title: iDC-MuV1, Input

first: Mijia

last: Lu

address: 180 Tianmushan Rd

institute: Hangzhou Medical College

description: Library name: SAMPLE11

data_processing:
Raw reads (Raw Data) are generated after sequencing on a sequencer, image analysis, base identification and QC. Q30 was first used for quality control. Then, cutadapt software (v1.9.3) was used to remove splice information and remove low quality reads to obtain high quality clean reads. The clean reads were matched to the reference genome using Hisat2 software (v2.0.4). Methylated genes in each sample were then identified using MACS software (1.4.2). Differential methylation gene identification was performed using diffReps software (1.55.6). The peaks located on exons were mRNA or LncRNA were screened using our own programs and annotated accordingly. GO and Pathway analyses were performed for differentially methylated mRNA and associated genes of LncRNA origin, respectively. circRNA: High quality reads were compared to the reference genome using STAR (v2.5.1b), and circular RNA was detected and identified using DCC(v0.4.4). circBase database and Circ2Traits were used to annotate the identified circular RNA. The peaks located on circRNA were screened, and the source genes of differentially modified circRNA were analyzed by GO and KEGG.
Assembly: GRch38/hg38
Supplementary files format and content: .xlsx. Column A ~ E: the coordinates of the methylated RNA sites in bed format, please ref http://genome.ucsc.edu/FAQ/FAQformat.html#format1. Column F: the length of the methylated RNA sites Column G ~ H: the transcript id and gene symbol of methylated RNA. Column I ~ K: the enrichment results calculated by MACS. Column L ~ S: the annotation of the methylated gene.

source_name: iDC-MuV1, IP

extract_protocol:
The infected or mock-infected cells was collected at 16 h post-infection (hpi) for total RNA extraction using TRIzol reagent according to the product manual.
The total RNA was subjected to immunoprecipitation using the GenSeq® m6A MeRIP Kit (GenSeq Inc.), following the manufacturer’s instructions. Briefly, RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents.  Protein A/G beads were coupled to the m6A antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. After incubation, the RNA/antibody complexes were washed several times, and then, the captured RNA was eluted from the complexes and purified. RNA libraries for IP and input samples were then constructed with GenSeq® Low Input Whole RNA Library Prep Kit (GenSeq, Inc.) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer (Agilent) and then sequenced.

treatment_protocol: THP1-iDC was infected with rhMPV or rMuV, with the control of DMEM (n=2) for 16 hours.

value: iDC-MuV1, IP

value: MuV-infection


title: ATAC-seq, hPIB-142_d9_G_CD45_2

status: Public on Jul 10 2026

type: SRA

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

description: Library name: hPIB-142_d9_G_CD45_2

library_source: genomic

data_processing:
In order to pre-process the FASTQ files of ATAC-Seq experiments, we used the nf-core ATAC-seq pipeline version 1.2.2 with default parameters. Technical replicates were merged together.
Reads were mapped to the GRCh38 reference genome using BWA. Peak calling was performed with MACS2 separately for each sample. A combined peak list for all samples was obtained using BEDTools. Finally, read counts on a combined peak list were calculated using featureCounts.
Assembly: hg38
Supplementary files format and content: count tables (.txt)

molecule: genomic DNA

organism: Homo sapiens

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.

extract_protocol:
5000-10000 cells were sorted intro PBS with 2 % FBS and processed according to the procedure described by Buenrostro et al. (2015).
ATAC-seq primers were prepared according to the procedure described by Buenrostro et al. (2015), with 96-plex indexing primers.

treatment_protocol: HDFs were transduced on day -1 with lentiviral vectors encoding for PIB and with lentiviral vectors encoding for miRNA hairpins. Cells were sorted on day 3, 6 or 9. Human dendritic cells were enriched from peripheral blood and sorted for subtype-specific markers.

tag: tissue

value: skin

tag: cell type

value: human dermal fibroblast

tag: genotype

value: WT

tag: treatment

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-142 on day -1 of reprogramming.

tag: time

value: Cells were collected on day 9 of reprogramming.

tag: sorted cells

value: live (DAPI-) and CD45+ HLA-DR-

tag: technical replicates


title: iDC-hMPV1, Input

city: Hangzhou

country: China

description: Library name: SAMPLE9

library_source: transcriptomic

molecule: total RNA

source_name: iDC-hMPV1, IP

value: iDC-hMPV1, IP

tag: cell line

value: hMPV-infection


title: ATAC-seq, hPIB-124_d9_L_CD45_2

description: Library name: hPIB-124_d9_L_CD45_2

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-124 on day -1 of reprogramming.


title: ATAC-seq, hPIB-142_d9_S_CD45_2

description: Library name: hPIB-142_d9_S_CD45_2


title: iDC-Ctrl2, Input

description: Library name: SAMPLE8

source_name: iDC-Ctrl2, IP

value: iDC-Ctrl2, IP

value: Mock infection


title: ATAC-seq, hPIB-124_d9_G_CD45_2

description: Library name: hPIB-124_d9_G_CD45_2


title: iDC-MuV2, IP

description: Library name: SAMPLE6

data_processing:
Raw reads (Raw Data) are generated after sequencing on a sequencer, image analysis, base identification and QC. Q30 was first used for quality control. Then, cutadapt software (v1.9.3) was used to remove splice information and remove low quality reads to obtain high quality clean reads. The clean reads were matched to the reference genome using Hisat2 software (v2.0.4). Methylated genes in each sample were then identified using MACS software (1.4.2). Differential methylation gene identification was performed using diffReps software (1.55.6). The peaks located on exons were mRNA or LncRNA were screened using our own programs and annotated accordingly. GO and Pathway analyses were performed for differentially methylated mRNA and associated genes of LncRNA origin, respectively. circRNA: High quality reads were compared to the reference genome using STAR (v2.5.1b), and circular RNA was detected and identified using DCC(v0.4.4). circBase database and Circ2Traits were used to annotate the identified circular RNA. The peaks located on circRNA were screened, and the source genes of differentially modified circRNA were analyzed by GO and KEGG.
Assembly: GRch38/hg38
Supplementary files format and content: .xlsx. Column A ~ E: the coordinates of the methylated RNA sites in bed format, please ref http://genome.ucsc.edu/FAQ/FAQformat.html#format1. Column F: the length of the methylated RNA sites Column G ~ H: the transcript id and gene symbol of methylated RNA. Column I ~ K: the enrichment results calculated by MACS. Column L ~ S: the annotation of the methylated gene.
Library strategy: MeRIP-Seq

source_name: iDC-MuV2, IP

value: iDC-MuV2, IP


title: ATAC-seq, hPIB-SCR_d9_L_CD45_2

description: Library name: hPIB-SCR_d9_L_CD45_2

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for a scrambled control hairpin on day -1 of reprogramming.


title: ATAC-seq, hPIB-124_d9_S_CD45_2

description: Library name: hPIB-124_d9_S_CD45_2


title: ATAC-seq, hPIB-SCR_d9_G_CD45_2

description: Library name: hPIB-SCR_d9_G_CD45_2


title: iDC-MuV1, IP

description: Library name: SAMPLE5


title: iDC-hMPV2, IP

description: Library name: SAMPLE4

source_name: iDC-hMPV2, IP

value: iDC-hMPV2, IP


title: iDC-hMPV1, IP

description: Library name: SAMPLE3


title: ATAC-seq, hPIB-SCR_d9_S_CD45_2

description: Library name: hPIB-SCR_d9_S_CD45_2


title: ATAC-seq, hPIB-142_d6_L_DP_2

description: Library name: hPIB-142_d6_L_DP_2

value: Cells were collected on day 6 of reprogramming.

value: live (DAPI-) and CD45+ HLA-DR+


title: ATAC-seq, hPIB-142_d6_G_DP_2

description: Library name: hPIB-142_d6_G_DP_2


title: iDC-Ctrl1, IP

description: Library name: SAMPLE1

source_name: iDC-Ctrl1, IP

value: iDC-Ctrl1, IP


title: ATAC-seq, hPIB-142_d6_S_DP_2

description: Library name: hPIB-142_d6_S_DP_2

value: skin


title: MuV2, Input

description:
Library name: SAMPLE12
modification_mRNA_sites.xlsx
MuV.modification_mRNA_sites.xlsx

data_processing:
After sequencing, image analysis, base identification and QC, raw reads (Raw Data) are generated. QC was first performed using Q30.
Then cutadapt software (v1.9.3) was used to de-join and remove low quality reads to obtain clean reads.
The clean reads were compared to the reference genome and bam files were obtained using STAR (v.2.7) and bowtie2 (v.2.2.4) software.
The GLORI-tools (https://github.com/liucongcas/) tool was used and based on multiple filtering to calculate the conversion rate of A-G at single base loci.
GO and Pathway enrichment analysis were performed based on differentially modified Mrna.
Assembly: GRCh38.92_UCSC, hMPV (GenBank: AF371337.2), MuV (GenBank: AF345290.1)
Supplementary files format and content: .xlsx files including all samples' sequencing depth, m6A depth and m6A ratio
Library strategy: RNA methylation

extract_protocol:
The infected or mock-infected cells was collected at 20 h post-infection (hpi) for total RNA extraction using TRIzol reagent according to the product manual.
The total RNA samples of infected or mock-infected A549 (n=2) were treated with GenSeq® GLORI kit (GenSeq Biotech Inc., Shanghai) according to the manufacturer’s instruction. Briefly, RNA was incubated with fragmentation buffer for 4 min at 94ºC, then glyoxal solution and DMSO were added, and the mixture was incubated for 30 min at 50ºC in a preheated thermocycler. The samples were cooled down to room temperature, mixed with saturated H3BO3 solution, and incubated at 50ºC for 30 min, followed by the addition of deamination buffer and 8 h incubation at 16ºC. Finally, the RNA was purified by ethanol precipitation, and sequencing libraries were constructed with GenSeq® eCLIP RNA Library Prep Kit (GenSeq Biotech Inc., Shanghai) following the manufacturer’s instructions. The constructed sequencing libraries were subjected to quality control and quantification by the BioAnalyzer 2100 system (Agilent Technologies, USA), followed by 150 bp double-end sequencing.

treatment_protocol: A549 cells were infected with rhMPV or rMuV, with the control of DMEM (n=2) for 20 hours.

value: MuV-infection


title: ATAC-seq, hPIB-124_d6_L_DP_2

description: Library name: hPIB-124_d6_L_DP_2

value: human dermal fibroblast

value: WT


title: MuV1, Input

description:
Library name: SAMPLE11
modification_mRNA_sites.xlsx
MuV.modification_mRNA_sites.xlsx


title: ATAC-seq, hPIB-124_d6_G_DP_2

description: Library name: hPIB-124_d6_G_DP_2


title: hMPV2, Input

description:
Library name: SAMPLE10
modification_mRNA_sites.xlsx
hMPV.modification_mRNA_sites.xlsx


title: ATAC-seq, hPIB-124_d6_S_DP_2

description: Library name: hPIB-124_d6_S_DP_2


title: hMPV1, Input

description:
Library name: SAMPLE9
modification_mRNA_sites.xlsx
hMPV.modification_mRNA_sites.xlsx


title: ATAC-seq, hPIB-SCR_d6_L_DP_2

description: Library name: hPIB-SCR_d6_L_DP_2


title: Mock2, Input

description:
Library name: SAMPLE8
modification_mRNA_sites.xlsx


title: Liver, Vehicle 1

status: Public on Jul 11 2026

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5607 Baum Blvd

country: USA

institute: University of Pittsburgh

data_processing:
Cutadapt trimmed reads were aligned to the rat reference genome using HISAT2
Raw read counts for all samples were counted using HTSeq
Assembly: Rattus norvegicus, mRatBN7.2 v107
Supplementary files format and content: text file includes raw counts for each sample ( columns: 1. Ensembl ID and 2. raw counts).

organism: Rattus norvegicus

source_name: postnatal day 6 liver

growth_protocol: pups from postnatal day 1-6 were nursed from mothers with free access to food (Prolab Isopro RMH 3000, LabDiet) and water

extract_protocol:
RNA was isolated from frozen rat lung and liver by digesting tissue in Trizol (Invitrogen) using a Lysing Matrix in a MP Biomedicals FastPrep-25 5G homogenizer followed by a chloroform extraction.
Directional mRNA library preparation (poly A enrichment). Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

treatment_protocol: beginning on postnatal day 1, pups were injected subcutaneously in the morning daily for 5 days with various treatments and  total liver and lung tissue harvested on postnatal day 6 and snap frozen 24 hours following final treatment

value: postnatal day 6 liver

tag: strain

value: Sprague Dawley

value: 24 hours Vehicle


title: HS02 DMSO A2

city: Orlando

first: Cristina

last: Fernandez-Valle

state: FL

address: 6850 Lake Nona Blvd.

