title: 7G_AZA_250620, NOMe

data_processing:
Single-cell bisulfite libraries were processed using Bismark (v0.22.3) as described [Clark, S. J. et al. scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells. Nature Communications (2018)] [Clark, S. J. et al. Genome-wide base-resolution mapping of DNA methylation in single cells using single-cell bisulfite sequencing (scBS-seq). Nature Protocols  (2017)]
Following demultiplexing, samples with multiple sequencing lanes per read were concatenated into single R1 and R2 fastq files per sample (uploaded NOMeSeq files are already concatenated).
Reads were trimmed using Trim Galore (v0.6.6) with cutadapt (v1.18) to remove automatically detected illumina adaptors and the first 9 reads ‘--Clip_R1 9’ in single end mode.
Reads were then mapped by single-end non-directional alignment to Bowtie2 indexed human genome GRCh38.
Sample reads were deduplicated in single-end mode and concatenated into a single file per sample by ‘deduplicate_bismark --multiple --single’.
Methylation extraction and coverage file generation was performed separately on samples with ‘bismark_methylation_extractor --single-end --bedGraph --gzip --cx’, followed by ‘coverage2cytosine --gzip --nome --seq’.
Assembly: GRCh38
Supplementary files format and content: Bismark output file: genome-wide CpG methylation reports (CpG.cov.gz) are tab-delimited, use 1-based genomic coordinates and are in the following format: <chromosome> <position> <methylation rate>
Supplementary files format and content: Bismark output file: genome-wide GpC methylation reports (GpC.cov.gz) are tab-delimited, use 1-based genomic coordinates and are in the following format: <chromosome> <position> <methylation rate>
Supplementary files format and content: Count table (tab-deliminated) compiled from TEtranscripts results. First column contains gene (ensembl ID) and transposable element (TE) ID and column two contains hgnc symbol equiavelnt (gene IDs). Columns 3-7 contains TE information and columns 7-13  contains gene informations. Counts for individual samples are contained in column 14 onwards.
Library strategy: scNOMe-seq

value: Peripheral blood


title: Unstimulated Donor 122 Replicate 1

status: Public on Jul 21 2025

type: SRA

city: Mountain View

first: Kitt

middle: D

last: Paraiso

state: CA

address: 320 Logue Ave.

department: Bioinformatics

country: USA

institute: Cellecta, Inc.

description:
Library name: UN-1
FC348_clonotype_counts.xlsx

library_source: transcriptomic

data_processing:
Reads were then aligned to the IMGT reference database with MiXCR v4.5.0. The preset cellecta-human-rna-xcr-umi-drivermap-air to define MiXCR alignment settings was used.
The repertoire space analysis and the diversity estimation along with data visualization were performed using the immunarch package on R version 4.3.2.
Due to high reproducibility across samples of the same treatment (i.e. untreated, IST, mDC), we focused on the clonotypes with the greatest effect size and statistical significance. The following cut-offs were used to categorize a clonotype to be activated/inactivated when comparing two conditions: fold change >= 50x, false discovery rate (FDR) <= 10-5, clonotype counts (in UMI) >=20.
Assembly: IMGT
Supplementary files format and content: XLSX containing RNA read counts
Library strategy: TCR-Seq

molecule: total RNA

organism: Homo sapiens

source_name: Naive CD8+ T cell

growth_protocol: Isolated naïve CD8+ T cells were cultured in Iscove's Modified Dulbecco's medium (Corning, Ref# 10-016-CV) supplemented with 10% FBS, 1X GlutaMAX (Gibco, Ref# 35050-061), 1X Penicillin-Streptomycin Solution (Corning, Ref# 30-002-CI), and 100 mM HEPES buffer (I-10 media) in a humidified 5% CO2 atmosphere at 37°C and regularly tested for mycoplasma contamination

extract_protocol:
RNA for TCR immunoprofiling was isolated from whole cultures or highly purified MART-1-specific CD8+ T cells sorted by. flow cytometry from two combined replicates. For unsorted samples, 2 × 10⁶ cells were harvested from cultures stimulated with 100 nM MART-1-IST, MART-1-peptide-loaded mDCs, or left untreated, and RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, Cat# 74034).  For sorted MART-1-specific CD8+ T cells, 1 × 10⁷ cells from two wells with similar tetramer percentages were collected, washed, and resuspended in FACS buffer. Cells were incubated with FcR Blocking Reagent (1:50 dilution) for 10 minutes at room temperature, followed by a 15-minute incubation with MART-1-tetramer-BV421 (1:350 dilution). After washing and filtering through a cell strainer cap, approximately 2 million CD8+ MART-1-tetramer-positive cells were sorted using a BD FACSAria™ II sorter, and RNA was immediately isolated using the RNeasy Plus Micro Kit.
DriverMap™ Multiplex PCR technology uses gene-specific primers which significantly reduce the level of non-specific binding and primer-dimer amplification products, and are designed to target only TCR/BCR isoforms. Unique Molecular Identifiers (UMIs) facilitate accurate quantitation of the copy number of cDNA or DNA molecules in amplification steps, as well as detection of low abundance clonotypes and correction of amplification biases and sequencing errors. Dual-index amplicon labeling strategy minimizes index hopping during NGS allowing for comprehensive readouts. Full profiles of the antigen-recognition CDR3 region enable assessment of CDR3 length distribution, V(D)J segment usage, isotype composition for BCRs, somatic mutations, and similar characteristics with immune receptor profiling software such as MiXCR (MiLabs).
All RNA samples were shipped on dry ice to Cellecta, Inc. (Mountain View, CA) for TCR immunoprofiling analysis using the Cellecta DriverMap Adaptive Immune Receptor (AIR) system. DriverMap AIR sequencing reads quality were assessed using FastQC v0.11.9.

