AD, 82yo F, 207215830074_R05C01

value: Female

value: Alzheimer's disease


title: CnR_BRG1_DKO_Day3_Rep2

value: ASCL1-KO; K27M-KO

value: Serum differentiation


title: DN_d0143

description: Library name: DN_d0143

value: DN

value: No treatment

value: TimeNA


title: SAM non-converted 3

description:
Library name: SAM non-converted 3
amplicon


title: Whole blood DNA methylation, AA AD, 81yo M, 207215820094_R07C01

value: Male


title: CnR_ASCL1_Control_Sph_Wk10_Rep2

value: WT

value: ASCL1 (Abcam, ab74065)


title: SAM non-converted 2

description:
Library name: SAM non-converted 2
amplicon

value: BJ-T converted to iKCs


title: Whole blood DNA methylation, AA CONTROL, 86yo F, 207097650075_R05C01

value: Healthy control


title: CnR_ASCL1_Control_Sph_Wk10_Rep1


title: DN_d4147

description: Library name: DN_d4147

value: Blood

value: Healthy


title: SAM non-converted 1

description:
Library name: SAM non-converted 1
amplicon

value: iKCs conversion


title: Teff_d0957

description: Library name: Teff_d0957

value: Teff


title: SAM converted 4

description:
Library name: SAM converted 4
amplicon


title: Whole blood DNA methylation, AA CONTROL, 70yo F, 207215830119_R07C01

value: whole blood

value: AA

value: REAAADI


title: Whole blood DNA methylation, AA AD, 72yo F, 207215820055_R04C01

value: Female

value: Alzheimer's disease


title: SAM converted 3

description:
Library name: SAM converted 3
amplicon


title: CnR_ASCL1_Control_Adh_Wk10_Rep2

value: DIPG-XIII

value: Glioma

value: Serum differentiation


title: Whole blood DNA methylation, AA AD, 82yo F, 207215830027_R06C01


title: SAM converted 2

description:
Library name: SAM converted 2
amplicon


title: Teff_d0143

description: Library name: Teff_d0143

value: No treatment

value: TimeNA


title: CnR_ASCL1_Control_Adh_Wk10_Rep1

value: WT

value: ASCL1 (Abcam, ab74065)


title: Whole blood DNA methylation, AA CONTROL, 68yo F, 207228480080_R05C01

value: Healthy control


title: CnR_ASCL1_ASCL1KO_TSM

value: Day 0


title: Whole blood DNA methylation, AA AD, 84yo M, 207215820034_R06C01

value: Male


title: Teff_d4147

description: Library name: Teff_d4147

value: Blood

value: Healthy


title: DBD non-converted 4

description:
Library name: DBD non-converted 4
amplicon

value: BJ-T converted to iKCs

value: iKCs conversion


title: Whole blood DNA methylation, NHW AD, 79yo F, 207097650067_R03C01

value: whole blood

value: NHW


title: CUTAC_K27MKO_TSM_Rep2

data_processing:
*library strategy: CUTAC
Reads were aligned to the human hg38 genome using Bowtie2 v2.3.5.1, with settings --no-unal --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700
Bigwig track files were created using bamCoverage from deepTools v3.3.1, with settings --binSize=20 --smoothLength=60 --normalizeUsing BPM
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
CUTAC was performed with anti-H3K4me2 (Sigma-Aldrich 07-030). Tagmented genomic DNA was extracted using 1%SDS/Proteinase K
Released, tagmented DNA from ~50,000 starting cells was amplified using non-hot-start polymerase (NEB M0541S) using the following program: 58oC, 5 mins; 72oC, 5mins; 98oC 30s; (98oC 10s, 63oC 30s) x 12 cycles total, 72oC, 1min.

tag: cutac antibody

value: anti-H3K4me2 (Sigma Aldrich 07-030)


title: Tr1_d0957

description: Library name: Tr1_d0957

tag: cell type


title: DBD non-converted 3

description:
Library name: DBD non-converted 3
amplicon


title: CUTAC_K27MKO_TSM_Rep1

value: DIPG-XIII

tag: genotype


title: Whole blood DNA methylation, NHW AD, 77yo M, 207215820097_R01C01

value: Alzheimer's disease


title: Tr1_d0008

description: Library name: Tr1_d0008


title: DBD non-converted 2

description:
Library name: DBD non-converted 2
amplicon


title: CUTAC_K27MKO_Day3_Rep2

value: Glioma

value: Serum differentiation


title: Whole blood DNA methylation, NHW AD, 83yo M, 207215830104_R03C01


title: DBD non-converted 1

description:
Library name: DBD non-converted 1
amplicon


title: Tr1_d0143

description: Library name: Tr1_d0143

value: No treatment

value: TimeNA


title: Whole blood DNA methylation, AA AD, 89yo F, 207215820047_R07C01

value: Female

value: AA

value: REAAADI


title: CUTAC_K27MKO_Day3_Rep1


title: Tr1_d0587

description: Library name: Tr1_d0587


title: DBD converted 4

description:
Library name: DBD converted 4
amplicon


title: CUTAC_DKO_TSM_Rep2

value: DKO


title: Whole blood DNA methylation, NHW AD, 76yo F, 207097650070_R07C01


title: Tr1_d4147

description: Library name: Tr1_d4147

value: Blood


title: DBD converted 3

description:
Library name: DBD converted 3
amplicon


title: Whole blood DNA methylation, NHW AD, 78yo F, 207215820055_R01C01


title: CUTAC_DKO_TSM_Rep1


title: CD4_d0008

description: Library name: CD4_d0008

data_processing:
sequencing reads were mapped and aligned to the reference human genome (GENCODE v32) and quantified using Salmon (v1.10.2), then aggregated to gene level, and imported into R using tximport.
Assembly: GENCODE v32
Supplementary files format and content: Individual sample files are in Salmon quant.sf format (tab-delimited text)

growth_protocol: Tr1 and non-Tr1 cells were isolated from T-allo10 cell products, and Teff isolated from T-allo cell products at day 10 of culture by FACS

extract_protocol:
RNA was extracted using the RNAqueous Micro Total RNA Isolation Kit (Invitrogen)
cDNA was generated from 1.2 ng of total RNA using the SMARTer Ultra Low Input RNA Kit for Sequencing (Takara Bio). RNA-seq libraries were generated from by the Nextera XT Library Prep Kit (Illumina).