institute: Unviersity of Central Florida College of Medicine

description: Library name: A2

data_processing:
Raw sequencing data was processed using the nf-core/atacseq pipeline (v2.1.2, commit hash: 1a1dbe52ffbd82256c941a032b0e22abbd925b8a) running on Nextflow (v23.10.1).
Quality control was performed using FastQC (v0.11.9) and MultiQC to assess read quality metrics.
Reads were aligned to the GRCh38 human reference genome using BWA-MEM (v0.7.17-r1188). Duplicate reads were marked using Picard MarkDuplicates (v3.0.0).
Peak calling was performed using MACS2 (v2.2.7.1) with broad peak settings for BRD4 ChIP-seq analysis. Signal tracks were generated in bigWig format using deepTools (v3.5.1).
Assembly: GRCh38
Supplementary files format and content: BigWig files containing normalized ChIP-seq signal tracks generated from MACS2 peak calling and deepTools normalization.

growth_protocol: HS02 cells were seeded at 10^6 cells/flask, two t75 CellBIND flasks per condition in Schwann Cell Media with 10x Schwann Cell Growth Supplement (ScienCell) and 10% FBS.

extract_protocol:
Flasks were crosslinked for using 10% formaldehyde for 10 min at room temperature and quenched with 25M glycine for 5 min. Nuclear extracted was performed and DNA was digested with MNase (50units/10^6 cells) followed by sonication (30% amplitude, 6 cycles, 10 sec ON, 30 sec OFF). Immunoprecipitation was performed overnight with rabbit anti-BRD4 antibodies (#BL-149-2H5, Fortis) conjugated to Dynabeads Protein A (ThermoFisher). After elution, DNA was reverse crosslinked, thenRNase and proteinase K treated. DNA was extracted using the ChIP DNA Clean & Concentrator Kit (Zymo) and analyzed using Nanodrop8000 and Tapestation 4150 bioanalyzer (Agilent).
Samples were sent to Novogene for library construction. From the quality analysis report "The DNA fragments were repaired, A-tailed and further ligated with Illumina adapter. The final DNA library was obtained by size selection and PCR amplification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. The library was then sequenced using the Illumina NovaSeq platform (12G raw data per sample; 150bp, paired end reads).

treatment_protocol: Cells were treated the following day. Treatments were given at 5x concentration. 3mL media was removed from the 15mL total volume (per flask) and replaced with the respective treatment. Flasks were gently mixed and then incubated for 4h at 37C, 5% CO2.

value: schwann cells

value: DMSO

tag: chip antibody

tag: batch

value: A


title: Lung, desisobutyryl ciclesonide 4

source_name: postnatal day 6 lung

value: postnatal day 6 lung

value: 24 hours desisobutyryl ciclesonide


title: HS02 DMSO A3

description: Library name: A3


title: ATAC-seq, hPIB-SCR_d6_G_DP_2

description: Library name: hPIB-SCR_d6_G_DP_2

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for a scrambled control hairpin on day -1 of reprogramming.


title: Mock1, Input

description:
Library name: SAMPLE7
modification_mRNA_sites.xlsx

value: Mock infection


title: ATAC-seq, hPIB-SCR_d6_S_DP_2

description: Library name: hPIB-SCR_d6_S_DP_2

value: Cells were collected on day 6 of reprogramming.


title: ATAC-seq, hPIB-142_d6_L_CD45_2

description: Library name: hPIB-142_d6_L_CD45_2

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-142 on day -1 of reprogramming.

value: live (DAPI-) and CD45+ HLA-DR-


title: MuV2, IP

description:
Library name: SAMPLE6
modification_mRNA_sites.xlsx
MuV.modification_mRNA_sites.xlsx


title: MuV1, IP

description:
Library name: SAMPLE5
modification_mRNA_sites.xlsx
MuV.modification_mRNA_sites.xlsx


title: ATAC-seq, hPIB-142_d6_G_CD45_2

description: Library name: hPIB-142_d6_G_CD45_2

value: skin


title: hMPV2, IP

description:
Library name: SAMPLE4
modification_mRNA_sites.xlsx
hMPV.modification_mRNA_sites.xlsx

value: hMPV-infection


title: ATAC-seq, hPIB-142_d6_S_CD45_2

description: Library name: hPIB-142_d6_S_CD45_2

value: human dermal fibroblast


title: ATAC-seq, hPIB-124_d6_L_CD45_2

description: Library name: hPIB-124_d6_L_CD45_2

value: WT

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-124 on day -1 of reprogramming.


title: hMPV1, IP

description:
Library name: SAMPLE3
modification_mRNA_sites.xlsx
hMPV.modification_mRNA_sites.xlsx


title: ATAC-seq, hPIB-124_d6_G_CD45_2

description: Library name: hPIB-124_d6_G_CD45_2


title: Mock2, IP

description:
Library name: SAMPLE2
modification_mRNA_sites.xlsx


title: iDC-Ctrl2, IP

description: Library name: SAMPLE2

value: iDC-Ctrl2, IP


title: ATAC-seq, hPIB-124_d6_S_CD45_2

description: Library name: hPIB-124_d6_S_CD45_2


title: Mock1, IP

description:
Library name: SAMPLE1
modification_mRNA_sites.xlsx


title: SeV3

description: Library name: SAMPLE15

data_processing:
To identify DEGs ( differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM was used to quantify gene abundances.
Essentially, differential expression analysis was performed using the DESeq2 or DEGseq. DEGs with |log2FC| ≧ 1 and FDR≤ 0.05(DESeq2 ) or FDR ≤0.001(DEGseq) were considered to be significantly different expressed genes.
In addition, functional- enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferronicorrected P-value ≤0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools and KOBAS, respectively.
Assembly: GRCh38
Supplementary files format and content: .txt file includes TPM values for each Sample

extract_protocol:
A549 cells were infected with hMPV, MuV, VSV, SeV or mock-infected with DMEM (n=3).
The RNA-seq transcriptome library was prepared following Illumina® Stranded mRNA Prep Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Briefly, messenger RNA was isolated according to the polyA selection method by oligo(dT) beads and then fragmented by the fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size-selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplification using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantification by Qubit 4.0, the paired-end RNA-seq sequencing library was sequenced with the NovaSeq X plus sequencer (2 × 150 bp read length).

value: SeV-infection


title: ATAC-seq, hPIB-SCR_d6_L_CD45_2

description: Library name: hPIB-SCR_d6_L_CD45_2


title: SeV2

description: Library name: SAMPLE14


title: ATAC-seq, hPIB-SCR_d6_G_CD45_2

description: Library name: hPIB-SCR_d6_G_CD45_2


title: ATAC-seq, hPIB-SCR_d6_S_CD45_2

description: Library name: hPIB-SCR_d6_S_CD45_2


title: VSV3

description: Library name: SAMPLE12

value: VSV-infection


title: ATAC-seq, hPIB-142_d3_L_CD45_2

description: Library name: hPIB-142_d3_L_CD45_2

value: Cells were collected on day 3 of reprogramming.

value: live (DAPI-) and CD45+


title: VSV2

description: Library name: SAMPLE11


title: SeV1

description: Library name: SAMPLE13


title: ATAC-seq, hPIB-142_d3_G_CD45_2

description: Library name: hPIB-142_d3_G_CD45_2


title: VSV1

description: Library name: SAMPLE10


title: ATAC-seq, hPIB-142_d3_S_CD45_2

description: Library name: hPIB-142_d3_S_CD45_2


title: MuV3

description: Library name: SAMPLE9

value: MuV-infection


title: ATAC-seq, hPIB-124_d3_L_CD45_2

description: Library name: hPIB-124_d3_L_CD45_2


title: MuV2

description: Library name: SAMPLE8


title: ATAC-seq, hPIB-124_d3_G_CD45_2

description: Library name: hPIB-124_d3_G_CD45_2


title: MuV1

description: Library name: SAMPLE7


title: ATAC-seq, hPIB-124_d3_S_CD45_2

description: Library name: hPIB-124_d3_S_CD45_2


title: hMPV3

description: Library name: SAMPLE6


title: ATAC-seq, hPIB-SCR_d3_L_CD45_2

description: Library name: hPIB-SCR_d3_L_CD45_2


title: ATAC-seq, hPIB-SCR_d3_G_CD45_2

description: Library name: hPIB-SCR_d3_G_CD45_2


title: hMPV2

description: Library name: SAMPLE5


title: hMPV1

description: Library name: SAMPLE4


title: ATAC-seq, hPIB-SCR_d3_S_CD45_2

description: Library name: hPIB-SCR_d3_S_CD45_2


title: Mock3

description: Library name: SAMPLE3


title: VDJ_SampleB

city: Stanford

first: Laura

last: Amaya

state: CA

address: 269 Campus Drive

institute: Stanford University

description: Library name: VDJ_SampleB

data_processing:
Cell Ranger Single-Cell Software Suite (10X Genomics) was employed for sample demultiplexing, alignment, filtering, and UMI counting for RNA-seq libraries, using the human GRCh38 genome assembly and RefSeq gene model. For V(D)J libraries, the Cell Ranger Single-Cell Software (10X Genomics) was used for sample demultiplexing, de novo assembly, alignment, annotation against germline segment V(D)J reference sequences and clonotype grouping.
Assembly: GRCh38
Supplementary files format and content: fragments.tsv for scATAC, filtered_feature_matrix.h5 for scRNA and contig_annotations.csv for scTCR.

source_name: Blood

extract_protocol: Live singlet CD3+CD4+ T cells from T-allo10 cell products were purified by FACS, counted, and their cell concentration adjusted in PBS with 0.04% BSA to allow capture up to 10,000 cells per well of the Chromium Next GEM chip, which was then loaded onto a Chromium Single Cell Instrument (10x Genomics, Pleasanton, CA). RNA-seq and V(D)J libraries were prepared using the Chromium Single Cell 5′ Library, Gel Beads, & Multiplex Kit according to manufacturer’s instructions.

value: Blood

value: CD4 T cells

tag: disease state

value: Healthy

value: TimeNA

value: No treatment


title: ATAC-seq, MCS_d3_L_alive_2

description: Library name: MCS_d3_L_alive_2

value: Cells were transduced with an empty lentiviral vector on day -1.


title: ATAC-seq, MCS_d3_G_alive_2

description: Library name: MCS_d3_G_alive_2

value: skin


title: Mock2

description: Library name: SAMPLE2

value: Mock infection


title: Old_Pbx1_CutTag_rep1

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: Old_Pbx1_CutTag_rep1
Old hematopoietic stem cells (CD150+CD48-CD34-LSK) were retrovirally transduced with Pbx1-IRES-GFP and subjected to Cut&Tag for H3K9me2 on day 3, rep1

data_processing:
Fastq files were trimmed using Trim Galore and aligned to the reference mouse genome (mm10) using bowtie2 with a --very-sensitive and single-read mode. Mitochondrial genome, Y chromosome, and scaffold chromosomes were removed using samtools, and duplicate reads were removed using picard MarkDuplicates. Peak calling was performed using MACS3 for each group with -q = 0.05, --extsize =100, and --shift = 50 with narrow peak mode. All peaks called in each group were merged, and peaks overlapping with blacklist region were excluded, and peaks within a distance smaller than 50bp considered as an identical peak. After further removing peaks with average of log CPM < -1, peak count around +/- 125bp of each summit was performed using csaw package of R.
Assembly: mm10
Supplementary files format and content: BigWig files were generated using Deeptools from BAM files removing duplicated reads after normalized to peak counts, and biological replicates were merged with DeepTools.
Supplementary files format and content: PeakCounts_th0.txt provides a tab-deliminated raw count data, counting reads 250bp around each summit.
Supplementary files format and content: Peak_250bp_noBL.bed is a BED file providing a +/- 125bp around summits detected by MACS3. Problematic regions ("blacklist") were removed.
Supplementary files format and content: Peaks_gene10kb.bed is a BED file defining regions spanning +/- 10 kb around gene bodies, based on annotations from mm10 RefSeq genes.
Supplementary files format and content: PeakCounts_gene10kb.txt is a tab-delimited file containing raw read count data for the regions specified in Peaks_gene10kb.bed.
Library strategy: CUT&TAG