treatment_protocol: On day -1, PBMCs were thawed quickly in a 37°C water bath and washed twice with pre-warmed Iscove's Modified Dulbecco's medium (Corning, Ref# 10-016-CV) supplemented with 10% FBS, 1X GlutaMAX (Gibco, Ref# 35050-061), 1X Penicillin-Streptomycin Solution (Corning, Ref# 30-002-CI), and 100 mM HEPES buffer (I-10 media). On the same day, naïve CD8+ cells were isolated by immunomagnetic sorting using the naïve CD8+ T Cell Isolation Kit (Miltenyi Biotec, cat# 130-093-244) according to the manufacturer’s instructions and rested overnight in I-10 media supplemented with 5 ng/mL IL-7 (NIH) at 3 x 106 cells per mL in a flask.  Naïve CD8+ T cells activation and expansion was performed as described [32]. On day 0, cells were resuspended at 1 × 10⁶ cells/mL in I-10 media with 30 ng/mL IL-21, plated at 500K cells/well in 48-well plates, and stimulated with peptide-loaded mDCs (4:1 mDC:T ratio) or Immuno-STAT at specified concentrations for 72 hours. On day 3, cells were supplemented with fresh media containing IL-7 and IL-15 (5 ng/mL each, final concentrations). On day 7, cultures were transferred to 12-well plates and supplemented with additional media to maintain 5 ng/mL of each cytokine in a 2 mL volume. On day 10, cultures were transferred to 6-well plates, supplemented with additional media to maintain 10 ng/mL of each cytokine in a 3 mL volume. Media was exchanged every 2–3 days thereafter, maintaining 10 ng/mL IL-7 and IL-15.  For alternative cytokine conditions, cells were cultured with either IL-2 (100 U/mL) or IL-15 (10 ng/mL) at all time points (days 0, 3, 7, and beyond).

tag: cell type

value: Naive CD8+ T cell

tag: genotype

value: WT

tag: treatment

value: Unstimulated Donor 122

tag: batch


title: Comp30_24hRec_rep1

city: Münster

first: Sara

middle: A

last: Wickström

address: Röntgenstraße 20

department: Cell & Tissue Dynamics

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: scRNAseq and scATACseq

library_source: other

data_processing:
Initial transcript count and peak accessibility matrices were obtained with Cell Ranger Arc (v.1.1.2).Raw counts were subsequently imported into Python (3.8) as AnnData (0.8.0) objects. Cells with more than 25% mitochondrial RNA content were removed.
Doublet prediction on scRNA-seq data was performed using scrublet (0.2.3). Raw scRNA-seq counts were normalized using scran (1.22.1) with Leiden clustering input at resolution 0.5. scRNA-seq and scATAC-seq data were integrated as MuData objects (0.2.2) using Muon (0.1.2). Raw scATAC-seq counts were filtered for noise, and subsequently TF-IDF transformed using muon.atac.pp.tfidf with scale factor 10,000.
scRNA-seq data was further processed using scanpy (1.8.2): for 2D embedding, the expression matrix was subset to the 2,000 most highly variable genes (sc.pp.highly_variable_genes, flavor “seurat”). The top 50 principal components (PCs) were calculated, and served as basis for k-nearest neighbor calculation (sc.pp.neighbors, n_neighbors=30), which were used as input for UMAP (<https://doi.org/10.48550/arXiv.1802.03426>) layout (sc.tl.umap, min_dist=0.3).
Assembly: hg38
Supplementary files format and content: AnnData files
Library strategy: scRNAseq and scATACseq

molecule: other

source_name: iPS

growth_protocol: Human iPSCs were purchased from Allen Institute (Allen Cell Collection). Sox2-GFP tagged cells were used for experiments unless indicated otherwise. Cells were cultured on Matrigel-coated plates in mTeSR (StemCell technologies) medium.