tag: donor


title: DBD converted 2

description:
Library name: DBD converted 2
amplicon


title: CUTAC_DKO_Day3_Rep2


title: Whole blood DNA methylation, AA AD, 78yo F, 207215820077_R01C01

tag: Sex


title: CD4_d0587

description: Library name: CD4_d0587


title: DBD converted 1

description:
Library name: DBD converted 1
amplicon


title: DN_d0587

description: Library name: DN_d0587

value: DN

tag: disease state

value: Healthy


title: CnR_ASCL1_Control_Day3_Rep2

value: WT

value: ASCL1 (Abcam, ab74065)


title: CD4_d4147

description: Library name: CD4_d4147

tag: tissue


title: CUTAC_DKO_Day3_Rep1


title: CnR_ASCL1_Control_Day3_Rep1


title: Whole blood DNA methylation, AA AD, 76yo F, 207215820094_R04C01

value: whole blood

tag: ethnicity


title: CUTAC_Control_TSM_Rep2

value: Control

value: anti-H3K4me2 (Sigma Aldrich 07-030)


title: scRNA-seq of Mus musculus: Young_CD41

city: Sendai

first: Keiyo

last: Takubo

address: 2-1 Seiryo-machi Aoba-ku

department: Graduate School of Medicine

country: Japan

institute: Tohoku University

description:
Library name: Young_CD41_1_scRNAseq
Young CD41+ megakaryocyte progenitors were freshly isolated, then subjected to scRNAseq

library_source: transcriptomic single cell

data_processing:
Sequencing was performed using an Illumina HiSeq2000 system. Sequence reads were aligned to the murine genome mm10 using Cufflinks version 2.1.1. Downstream analysis was performed by R package Seurat (version 4)
Assembly: mm10
Supplementary files format and content: count.txt provides a tab-deliminated raw count data generated by featureCounts.

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
Single-cell cDNA synthesis was performed with a C1 Single-Cell Auto Prep System (Fluidigm). Reverse transcription and preamplification were performed according to the manufacturer’s instructions using a SMARTer Ultra Low RNA Kit for the Fluidigm C1 System (Clontech) and a C1 Single-Cell Auto Prep Reagent Kit for mRNA Seq (Fluidigm). For RNA controls, tubes #1, #4, and #7 of ArrayControl RNA Spikes (Thermo Fisher Scientific) were mixed at a ratio of 100:10:1, and the RNA Spikes mixture was diluted 1:10000 in C1 Loading Reagent (Fluidigm). Sorted HSCs were diluted in Suspension Reagent to ~1000 cells/μL and loaded into a C1-Single-Cell Auto Prep IFC for mRNA-seq (5-10 μm). After loading the cells, the integrated fluidic circuit (IFC) was observed microscopically using an INCell Analyzer 6000 (GE Healthcare) to ensure that single cells were captured in each well. Wells with 0, >1, or shrunken cells were excluded.
The thermal cycling conditions for cell lysis, reverse transcription, and preamplification were as follows: 72°C for 3 min, 4°C for 10 min, and 25°C for 10 min for cell lysis; 42°C for 90 min and 70°C for 10 min for reverse transcription; 95°C for 1 min and 5 cycles at 95°C for 20 s, 58°C for 4 min, and 68°C for 6 min, 9 cycles at 95°C for 20 s, 64°C for 30 s, and 68°C for 6 min, 7 cycles at 95°C for 30 s, 64°C for 30 s, and 68°C for 7 min, and 1 cycle at 72°C for 10 min for preamplification; and holding at 4°C until harvest. Amplified cDNA (approximately 3.5 μL) from each well was diluted with 10 μL of C1 DNA Dilution Reagent (Fluidigm) and frozen at -30°C until use. The sample in each well was further diluted 1:2 with C1 Harvest Reagent and subjected to tagmentation and Illumina sequencing library preparation using a Nextera XT DNA Sample Preparation Kit (Illumina) and a Nextera XT DNA Sample Preparation Index Kit (96 indices, Illumina). Then, 2.5 μL of Tagment DNA Buffer, 1.25 μL of Amplification Tagment Mix and 1.25 μL of the diluted cDNA sample were mixed and incubated at 55°C for 10 min in a thermal cycler. The tagmentation reaction was then stopped by adding 1.25 μL of neutralizing buffer (NT buffer). Next, the samples were subjected to PCR amplification. A 6.25 μL aliquot of each sample was mixed with NPM buffer, and 1.25 μL each of Index Primer 1 and Index Primer 2. The thermal cycling conditions were as follows: 72°C for 3 min, 95°C for 30 s, 12 cycles at 95°C for 10 s, 55°C for 30 s, and 72°C for 1 min, and 1 cycle at 72°C for 5 min. A 1 μL aliquot from each well of amplified DNA was processed by two rounds of mixing and cleanup with AMPure XP beads (Beckman Coulter), and DNA was then eluted with 144 μL of DNA suspension buffer.

treatment_protocol: Fresh CD150+CD48-CD41-CD34- LSK cells (HSCs) or CD150+CD48-CD41+ LSK cells from 10-week-old mice or CD150+CD48-CD41-CD34- LSK cells from 7 month-old, 12 month-old, 18 month-old or 2-year old were sorted into 500 µL SF-O3. Either GFP+ or GFP- CD150+CD48-CD34- LSK cells from Scl-tTA:H2B-GFP mice treated with doxycycline from 1 year old for 2.5 months were sorted as well.

value: Bone marrow

value: Wild type

value: Freshly isolated


title: Teff_d0008

description: Library name: Teff_d0008

value: Teff

value: No treatment


title: Whole blood DNA methylation, NHW AD, 77yo M, 207221680026_R02C01

value: Male

value: Alzheimer's disease

value: NHW

tag: cohort


title: DN_d0008

description: Library name: DN_d0008


title: scRNA-seq of Mus musculus: H2B_low

description:
Library name: H2B_low_1_scRNAseq
GFP-low HSCs from 14.5m Scl-tTA::H2B-GFP mouse treated with DOX for 2m were freshly isolated, then subjected to scRNA-seq


title: Whole blood DNA methylation, AA AD, 77yo F, 207215820075_R05C01

value: Female

value: AA

value: REAAADI

tag: age


title: DN_d0587

description: Library name: DN_d0587

value: Blood

value: DN


title: SAM converted 1

description:
Library name: SAM converted 1
amplicon

value: BJ-T converted to iKCs

tag: treatment

value: iKCs conversion


title: scRNA-seq of Mus musculus: H2B_high

description:
Library name: H2B_high_1_scRNAseq
GFP-high HSCs from 14.5m Scl-tTA::H2B-GFP mouse treated with DOX for 2m were freshly isolated, then subjected to scRNA-seq


title: Teff_d0587

description: Library name: Teff_d0587

value: Healthy

tag: time

value: TimeNA


title: CUTAC_Control_Day3_Rep2

value: DIPG-XIII

value: Glioma

value: Control

value: Serum differentiation

value: anti-H3K4me2 (Sigma Aldrich 07-030)


title: scRNA-seq of Mus musculus: Old_HSC

description:
Library name: OldHSC2_1_scRNAseq
HSCs from 2yo mouse were freshly isolated, then subjected to RNA-seq

value: Bone marrow

value: Wild type

value: Freshly isolated


title: CUTAC_Control_Day3_Rep1


title: DN_d4147

description: Library name: DN_d4147


title: Whole blood DNA methylation, AA AD, 82yo F, 207215830103_R01C01

value: Female

value: Alzheimer's disease

value: whole blood


title: scRNA-seq of Mus musculus: 1half

description:
Library name: 1half_1_scRNAseq
HSCs from 18mo mouse were freshly isolated, then subjected to RNA-seq