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
A tatoal of 50000 Mock- or Pbx1-transduced HSCs were subjected to the CUT&Tag assay, utilizing the CUT&Tag Assay Kit (Cell Signaling Technology) according to the manufacturer's instructions with minor modifications.
For the detection of di-methyl H3K9 (H3K9me2), 2 uL of Rabbit anti-H3K9me2 monoclonal antibody (Cell Signaling Technology) per sample was bound to activated concanavalin A beads and incubated with the cell suspension overnight at 4°C. Subsequently, 1 uL of goat anti-rabbit IgG (H+L) antibody was used as the secondary antibody and was bound for 30 minutes at room temperature. pAG-Tn5 was then bound to the secondary antibody for tagmentation for 1 hour at room temperature. Following this, the fragmented DNA was released, purified using a spin column, and amplified using KAPA HiFi HotStart ReadyMix (KAPA BIOSYSTEMS) to incorporate the Nextera XT Index Kit v2. Each sample was prepared using 25 uL of 2X KAPA HiFi HS RM, 5 uL each of index 1 and index 2 primers, and 15 μL of the tagmented library. The thermal cycler conditions were set as follows: 72°C for 5 min, 98°C for 30 s, and 13 cycles of 98°C for 10 s followed by 60°C for 11 s. The residual PCR products were further elongated at 72°C for 1 min and maintained at 4°C. The library was purified using AMPure XP beads and sequenced on the NovaSeq 6000 platform with a paired-end read length of 150 bp.

treatment_protocol: Either CD150+CD48-CD41-CD34- LSK cells from 4 young (2.5mo) mice per sample, or CD150+CD48- CD34- LSK cells from 1 old (18mo) mouse per sample was isolated. Each experimental sample comprised cells from four young mice or one old mouse per sample. All isolated cells underwent retroviral transduction with mock or Pbx1-expressing vectors, after which 50,000 GFP+ cells for Cut&Tag were selected.

value: Bone marrow

value: anti-H3K9me2 (Cell Signaling Technology)

value: Old HSC

value: Wild type


title: Mock1

description: Library name: SAMPLE1


title: Old_Mock_CutTag_rep1

description:
Library name: Old_Mock_CutTag_rep1
Old hematopoietic stem cells (CD150+CD48-CD34-LSK) were retrovirally transduced with pMYs-IRES-GFP and subjected to Cut&Tag for H3K9me2 on day 3, rep1

value: Mock-transduced


title: BJ-T, MYOD1 mut, biol rep 2.2

city: Pozzuoli

first: Davide

last: Cacchiarelli

state: Napoli

address: via campi flegrei,34

country: Italy

institute: TIGEM

description: Library name: BJ-T, MYOD1 mut, biol rep 2.2

library_source: transcriptomic single cell

data_processing:
Single cell sequencing data were processed using the zUMIs pipeline (v. 2.9.7) for demultiplexing, read alignment, and UMI quantification to generate a gene-level count matrix and a cell-specific bam alignment file for each sample. The output of zUMI was used for both expression analysis and cell-level genotyping of the gene of interest.
Assembly: hg38
Supplementary files format and content: tab-separated files and matrix

molecule: polyA RNA

source_name: BJ-T

growth_protocol: BJ-T cells were grown in alphamem (Euroclone # ECM0095) supplemented with 10% FBS (Euroclone #ECS0186L), 1x Glutamax (Thermo #35050061)

extract_protocol:
cells were sorted in 300 nL lysis buffer overlayed with 3 μL Silicon Oil (5 cSt; Sigma-Aldrich) using a CytoFlex SRT sorter (100 μm nozzle; Beckmann Coulter).
reverse transcription was carried out by adding 100 nL reverse transcription master mix. Preamplification of cDNA was performed in 1 μl total volume using SeqAmp polymerase (Takara Bio #) for 14 cycles. Subsequently, amplified cDNA was diluted with 9 μl H2O and we used 1 μl for downstream tagmentation using 0.004 μl TDE1 enzyme per cell. Final, indexed libraries were pooled per 384-well plate, cleaned and equimolarly pooled before sequencing

treatment_protocol: Two days after transduction, the medium was supplemented with 1 ug/ml puromycin (Thermo #A1113903), for two days. After antibiotic selection, cells were allowed to overexpress exogenous gene for 72h.

value: BJ-T

value: Fibroblasts

value: transgene overexpresison


title: ATAC-seq, MCS_d3_S_alive_2

description: Library name: MCS_d3_S_alive_2

value: human dermal fibroblast

value: WT

value: Cells were collected on day 3 of reprogramming.

value: live (DAPI-) and CD45+


title: ATAC-seq, pDC_d3_C_Villani_2

description: Library name: pDC_d3_C_Villani_2

source_name: blood

value: blood

value: human dendritic cell

value: live (7-AAD-) and HLA-DR+ CD11c- CD123+


title: IMR32_KO_rescue1_Rep2

city: Segrate

first: Simona

last: Di Lascio

address: Via Fratelli Cervi 93

institute: University of Milan

description:
Library name: Sample 8
Column name in  raw_counts_All_Samples.txt : IMR32_KO_rescue1_Rep2

data_processing:
Base calling, demultiplexing and adapter masking were performed using Illumina BCL Convert v3.9.3
Sequence reads were trimmed for adaptor sequence/low-quality bases using ERNE software
Reads were aligned on hg38-iGenomes genome with STAR (default parameters),
Assembling and quantitation of full-length transcripts for each gene locus were performed by Stringtie (default parameters).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: The human neuroblastoma cell line IMR32 was grown in RPMI 1640 medium, supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin, 100 mg/mL streptomycin, 2 mM L-glutamine. The IMR32 PHOX2B KO stable clone was maintained under selection with 0.150 mg/mL Puromycin dihydrochloride. The IMR32 KO clones re-expressing PHOX2B (rescue_1 and rescue_2) were maintained under selection by adding Puromycin dihydrochloride and Geneticin (G-161 418 Sulphate) at 0.150 mg/mL and 0.170 mg/mL final concentration, respectively. All cell lines grow in adhesion at 37°C in a humified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini Kit.
VAHTS Universal v10 RNA-Seq kit (Vazyme, Nanjing, PRC) has been used for library preparation following the manufacturer’s instructions (library type: fr-firststrand).

value: Neuroblastoma

value: PHOX2B Knockdown + PHOX2B re-expression


title: BJ-T, MYOD1 mut, biol rep 1.2

description: Library name: BJ-T, MYOD1 mut, biol rep 1.2


title: IMR32_KO_rescue1_Rep3

description:
Library name: Sample 9
Column name in  raw_counts_All_Samples.txt : IMR32_KO_rescue1_Rep3


title: BJ-T, SAM mut, biol rep 2.2

description: Library name: BJ-T, SAM mut, biol rep 2.2

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)

treatment_protocol: Two days after transduction, the medium was supplemented with 10 ug/ml blasticidin (Thermo #A1113903), for four days. After antibiotic selection, cells were allowed to overexpress exogenous gene for 72h.


title: ATAC-seq, pDC_d3_B_Villani_2

description: Library name: pDC_d3_B_Villani_2


title: ATAC-seq, pDC_d3_A_Villani_2

description: Library name: pDC_d3_A_Villani_2


title: BJ-T, SAM mut, biol rep 1.2

description: Library name: BJ-T, SAM mut, biol rep 1.2


title: ATAC-seq, DC2_d3_C_Villani_2

description: Library name: DC2_d3_C_Villani_2

value: live (7-AAD-) and HLA-DR+ CD11c+ CD1c+ CD141-


title: ATAC-seq, DC2_d3_B_Villani_2

description: Library name: DC2_d3_B_Villani_2


title: WI38-RsaI

city: Singapore

first: XIAORAN

last: CHAI

address: 8 College Rd, Singapore 169857

country: Singapore

institute: Duke-NUS Medical School

description: Library name: Sample 18

data_processing:
For PacBio 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 PacBio sequencing, SMRTBELL EXPRESS TEMPLATE PREP KIT 2.0 was used. For Nanopore sequencing, Ligation Sequencing Kit V14 was used.

value: fibroblast


title: SJSA1-RsaI

description: Library name: Sample 16


title: ATAC-seq, DC2_d3_A_Villani_2

description: Library name: DC2_d3_A_Villani_2


title: Raji-RsaI

description: Library name: Sample 13

source_name: Raji

value: Raji

value: B lymphocyte


title: ATAC-seq, DC1_d3_C_Villani_2

description: Library name: DC1_d3_C_Villani_2

value: live (7-AAD-) and HLA-DR+ CD11c+ CD141+


title: HeLa-RsaI

description: Library name: Sample 7

source_name: HeLa

value: HeLa

value: human epithelial cell


title: IMR90-RsaI

description: Library name: Sample 10


title: ATAC-seq, DC1_d3_B_Villani_2

description: Library name: DC1_d3_B_Villani_2


title: ATAC-seq, DC1_d3_A_Villani_2

description: Library name: DC1_d3_A_Villani_2


title: 293T-RsaI, rep5

description: Library name: Sample 5

value: human embryonic kidney


title: ATAC-seq, hPIB-142_d9_L_DP_1

description: Library name: hPIB-142_d9_L_DP_1

value: skin

value: human dermal fibroblast

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-142 on day -1 of reprogramming.

value: Cells were collected on day 9 of reprogramming.

value: live (DAPI-) and CD45+ HLA-DR+


title: 293T-RsaI, rep4

description: Library name: Sample 4


title: ATAC-seq, hPIB-142_d9_G_DP_1

description: Library name: hPIB-142_d9_G_DP_1

value: WT


title: Old_Pbx1_ATAC-seq_rep3

description:
Library name: Old_Pbx1_ATAC-seq_rep3
Old hematopoietic stem cells (CD150+CD48-CD34-LSK) were retrovirally transduced with Pbx1-IRES-GFP and subjected to ATAC-seq on day 3, rep3

data_processing:
Fastq files were trimmed using Trim Galore and aligned to the reference mouse genome (mm10) using bowtie2 with a --very-sensitive and single-read mode. Mitochondrial genome, Y chromosome, and scaffold chromosomes were removed using samtools, and duplicate reads were removed using picard MarkDuplicates. Peak calling was performed using MACS3 for each group with -q = 0.05, --extsize =100, and --shift = 50 with narrow peak mode. All peaks called in each group were merged, and peaks overlapping with blacklist region were excluded, and peaks within a distance smaller than 50bp considered as an identical peak. After further removing peaks with average of log CPM < -1, peak count around +/- 125bp of each summit was performed using csaw package of R.
Assembly: mm10
Supplementary files format and content: BigWig files were generated using Deeptools from BAM files removing duplicated reads after normalized to peak counts, and biological replicates were merged with DeepTools.
Supplementary files format and content: PeakCounts_th0.txt provides a tab-deliminated raw count data, counting reads 250bp around each summit following removal of peaks with low signal.
Supplementary files format and content: Peak_250bp_noBL.bed is a BED file providing a +/- 125bp around summits detected by MACS3. Problematic regions ("blacklist") were removed.

extract_protocol:
A total of 50000 Mock- or Pbx1 transduced young or old HSCs were sorted into 1.5-mL tubes containing 500 uL of SF-O3 medium and pelleted by centrifugation for 5 minutes at 700g. The cells were then incubated with ATAC-S buffer 25uL and ATAC-lysis buffer 25uL of Zymo-Seq ATAC Library Kit (Zymo Research) for 3 minutes on ice. Then 1 mL of ATAC-wash buffer was added and centrifuged at 1000 x g for 10 minutes to collect nuclei.
Extracted nuclei were treated with Tn5 transposase bound with adaptor sequences for 30 minutes at 37°C with gentle shaking, followed by amplification with PCR. Sequencing was performed using NovaSeq6000 with a paired-end sequencing length of 150bp.

treatment_protocol: Either CD150+CD48-CD41-CD34- LSK cells from 4 young (2.5mo) mice per sample, or CD150+CD48- CD34- LSK cells from 1 old (18mo) mouse per sample was isolated. Each experimental sample comprised cells from four young mice or one old mouse per sample. All isolated cells underwent retroviral transduction with mock or Pbx1-expressing vectors, after which 5,000 GFP+ cells for RNA-seq and 50,000 GFP+ cells for ATAC-seq were selected.