extract_protocol:
single nuclei were harvested using Nuclei buffer and following manufacturer instructions (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit)
Single-nuclei encapsulation and library preparation were performed according to the manufacturer’s protocol (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit).

treatment_protocol: Cells were compressed for 5 or 30 min in pluripotency medium, and another group was compressed for 30min followed by 24h recovery in pluripotency-supporting media. Uncompressed cells in the respective media were used as controls (2 biological replicates/condition).

tag: cell line

value: iPS


title: COVID-19,Convalescent,individual031,Visit1

city: Ulsan

first: Jong

last: Bhak

state: Ulju-gun/Eonyang-eup

address: 50 UNIST-gil,

department: Biomedical Engineering (BME)

country: South Korea

institute: Korean Genomics Center (KOGIC)

description:
Library name: C19-R031-V1
sample_age:43,sample_sex:M,severity_scale:0,severity_class:NA

data_processing:
Raw sequencing reads were processed using Fastp (v0.23.1) to remove adapters and low-quality bases, with the following parameters: --cut_front 1 --cut_right 0 --cut_tail 1 --detect_adapter_for_pe --trim_front1 15 --trim_front2 15 --trim_tail1 0 --trim_tail2 0 --cut_mean_quality 20 --n_base_limit 1 --average_qual 20 34. Read quality was assessed before and after filtering reads using FastQC (v0.11.9).
Filtered reads were aligned to the human reference genome (GRCh38.p13) using STAR (v2.7.10b), a splice-aware aligner, with default settings.
Gene-level quantification was performed using RSEM (v1.3.3) using default options, with gene annotations from GENCODE v42 (GFF3 format).
Raw expected gene counts were normalized using the DESeq2 R package (v1.38.3). A variance stabilizing transformation (VST) was subsequently applied to the normalized counts.
Assembly: GRCh38.p13 (GENCODE v42)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

molecule: polyA RNA

source_name: Whole blood

extract_protocol:
Frozen whole blood samples collected in PAXgene® Blood RNA Tubes (PreAnalytiX, #762174) were used for total RNA extraction. RNA integrity and concentration were assessed using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific, #Q32866) and the Qubit RNA HS Assay Kit (Thermo Fisher Scientific, #Q32854). For mRNA enrichment, 200 ng of total RNA per sample was processed using the Dynabeads mRNA Purification Kit (Thermo Fisher Scientific, #01152851), which depletes rRNA and isolates polyadenylated transcripts using oligo(dT) beads.
Library preparation was performed using the MGIEasy RNA Directional Library Prep Set (MGI, #MG1000006386), following the manufacturer’s protocol. Fragment size distribution was checked using 4150 TapeStation (Agilent, #G2992A) with the cDNA D1000 ScreenTape (Agilent, #5067-5582). Final libraries were quantitated using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific, Q32866). RNA sequencing was run on DNBSEQ-T7RS (MGI) platform, generating 150 bp paired-end reads.

tag: tissue

value: Whole blood

tag: age

tag: Sex

value: Male

tag: severity scale

tag: severity class

tag: visit number


title: COVID-19,Convalescent,individual030,Visit1

description:
Library name: C19-R030-V1
sample_age:33,sample_sex:M,severity_scale:0,severity_class:NA


title: 7D_DAC_250620, NOMe

city: Newcastle

first: Heather

last: Lee

state: NSW

address: University Drive, Callaghan

country: Australia

institute: The University of Newcastle

library_source: genomic

molecule: genomic DNA

source_name: Peripheral blood

growth_protocol: AML cell line, HL-60 (ATCC #CCL-240), were maintained in tissue culture flasks (Greiner Bio-One) at 37°C, 5% CO2, and sub-cultured at 500,000 cells/mL every 2-3 days with fresh medium. HL-60 cells were maintained in Iscove′s Modified Dulbecco′s media (IMDM; Sigma-Aldrich) supplemented with 4mM GlutaMAX (Thermo Fisher Scientific) and 10% Fetal Bovine Serum (FBS; Sigma-Aldrich).