title: CUTAC_ASCL1KO_TSM_Rep2


title: Whole blood DNA methylation, AA AD, 84yo F, 207215820062_R03C01

value: AA

value: REAAADI


title: Whole blood DNA methylation, NHW AD, 71yo F, 207215830126_R05C01

value: NHW


title: Teff_d4147

description: Library name: Teff_d4147

value: Blood

value: Teff


title: Teff_d0008

description: Library name: Teff_d0008


title: scRNA-seq of Mus musculus: 1yo

description:
Library name: 1yo_1_scRNAseq
HSCs from 12mo mouse were freshly isolated, then subjected to RNA-seq


title: CUTAC_ASCL1KO_TSM_Rep1


title: Tr1_d0008

description: Library name: Tr1_d0008


title: Whole blood DNA methylation, NHW CONTROL, 69yo F, 207215830065_R02C01

value: Healthy control


title: scRNA-seq of Mus musculus: 7mo

description:
Library name: 7mo_1_scRNAseq
HSCs from 7mo mouse were freshly isolated, then subjected to RNA-seq


title: Whole blood DNA methylation, NHW AD, 97yo F, 207221680026_R07C01


title: scRNA-seq of Mus musculus: Young_HSC

description:
Library name: YoungHSC2_1_scRNAseq
Young HSCs were freshly isolated, then subjected to RNA-seq


title: Whole blood DNA methylation, AA AD, 76yo F, 207096540063_R01C01


title: Tr1_d0587

description: Library name: Tr1_d0587


title: CUTAC_ASCL1KO_Day3_Rep1

value: DIPG-XIII


title: RNA-seq of HEK293T cells: STV-C8_EGFP replicate 2

status: Public on Jul 09 2026

city: Neuherberg

first: Florian

last: Giesert

state: Bavaria

address: Ingolstaedter Landstrasse 1

department: Stem Cell Department

institute: Helmholtz Munich

description: Library name: cd2

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the GRCh38_90-982227366 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Below are the statistics of mapping the reads to the reference genome
Assembly: GRCh38_90-982227366 reference genome
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
STV-C8 particles (supernatant) and corresponding producer cells (cells) were processed for RNA isolation (Monarch Total RNA Miniprep Kit, NEB).
mRNA enrichment, mRNA Fragmentation and rondom priming. cDNA Synthesism End Pair, 5'phoshorylation and dA-Tailing, Adaptor Ligation, PCR Enrichment and sequencing

value: human embryonic kidney


title: RNA-seq of HEK293T cells: STV-C8_EGFP replicate 1

description: Library name: cd1


title: CUTAC_ASCL1KO_Day3_Rep2

value: Glioma


title: RNA-seq of HEK293T cells: STV-C8_EGFP replicate 4

description: Library name: cd4


title: RNA-seq of HEK293T cells: STV-C8_EGFP replicate 3

description: Library name: cd3


title: Tr1_d4147

description: Library name: Tr1_d4147


title: RNA-seq of HEK293T supernatant: STV-C8_EGFP replicate 1

description: Library name: SN1


title: RNA-seq of HEK293T supernatant: STV-C8_EGFP replicate 3

description: Library name: SN3


title: RNA-seq of HEK293T supernatant: STV-C8_EGFP replicate 4

description: Library name: SN4


title: RNA-seq of HEK293T supernatant: STV-C8_EGFP replicate 2

description: Library name: SN2


title: ROPE_eGFP_CAAAAG_L007_R1_001

description: Library name: ROPE_eGFP

molecule: nuclear RNA

extract_protocol:
eCLIP is performed according to Van Nostrand, E., Pratt, G., Shishkin, A. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–514 (2016). https://doi.org/10.1038/nmeth.3810
Samples are quantified using Bioanalyzer and sequenced with Nova X 25B paired-reads 300-cycle on the NovaSeq X Plus platform


title: ROPE_3A_CAACTA_L007_R1_001

description: Library name: ROPE_3A


title: eCLIP_eGFP_ATGAGC_L007_R1_001

description: Library name: eCLIP_eGFP


title: eCLIP_3A_ATTCCT_L007_R1_001

description: Library name: eCLIP_3A


title: H3K9me3 sh SETDB1

city: lexington

first: ka wing

last: Fong

state: KY

address: 760 press ave

institute: University of Kentucky

description: Library name: H3K9me3 shSETDB1

data_processing:
Paired-end sequencing reads were trimmed using Trimmomatic(v0.39) to remove adapters and low quality bases. Trimmed reads were mapped to the human reference genome assembly GRCh37 (hg19) using Bowtie2 (v2.3.5.1), allowing fragments up to 2kb to be aligned.
The alignment result was further filtered by SAMtools to remove reads unmapped, not primary alignment, reads failing platform, reads mapped to mitochondria, reads mapped to ENCODE blacklisted genomic regions and multi-mapped reads.
PCR duplicates were removed using Picard(v2.26.8). Peaks were called by MACS2(v2.2.7.1). The coverage track bigwig files were generated with bin size 10 and were normalized by reads per genome coverage using deeptools (v3.5.1).
Assembly: GRCH38
Supplementary files format and content: bigwig
Library strategy: CUT&Run

source_name: LNCaP

growth_protocol: LNCaP cells were grown in RPMI + 10% FBS and 1% PS.

extract_protocol:
For CUT&RUN assay, 0.5x10^6  cells bound to Concanavalin A-coated beads were incubated with indicated primary antibodies and secondary antibody.  pA-MNase was used to digest chromatin/DNA bound by the antibodies-protein complex in CUT&RUN, followed by Proteinase K digestion and PCI extraction.
CUT&RUN libraries were prepared from 15-20ng DNA using NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645S), according to the manufacturer’s instructions. Postamplification libraries were size selected at 160-320bp (CUT&RUN) in length using Agencourt AMPure XP beads from Beckman Coulter and were quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems, KK4603). All CUT&RUN Libraries were pooled to a final concentration of 10nM and sequenced single-end using the Illumina HiSeq 4000.

value: LNCaP

value: Human prostate cancer cells

tag: chip antibody


title: SETDB1 shSETDB1

description: Library name: SETDB1 shSETDB1

tag: cell line

value: SETDB1 proteintech 11231-1-AP


title: H3K9me3

description: Library name: H3K9me3


title: SETDB1

description: Library name: SETDB1


title: siSETDB1-2 rep1

description: Library name: siSETDB1-2 rep1

data_processing:
Sequencing reads were trimmed and filtered using Trimmomatic (V0.39) to remove adapters and low quality reads. Reads from samples were mapped to Ensembl GRCh38 transcripts annotation, using RSEM (v1.3.2) and STAR (2.6.1d) with default settings.
Assembly: GRCh38
Supplementary files format and content: Count data: gene.count.annotated.tsv

extract_protocol:
Total RNA was isolated from cells using the nucleospin RNA kit (Takara) according to the manufacturer's recommended protocol.
RNA-seq libraries were prepared from 0.5 μg high-quality DNA-free total RNA by using NEBNext® Ultra RNA Library Prep Kit, according to the manufacturer’s instructions. The libraries passing quality control (equal size distribution between 250-400 bp, no adapter contamination peaks, no degradation peaks) were quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems, KK4603) using the Illumina provided protocol.