value: Bone marrow

value: Old HSC

value: Wild type


title: IMR32_CTRL_Rep2

description:
Library name: Sample 2
Column name in  raw_counts_All_Samples.txt : IMR32_CTRL_Rep2

value: Neuroblastoma


title: 293T-RsaI, rep3

description: Library name: Sample 3


title: ATAC-seq, hPIB-142_d9_S_DP_1

description: Library name: hPIB-142_d9_S_DP_1


title: ATAC-seq, hPIB-142_d9_L_DP_2

description: Library name: hPIB-142_d9_L_DP_2


title: 293T-RsaI, rep2

description: Library name: Sample 2


title: ATAC-seq, hPIB-124_d9_L_DP_1

description: Library name: hPIB-124_d9_L_DP_1

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-124 on day -1 of reprogramming.


title: ATAC-seq, hPIB-124_d9_L_DP_2

description: Library name: hPIB-124_d9_L_DP_2


title: 293T-RsaI, rep1

description: Library name: Sample 1


title: ATAC-seq, hPIB-124_d9_G_DP_1

description: Library name: hPIB-124_d9_G_DP_1


title: ATAC-seq, hPIB-124_d9_S_DP_1

description: Library name: hPIB-124_d9_S_DP_1


title: ht1080b3.RsaIrep1

description: Library name: ht1080b3.RsaIrep1

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 fibrosarcoma cell line


title: ATAC-seq, hPIB-SCR_d9_L_DP_1

description: Library name: hPIB-SCR_d9_L_DP_1

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for a scrambled control hairpin on day -1 of reprogramming.


title: ht1080b2.RsaIrep2

description: Library name: ht1080b2.RsaIrep2


title: ATAC-seq, hPIB-SCR_d9_G_DP_1

description: Library name: hPIB-SCR_d9_G_DP_1


title: ht1080b2.RsaIrep1

description: Library name: ht1080b2.RsaIrep1


title: ATAC-seq, hPIB-142_d9_L_CD45_1

description: Library name: hPIB-142_d9_L_CD45_1

value: live (DAPI-) and CD45+ HLA-DR-


title: ht1080b3.RsaIrep2

description: Library name: ht1080b3.RsaIrep2


title: ht1080a6.RsaIrep3

description: Library name: ht1080a6.RsaIrep3


title: ATAC-seq, hPIB-142_d9_G_CD45_1

description: Library name: hPIB-142_d9_G_CD45_1


title: ht1080a6.RsaIrep2

description: Library name: ht1080a6.RsaIrep2


title: ht1080a6.RsaIrep1

description: Library name: ht1080a6.RsaIrep1


title: ATAC-seq, hPIB-SCR_d9_S_DP_1

description: Library name: hPIB-SCR_d9_S_DP_1


title: hct116.SmiIrep3

description: Library name: hct116.SmiIrep3

value: human colorectal carcinoma cell line


title: ATAC-seq, hPIB-142_d9_S_CD45_1

description: Library name: hPIB-142_d9_S_CD45_1


title: hct116.SmiIrep2

description: Library name: hct116.SmiIrep2


title: ATAC-seq, hPIB-124_d9_G_CD45_1

description: Library name: hPIB-124_d9_G_CD45_1


title: hct116.SmiIrep1

description: Library name: hct116.SmiIrep1


title: ATAC-seq, hPIB-124_d9_S_CD45_1

description: Library name: hPIB-124_d9_S_CD45_1


title: hct116.RsaIrep6

description: Library name: hct116.RsaIrep6


title: ATAC-seq, hPIB-124_d9_L_CD45_1

description: Library name: hPIB-124_d9_L_CD45_1


title: ATAC-seq, hPIB-SCR_d9_L_CD45_1

description: Library name: hPIB-SCR_d9_L_CD45_1


title: hct116.RsaIrep5

description: Library name: hct116.RsaIrep5


title: hct116.RsaIrep4

description: Library name: hct116.RsaIrep4


title: ATAC-seq, hPIB-SCR_d9_G_CD45_1

description: Library name: hPIB-SCR_d9_G_CD45_1


title: ATAC-seq, hPIB-SCR_d9_S_CD45_1

description: Library name: hPIB-SCR_d9_S_CD45_1


title: ATAC-seq, hPIB-142_d6_L_DP_1

description: Library name: hPIB-142_d6_L_DP_1

value: Cells were collected on day 6 of reprogramming.


title: hct116.RsaIrep3

description: Library name: hct116.RsaIrep3


title: hct116.RsaIrep2

description: Library name: hct116.RsaIrep2


title: ATAC-seq, hPIB-142_d6_G_DP_1

description: Library name: hPIB-142_d6_G_DP_1


title: hct116.RsaIrep1

description: Library name: hct116.RsaIrep1


title: ATAC-seq, hPIB-142_d6_S_DP_1

description: Library name: hPIB-142_d6_S_DP_1


title: ATAC-seq, hPIB-124_d6_G_DP_1

description: Library name: hPIB-124_d6_G_DP_1


title: inhibitor4

city: Shijiazhuang

first: Ya

last: Wen

state: Hebei

address: No. 215, Heping West Road, Xinhua District

department: Neurology

institute: The Second Hospital of Hebei Medical University

description:
Library name: sample12
Column name in mRNA_readcounts.txt:inhibitor4

data_processing:
Quality Control of Sequencing Data Raw sequencing data may contain adapter sequences, low-quality reads, and short sequences, which can affect subsequent analyses. To ensure accuracy, raw data is filtered to obtain high-quality clean data. The steps are as follows: 1. Remove adapter sequences and reads without inserts due to adapter self-ligation. 2. Trim low-quality bases (quality score < 20) from the 3’ end of the reads. If any bases in the remaining sequence have a quality score < 10, discard the entire read; otherwise, keep the read. 3. Remove reads containing N (ambiguous bases). 4. Discard sequences shorter than 30 bp after adapter trimming and quality filtering. Software used: fastp (https://github.com/OpenGene/fastp); v0.20.1 Mapping to the Reference Genome The high-quality clean data (reads) were mapped to the reference genome to obtain mapped data (reads) for subsequent transcriptome assembly, expression quantification, etc. Quality assessment of the alignment results is also performed. Software used: STAR (https://github.com/alexdobin/STAR); v2.7.7a FeatureCounts (https://github.com/topics/featurecounts); v2.0.0 Expression Level AnalysisTranscript abundance reflects gene expression levels; the higher the transcript abundance, the higher the gene expression level. In RNA-Seq analysis, gene expression levels are calculated by counting the number of sequences (clean reads) aligned to genomic regions. StringTie, a transcriptome assembly tool based on locus junctions, was used to convert raw data into gene transcript expression matrices and to discover new transcripts, identify differential expression, and detect alternative splicing events. The quantification results included raw counts, FPKM (Fragments Per Kilobase of transcript per Million mapped reads), and TPM (Transcripts Per Million). Software used: StringTie (https://ccb.jhu.edu/software/stringtie/index.shtml) Differential Expression Analysis Differential expression analysis was performed using edgeR, which calculates differential expression based on read count data aligned to genes, using a negative binomial distribution model. The default criteria for identifying significantly differentially expressed genes (DEGs) are FDR < 0.05 and |log2FC| ≥ 1. A gene meeting both criteria is considered a DEG. Software used: edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html) Enrichment Analysis GO/KEGG pathway enrichment analysis was performed using clusterProfiler with Fisher's exact test for calculation. The Benjamini-Hochberg (BH) method was used for multiple testing correction to control the false discovery rate (FDR), with a corrected p-value threshold of 0.05. GO terms/KEGG pathways meeting this criterion were considered significantly enriched in DEGs. Software used: clusterProfiler (https://github.com/YuLab-SMU/clusterProfiler); v4.0.2
Assembly: GRCm39.106
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: cs files include TPM values for each Sample

growth_protocol: Neuro-2a cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO₂ at 37°C

extract_protocol:
Total RNA was extracted using the TransZol Up reagent (TransGen Biotech) according to themanufacturer’s instructions. After extraction, the RNA integrity was checked using 1.5% agarose gel electrophoresis or a fragment analyzer. The concentration and purity of the RNAwere measured using a Nanodrop spectrophotometer.
The transcriptome library was constructed using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina according to the manufacturer’s protocol. The steps are as follows: 1. Add fragmentation buffer and random primers to fragment the target RNA and allow random primers to bind to the target RNA. 2. Add first-strand reverse transcription reagents to reverse transcribe the target RNA into cDNA, forming RNA-cDNA hybrids. 3. Add second-strand synthesis reagents to cleave the RNA from the RNA-cDNA hybrids and use the remaining RNA as primers to synthesize double-stranded cDNA. 4. Perform end-repair and add an A-tail to the double-stranded cDNA, then ligate Y-shaped adapters. 5. Use magnetic beads to remove adapter dimers. 6. Enrich the library templates using PCR amplification. 7. Recover the library using magnetic beads.

treatment_protocol: Cells were transfected with miR-Control, miR-155 mimic, and miR-155 inhibitor using RNA Fit under serum-free and antibiotic-free conditions. After 4 hours, the medium was replaced with complete growth medium, and cells were cultured in a humidified incubator at 37°C with 5% CO₂ until day 2.

value: neuroblastoma cells

value: miR-155 inhibitor


title: ATAC-seq, hPIB-124_d6_S_DP_1

description: Library name: hPIB-124_d6_S_DP_1

value: skin

value: human dermal fibroblast


title: ATAC-seq, hPIB-SCR_d6_L_DP_1

description: Library name: hPIB-SCR_d6_L_DP_1


title: inhibitor2

description:
Library name: sample10
Column name in mRNA_readcounts.txt:inhibitor2


title: Mouse lung scRNA-seq GEM-X Flex P0.5 pool 1

city: Seoul

first: SeJin

last: Kim

address: 50-1, Yonsei-ro

country: South Korea

institute: Yonsei university

description:
Library name: Lung_pool_FLX
Pooled P0.5 mouse lung single-cell samples including wild type, Wfdc2 p.C147W knock-in, Wfdc2 knockout, and amiloride-treated Wfdc2 knockout conditions, processed using the 10x Genomics GEM-X Flex workflow.

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger software v7.2(https://www.10xgenomics.com/support/software/cell-ranger/).
Assembly: Mouse mm10
Supplementary files format and content: Processed data are provided as 10x Genomics feature-barcode matrices in Matrix Market format. The files include matrix.mtx.gz, features.tsv.gz, and barcodes.tsv.gz generated by Cell Ranger. Rows correspond to genes/features, columns correspond to cell barcodes, and values represent raw count values for each gene in each cell.

source_name: lung

extract_protocol:
Fresh tissue specimens were kept at 4°C in Tissue Storage Solution (Miltenyi Biotec) until processing. Before dissociation, tissues were rinsed with cold PBS, minced into 1-2 mm pieces, and dissociated using the Multi Tissue Dissociation Kit 2 and gentleMACS Dissociator according to the manufacturer's instructions. The resulting cell suspensions were filtered sequentially through 70- and 30-um strainers to remove debris and undigested tissue. Cells were pelleted at 300 x g for 5 min at 4°C and resuspended in ice-cold Ca2+/Mg2+-free PBS containing 0.04% BSA. Cell number and viability were assessed with AO/PI staining using a LUNA-FX7 automated fluorescence cell counter. Cells were cryopreserved in Cellbanker2 and, before downstream processing, thawed in 37°C 10% FBS/DMEM for 1-2 min, washed twice with cold Ca2+/Mg2+-free 0.04% BSA/PBS at 300 x g for 5 min at 4°C, resuspended, and recounted. For GEM-X Flex processing, cells were fixed using the 10x Genomics GEM-X Flex Sample Preparation Kit following the 10x Genomics Fixation of Cells & Nuclei for GEM-X Flex Gene Expression protocol. Cells were centrifuged, resuspended in Fixation Buffer B containing 4% formaldehyde, incubated at 4°C for 22.5 h, pelleted at 850 rcf for 5 min at room temperature, and quenched with Quenching Buffer B.
Probe hybridization and fixed RNA profiling library construction were performed using the 10x Genomics GEM-X Flex Mouse Transcriptome Probe Kit and the GEM-X Flex Multiplexed Samples protocol. Fixed samples were hybridized with transcriptome probes at 42°C for 22.5 h, then counted and pooled. The pooled fixed cells, with a total target recovery of 20,000 cells, were combined with GEM master mix and loaded with GEM-X Flex Gel Beads and Partitioning Oil on a GEM-X Flex Gene Expression Chip using the 10x Chromium X system to generate single-cell GEMs. Within GEMs, probe-hybridized RNA molecules were barcoded and reverse-transcribed. After GEM-RT incubation, barcoded cDNA was pre-amplified by PCR, and fixed RNA gene expression libraries were generated by index PCR from enriched cDNA. Purified libraries were quantified by qPCR, assessed with an Agilent 4200 TapeStation, and sequenced on an Illumina NovaSeq X Plus.