extract_protocol:
At 72 hours, viable (propidium iodide negative) single cells were isolated by Fluoresence activated cell sorting (FACS) and sorted into 2.5µL of RLT PLUS buffer (Qiagen) containing 2.5U SUPERas-In (Thermo Fisher Scientific) in LoBind 96-well full skirted plates (Eppendorf) using indexed sorting on a FACS Aria II (BD Biosciences). Plates were sealed and briefly centrifuged before storage at -80°C for sequencing analyses.
For scNMT-seq, matched scNOMe-seq and scRNA-seq libraries were prepared from sorted HL-60 single cells, as previously described (Clark, S. J. et al. scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells. Nature Communications [2018]) with minor modifications described below and within the associated manuscript.
Cell lysates were incubated with magnetic Dynabeads conjugated to the Bio-dT30VN oligonucleotide (5’- AAG CAG TGG TAT CAA CGC AGA GTA CT30VN-3’). Poly-adenylated mRNA captured on the Dynabeads underwent reverse transcription and cDNA amplification (for scRNA-seq), while genomic DNA was transferred to a new multi-well plate for bisulphite conversion (for scNOMe-seq).
For reverse transcription, Dynabeads were resuspended in 10µL reaction mix containing: 100U SuperScript II reverse transcriptase (Thermofisher), 1X First-strand buffer (Thermofisher), 2.5mM DTT (Thermofisher), 1M Betaine (Sigma-Aldrich), 9mM MgCl2 (Thermofisher), 1μM Template switching oligo (5’AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’), 1mM dNTPs (New England Biolabs) and 5U SUPERase-In RNAse inhibitor (Thermofisher). First-strand synthesis and template switching was then performed by incubating at 42 °C for 60 min, 50 °C for 30 min and 60 °C for 10 min. Amplification of cDNA was performed by adding KAPA HiFi HotStart ReadyMix (final concentration 1x, Roche sequencing) and ISPCR primer (5’-AAGCAGTGGTATCAACGCAGAGT-3’, final concentration 0.11μM) to the reverse transcription mix and amplifying as follows: 98 °C for 3 min, 23 repeats of (98 °C for 20s, 67 °C for 15 s, 72 °C for 6 min) and 72 °C for 5 min. Amplified cDNA was stored at -20 °C for later scRNA-seq library preparation.
Genomic DNA was purified using a 0.8x volume of AMPure XP beads (Beckman Coulter), and bisulphite converted using the Zymo EZ-96 DNA Methylation-Direct MagPrep Kit (Zymo Research) with halved reaction volumes. Converted DNA was eluted in first-strand synthesis mix containing: 1X Blue Buffer, 0.4mM dNTPs, 0.4 μM oligo1 - 5’CTACACGACGCTCTTCCGATCTNNNNNN 3’. Samples were incubated at 65 °C for 3 min and rapidly cooled before addition of 50 U of Klenow 3’ -> 5’ exo– (Enzymatics). The final reaction volume was 40µL, and samples were incubated as follows: 4°C 5 min, +1°C/15 s to 37°C, 37°C 30 min. Samples were heated to 95°C for 45s and rapidly cooled before addition of 2.5µL containing: 1X Blue Buffer, 0.4mM dNTPs, 0.4 μM oligo1 and 25U of Klenow 3’ -> 5’ exo–. The first strand synthesis step was then repeated (4°C 5 min, +1°C/15 s to 37°C, 37°C 30 min). In total, 5 rounds of first-strand synthesis were performed with the final round having an extended incubation for strand extension (4°C 5 min, +1°C/15 s to 37°C, 37°C 90 min). Samples were then incubated with 40 U exonuclease I (New England Bio-labs) for 1 h at 37 °C before DNA was purified using a 0.65x volume of AMPure XP beads. Samples were eluted in second-strand synthesis mix containing: 1X Blue Buffer, 0.4mM dNTP mix, 0.4 μM oligo2 (5’-TGCTGAACCGCTCTTCCGATCTNNNNNN-3’. Samples were incubated at 95°C for 45s and rapidly cooled before addition of 50 U of Klenow 3’ -> 5’ exo–. The final reaction volume was 40µL, and samples were incubated as follows: 4 °C for 5 min, +1 °C/15 s to 37 °C, 37 °C for 90 min. DNA purification was carried out using a 0.65x volume of AMPure XP bead buffer. Beads were resuspended in 1X KAPA HiFi HotStart ReadyMix with 0.2μM of i5 and i7 indexed primers from the NEBNext Multiplex Oligos for Illumina Dual Index Primer Sets (New England Biolabs, USA). Libraries were then amplified by PCR as follows: 95 °C 2 min, 12–14 repeats of (94 °C for 80 s, 65 °C for 30 s, 72 °C for 30 s), 72 °C for 3 min and 4 °C hold. Amplified libraries were purified using a 0.65x volume of AMPure XP beads and eluted in nuclease free water.
Amplified cDNA samples were quantified using Qubit dsDNA HS Assay Kit (ThermoFisher Scientific) and normalised to 0.2 ng/μL with nuclease free water before proceeding with RNA-seq library preparation. The Nextera XT DNA library preparation kit (Illumina) was used according to the manufacturer’s guidelines, but with halved reaction volumes and one in five dilutions of i5 and i7 indexed primers.

treatment_protocol: HL-60 cells were treated in suspension culture, every 24h for 72h total, with 100nM decitabine (DAC; Selleckchem #S1200) or with 2000nM azacytidine (AZA; Selleckchem # S1782). Untreated cells (UNT) were given an equal volume of 0.1% DMSO in UltraPure™ DNase/RNase-Free Distilled Water (Thermo Fisher Scientific) and served as a negative control.