treatment_protocol: LNCaP cells were transfected by 100nM non-targeting siRNA and SETDB1 siRNA for 4 days


title: siSETDB1-2 rep3

description: Library name: siSETDB1-2 rep3


title: siSETDB1-2 rep2

description: Library name: siSETDB1-2 rep2


title: siSETDB1-1 rep2

description: Library name: siSETDB1-1 rep2


title: siSETDB1-1 rep3

description: Library name: siSETDB1-1 rep3


title: siCont rep3

description: Library name: siCont rep3

value: siCon


title: siCont rep2

description: Library name: siCont rep2


title: siSETDB1-1 rep1

description: Library name: siSETDB1-1 rep1


title: siCont rep1

description: Library name: siCont rep1


title: THP1, 2h,Romidepsin50nM,sRNA, biol rep 3

description: Library name: THP1_2h_Romidepsin50nM_sRNA_3

data_processing:
ATAC seq data are trimmed with Trim_Galore/0.6.5, aligned to genome GRCh38, sorted and indexed using Bowtie2/2.3.5.1 and SAMtools/1.9-IGB-gcc-4.9.4. Then unmapped reads, reads shorter than 20bp, and reads mapping to mitochondrial chromosomes are removed. Duplicated reads are removed using picard/2.9.4. Each replicate is downsampled to ~120 million reads to remove bias, using samtools view -s function. Reads counts at RNA central noncoding genes (gene body +-150bp) are extracted with bedtools coverage -counts BEDTools/2.26.0. Peaks are called with MACS2/2.2.5
ChIP-seq data were processed following a standardized pipeline. Raw paired-end reads were trimmed with Trim_Galore/0.6.5, and read quality was assessed using FastQC. Trimmed reads were aligned to the human reference genome GRCh38_noalt_as using Bowtie2/2.3.5.1, and resulting SAM files were converted to BAM, sorted, and indexed using SAMtools/1.9-IGB-gcc-4.9.4. Normalized signal tracks (20 bp bin size, smoothed over 60 bp) were generated with deepTools/3.2.1 using bamCoverage with RPGC normalization. Read coverage over RNA central noncoding genes (gene body +-150bp) s or custom-defined genomic windows was computed using BEDTools/2.26.0 with the coverage function. Peaks were identified using MACS2/2.2.5.
Small RNA sequencing (sRNA-seq) reads were processed using a standardized pipeline. Raw single-end reads were trimmed with Trim_Galore to remove adapter sequences and low-quality bases, and read quality was assessed using FastQC. Trimmed reads were aligned to the custom THP1_active_PolIIIgenes_100exp index using Bowtie2/2.3.5.1, and resulting SAM files were converted, sorted, and indexed as BAM files using SAMtools/1.9-IGB-gcc-4.9.4. Genome-normalized coverage tracks were generated using deepTools/3.2.1.  Reads counts at RNA central noncoding genes (gene body +- 50bp) were obtained with BEDTools/2.28.0 (coverage function, -counts mode).
Assembly: GRCh38.109
Supplementary files format and content: Bigwig

growth_protocol: THP−1 cells were obtained from ATCC (Batch# 62454382) and propagated in T-75 flasks between 0.2 and 1 × 106 cells/mL in an RPMI-1640 (Catalog# 11875093, Gibco, Billings, MT, USA) growth medium. THP−1 experiments were conducted on cells between passage 10 and 15.

extract_protocol:
ATAC seq samples of DMSO and 50nM Romidepsin treated THP1 cells  are prepared from 70k cells per sample using ATAC-Seq Kit (Cat #53156 Active Motif), following manufacturer's protocol for Cell Sample Preparation. Libraries are quantified using bioanalyzer and sequenced on a NovaSeq X Plus on a 25B lane with 2x150nt reads. for ChIP seq Equal numbers of THP-1 monocytes, THP-1 derived macrophages, and ML-60218 treated monocytes were collected (~10 million cells per ChIP experiment) and resuspended in growth media at 1 × 10^6 cells/mL and cross-linked with rotation at room temperature in 1% formaldehyde for 10 min. Cross-linking was quenched with the addition of 200 mM glycine and an additional 5 min of rotation at room temperature. Cross-linked cells were then spun down and resuspended in 1× RIPA lysis buffer, followed by chromatin shearing via sonication (3 cycles using a Branson sonicator: 30 s on, 60 s off; 20 additional cycles on a Bioruptor sonicator: 30 s on, 30 s off). Individual ChIP experiments were performed on pre-cleared chromatin using antibody-coupled ChIP grade Protein G magnetic beads (Cell Signaling Technology). Antibody used in this study are: MTA3 (Proteintech, #14682-1-AP), MTA2 (Invitrogen, #PA1-41581), MTA1 (Proteintech, #30545-1-AP), MBD2 (Proteintech, #55200-1-AP), HDAC2 (ActiveMotif AbFlex, #91197), HDAC1 (Proteintech, #10197-1-AP), and CDK2AP1 (Proteintech, #13060-2-AP). 5 ug of antibody per ChIP was coupled to 60 uL of beads and rotated overnight with sheared chromatin at 4°C. Beads were then washed 5× in ChIP wash buffer (Santa Cruz), 1× in TE, and chromatin eluted in TE + 1% SDS. Cross-linking was then reversed by incubation at 65°C overnight, followed by digestion of RNA (30 min RNase (Cell Signaling Technology cat #7012), 1mg/exp incubation at 37°C) and digestion of protein (30 min, 30ug/1 exp proteinase K (Cell Signaling Technology cat #10012) incubation at 45°C). ChIP DNA was then purified on a minElute column (Qiagen), followed by DNA library preparation (NEBNext Ultra II DNA Library Prep Kit for Illumina) and size selection of 350-550 bp fragments via gel extraction (Qiagen). small RNA seq: Total steady-state small RNA was purified from equal numbers (~2 million cells per small RNA-seq experiment) of THP-1 monocytes ± Romidepsin exposure using the mirVana™ PARIS™ RNA and Native Protein Purification Kit (Catalog# AM1556, Invitrogen) according to manufacturer's protocol for sRNA enrichment . The small RNA were treated with Antartic Phosphatase and PNK and libraries were constructed with the NEBNext Small RNA Sample Prep kit (NEB).
Samples are quantified using Bioanalyzer and sequenced with Nova X 25B paired-reads 300-cycle on the NovaSeq X Plus platform

treatment_protocol: THP-1 derived macrophages were collected after 72-h exposure to PMA by aspirating media and any non-adherent cells, and incubating adherent cells with TrypLE (ThermoFisher) for 15 min followed by cell wash in phosphate-buffered saline (PBS) buffer. THP-1 cells by treatment with RNA polymerase III inhibitor ML-60218 (Catalog# 557403-10MG, SigmaAldrich) at a final concentration of 25 μM or Romidepsin (FK 228)(Catalog# HY-15149, MedChemExpress) at a final concentration at 50 nM and cells collected at 2 h post-exposure followed by cell wash in PBS buffer.