value: lung

value: single cells

value: wild type; Wfdc2 p.C147W knock-in; Wfdc2 knockout

value: none; amiloride

value: P0.5 pool 1


title: inhibitor1

description:
Library name: sample9
Column name in mRNA_readcounts.txt:inhibitor1

value: WT


title: ATAC-seq, hPIB-SCR_d6_G_DP_1

description: Library name: hPIB-SCR_d6_G_DP_1

value: live (DAPI-) and CD45+ HLA-DR+


title: Mouse lung scRNA-seq GEM-X Flex P4 pool 2

description:
Library name: Lung_2_Pool_FLX
Pooled P4 mouse lung single-cell samples including wild type, amiloride-treated wild type, Wfdc2 knockout, and amiloride-treated Wfdc2 knockout conditions, processed using the 10x Genomics GEM-X Flex workflow.

value: wild type; Wfdc2 knockout

value: P4 pool 2


title: inhibitor3

description:
Library name: sample11
Column name in mRNA_readcounts.txt:inhibitor3


title: ATAC-seq, hPIB-SCR_d6_S_DP_1

description: Library name: hPIB-SCR_d6_S_DP_1

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for a scrambled control hairpin on day -1 of reprogramming.


title: mimic4

description:
Library name: sample8
Column name in mRNA_readcounts.txt:mimic4

value: miR-155 mimic


title: ATAC-seq, hPIB-142_d6_L_CD45_1

description: Library name: hPIB-142_d6_L_CD45_1

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-142 on day -1 of reprogramming.

value: live (DAPI-) and CD45+ HLA-DR-


title: ATAC-seq, hPIB-142_d6_G_CD45_1

description: Library name: hPIB-142_d6_G_CD45_1

value: Cells were collected on day 6 of reprogramming.


title: mimic3

description:
Library name: sample7
Column name in mRNA_readcounts.txt:mimic3

value: neuroblastoma cells


title: ATAC-seq, hPIB-142_d6_S_CD45_1

description: Library name: hPIB-142_d6_S_CD45_1

value: skin


title: ATAC-seq, hPIB-124_d6_L_CD45_1

description: Library name: hPIB-124_d6_L_CD45_1

value: human dermal fibroblast

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-124 on day -1 of reprogramming.


title: NC4

description:
Library name: sample4
Column name in mRNA_readcounts.txt:NC4

value: miR-Con


title: NC3

description:
Library name: sample3
Column name in mRNA_readcounts.txt:NC3


title: ATAC-seq, hPIB-124_d6_G_CD45_1

description: Library name: hPIB-124_d6_G_CD45_1


title: ATAC-seq, hPIB-124_d6_S_CD45_1

description: Library name: hPIB-124_d6_S_CD45_1


title: ATAC-seq, hPIB-SCR_d6_G_CD45_1

description: Library name: hPIB-SCR_d6_G_CD45_1


title: ATAC-seq, hPIB-SCR_d6_L_CD45_1

description: Library name: hPIB-SCR_d6_L_CD45_1


title: NC1

description:
Library name: sample1
Column name in mRNA_readcounts.txt:NC1


title: bulge hair follicle stem cells, P69, cKO 2-input

city: Guangzhou

first: Kechen

last: Chen

state: Guangdong

address: Shatai South Road

institute: Southern Medical University

description: Library name: 145 B

data_processing:
Bulk RNA-seq data were processed through a streamlined analysis pipeline. Raw reads underwent quality assessment with FastQC and adapter trimming with TrimGalore. Clean reads were aligned to the mouse GRCm38/mm10 reference genome using STAR. PCR duplicates were removed with sambamba, and gene-level read quantification was performed using featureCounts. Differential expression analysis was conducted with DESeq2, and functional enrichment of GO terms and KEGG pathways was carried out using clusterProfiler.For MeRIP-seq data, IP and input samples were aligned to the mouse GRCm38/mm10 genome using the same pipeline as bulk RNA-seq. m⁶A peak calling was performed with MACS2 using parameters optimized for broad peak detection. Identified peaks were annotated with ChIPseeker to determine their associated genes and genomic features. Motif enrichment analysis of m⁶A peak regions was conducted using HOMER to identify sequence motifs enriched within modified regions.
Assembly: GRCm38/mm10
Supplementary files format and content: text file include raw count for each Sample
Supplementary files format and content: bw file includes raw signal intensity for each genomic position.
Library strategy: MeRIP-Seq

extract_protocol:
Cells were isolated by flow cytometric sorting, and total RNA was extracted using TRIzol. Libraries were constructed using 200 ng of total RNA for bulge hair follicle stem cells and 40 ng of total RNA for hair germ stem cells.
RNA-seq libraries were prepared using the SHERRY2 protocol, and m⁶A-seq libraries were generated using the m⁶A-CT-seq method based on the CUT&Tag principle.

value: hair follicle stem cell

value: Alkbh5 cKO


title: ATAC-seq, hPIB-SCR_d6_S_CD45_1

description: Library name: hPIB-SCR_d6_S_CD45_1


title: ATAC-seq, hPIB-142_d3_L_CD45_1

description: Library name: hPIB-142_d3_L_CD45_1

value: Cells were collected on day 3 of reprogramming.

value: live (DAPI-) and CD45+


title: bulge hair follicle stem cells, P69, WT 1-input

description: Library name: 142 B

value: wild-type


title: ATAC-seq, hPIB-142_d3_G_CD45_1

description: Library name: hPIB-142_d3_G_CD45_1

value: WT


title: ATAC-seq, hPIB-142_d3_S_CD45_1

description: Library name: hPIB-142_d3_S_CD45_1


title: bulge hair follicle stem cells, P69, cKO 2-IP

description: Library name: 145 B-CT


title: bulge hair follicle stem cells, P69, WT 2-IP

description: Library name: 143 B-CT


title: ATAC-seq, hPIB-124_d3_L_CD45_1

description: Library name: hPIB-124_d3_L_CD45_1


title: ATAC-seq, hPIB-124_d3_G_CD45_1

description: Library name: hPIB-124_d3_G_CD45_1


title: ATAC-seq, hPIB-124_d3_S_CD45_1

description: Library name: hPIB-124_d3_S_CD45_1


title: bulge hair follicle stem cells, P69, WT 1-IP

description: Library name: 142 B-CT


title: ATAC-seq, hPIB-SCR_d3_L_CD45_1

description: Library name: hPIB-SCR_d3_L_CD45_1


title: bulge hair follicle stem cells, P69, WT 2-input

description: Library name: 143 B


title: ATAC-seq, hPIB-SCR_d3_G_CD45_1

description: Library name: hPIB-SCR_d3_G_CD45_1


title: ATAC-seq, hPIB-SCR_d3_S_CD45_1

description: Library name: hPIB-SCR_d3_S_CD45_1


title: hair germ stem cells, P69, cKO mouse 1

description: Library name: 73H

data_processing:
Bulk RNA-seq data were processed through a streamlined analysis pipeline. Raw reads underwent quality assessment with FastQC and adapter trimming with TrimGalore. Clean reads were aligned to the mouse GRCm38/mm10 reference genome using STAR. PCR duplicates were removed with sambamba, and gene-level read quantification was performed using featureCounts. Differential expression analysis was conducted with DESeq2, and functional enrichment of GO terms and KEGG pathways was carried out using clusterProfiler.For MeRIP-seq data, IP and input samples were aligned to the mouse GRCm38/mm10 genome using the same pipeline as bulk RNA-seq. m⁶A peak calling was performed with MACS2 using parameters optimized for broad peak detection. Identified peaks were annotated with ChIPseeker to determine their associated genes and genomic features. Motif enrichment analysis of m⁶A peak regions was conducted using HOMER to identify sequence motifs enriched within modified regions.
Assembly: GRCm38/mm10
Supplementary files format and content: text file include raw count for each Sample
Supplementary files format and content: bw file includes raw signal intensity for each genomic position.


title: ATAC-seq, MCS_d3_G_alive_1

description: Library name: MCS_d3_G_alive_1

data_processing:
In order to pre-process the FASTQ files of ATAC-Seq experiments, we used the nf-core ATAC-seq pipeline version 1.2.2 with default parameters. Technical replicates were merged together.
Reads were mapped to the GRCh38 reference genome using BWA. Peak calling was performed with MACS2 separately for each sample. A combined peak list for all samples was obtained using BEDTools. Finally, read counts on a combined peak list were calculated using featureCounts.
Assembly: hg38
Supplementary files format and content: count tables (.txt)

value: Cells were transduced with an empty lentiviral vector on day -1.


title: bulge hair follicle stem cells, P69, cKO mouse 2

description: Library name: 5288CKO-B


title: ATAC-seq, pDC_d3_C_Villani_1

description: Library name: pDC_d3_C_Villani_1

value: blood

value: human dendritic cell

value: live (7-AAD-) and HLA-DR+ CD11c- CD123+


title: bulge hair follicle stem cells, P69, cKO mouse 1

description: Library name: 5285CKO-B


title: ATAC-seq, pDC_d3_B_Villani_1

description: Library name: pDC_d3_B_Villani_1


title: bulge hair follicle stem cells, P69, WT mouse 1

description: Library name: 5283WT-B


title: ATAC-seq, pDC_d3_A_Villani_1

description: Library name: pDC_d3_A_Villani_1


title: GBM|014|Full.ROI

city: Frankfurt am Main

first: Katharina

last: Imkeller

address: Heinrich-Hoffmann-Str. 7

country: Germany

institute: University Hospital Frankfurt

description: Library name: GBM|014|Full.ROI

data_processing:
Reads generated were filtered and normalised on GeoMx DSP Analysis Suite using the default settings. The reads were then scaled to nuclei prior to downstream analysis in R.
Assembly: GRCh38/hg38
Supplementary files format and content: counts_NS.csv: Comma-delimited csv file includes the raw counts from each roi form a sample. Each column is a ROI and each row is a gene.
Supplementary files format and content: metadata_NS.csv: Comma-delimited csv metadata file containing additional information about the each roi  in the count matrix file.

source_name: Glioma(GBM)

extract_protocol:
FFPE tissue cuts (5 μm) were placed onto microscope slides and the GeoMx ® Human Whole Transcriptome Atlas Assay (NanoString Technologies, United States) was conducted following the manufacturer’s protocol.
The library was constructed according to Nanostring GeoMx DSP manufacturer’s protocol.

value: Glioma(GBM)

value: TLS

tag: patient


title: ATAC-seq, DC2_d3_C_Villani_1

description: Library name: DC2_d3_C_Villani_1

value: live (7-AAD-) and HLA-DR+ CD11c+ CD1c+ CD141-


title: GBM|007|Full.ROI

description: Library name: GBM|007|Full.ROI

value: tumor


title: ATAC-seq, DC2_d3_B_Villani_1

description: Library name: DC2_d3_B_Villani_1


title: ATAC-seq, hPIB-124_d6_L_DP_1

description: Library name: hPIB-124_d6_L_DP_1

value: skin

value: human dermal fibroblast

value: Cells were collected on day 6 of reprogramming.

value: live (DAPI-) and CD45+ HLA-DR+


title: GBM|006|Full.ROI

description: Library name: GBM|006|Full.ROI


title: GBM|005|Full.ROI

description: Library name: GBM|005|Full.ROI


title: ATAC-seq, DC2_d3_A_Villani_1

description: Library name: DC2_d3_A_Villani_1


title: mimic2

description:
Library name: sample6
Column name in mRNA_readcounts.txt:mimic2

value: neuroblastoma cells

value: miR-155 mimic


title: ATAC-seq, DC1_d3_C_Villani_1

description: Library name: DC1_d3_C_Villani_1

value: live (7-AAD-) and HLA-DR+ CD11c+ CD141+


title: ATAC-seq, DC1_d3_B_Villani_1

description: Library name: DC1_d3_B_Villani_1


title: GBM|003|Full.ROI

description: Library name: GBM|003|Full.ROI


title: GBM|004|Full.ROI

description: Library name: GBM|004|Full.ROI


title: ATAC-seq, DC1_d3_A_Villani_1

description: Library name: DC1_d3_A_Villani_1


title: mimic1

description:
Library name: sample5
Column name in mRNA_readcounts.txt:mimic1


title: GBM|002|Full.ROI

description: Library name: GBM|002|Full.ROI


title: hPIB-142_d9_L_DP_2

description: Library name: hPIB-142_d9_L_DP_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}).*". Technical replicates were merged together.
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)

extract_protocol:
1000-2000 cells were sorted intro PBS with 2 % FBS, pelleted and frozen at -80 °C. RNA was exracted using TRIzol according to manufacturer's protocol.
Libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian kit by Takara.