value: promyeloblast

tag: disease/cancer type

value: Acute promyelocytic leukemia

value: Female

value: decitabine


title: Comp30min_rep2

description: scRNAseq and scATACseq


title: COVID-19,Convalescent,individual035,Visit1

description:
Library name: C19-R035-V1
sample_age:22,sample_sex:F,severity_scale:0,severity_class:NA


title: 8A_DAC_250620, NOMe


title: CNL_rep2

description: scRNAseq and scATACseq

value: control


title: Comp30min_rep1

description: scRNAseq and scATACseq


title: CNL_rep1

description: scRNAseq and scATACseq


title: iPS_HyperPluri_TTseq_rep3

data_processing:
Trimmed reads were aligned to the human genome assembly (hg38) using STAR2.4.2 68.
For coverage profiles and visualization, reads were uniquely mapped, de-stranded, antisense corrected. Counts were generated from HTSeq. Counts from the forward strand were included with labelled and unlabelled ERCC spike-in counts, which can subsequently be used for normalization.
Assembly: hg38
Supplementary files format and content: non-normalized HTSeq counts
Library strategy: TT-seq

growth_protocol: Human iPSCs were purchased from Allen Institute (Allen Cell Collection). Sox2-GFP tagged cells were used for experiments unless indicated otherwise. Cells were cultured on Matrigel-coated plates in mTeSR (StemCell technologies) medium and placed in E6 basal medium (Gibco) directly at the onset of experiments wherever indicated.

extract_protocol:
After treatment, cells were harvested and lysed with Trizol. ERCC spike-ins (00043, 00170, 00136) were added to lysates after which RNA was isolated, fragmented and biotinylated with EZ-link HPDP-biotin (Thermo Fischer. Biotinylated nascent RNAs were purified with streptavidin-conjugated magnetic beads (µMACS; Miltenyi) and libraries of total and biotinylated RNA were prepared with Illumina TruSeq total RNA kit. Libraries were quantified using the KAPA Library Quantification Kit and sequenced with Illumina NextSeq 500 using the High Output Kit v2.5 (150 cycles, Illumina) for 2 × 75 bp paired-end reads.
Libraries of biotinylated RNA were prepared with Illumina TruSeq total RNA kit. Libraries were quantified using the KAPA Library Quantification Kit and sequenced with Illumina NextSeq 500 using the High Output Kit v2.5 (150 cycles, Illumina) for 2 × 75 bp paired-end reads.

treatment_protocol: Human iPS cells were compressed for 30min either in pluripotency growth factor supplemented media or basal media without growth factor supplementation. As a control for osmotic regulation, a condition of hypertonic shock for 30min was included. Cells were labeled with 500 µM 4‐thiouridine (4sU) for the last 10 min of the indicated 30 min treatments. Labeled and unlabeled RNA was extracted and libraries were prepared. Labeled RNA was sequenced.


title: 7C_DAC_250620, NOMe


title: 7B_DAC_250620, NOMe


title: iPS_HyperPluri_TTseq_rep1


title: Unstimulated Donor 86 Replicate 3

description:
Library name: UN_3_S67
FC345_clonotype_counts.xlsx

value: Unstimulated Donor 86


title: iPS_HyperPluri_TTseq_rep2


title: COVID-19,Convalescent,individual029,Visit1

description:
Library name: C19-R029-V1
sample_age:31,sample_sex:F,severity_scale:0,severity_class:NA


title: 7A_DAC_250620, NOMe


title: COVID-19,Convalescent,individual028,Visit1

description:
Library name: C19-R028-V1
sample_age:44,sample_sex:M,severity_scale:0,severity_class:NA


title: iPS_ComprPluri_TTseq_rep3


title: Comp30_24hRec_rep2

description: scRNAseq and scATACseq


title: iPS_ComprPluri_TTseq_rep2


title: iPS_ComprPluri_TTseq_rep1


title: 6H_AZA_250620, NOMe

value: azacytidine


title: COVID-19,Convalescent,individual028,Visit5

description:
Library name: C19-R028-L1
sample_age:45,sample_sex:M,severity_scale:0,severity_class:NA


title: iPS_ComprBasal_TTseq_rep3


title: 7E_AZA_250620, NOMe


title: iPS_ComprBasal_TTseq_rep2


title: COVID-19,Convalescent,individual027,Visit1

description:
Library name: C19-R027-V1
sample_age:25,sample_sex:M,severity_scale:0,severity_class:NA


title: 6G_AZA_250620, NOMe


title: iPS_ComprBasal_TTseq_rep1


title: 6F_AZA_250620, NOMe


title: iPS_PluriCnl_TTseq_rep3


title: COVID-19,Convalescent,individual030,Visit5

description:
Library name: C19-R030-L1
sample_age:34,sample_sex:M,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual026,Visit1