value: Romidepsin 50nM 2h


title: THP1, 2h,DMSO,sRNA, biol rep 2

description: Library name: THP1_2h_DMSO_sRNA_2

value: DMSO


title: THP1, 2h,Romidepsin50nM,sRNA, biol rep 1

description: Library name: THP1_2h_Romidepsin50nM_sRNA_1


title: THP1, 2h,Romidepsin50nM,sRNA, biol rep 2

description: Library name: THP1_2h_Romidepsin50nM_sRNA_2


title: CDK2AP1,THP1, biol rep 1

description: Library name: CDK2AP1_THP1_1


title: CDK2AP1,THP1, biol rep 2

description: Library name: CDK2AP1_THP1_2


title: THP1, 2h,DMSO,sRNA, biol rep 1

description: Library name: THP1_2h_DMSO_sRNA_1


title: CDK2AP1,THP1,ML6, biol rep 2

description: Library name: CDK2AP1_THP1_ML6_2


title: CDK2AP1,THP1,ML6, biol rep 1

description: Library name: CDK2AP1_THP1_ML6_1


title: THP1, 2h,DMSO,sRNA, biol rep 3

description: Library name: THP1_2h_DMSO_sRNA_3


title: CDK2AP1,THP1,PMA, biol rep 1

description: Library name: CDK2AP1_THP1_PMA_1

value: PMA


title: CDK2AP1,THP1,PMA, biol rep 2

description: Library name: CDK2AP1_THP1_PMA_2


title: HDAC1,THP1, biol rep 2

description: Library name: HDAC1_THP1_2


title: HDAC1,THP1, biol rep 1

description: Library name: HDAC1_THP1_1


title: HDAC1,THP1,ML6, biol rep 1

description: Library name: HDAC1_THP1_ML6_1


title: HDAC1,THP1,ML6, biol rep 2

description: Library name: HDAC1_THP1_ML6_2


title: HDAC1,THP1,PMA, biol rep 2

description: Library name: HDAC1_THP1_PMA_2


title: HDAC1,THP1,PMA, biol rep 1

description: Library name: HDAC1_THP1_PMA_1


title: HDAC2,THP1, biol rep 2

description: Library name: HDAC2_THP1_2


title: HDAC2,THP1, biol rep 1

description: Library name: HDAC2_THP1_1


title: HDAC2,THP1,ML6, biol rep 1

description: Library name: HDAC2_THP1_ML6_1


title: HDAC2,THP1,ML6, biol rep 2

description: Library name: HDAC2_THP1_ML6_2


title: HDAC2,THP1,PMA, biol rep 2

description: Library name: HDAC2_THP1_PMA_2


title: HDAC2,THP1,PMA, biol rep 1

description: Library name: HDAC2_THP1_PMA_1


title: MBD2,THP1, biol rep 2

description: Library name: MBD2_THP1_2


title: MBD2,THP1,ML6, biol rep 1

description: Library name: MBD2_THP1_ML6_1


title: MBD2,THP1,ML6, biol rep 2

description: Library name: MBD2_THP1_ML6_2


title: MBD2,THP1, biol rep 1

description: Library name: MBD2_THP1_1


title: MBD2,THP1,PMA, biol rep 1

description: Library name: MBD2_THP1_PMA_1


title: MBD2,THP1,PMA, biol rep 2

description: Library name: MBD2_THP1_PMA_2


title: MTA1,THP1, biol rep 2

description: Library name: MTA1_THP1_2


title: MTA1,THP1, biol rep 1

description: Library name: MTA1_THP1_1


title: MTA1,THP1,ML6, biol rep 2

description: Library name: MTA1_THP1_ML6_2


title: MTA1,THP1,PMA, biol rep 1

description: Library name: MTA1_THP1_PMA_1


title: MTA1,THP1,PMA, biol rep 2

description: Library name: MTA1_THP1_PMA_2


title: MTA1,THP1,ML6, biol rep 1

description: Library name: MTA1_THP1_ML6_1


title: MTA2,THP1, biol rep 1

description: Library name: MTA2_THP1_1


title: MTA2,THP1, biol rep 2

description: Library name: MTA2_THP1_2


title: MTA2,THP1,ML6, biol rep 1

description: Library name: MTA2_THP1_ML6_1


title: MTA2,THP1,PMA, biol rep 1

description: Library name: MTA2_THP1_PMA_1


title: MTA2,THP1,PMA, biol rep 2

description: Library name: MTA2_THP1_PMA_2


title: MTA2,THP1,ML6, biol rep 2

description: Library name: MTA2_THP1_ML6_2


title: MTA3,THP1, biol rep 1

description: Library name: MTA3_THP1_1


title: MTA3,THP1,ML6, biol rep 1

description: Library name: MTA3_THP1_ML6_1


title: MTA3,THP1, biol rep 2

description: Library name: MTA3_THP1_2


title: MTA3,THP1,PMA, biol rep 2

description: Library name: MTA3_THP1_PMA_2


title: THP1,Romidepsin 2h, biol rep  2

description: Library name: THP1_Romidepsin_2


title: MTA3,THP1,PMA, biol rep 1

description: Library name: MTA3_THP1_PMA_1


title: THP1,DMSO 2h, biol rep  2

description: Library name: THP1_DMSO_2


title: THP1,DMSO 2h, biol rep  3

description: Library name: THP1_DMSO_3


title: 3290464_JW_G2_1_3

city: Memphis

first: Rashid

last: Mehmood

state: Tennessee

address: 324 NIGHT SAIL DR N APT 112, UNIT # 04-112

department: Hematology

institute: St Jude Children's Research Hospital

description: Library name: 3290464_JW_G2_1_3

data_processing:
Single-cell RNA libraries, sequenced by 10x Genomics, were processed using CellRanger software (v7.0.0) with default parameters. The count function mapped the raw reads to the human reference genome GRCh38 and generated a gene expression count matrix. The filtered_feature_bc_matrix were used for downstream analysis in Seurat (V. 5.3.0) using R (V. 4.2.3). Seurat tutorial(https://satijalab.org/seurat/articles/seurat5_integration) was followed for downstream analysis, where batch effects were corrected using harmony integration method.
Assembly: hg38
Supplementary files format and content: filterd_featured_bc_matrix.h5

source_name: hCD34 cells

growth_protocol: CD34⁺ hematopoietic stem and progenitor cells (HSPCs) mobilized with G-CSF from healthy donors were expanded 7 days in StemSpan™ SFEM II with CD34⁺ Expansion Supplement, human LDL, and Penicillin-Streptomycin. Cells were then cultured with thrombopoietin (50 ng/mL, increased to 100 ng/mL after 3 days) to induce megakaryocyte differentiation. On day 14, cells were harvested.