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-142 on day -1 of reprogramming.

value: Cells were collected on day 9 of reprogramming.


title: BM|006|Full.ROI

description: Library name: BM|006|Full.ROI

source_name: Brain Metastases (BM)

value: Brain Metastases (BM)


title: NC2

description:
Library name: sample2
Column name in mRNA_readcounts.txt:NC2

value: WT

value: miR-Con


title: hPIB-142_d9_G_DP_2

description: Library name: hPIB-142_d9_G_DP_2

source_name: skin


title: BM|005|Full.ROI

description: Library name: BM|005|Full.ROI


title: BM|004|Full.ROI

description: Library name: BM|004|Full.ROI


title: hPIB-142_d9_S_DP_2

description: Library name: hPIB-142_d9_S_DP_2


title: BM|003|Full.ROI

description: Library name: BM|003|Full.ROI


title: hPIB-124_d9_L_DP_2

description: Library name: hPIB-124_d9_L_DP_2

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-124 on day -1 of reprogramming.


title: bulge hair follicle stem cells, P69, cKO 1-input

description: Library name: 141 B

value: hair follicle stem cell

value: Alkbh5 cKO


title: hPIB-124_d9_G_DP_2

description: Library name: hPIB-124_d9_G_DP_2


title: BM|002|Full.ROI

description: Library name: BM|002|Full.ROI


title: bulge hair follicle stem cells, P69, cKO 1-IP

description: Library name: 141 B-CT


title: hPIB-124_d9_S_DP_2

description: Library name: hPIB-124_d9_S_DP_2


title: BM|001|Full.ROI

description: Library name: BM|001|Full.ROI

value: TLS


title: hair germ stem cells, P69, cKO mouse 2

description: Library name: 76H


title: hPIB-SCR_d9_L_DP_2

description: Library name: hPIB-SCR_d9_L_DP_2

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for a scrambled control hairpin on day -1 of reprogramming.


title: hPIB-SCR_d9_G_DP_2

description: Library name: hPIB-SCR_d9_G_DP_2

value: skin


title: Whole blood DNA methylation, NHW AD, 75yo M, 207215820065_R04C01

type: genomic

city: San Francisco

first: Sebastián

last: Cruz-González

state: California

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

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: Male

value: Alzheimer's disease

value: whole blood

tag: ethnicity

value: NHW

tag: cohort

tag: age


title: Whole blood DNA methylation, NHW AD, 82yo M, 207215820085_R02C01

tag: tissue


title: ATAC-seq, MCS_d3_L_alive_1

description: Library name: MCS_d3_L_alive_1

extract_protocol:
5000-10000 cells were sorted intro PBS with 2 % FBS and processed according to the procedure described by Buenrostro et al. (2015).
ATAC-seq primers were prepared according to the procedure described by Buenrostro et al. (2015), with 96-plex indexing primers.

tag: cell type

value: human dermal fibroblast

value: Cells were transduced with an empty lentiviral vector on day -1.

value: Cells were collected on day 3 of reprogramming.

value: live (DAPI-) and CD45+


title: hair germ stem cells, P69, WT mouse 2

description: Library name: 75H

tag: genotype

value: wild-type


title: hPIB-SCR_d9_S_DP_2

description: Library name: hPIB-SCR_d9_S_DP_2

value: WT

tag: treatment

value: Cells were collected on day 9 of reprogramming.

value: live (DAPI-) and CD45+ HLA-DR+


title: hPIB-142_d9_L_CD45_2

description: Library name: hPIB-142_d9_L_CD45_2

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-142 on day -1 of reprogramming.

tag: time

value: live (DAPI-) and CD45+ HLA-DR-


title: Whole blood DNA methylation, AA AD, 97yo F, 207221680059_R01C01

value: Female

value: AA

value: REAAADI


title: hair germ stem cells, P69, WT mouse 1

description: Library name: 74H

value: skin

value: hair follicle stem cell


title: Whole blood DNA methylation, AA AD, 82yo M, 207215820121_R07C01

value: Male

value: Alzheimer's disease

value: whole blood


title: Whole blood DNA methylation, NHW AD, 71yo M, 207215820094_R03C01

value: NHW


title: ATAC-seq, MCS_d3_S_alive_1

description: Library name: MCS_d3_S_alive_1

value: human dermal fibroblast

value: Cells were transduced with an empty lentiviral vector on day -1.

value: Cells were collected on day 3 of reprogramming.

tag: sorted cells


title: hPIB-142_d9_G_CD45_2

description: Library name: hPIB-142_d9_G_CD45_2

value: WT

tag: technical replicates


title: hPIB-142_d9_S_CD45_2

description: Library name: hPIB-142_d9_S_CD45_2

value: Cells were collected on day 9 of reprogramming.


title: bulge hair follicle stem cells, P69, WT mouse 2

description: Library name: 5287WT-B

value: wild-type


title: Whole blood DNA methylation, AA AD, 80yo F, 207221680059_R03C01


title: hPIB-124_d9_L_CD45_2

description: Library name: hPIB-124_d9_L_CD45_2

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-124 on day -1 of reprogramming.


title: Whole blood DNA methylation, AA CONTROL, 76yo M, 207215830018_R06C01

value: Healthy control


title: hPIB-124_d9_G_CD45_2

description: Library name: hPIB-124_d9_G_CD45_2

value: live (DAPI-) and CD45+ HLA-DR-


title: Whole blood DNA methylation, AA CONTROL, 69yo F, 207215820086_R08C01

value: Female

value: AA


title: hPIB-124_d9_S_CD45_2

description: Library name: hPIB-124_d9_S_CD45_2

value: skin


title: hPIB-SCR_d9_L_CD45_2

description: Library name: hPIB-SCR_d9_L_CD45_2

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for a scrambled control hairpin on day -1 of reprogramming.


title: hPIB-SCR_d9_G_CD45_2

description: Library name: hPIB-SCR_d9_G_CD45_2


title: Whole blood DNA methylation, AA AD, 86yo F, 207219770143_R03C01

value: REAAADI


title: hPIB-SCR_d9_S_CD45_2

description: Library name: hPIB-SCR_d9_S_CD45_2


title: Whole blood DNA methylation, AA AD, 79yo F, 207215820013_R03C01

value: Alzheimer's disease


title: Whole blood DNA methylation, AA CONTROL, 76yo F, 207215820034_R02C01

value: whole blood


title: Whole blood DNA methylation, AA CONTROL, 69yo F, 207215820121_R01C01


title: hPIB-142_d6_G_DP_2

description: Library name: hPIB-142_d6_G_DP_2

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-142 on day -1 of reprogramming.

value: Cells were collected on day 6 of reprogramming.

value: live (DAPI-) and CD45+ HLA-DR+


title: hPIB-142_d6_S_DP_2

description: Library name: hPIB-142_d6_S_DP_2

value: human dermal fibroblast


title: Whole blood DNA methylation, AA CONTROL, 66yo F, 207215820006_R04C01


title: hPIB-142_d6_L_DP_2

description: Library name: hPIB-142_d6_L_DP_2

value: WT


title: Whole blood DNA methylation, AA AD, 90yo F, 207215820048_R06C01


title: Whole blood DNA methylation, AA AD, 87yo F, 207215820044_R03C01


title: hPIB-124_d6_L_DP_2

description: Library name: hPIB-124_d6_L_DP_2


title: Whole blood DNA methylation, AA CONTROL, 68yo M, 207228480079_R07C01

value: Male


title: hPIB-124_d6_S_DP_2

description: Library name: hPIB-124_d6_S_DP_2


title: Whole blood DNA methylation, NHW AD, 89yo F, 207228480079_R04C01

value: NHW


title: Whole blood DNA methylation, AA AD, 93yo F, 207215830065_R01C01


title: hPIB-124_d6_G_DP_2

description: Library name: hPIB-124_d6_G_DP_2

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-124 on day -1 of reprogramming.


title: hPIB-SCR_d6_L_DP_2

description: Library name: hPIB-SCR_d6_L_DP_2


title: Whole blood DNA methylation, AA CONTROL, 73yo F, 207219630122_R04C01

value: Healthy control


title: hPIB-SCR_d6_G_DP_2

description: Library name: hPIB-SCR_d6_G_DP_2


title: Whole blood DNA methylation, AA CONTROL, 66yo F, 207215830114_R01C01


title: Whole blood DNA methylation, AA AD, 85yo F, 207215820048_R01C01


title: hPIB-SCR_d6_S_DP_2

description: Library name: hPIB-SCR_d6_S_DP_2


title: hPIB-142_d6_L_CD45_2

description: Library name: hPIB-142_d6_L_CD45_2

value: live (DAPI-) and CD45+ HLA-DR-


title: hPIB-142_d6_S_CD45_2

description: Library name: hPIB-142_d6_S_CD45_2


title: Whole blood DNA methylation, AA CONTROL, 71yo F, 207215820034_R08C01

value: Female


title: Whole blood DNA methylation, AA AD, 88yo F, 207215820094_R01C01

value: AA


title: hPIB-142_d6_G_CD45_2

description: Library name: hPIB-142_d6_G_CD45_2

value: skin


title: Whole blood DNA methylation, AA AD, 83yo F, 207215830065_R08C01


title: hPIB-124_d6_L_CD45_2

description: Library name: hPIB-124_d6_L_CD45_2


title: hPIB-124_d6_G_CD45_2

description: Library name: hPIB-124_d6_G_CD45_2


title: Whole blood DNA methylation, NHW AD, 83yo F, 207215830113_R03C01


title: Whole blood DNA methylation, NHW CONTROL, 77yo F, 207215820013_R08C01


title: hPIB-124_d6_S_CD45_2

description: Library name: hPIB-124_d6_S_CD45_2


title: Whole blood DNA methylation, NHW AD, 77yo M, 207097650112_R04C01


title: hPIB-SCR_d6_L_CD45_2

description: Library name: hPIB-SCR_d6_L_CD45_2

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for a scrambled control hairpin on day -1 of reprogramming.


title: hPIB-SCR_d6_G_CD45_2

description: Library name: hPIB-SCR_d6_G_CD45_2


title: Whole blood DNA methylation, AA AD, 80yo M, 207219630122_R08C01

value: REAAADI


title: Whole blood DNA methylation, AA AD, 85yo F, 207215820006_R03C01

value: Alzheimer's disease


title: hPIB-142_d3_L_CD45_2

description: Library name: hPIB-142_d3_L_CD45_2

value: Cells were collected on day 3 of reprogramming.

value: live (DAPI-) and CD45+


title: Whole blood DNA methylation, AA AD, 67yo M, 207219630048_R02C01

value: whole blood


title: Whole blood DNA methylation, AA AD, 83yo F, 207215820047_R06C01


title: hPIB-142_d3_G_CD45_2

description: Library name: hPIB-142_d3_G_CD45_2

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-142 on day -1 of reprogramming.


title: hPIB-142_d3_S_CD45_2

description: Library name: hPIB-142_d3_S_CD45_2

value: human dermal fibroblast


title: Whole blood DNA methylation, AA CONTROL, 68yo F, 207215820013_R06C01


title: hPIB-124_d3_L_CD45_2

description: Library name: hPIB-124_d3_L_CD45_2

value: WT


title: Whole blood DNA methylation, AA AD, 89yo F, 207215820034_R01C01


title: Whole blood DNA methylation, AA AD, 68yo F, 207215820089_R06C01


title: Whole blood DNA methylation, AA CONTROL, 69yo F, 207221680011_R02C01


title: hPIB-124_d3_G_CD45_2

description: Library name: hPIB-124_d3_G_CD45_2


title: Whole blood DNA methylation, AA AD, 81yo F, 207219630047_R06C01


title: hPIB-SCR_d3_L_CD45_2

description: Library name: hPIB-SCR_d3_L_CD45_2


title: hPIB-SCR_d3_G_CD45_2

description: Library name: hPIB-SCR_d3_G_CD45_2


title: hPIB-124_d3_S_CD45_2

description: Library name: hPIB-124_d3_S_CD45_2


title: hPIB-SCR_d3_S_CD45_2

description: Library name: hPIB-SCR_d3_S_CD45_2


title: Whole blood DNA methylation, NHW AD, 78yo F, 207215820121_R02C01


title: MCS_d3_L_alive_2

description: Library name: MCS_d3_L_alive_2

value: Cells were transduced with an empty lentiviral vector on day -1.