description:
Library name: C19-R026-V1
sample_age:36,sample_sex:M,severity_scale:0,severity_class:NA


title: 6E_AZA_250620, NOMe


title: COVID-19,Convalescent,individual025,Visit1

description:
Library name: C19-R025-V1
sample_age:48,sample_sex:F,severity_scale:0,severity_class:NA


title: iPS_PluriCnl_TTseq_rep1


title: iPS_PluriCnl_TTseq_rep2


title: iPS_BasalCnl_TTseq_rep3


title: iPS_BasalCnl_TTseq_rep2


title: iPS_BasalCnl_TTseq_rep1


title: 6C_DAC_250620, NOMe


title: COVID-19,Convalescent,individual036,Visit1

description:
Library name: C19-R036-V1
sample_age:39,sample_sex:F,severity_scale:0,severity_class:NA


title: HyperBasal_24hr_rep1

data_processing:
Unmapped paired-end reads were trimmed to remove adapters and poor-quality sequences using fastp v0.23.2 and subsequently filtered for a quality score of at least 20. Paired-end reads were mapped to the human genome hg38 using bwa-mem2 v.2.2.1 using default settings.
Filtered reads were mapped to the GRCh38 reference genome merged with ERCC92 spike-in sequence reference using STAR (2.7.10a) (--outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outFilterMultimapNmax 1 --winAnchorMultimapNmax 50 --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1500000 --alignMatesGapMax 1500000 --chimSegmentMin 15 --chimOutType WithinBAM --outSAMattributes All). Gene expression counts were generated from mapped reads using Gencode v35 and ERCC92 annotations with htseq-count (2.0.3). Raw counts produced from HTSeq-count were transformed to variance-stabilized counts (VST) using DESeq2 and subsequently annotated with ENSEMBL IDs.
Assembly: hg38

growth_protocol: Human iPSCs were purchased from Allen Institute (Allen Cell Collection). Sox2-GFP tagged cells were used for experiments unless indicated otherwise. Cells were cultured on Matrigel-coated plates in mTeSR (StemCell technologies) medium and placed in E6 basal medium (Gibco) directly at the onset of experiments wherever indicated. TGFβ1 (5 ng/mL) and bFGF (100 ng/mL) were purchased from StemCell Technologies and were supplemented to basal media where indicated.

extract_protocol:
Total RNA was isolated using the NucleoSpin RNA Plus kit (Macherey&Nagel). After quantification and quality control using Agilent 2200 TapeStation, total RNA amounts were adjusted.
libraries were prepared using the TruSeq Stranded Total RNA kit with Ribo- zero gold rRNA depletion (Illumina). RNA sequencing was carried out on Illumina NextSeq 500 using the High Output Kit v2.5 (150 cycles, Illumina) for 2 × 75 bp paired-end reads

treatment_protocol: Human iPS cells were compressed for 30min either in pluripotency growth factor supplemented media or basal media without growth factor supplementation. As a control for osmotic regulation, a condition of hypertonic shock for 30min was included for both media conditions. After 24 hours recovery from 30min treatments, cells were lysed and RNA collected.


title: 6B_DAC_250620, NOMe


title: HyperPluri_24hr_rep1


title: HyperPluri_24hr_rep2


title: 6A_DAC_250620, NOMe


title: BasalCompr_24hr_rep3


title: 5H_AZA_250620, NOMe


title: COVID-19,Convalescent,individual022,Visit1

description:
Library name: C19-R022-V1
sample_age:59,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual021,Visit1

description:
Library name: C19-R021-V1
sample_age:47,sample_sex:M,severity_scale:0,severity_class:NA


title: 5G_AZA_250620, NOMe


title: COVID-19,Convalescent,individual020,Visit1

description:
Library name: C19-R020-V1
sample_age:44,sample_sex:F,severity_scale:0,severity_class:NA


title: BasalCnl_24hr_rep3


title: BasalCnl_24hr_rep2


title: 5F_AZA_250620, NOMe


title: BasalCnl_24hr_rep1


title: COVID-19,Convalescent,individual024,Visit1

description:
Library name: C19-R024-V1
sample_age:44,sample_sex:F,severity_scale:0,severity_class:NA


title: 6D_DAC_250620, NOMe


title: HyperBasal_24hr_rep2


title: PluriComp_24hr_rep2


title: COVID-19,Convalescent,individual024,Visit5

description:
Library name: C19-R024-L1
sample_age:45,sample_sex:F,severity_scale:0,severity_class:NA


title: 5E_AZA_250620, NOMe


title: COVID-19,Convalescent,individual019,Visit1

description:
Library name: C19-R019-V1
sample_age:57,sample_sex:M,severity_scale:0,severity_class:NA