extract_protocol:
Cells were processed for single cell RNA-seq via the 10X Genomics 3' v3.1 kit
Libraries were constructed via the 10X Genomics 3' v3.1 kit

treatment_protocol: For each experimental condition (DMSO vs. treatment; non-targeting vs. sgRNA), equal number of cells were allocated per group when thrombopoietin was added to the cells. The cells were cultured with thrombopoietin for 7 days and at the end of the 7 days, the cells were harvested.

value: hCD34 cells

value: Wild type

value: MEN1 gRNA 13

tag: batch


title: 3290465_JW_G2_2_3

description: Library name: 3290465_JW_G2_2_3


title: 3290463_JW_G1_2_3

description: Library name: 3290463_JW_G1_2_3

value: MEN1 gRNA 1


title: 3290462_JW_G1_1_3

description: Library name: 3290462_JW_G1_1_3


title: 3290460_JW_NT_1_3

description: Library name: 3290460_JW_NT_1_3

value: Non targeting sgRNA


title: 3274817_JW_G2_2_2

description: Library name: 3274817_JW_G2_2_2


title: 3274815_JW_G1_2_2

description: Library name: 3274815_JW_G1_2_2


title: 3274816_JW_G2_1_2

description: Library name: 3274816_JW_G2_1_2


title: 3274812_JW_NT_1_2

description: Library name: 3274812_JW_NT_1_2


title: 3260159_JW_G2_2

description: Library name: 3260159_JW_G2_2


title: 3260158_JW_G2_1

description: Library name: 3260158_JW_G2_1


title: 3260157_JW_G1_2

description: Library name: 3260157_JW_G1_2


title: 3260155_JW_NT_2

description: Library name: 3260155_JW_NT_2


title: 3260154_JW_NT_1

description: Library name: 3260154_JW_NT_1


title: 3260156_JW_G1_1

description: Library name: 3260156_JW_G1_1


title: 2693268_JW_011

description: Library name: 2693268_JW_011

value: Revumenib


title: 2693266_JW_009

description: Library name: 2693266_JW_009


title: 2693267_JW_010

description: Library name: 2693267_JW_010


title: 2668333_JW_008

description: Library name: 2668333_JW_008


title: 2668332_JW_007

description: Library name: 2668332_JW_007


title: 2668331_JW_006

description: Library name: 2668331_JW_006


title: 2668330_JW_005

description: Library name: 2668330_JW_005


title: 2658300_JW_004

description: Library name: 2658300_JW_004


title: 2658298_JW_002

description: Library name: 2658298_JW_002


title: GM12878 cells, DMSO vehicle, 24 h, biol rep 4

city: Chicago

first: Jingxin

last: Wang

address: Abbott Memorial Hall 210A, 947 E 58th St.

department: Section of Genetic Medicine

institute: University of Chicago

description:
Library name: Exp2_GM12878_polyA_DMSO_NA_4
Column 'Exp2_GM12878_polyA_DMSO_NA_4' in Exp2_GeneCounts.tsv.gz and Exp2_leafcutter_perind_numers.counts.gz.

data_processing:
Reads were aligned to the human reference genome GRCh38 with STAR using two-pass mode per sample, using the Gencode v44 comprehensive gene annotation.
Gene-level read counts were generated with featureCounts (Subread) against Gencode v44 comprehensive gene models, in unstranded mode.
Intron-junction-level counts were generated with leafcutter (extract junctions from STAR-aligned BAMs; leafcutter_cluster.py to define junction clusters); the per-cluster numerator count matrix (`*_perind_numers.counts.gz`) is provided as a processed data file.
Assembly: GRCh38 (Gencode Release 44 comprehensive annotation)
Supplementary files format and content: Two file types are provided. (1) Gzipped tab-separated featureCounts gene-by-sample raw read-count tables (`Exp1_GeneCounts.tsv.gz`, `Exp2_GeneCounts.tsv.gz`): first 6 columns are Geneid/Chr/Start/End/Strand/Length followed by one column of integer counts per sample. (2) Gzipped space-separated leafcutter junction-cluster-by-sample numerator count tables (`Exp1_leafcutter_perind_numers.counts.gz`, `Exp2_leafcutter_perind_numers.counts.gz`): header row lists sample names; each data row has `chrom:start:end:cluster_id` followed by one integer per sample (junction-supporting reads).

growth_protocol: LN-229 glioblastoma cells were cultured in DMEM supplemented with 5% FBS, 1x ThermoFisher anti(biotic)-anti(mycotic), at 37 °C, 5% CO2. GM12878 lymphoblastoid cells were cultured in RPMI 1640 supplemented with 15% FBS, 1x ThermoFisher anti-anti, at 37 °C, 5% CO2.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy column-based purification kit following the manufacturer's protocol.
Strand-specific polyA-enriched RNA-seq libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, following the manufacturer's protocol.

treatment_protocol: Cells were treated with the indicated splicing-modulator compound (or DMSO vehicle) at the specified dose for 24 hours prior to harvest.

value: B-lymphocyte (lymphoblastoid)

value: DMSO vehicle (24 h)


title: GM12878 cells, DMSO vehicle, 24 h, biol rep 3

description:
Library name: Exp2_GM12878_polyA_DMSO_NA_3
Column 'Exp2_GM12878_polyA_DMSO_NA_3' in Exp2_GeneCounts.tsv.gz and Exp2_leafcutter_perind_numers.counts.gz.


title: GM12878 cells, DMSO vehicle, 24 h, biol rep 1

description:
Library name: Exp2_GM12878_polyA_DMSO_NA_1
Column 'Exp2_GM12878_polyA_DMSO_NA_1' in Exp2_GeneCounts.tsv.gz and Exp2_leafcutter_perind_numers.counts.gz.


title: GM12878 cells, BPN15477 25000 nM, 24 h, biol rep 2

description:
Library name: Exp2_GM12878_polyA_BPN15477_25000_2
Column 'Exp2_GM12878_polyA_BPN15477_25000_2' in Exp2_GeneCounts.tsv.gz and Exp2_leafcutter_perind_numers.counts.gz.


title: THP1,Romidepsin 2h, biol rep  3

description: Library name: THP1_Romidepsin_3


title: THP1,Romidepsin 2h, biol rep  1

description: Library name: THP1_Romidepsin_1


title: THP1,DMSO 2h, biol rep  1

description: Library name: THP1_DMSO_1


title: GM12878 cells, BPN15477 25000 nM, 24 h, biol rep 1

description:
Library name: Exp2_GM12878_polyA_BPN15477_25000_1
Column 'Exp2_GM12878_polyA_BPN15477_25000_1' in Exp2_GeneCounts.tsv.gz and Exp2_leafcutter_perind_numers.counts.gz.