title: Whole blood DNA methylation, AA AD, 77yo M, 207215820045_R02C01

value: Male


title: MCS_d3_G_alive_2

description: Library name: MCS_d3_G_alive_2


title: Whole blood DNA methylation, AA CONTROL, 68yo F, 207219630047_R08C01


title: MCS_d3_S_alive_2

description: Library name: MCS_d3_S_alive_2


title: pDC_d3_C_Villani_2

description: Library name: pDC_d3_C_Villani_2

value: blood

value: human dendritic cell

value: live (7-AAD-) and HLA-DR+ CD11c- CD123+


title: Whole blood DNA methylation, AA CONTROL, 74yo F, 207215820075_R02C01

value: Female

value: Healthy control


title: Whole blood DNA methylation, NHW AD, 83yo F, 207097650075_R02C01

value: NHW


title: pDC_d3_A_Villani_2

description: Library name: pDC_d3_A_Villani_2


title: DC2_d3_C_Villani_2

description: Library name: DC2_d3_C_Villani_2

value: live (7-AAD-) and HLA-DR+ CD11c+ CD1c+ CD141-


title: DC2_d3_B_Villani_2

description: Library name: DC2_d3_B_Villani_2


title: Whole blood DNA methylation, AA AD, 86yo F, 207097650112_R01C01

value: AA

value: REAAADI


title: Whole blood DNA methylation, AA AD, 86yo F, 207215820047_R01C01

value: Alzheimer's disease


title: DC2_d3_A_Villani_2

description: Library name: DC2_d3_A_Villani_2


title: Whole blood DNA methylation, NHW CONTROL, 71yo F, 207215820077_R06C01


title: Whole blood DNA methylation, AA CONTROL, 68yo M, 207215820077_R02C01


title: DC1_d3_C_Villani_2

description: Library name: DC1_d3_C_Villani_2

value: live (7-AAD-) and HLA-DR+ CD11c+ CD141+


title: DC1_d3_B_Villani_2

description: Library name: DC1_d3_B_Villani_2


title: Whole blood DNA methylation, AA AD, 75yo M, 207219630122_R07C01

value: whole blood


title: Whole blood DNA methylation, AA AD, 78yo F, 207215820085_R01C01


title: hPIB-142_d9_G_DP_1

description: Library name: hPIB-142_d9_G_DP_1

value: skin

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-142 on day -1 of reprogramming.

value: Cells were collected on day 9 of reprogramming.

value: live (DAPI-) and CD45+ HLA-DR+


title: Whole blood DNA methylation, AA AD, 72yo M, 207215820085_R06C01

value: Male


title: Whole blood DNA methylation, AA CONTROL, 88yo F, 207221680011_R04C01


title: Whole blood DNA methylation, AA AD, 81yo F, 207215820097_R07C01


title: Whole blood DNA methylation, AA AD, 79yo M, 207219630128_R07C01


title: hPIB-124_d9_G_DP_1

description: Library name: hPIB-124_d9_G_DP_1

value: human dermal fibroblast

value: WT

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-124 on day -1 of reprogramming.


title: hPIB-124_d9_S_DP_1

description: Library name: hPIB-124_d9_S_DP_1


title: hPIB-SCR_d9_L_DP_1

description: Library name: hPIB-SCR_d9_L_DP_1

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for a scrambled control hairpin on day -1 of reprogramming.


title: Whole blood DNA methylation, AA CONTROL, 72yo F, 207215830057_R07C01

value: Female

value: Healthy control


title: hPIB-SCR_d9_G_DP_1

description: Library name: hPIB-SCR_d9_G_DP_1


title: Whole blood DNA methylation, AA CONTROL, 69yo F, 207228480014_R03C01


title: hPIB-SCR_d9_S_DP_1

description: Library name: hPIB-SCR_d9_S_DP_1


title: Whole blood DNA methylation, AA CONTROL, 69yo F, 207228480079_R05C01


title: hPIB-142_d9_L_CD45_1

description: Library name: hPIB-142_d9_L_CD45_1

value: live (DAPI-) and CD45+ HLA-DR-


title: Whole blood DNA methylation, AA CONTROL, 72yo F, 207096540017_R06C01

value: AA


title: hPIB-142_d9_G_CD45_1

description: Library name: hPIB-142_d9_G_CD45_1


title: Whole blood DNA methylation, AA CONTROL, 70yo F, 207221680026_R03C01

value: REAAADI


title: Whole blood DNA methylation, AA AD, 96yo F, 207215820046_R02C01

value: Alzheimer's disease


title: Whole blood DNA methylation, AA CONTROL, 71yo M, 207215820094_R06C01


title: hPIB-124_d9_L_CD45_1

description: Library name: hPIB-124_d9_L_CD45_1


title: hPIB-124_d9_G_CD45_1

description: Library name: hPIB-124_d9_G_CD45_1


title: Whole blood DNA methylation, AA CONTROL, 65yo F, 207215830018_R02C01


title: Whole blood DNA methylation, AA AD, 73yo F, 207215820047_R05C01


title: hPIB-124_d9_S_CD45_1

description: Library name: hPIB-124_d9_S_CD45_1


title: pDC_d3_B_Villani_2

description: Library name: pDC_d3_B_Villani_2

value: blood

value: human dendritic cell

value: live (7-AAD-) and HLA-DR+ CD11c- CD123+


title: Whole blood DNA methylation, NHW CONTROL, 75yo M, 207215820089_R03C01

value: whole blood

value: NHW


title: hPIB-SCR_d9_L_CD45_1

description: Library name: hPIB-SCR_d9_L_CD45_1

value: skin

value: Cells were collected on day 9 of reprogramming.


title: hPIB-SCR_d9_G_CD45_1

description: Library name: hPIB-SCR_d9_G_CD45_1

value: human dermal fibroblast


title: Whole blood DNA methylation, AA CONTROL, 75yo M, 207215830065_R03C01

value: Male


title: Whole blood DNA methylation, AA CONTROL, 65yo F, 207215820097_R03C01


title: hPIB-142_d6_L_DP_1

description: Library name: hPIB-142_d6_L_DP_1

value: WT

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-142 on day -1 of reprogramming.

value: Cells were collected on day 6 of reprogramming.

value: live (DAPI-) and CD45+ HLA-DR+


title: hPIB-SCR_d9_S_CD45_1

description: Library name: hPIB-SCR_d9_S_CD45_1

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for a scrambled control hairpin on day -1 of reprogramming.

value: live (DAPI-) and CD45+ HLA-DR-


title: Whole blood DNA methylation, AA CONTROL, 73yo F, 207215820045_R08C01

value: Female

value: Healthy control

value: AA

value: REAAADI


title: Whole blood DNA methylation, AA AD, 80yo F, 207215820006_R08C01

value: Alzheimer's disease


title: hPIB-142_d9_S_DP_1

description: Library name: hPIB-142_d9_S_DP_1


title: Whole blood DNA methylation, AA CONTROL, 75yo F, 207215820061_R08C01

value: whole blood


title: hPIB-124_d9_L_DP_1

description: Library name: hPIB-124_d9_L_DP_1

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-124 on day -1 of reprogramming.


title: hPIB-142_d6_G_DP_1

description: Library name: hPIB-142_d6_G_DP_1

value: skin


title: Whole blood DNA methylation, AA AD, 90yo M, 207221680059_R04C01


title: hPIB-142_d6_S_DP_1

description: Library name: hPIB-142_d6_S_DP_1


title: Whole blood DNA methylation, AA CONTROL, 75yo F, 207215820006_R07C01


title: hPIB-124_d6_L_DP_1

description: Library name: hPIB-124_d6_L_DP_1


title: Whole blood DNA methylation, NHW AD, 82yo F, 207219630048_R03C01

value: NHW


title: hPIB-124_d6_G_DP_1

description: Library name: hPIB-124_d6_G_DP_1

value: human dermal fibroblast


title: Whole blood DNA methylation, AA CONTROL, 65yo M, 207215820006_R01C01

value: Male


title: hPIB-124_d6_S_DP_1

description: Library name: hPIB-124_d6_S_DP_1

value: WT


title: hPIB-SCR_d6_L_DP_1

description: Library name: hPIB-SCR_d6_L_DP_1


title: Whole blood DNA methylation, AA CONTROL, 77yo F, 207219630048_R06C01


title: hPIB-SCR_d6_G_DP_1

description: Library name: hPIB-SCR_d6_G_DP_1


title: hPIB-SCR_d6_S_DP_1

description: Library name: hPIB-SCR_d6_S_DP_1


title: Whole blood DNA methylation, NHW CONTROL, 65yo F, 207215820132_R04C01


title: hPIB-142_d6_L_CD45_1

description: Library name: hPIB-142_d6_L_CD45_1

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-142 on day -1 of reprogramming.


title: Whole blood DNA methylation, AA CONTROL, 77yo F, 207219630122_R06C01


title: Whole blood DNA methylation, AA CONTROL, 85yo F, 207215830018_R07C01


title: hPIB-142_d6_S_CD45_1

description: Library name: hPIB-142_d6_S_CD45_1

value: Cells were collected on day 6 of reprogramming.


title: Whole blood DNA methylation, AA CONTROL, 71yo F, 207215830104_R08C01


title: hPIB-124_d6_L_CD45_1

description: Library name: hPIB-124_d6_L_CD45_1


title: Whole blood DNA methylation, NHW CONTROL, 80yo M, 207215820085_R05C01


title: hPIB-124_d6_G_CD45_1

description: Library name: hPIB-124_d6_G_CD45_1


title: hPIB-SCR_d6_L_CD45_1

description: Library name: hPIB-SCR_d6_L_CD45_1


title: Whole blood DNA methylation, NHW CONTROL, 72yo M, 207097650067_R05C01


title: hPIB-SCR_d6_G_CD45_1

description: Library name: hPIB-SCR_d6_G_CD45_1


title: hPIB-SCR_d6_S_CD45_1

description: Library name: hPIB-SCR_d6_S_CD45_1


title: hPIB-142_d3_L_CD45_1

description: Library name: hPIB-142_d3_L_CD45_1

value: Cells were collected on day 3 of reprogramming.

value: live (DAPI-) and CD45+


title: Whole blood DNA methylation, AA CONTROL, 83yo F, 207215820086_R02C01


title: hPIB-142_d3_G_CD45_1

description: Library name: hPIB-142_d3_G_CD45_1


title: Whole blood DNA methylation, AA CONTROL, 77yo F, 207215820061_R01C01


title: Whole blood DNA methylation, AA CONTROL, 66yo F, 207096540063_R06C01


title: Whole blood DNA methylation, NHW AD, 81yo M, 207215820131_R03C01


title: hPIB-142_d3_S_CD45_1

description: Library name: hPIB-142_d3_S_CD45_1


title: Whole blood DNA methylation, AA CONTROL, 69yo F, 207215820044_R04C01


title: hPIB-142_d6_G_CD45_1

description: Library name: hPIB-142_d6_G_CD45_1

value: live (DAPI-) and CD45+ HLA-DR-


title: hPIB-124_d3_L_CD45_1

description: Library name: hPIB-124_d3_L_CD45_1


title: Whole blood DNA methylation, AA CONTROL, 70yo M, 207228480080_R01C01


title: Whole blood DNA methylation, AA AD, 81yo F, 207215820055_R06C01

value: Female


title: hPIB-124_d3_G_CD45_1

description: Library name: hPIB-124_d3_G_CD45_1


title: Whole blood DNA methylation, AA CONTROL, 66yo M, 207215830104_R04C01

value: Healthy control


title: Whole blood DNA methylation, NHW AD, 83yo M, 207096540017_R02C01


title: hPIB-124_d6_S_CD45_1

description: Library name: hPIB-124_d6_S_CD45_1


title: Whole blood DNA methylation, AA CONTROL, 68yo F, 207215820132_R01C01

value: AA


title: Whole blood DNA methylation, NHW AD, 78yo M, 207215830114_R05C01


title: Whole blood DNA methylation, AA CONTROL, 76yo F, 207215830119_R03C01

value: REAAADI


title: hPIB-SCR_d3_L_CD45_1

description: Library name: hPIB-SCR_d3_L_CD45_1

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for a scrambled control hairpin on day -1 of reprogramming.


title: hPIB-SCR_d3_G_CD45_1

description: Library name: hPIB-SCR_d3_G_CD45_1


title: Whole blood DNA methylation, AA CONTROL, 72yo M, 207215830126_R08C01

value: whole blood


title: Whole blood DNA methylation, AA AD, 80yo F, 207228480032_R05C01

value: Alzheimer's disease


title: hPIB-124_d3_S_CD45_1

description: Library name: hPIB-124_d3_S_CD45_1

value: skin

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-124 on day -1 of reprogramming.