title: 5D_DAC_250620, NOMe


title: PluriComp_24hr_rep1


title: COVID-19,Convalescent,individual018,Visit1

description:
Library name: C19-R018-V1
sample_age:48,sample_sex:M,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual017,Visit1

description:
Library name: C19-R017-V1
sample_age:28,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual023,Visit1

description:
Library name: C19-R023-V1
sample_age:33,sample_sex:F,severity_scale:0,severity_class:NA


title: PluriCnl_24hr_rep2


title: BasalCompr_24hr_rep2


title: iPS_HyperPluri_H3K27ac_rep1

data_processing:
Unmapped paired-end reads were trimmed to remove adapters and poor-quality sequences using fastp v0.23.2 (--detect_adapter_for_pe). Paired-end reads were mapped to GRCh38 and Drosophila melanogaster (GCF_000001215.4_release_6_plus_iso1_mt) reference genomes using bwa-mem2 v.2.2.1 with default settings.
To define active enhancers and promoters, we performed peak calling using the callpeak function (“-f BAMPE -g hs -q 1e-5 --keep-dup all –nomodel”) from MACS2 (2.2.7.1) 62. PCR duplicates were removed using sambamba (v 1.0.1) 63 and the IgG negative control from the CBX2 Cut & Run experiment (see GSE267743) was used for estimating background. The final processed files are H3K27acenriched genomic regions from all experimental conditions and with peaks closer than 1 kb merged together, and peaks overlapping with the ENCODE blacklisted genomic regions discarded.
Assembly: hg38
Library strategy: CUT&Tag

extract_protocol:
Cells were collected from 10 cm dishes by brief incubation at 37℃ in 0.05M EDTA in HBSS to promote detachment followed by cell scraping. Briefly, cells were attached to Concanavalin-A-conjugated magnetic beads (ConA beads, Polysciences) before overnight binding of primary antibody H3K27ac (Abcam, ab4729). Samples were then incubated with secondary antibody and CUT&Tag-ITAssembled pA-Tn5 Transposomes, after which tagmented DNA was purified
This DNA was PCR amplified using a unique combination of i5/i7 indexing primers for each sample, cleaned using SPRI beads and pooled into an equimolar library for sequencing on an Illumina NextSeq 500 sequencing platform.

treatment_protocol: Human iPS cells were compressed for 30min either in pluripotency growth factor supplemented media or basal media without growth factor supplementation. As a control for osmotic regulation, a condition of hypertonic shock for 30min was included. At 30min, samples were collected to perform H3K27ac CUT&Tag.

value: Hypertonic Pluripotency


title: PluriCnl_24hr_rep1


title: COVID-19,Convalescent,individual016,Visit1

description:
Library name: C19-R016-V1
sample_age:28,sample_sex:M,severity_scale:0,severity_class:NA


title: 5B_DAC_250620, NOMe


title: iPS_BasalComp_H3K27ac_rep2

value: Compressed Basal


title: COVID-19,Convalescent,individual015,Visit1

description:
Library name: C19-R015-V1
sample_age:51,sample_sex:M,severity_scale:0,severity_class:NA


title: iPS_BasalComp_H3K27ac_rep1


title: HyperPluri_24hr_rep3


title: COVID-19,Convalescent,individual014,Visit1

description:
Library name: C19-R014-V1
sample_age:56,sample_sex:M,severity_scale:0,severity_class:NA


title: BasalCompr_24hr_rep1


title: iPS_BasalCnl_H3K27ac_rep2

value: Control Basal


title: PluriCnl_24hr_rep3


title: 5A_DAC_250620, NOMe

value: Peripheral blood


title: COVID-19,Convalescent,individual013,Visit1

description:
Library name: C19-R013-V1
sample_age:44,sample_sex:M,severity_scale:0,severity_class:NA


title: iPS_PluriComp_H3K27ac_rep2

value: Compressed Pluripotency


title: 4H_AZA_250620, NOMe


title: iPS_BasalCnl_H3K27ac_rep1


title: iPS_PluriComp_H3K27ac_rep1


title: iPS_PluriCnl_H3K27ac_rep1

value: Control Pluripotency


title: COVID-19,Convalescent,individual012,Visit1

description:
Library name: C19-R012-V1
sample_age:37,sample_sex:M,severity_scale:0,severity_class:NA


title: 4F_AZA_250620, NOMe


title: iPS_HyperPluri_H3K27ac_rep2


title: 5C_DAC_250620, NOMe


title: COVID-19,Convalescent,individual011,Visit1

description:
Library name: C19-R011-V1
sample_age:29,sample_sex:F,severity_scale:0,severity_class:NA