title: LN-229 cells, SMSM74 3160 nM, 24 h, biol rep 1

description:
Library name: Exp1_LN229_polyA_SMSM74_3160_1
Column 'Exp1_LN229_polyA_SMSM74_3160_1' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.

value: glioblastoma


title: 3290461_JW_NT_2_3

description: Library name: 3290461_JW_NT_2_3


title: 3274814_JW_G1_1_2

description: Library name: 3274814_JW_G1_1_2


title: LN-229 cells, SMSM74 1000 nM, 24 h, biol rep 1

description:
Library name: Exp1_LN229_polyA_SMSM74_1000_1
Column 'Exp1_LN229_polyA_SMSM74_1000_1' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.


title: LN-229 cells, SMSM74 10000 nM, 24 h, biol rep 1

description:
Library name: Exp1_LN229_polyA_SMSM74_10000_1
Column 'Exp1_LN229_polyA_SMSM74_10000_1' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.


title: LN-229 cells, SMSM74 31600 nM, 24 h, biol rep 1

description:
Library name: Exp1_LN229_polyA_SMSM74_31600_1
Column 'Exp1_LN229_polyA_SMSM74_31600_1' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.


title: LN-229 cells, Risdiplam 3160 nM, 24 h, biol rep 1

description:
Library name: Exp1_LN229_polyA_Risdiplam_3160_1
Column 'Exp1_LN229_polyA_Risdiplam_3160_1' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.

value: Risdiplam at 3160 nM (24 h)


title: 3274813_JW_NT_2_2

description: Library name: 3274813_JW_NT_2_2


title: LN-229 cells, DMSO vehicle, 24 h, biol rep 4

description:
Library name: Exp1_LN229_polyA_DMSO_NA_4
Column 'Exp1_LN229_polyA_DMSO_NA_4' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.


title: LN-229 cells, Risdiplam 10000 nM, 24 h, biol rep 1

description:
Library name: Exp1_LN229_polyA_Risdiplam_10000_1
Column 'Exp1_LN229_polyA_Risdiplam_10000_1' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.

value: Risdiplam at 10000 nM (24 h)


title: LN-229 cells, Risdiplam 1000 nM, 24 h, biol rep 1

description:
Library name: Exp1_LN229_polyA_Risdiplam_1000_1
Column 'Exp1_LN229_polyA_Risdiplam_1000_1' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.

value: Risdiplam at 1000 nM (24 h)


title: LN-229 cells, DMSO vehicle, 24 h, biol rep 2

description:
Library name: Exp1_LN229_polyA_DMSO_NA_2
Column 'Exp1_LN229_polyA_DMSO_NA_2' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.


title: LN-229 cells, DMSO vehicle, 24 h, biol rep 1

description:
Library name: Exp1_LN229_polyA_DMSO_NA_1
Column 'Exp1_LN229_polyA_DMSO_NA_1' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.


title: LN-229 cells, Risdiplam 316 nM, 24 h, biol rep 1

description:
Library name: Exp1_LN229_polyA_Risdiplam_316_1
Column 'Exp1_LN229_polyA_Risdiplam_316_1' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.

value: Risdiplam at 316 nM (24 h)


title: RNA-seq of C. elegans with mutation in nlg-1 (tm474) young adult_biol rep 3

city: Ondo

first: Omamuyovwi

middle: Meashack

last: Ijomone

state: Ondo

address: Medical Village, Laje Road

department: Anatomy

country: Nigeria

institute: University of Medical Sciences

description:
Library name: Sample-63
Column name in raw_counts.csv: nlg-1 (tm474): Sample.63

data_processing:
The enriched RNAs were fragmented for 8 minutes at 94 °C. First-strand and second-strand cDNA were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. cDNA fragments were adenylated at 3’ends, and an indexed adapter was ligated to the cDNA fragments. Limited-cycle PCR was used for library enrichment.
The incorporated dUTP in the second-strand cDNA quenched the amplification of the second strand, which helped to preserve the strand specificity.
The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA) and quantified by using Qubit 4.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
The libraries were clustered on a flowcell and sequenced on an Illumina NovaSeq platform in a 2x150 bp paired-end configuration. Raw sequence data were converted to fastq files and de-multiplexed using Illumina's bcl2fastq 2.20 software.
Assembly: WBcel235 (Ensembl)
Supplementary files format and content: csv file contains raw counts for each sample

source_name: whole-organism

growth_protocol: All C. elegans strains were handled and maintained at 20 °C on Nematode Growth Medium (NGM) agar plates seeded with Escherichia coli OP50 as a food source. Worms were transferred periodically onto fresh NGM plates using a sterile worm pick or agar chunking technique to ensure healthy propagation

extract_protocol:
Approximately 20,000 worms were transferred into 15 mL tubes using 85 mM NaCl supplemented with 0.1% Tween 20. Following subsequent washes, the worms were transferred to 2.0 mL tubes, snap-frozen in liquid nitrogen, and stored at −80 °C for subsequent analysis. Total RNA was extracted from the resulting lysates using the RNeasy Plus Universal Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA concentration was quantified using a Qubit 4.0 Fluorometer (Life Technologies, Carlsbad, CA, USA), and RNA integrity was assessed using an Agilent 4200 TapeStation system (Agilent Technologies, Palo Alto, CA, USA).
rRNA depletion was performed using the QIAGEN FastSelect rRNA HMR Kit (Qiagen, Germantown, MD, USA). Strand-specific libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB, Ipswich, MA, USA) following the manufacturer’s instructions.

value: whole-organism


title: Whole blood DNA methylation, NHW AD, 79yo F, 207215830119_R01C01

data_processing:
All quality control and data normalization were performed using the openSeSAMe pipeline from the SeSAMe R package (Zhou et al., 2018). Probes of poor design were removed, as well as probes with detection P-value > 0.05 in more than 5% of samples. Non-CG probes and probes on X, Y, and mitochondrial chromosomes were also removed. Samples with incomplete bisulfite conversion (GCT score > 1.5) and principal component analysis outliers were excluded. Noob normalization was performed with SeSAMe using a nonlinear dye-bias correction.
processed value definition: Beta values representing the ratio of methylated probe intensity to overall intensity (methylated + unmethylated + offset). Values range from 0 (unmethylated) to 1 (fully methylated).

extract_protocol: Genomic DNA was extracted from whole blood samples at external processing sites associated with each cohort. Standard column-based DNA extraction methods were used according to each site's established protocols.

value: Female

value: Alzheimer's disease

value: whole blood

value: NHW


title: LN-229 cells, CP3 3160 nM, 24 h, biol rep 1

description:
Library name: Exp1_LN229_polyA_CP3_3160_1
Column 'Exp1_LN229_polyA_CP3_3160_1' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.


title: LN-229 cells, CP3 31600 nM, 24 h, biol rep 1

description:
Library name: Exp1_LN229_polyA_CP3_31600_1
Column 'Exp1_LN229_polyA_CP3_31600_1' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.


title: LN-229 cells, CP3 10000 nM, 24 h, biol rep 1

description:
Library name: Exp1_LN229_polyA_CP3_10000_1
Column 'Exp1_LN229_polyA_CP3_10000_1' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.