title: hPIB-SCR_d3_S_CD45_1

description: Library name: hPIB-SCR_d3_S_CD45_1

value: human dermal fibroblast


title: Whole blood DNA methylation, NHW AD, 86yo F, 207219770143_R02C01

value: NHW


title: MCS_d3_L_alive_1

description: Library name: MCS_d3_L_alive_1

value: WT

value: Cells were transduced with an empty lentiviral vector on day -1.


title: Whole blood DNA methylation, AA AD, 74yo F, 207228480080_R08C01


title: Whole blood DNA methylation, AA AD, 74yo M, 207215820132_R06C01

value: Male


title: MCS_d3_G_alive_1

description: Library name: MCS_d3_G_alive_1

value: Cells were collected on day 3 of reprogramming.


title: MCS_d3_S_alive_1

description: Library name: MCS_d3_S_alive_1

value: live (DAPI-) and CD45+


title: Whole blood DNA methylation, AA AD, 94yo M, 207219630048_R04C01


title: DC1_d3_A_Villani_2

description: Library name: DC1_d3_A_Villani_2

value: blood

value: human dendritic cell

value: live (7-AAD-) and HLA-DR+ CD11c+ CD141+


title: Whole blood DNA methylation, AA AD, 81yo M, 207215830118_R06C01

value: AA


title: pDC_d3_C_Villani_1

description: Library name: pDC_d3_C_Villani_1

value: live (7-AAD-) and HLA-DR+ CD11c- CD123+


title: hPIB-142_d9_L_DP_1

description: Library name: hPIB-142_d9_L_DP_1

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-142 on day -1 of reprogramming.

value: Cells were collected on day 9 of reprogramming.

value: live (DAPI-) and CD45+ HLA-DR+


title: pDC_d3_B_Villani_1

description: Library name: pDC_d3_B_Villani_1


title: Whole blood DNA methylation, AA CONTROL, 65yo F, 207215830113_R05C01

value: Female

value: Healthy control

value: whole blood

value: REAAADI


title: pDC_d3_A_Villani_1

description: Library name: pDC_d3_A_Villani_1

value: WT


title: Whole blood DNA methylation, NHW CONTROL, 72yo F, 207219740068_R07C01

value: NHW


title: DC2_d3_C_Villani_1

description: Library name: DC2_d3_C_Villani_1

value: live (7-AAD-) and HLA-DR+ CD11c+ CD1c+ CD141-


title: DC2_d3_B_Villani_1

description: Library name: DC2_d3_B_Villani_1


title: Whole blood DNA methylation, NHW CONTROL, 70yo F, 207215820076_R04C01


title: Whole blood DNA methylation, AA AD, 88yo F, 207097650067_R02C01

value: Alzheimer's disease


title: Whole blood DNA methylation, AA CONTROL, 65yo F, 207215830113_R02C01


title: DC2_d3_A_Villani_1

description: Library name: DC2_d3_A_Villani_1


title: Whole blood DNA methylation, AA CONTROL, 79yo F, 207215820061_R05C01


title: Whole blood DNA methylation, NHW CONTROL, 72yo F, 207215830104_R05C01


title: DC1_d3_B_Villani_1

description: Library name: DC1_d3_B_Villani_1


title: DC1_d3_C_Villani_1

description: Library name: DC1_d3_C_Villani_1


title: Whole blood DNA methylation, AA AD, 86yo F, 207215820061_R02C01


title: Whole blood DNA methylation, AA CONTROL, 72yo F, 207215820045_R07C01


title: Whole blood DNA methylation, AA AD, 86yo F, 207215820086_R05C01


title: DC1_d3_A_Villani_1

description: Library name: DC1_d3_A_Villani_1


title: CTRL 2 NS cells DRIP

city: Debrecen

first: Zsolt

last: Karanyi

address: Nagyerdei krt.98

department: Internal Med.Dept.

country: Hungary

institute: University of Debrecen

description: Library name: CTRL_2_nsc_DRIP

data_processing:
Aligning reads to reference genome with Bowtie2.
Creating BAM files with SAMtools
Removing duplicate reads with Picard.jar
Creating coverage files with DeepTools program
Assembly: Homo sapiens; GRCh38.p12
Supplementary files format and content: DRIP-seq bigwig files

source_name: reprogrammed fibroblast

growth_protocol: Generation of NSCs was performed using the PSC Neural Induction Medium (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s indicated protocol. Briefly, the PSC Neural Induction Medium (Neurobasal plus 2% Induction supplement) was added to 15–25% confluent iPSCs colonies and maintained for 7 days. Thereafter, cells were harvested and expanded in complete Neural Expansion Medium (Neurobasal and advanced DMEM-F12 plus 2% Induction supplement) on Matrigel (Corning)-coated dishes for at least 6 passages as already described 35. Characterization of the obtained NSCs was performed by immunocytochemistry using the specific marker Nestin (Anti-Nestin antibody, BD Biosciences, 1:100).

extract_protocol:
DNA-RNA Immunoprecipitation (DRIP). The same cell lines were used for DRIP as for ChIP. 5 to 7 million cells were harvested for the DRIP experiment, subsequently stored at -70°C. Genomic and mitochondrial DNA were isolated using the Macherey-Nagel NucleoSpin Tissue Kit. We modified the manufacturer’s protocol by performing the lysis step at 55°C for 4 hours, instead of the recommended 70°C for 15 minutes, to preserve R-loops from degradation 46. Post-RNase A digestion (37°C, 18 min), DNA concentration was measured. For each sample type, 6 µg of genomic DNA (gDNA) was sonicated for 5 cycles at high intensity (1 cycle: 30s ON, 30s OFF) to achieve fragment sizes of 400-600 bp, verified by agarose gel electrophoresis. We reserved 2% of each sample as INPUT. As a negative control, 6 µg of DNA underwent RNase H digestion in a thermoshaker at 37°C for 2 hours (RNase H selectively cleaves RNA-DNA hybrids). RNase H-digested samples were then purified using the Kapa Pure bead system according to the manufacturer's instructions. For immunoprecipitation, 100 µL of protein G beads were washed twice with 0.5% BSA in PBS/EDTA, then incubated with 30 µg of S9.6 antibody (R-loop specific) in 0.5% BSA PBS/EDTA for 4 hours at 4°C on a rotator. The S9.6-bead complexes were washed twice, then immunoprecipitation was performed in IP buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 5 mM EDTA, 1% Triton-X, 0.1% Na-deoxycholate) containing Protease Inhibitor. The samples were added to the bead-S9.6 complex and incubated overnight at 4°C on a rotator. The next day, bead-S9.6-R-loop complexes were washed thrice with IP buffer and thrice with TE buffer, then resuspended in elution buffer (50 mM Tris/HCl pH 8, 10 mM EDTA, 1% SDS, proteinase K), and incubated at 55°C for 2 hours at 1000 rpm in a thermos shaker. The supernatant was then transferred to a new tube and purified using a 3X bead-to-sample ratio with Kapa Pure beads.
NGS library preparation and sequencing was performed using the Illumina TruSeq ChIP Sample Preparation protocol. Briefly, DRIP DNA was end-repaired and indexed adapters were ligated to the inserts. Purified ligation products were then amplified by PCR. Amplified libraries were sequenced

treatment_protocol: NSC cells were fixed in T175 flasks using 1% formaldehyde (20 mL) for 10 minutes at room temperature and crosslinking was quenched with 416 mM glycine for 5 minutes. After three washes with ice-cold PBS containing 0.1% Tween-20 (PBS/T), cells were scraped, pelleted at 1000 × g for 5 minutes at 4 °C, and stored at −80 °C until use.

value: reprogrammed fibroblast

tag: cell line

value: NSC

value: C9orf72 normal


title: ALS Patient 1 NS cells DRIP

description: Library name: ALS_Patient_1_nsc_DRIP

value: C9orf72 expanded


title: Whole blood DNA methylation, NHW CONTROL, 82yo F, 207215820006_R05C01


title: Whole blood DNA methylation, NHW CONTROL, 70yo F, 207215820131_R07C01


title: ALS Patient 3 NS cells (INPUT)

description: Library name: ALS_Patient_3_nsc_INPUT


title: Whole blood DNA methylation, NHW CONTROL, 82yo F, 207215820048_R07C01


title: Whole blood DNA methylation, AA CONTROL, 70yo F, 207215820085_R08C01

value: AA


title: ALS Patient 3 NS cells (DRIP)

description: Library name: ALS_Patient_3_nsc_DRIP


title: ALS Patient 3 NS cells (DRIP RnaseH)

description: Library name: ALS_Patient_3_nsc_RnaseH_DRIP


title: Whole blood DNA methylation, AA AD, 78yo M, 207215820055_R08C01

value: Male


title: Whole blood DNA methylation, AA CONTROL, 69yo F, 207215820097_R04C01


title: iKCs, SAM mut, biol rep 1

description:
Library name: iKCs, SAM mut, biol rep 1
Smarteseq3Express

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

value: Fibroblasts

value: iKCs conversion


title: Whole blood DNA methylation, AA CONTROL, 72yo F, 207215820089_R01C01

value: Female


title: iKCs, DBD mut, biol rep 1

description:
Library name: iKCs, DBD mut, biol rep 1
Smarteseq3Express


title: Whole blood DNA methylation, AA AD, 91yo F, 207215830118_R05C01


title: BJ-T, MYOD1 mut, biol rep 1.1

description: Library name: BJ-T, MYOD1 mut, biol rep 1.1

value: transgene overexpresison


title: BJ-T, SAM mut, biol rep 2.1

description: Library name: BJ-T, SAM mut, biol rep 2.1


title: Whole blood DNA methylation, AA CONTROL, 79yo F, 207215830027_R05C01

value: Healthy control

value: whole blood


title: BJ-T, SAM mut, biol rep 1.1

description: Library name: BJ-T, SAM mut, biol rep 1.1


title: BJ-T, EMPTY CTR, biol rep 4

description: Library name: BJ-T, EMPTY CTR, biol rep 4

data_processing:
Illumina NovaSeq base call (BCL) files were converted into FASTQ files through bcl2fastq. Sequence reads were trimmed using bbduk software (https://sourceforge.net/projects/bbmap/ - bbmap suite 37.31) to remove adapter sequences, poly-A tails, and low-quality end bases (regions with average quality below 6). Alignment was performed with STAR 2.6.0a on GRCh38. The expression levels of genes were determined with htseq-count 0.9.1
Assembly: hg38
Supplementary files format and content: tab-separated count matrix files

extract_protocol:
Prior to library preparation, RNA samples were extracted with RNadvance cell V2 kit (Beckman Coulter #A47943) and diluted to 50 ng/μL.
RNA libraries were prepared using or NEGEDIA 3’Digital RNAseq service

value: Lentiviral overexpression


title: Whole blood DNA methylation, AA AD, 84yo F, 207096540063_R04C01

value: REAAADI


title: BJ-T, EMPTY CTR, biol rep 3

description: Library name: BJ-T, EMPTY CTR, biol rep 3


title: Whole blood DNA methylation, AA AD, 80yo F, 207215830018_R01C01


title: BJ-T, EMPTY CTR, biol rep 2

description: Library name: BJ-T, EMPTY CTR, biol rep 2


title: Whole blood DNA methylation, AA CONTROL, 66yo F, 207215830103_R04C01


title: BJ-T, EMPTY CTR, biol rep 1

description: Library name: BJ-T, EMPTY CTR, biol rep 1


title: Whole blood DNA methylation, AA AD, 73yo M, 207215820006_R02C01


title: Whole blood DNA methylation, AA CONTROL, 71yo F, 207215820047_R04C01


title: BJ-T, WT CTR, biol rep 3

description: Library name: BJ-T, WT CTR, biol rep 3


title: BJ-T, WT CTR, biol rep 4

description: Library name: BJ-T, WT CTR, biol rep 4


title: Whole blood DNA methylation, AA CONTROL, 72yo F, 207219630048_R07C01


title: BJ-T, WT CTR, biol rep 1

description: Library name: BJ-T, WT CTR, biol rep 1


title: Whole blood DNA methylation, AA CONTROL, 66yo F, 207215830113_R04C01


title: BJ-T, EMPTY CTR, biol rep 4


title: Whole blood DNA methylation, AA AD, 90yo F, 207215820062_R08C01


title: BJ-T, EMPTY CTR, biol rep 3


title: Whole blood DNA methylation, AA AD, 63yo F, 207215830104_R07C01


title: BJ-T, EMPTY CTR, biol rep 2