title: LN-229 cells, CP3 316 nM + 25 µM BPN15477 co-treatment, 24 h, biol rep 2

description:
Library name: Exp1_LN229_polyA_CP3PlusBPN_316_2
Column 'Exp1_LN229_polyA_CP3PlusBPN_316_2' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.

value: CP3 at 316 nM + constant 25 µM BPN15477 co-treatment (24 h)


title: LN-229 cells, CP3 3160 nM + 25 µM BPN15477 co-treatment, 24 h, biol rep 2

description:
Library name: Exp1_LN229_polyA_CP3PlusBPN_3160_2
Column 'Exp1_LN229_polyA_CP3PlusBPN_3160_2' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.

value: CP3 at 3160 nM + constant 25 µM BPN15477 co-treatment (24 h)


title: LN-229 cells, CP3 3160 nM + 25 µM BPN15477 co-treatment, 24 h, biol rep 1

description:
Library name: Exp1_LN229_polyA_CP3PlusBPN_3160_1
Column 'Exp1_LN229_polyA_CP3PlusBPN_3160_1' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.


title: LN-229 cells, CP3 316 nM + 25 µM BPN15477 co-treatment, 24 h, biol rep 1

description:
Library name: Exp1_LN229_polyA_CP3PlusBPN_316_1
Column 'Exp1_LN229_polyA_CP3PlusBPN_316_1' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.


title: LN-229 cells, CP3 1000 nM + 25 µM BPN15477 co-treatment, 24 h, biol rep 1

description:
Library name: Exp1_LN229_polyA_CP3PlusBPN_1000_1
Column 'Exp1_LN229_polyA_CP3PlusBPN_1000_1' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.

value: CP3 at 1000 nM + constant 25 µM BPN15477 co-treatment (24 h)


title: TET2 KD, 144 h, RNA-seq, r2

city: Badalona

first: José

middle: Luis

last: Sardina

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukaemia Research Institute

description: Library name: TET2_KD_144h_r2

data_processing:
Reads were aligned using STAR, default mode for paired-end data
Aligned reads were quantified using featureCounts
Differential expression analysis was performed using the R package DESeq2
Assembly: GRCh38
Supplementary files format and content: Raw counts are provided as .txt file

source_name: B-ALL cell line

growth_protocol: BlaER cells and subclones were grown in suspension in RPMI 1640 supplemented with 10% heat-inactivated FBS, 1X Penicillin-Streptomycin, 1X L-glutamine and 0,1X β-mercaptoethanol.

extract_protocol:
Total RNA was extracted using Rneasy Mini Kit (Qiagen).
RNA-seq libraries were prepared by an external sequencing service provider. Briefly, mRNA enrichment was performed on total RNA using the RNase H to remove ribosomal RNA. The enriched mRNA was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double -stranded DNA was then end-repaired and 5'-phosphorylated, with a protruding 'A' at the 3' end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3' end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing the quality control. Sequencing was performed on DNBSEQ platform with PE100 (read length).

treatment_protocol: BlaER cells with shTET2 and shCTRL were first pre-treated with doxycycline (1 µg/ml) for 48 hours. Next, to induce transdifferentiation cells were supplemented with 100 nM of 17-beta estradiol (E2), human IL-3 (10 ng/ml), and human M-CSF (10 ng/ml) during 7 days. Doxycycline (1 µg/ml) was re-added every 48 hours during the process. Cells were collected at 0, 72 and 144 hours post induction.

value: B-ALL cell line

value: B-ALL cell line with shTET2

value: iMac

value: Doxycycline (1 µg/ml)


title: TET2 KD, 144 h, RNA-seq, r1

description: Library name: TET2_KD_144h_r1


title: TET2 KD, 72 h, RNA-seq, r2

description: Library name: TET2_KD_72h_r2

value: B cell intermediate to iMac


title: TET2 KD, 72 h, RNA-seq, r1

description: Library name: TET2_KD_72h_r1


title: DRG_rat_FishOilDiet_Injury_LeftSide2

description: Library name: G6_47L

data_processing:
Raw FASTQ reads underwent fastp QC (adapter/poly-N/low-quality removal; Q20/Q30/GC calculated). Clean reads were Hisat2-aligned (v2.0.5) to the reference genome (with splice junction database). Gene expression was quantified via featureCounts (v1.5.0-p3) as FPKM
Assembly: ncbi_rattus_norvegicus_gcf_000002265_2_rn_celera
Supplementary files format and content: tab delimited text file includes raw counts for each sample
Supplementary files format and content: cvs file for FPKM values of each sample

extract_protocol:
total mRNA of DRG was isolated using the Qiagen AllPrep kit (cat. no. 80004) for simultaneous mRNA/DNA/protein. RNA integrity was assessed via Bioanalyzer 2100 (Agilent Technologies, CA, USA).
Messenger RNA is purified from total RNA using poly-T magnetic beads, fragmented, and converted to cDNA using random hexamer primers, with second-strand synthesis using dTTP for non-strand-specific libraries or dUTP for strand-specific libraries. Both library types undergo end repair, A-tailing, adapter ligation, size selection, amplification, and purification, followed by quality control using Qubit, real-time PCR, and a bioanalyzer. Libraries are then pooled and sequenced on an Illumina platform to analyze gene expression.

value: Dorsal Root Ganglia

value: WT_Fish Oil Diet_CCI

value: chronic constriction injury of Sciatic Nerve


title: TET2 KD, 0 h, RNA-seq, r1

description: Library name: TET2_KD_0h_r1

value: B cell


title: RNA-seq of C. elegans with mutation in nlg-1 (ok259) young adult_biol rep 3

description:
Library name: Sample-48
Column name in raw_counts.csv: nlg-1 (ok259): Sample.48

value: whole-organism


title: Control, 144 h, RNA-seq, r1

description: Library name: CTRL_144h_r1

value: B-ALL cell line with shCTRL


title: Control, 72 h, RNA-seq, r2

description: Library name: CTRL_72h_r2


title: Control, 72 h, RNA-seq, r1

description: Library name: CTRL_72h_r1


title: Control, 144 h, r2

description: Library name: CTRL_144h_r2

extract_protocol:
Total RNA was extracted using Rneasy Mini Kit (Qiagen).
RNA-seq libraries were prepared by an external sequencing service provider. Briefly, mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads. The enriched mRNA with poly(A) tails was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double -stranded DNA was then end-repaired and 5'-phosphorylated, with a protruding 'A' at the 3' end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3' end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing the quality control. Sequencing was performed on DNBSEQ platform with PE150 (read length).

treatment_protocol: To induce transdifferentiation, the BlaER cells with shAGO2.1, shAGO2.2 and shCTRL were supplemented with 100 nM of 17-beta estradiol (E2), human IL-3 (10 ng/ml), and human M-CSF (10 ng/ml) during 7 days. Cells were collected at 0, 72 and 144 hours post induction.