title: Pluri_cnl_rep2

data_processing:
Raw FASTQ files were adapter-trimmed and quality-filtered using fastp (0.23.2) using default settings and the “—detect_adapter_for_pe” flag. Filtered reads were mapped to the GRCh38 and E.coli (ASM886v2) reference genome using bwa-mem2 (2.2.1). Mapped reads were quality-filtered using a cutoff of 3. Scaling-factor normalized tracks were generated according to Zheng et al. (dx.doi.org/10.17504/protocols.io.bjk2kkye). Regions were blacklisted using published CUT&RUN blacklists 60.
Coverage profiles for IgG and CBX2 were generated using MACS2 (2.2.9.1). Normalisation to IgG was performed using MACS2 “bdgcmp” and the “qpois” method, and peak calls were obtained using MACS2 “bdgbroadcall” (-c 5 -C 2 -g 1000 -G 2000 --no-trackline). Peaks were filtered for noise using reproducibility (called in > 1 sample of the same condition), minimum peak size (> 1000bp), and minimum mean CBX2 signal in one condition (>0.075).
Assembly: hg38
Supplementary files format and content: Normalized Tracks bigWig
Library strategy: CUT&Run

extract_protocol:
Briefly, 5000 0000 cells/replicate were harvested and absorbed with activated ConA beads, followed by incubation with 0.5 µg of Cbx2 antibody (mAb #25069, Cell signaling) overnight at +4. Chromatin was then digested and released followed by DNA purification.
Library prep was performed using the CUTANA Cut&Run Library Prep Kit (EpiCypher)

treatment_protocol: Cells were compressed from 30 min in basal or pluripotency medium followed by 24h recovery in the same media condition. Uncompressed cells in the respective media were used as controls (2 biological replicates/condition).

value: Pluripotency Control


title: 4E_AZA_250620, NOMe


title: 4G_AZA_250620, NOMe


title: COVID-19,Convalescent,individual010,Visit1

description:
Library name: C19-R010-V1
sample_age:38,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual010,Visit5

description:
Library name: C19-R010-L1
sample_age:39,sample_sex:F,severity_scale:0,severity_class:NA


title: 4D_DAC_250620, NOMe


title: CompPluri_rep3

value: iPS

value: Compressed Pluripotency Recovery


title: Pluri_cnl_rep3


title: CompPluri_rep2


title: CompPluri_rep1


title: 4C_DAC_250620, NOMe


title: Basal_cnl_rep3

value: Basal Control


title: COVID-19,Convalescent,individual009,Visit1

description:
Library name: C19-R009-V1
sample_age:56,sample_sex:M,severity_scale:0,severity_class:NA

value: Whole blood

value: Male


title: iPS_PluriCnl_H3K27ac_rep2


title: Basal_cnl_rep2


title: Basal_cnl_rep1


title: 4A_DAC_250620, NOMe

value: promyeloblast

value: Acute promyelocytic leukemia

value: Female


title: COVID-19,Convalescent,individual008,Visit1

description:
Library name: C19-R008-V1
sample_age:31,sample_sex:F,severity_scale:0,severity_class:NA


title: CompBasal_rep2

value: Compressed Basal Reco


title: 4B_DAC_250620, NOMe

value: decitabine


title: IgG_cnl

value: IgG control


title: CompBasal_rep1


title: COVID-19,Convalescent,individual007,Visit1

description:
Library name: C19-R007-V1
sample_age:63,sample_sex:F,severity_scale:0,severity_class:NA


title: 3H_AZA_250620, NOMe

value: azacytidine


title: ChIP_H3K27me3_H295R_rep1

city: Houston

first: H. Courtney

last: Hodges

state: TX

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

description: H3K27me3 ChIP-seq in H295R cells

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using Bowtie v2.4.1.
Fragments with read qualities greater than 10 were considered for further analysis.
All bigWig files are unscaled counts and require scaling before comparison across samples.
Assembly: hg38
Supplementary files format and content: Unscaled bigWig files of genome-wide coverage

growth_protocol: H295R Cells were cultured in DMEM: F12 medium (ATCC) supplemented with 2.5% of Nu-serum (Corning), 1% ITS (Corning) and 1% penicillin/streptomycin (PS)

extract_protocol:
Lysates were obtained from sonicated nuclei crosslinked with either 1% formaldehyde and 2 mM disuccinimidyl glutarate (double cross-linking) for SWI/SNF subunits and β-catenin, or 1% formaldehyde alone (single cross-linking) for all other targets. Protein-DNA complexes were isolated by immunoprecipitation.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with either either DMSO or 1 uM BRM014 for 1 h, "none" indicates no treatment was performed.

tag: chip antibody

value: Anti-H3K27me3, Active Motif #39155

value: WT


title: COVID-19,Convalescent,individual005,Visit1

description:
Library name: C19-R005-V1
sample_age:60,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual006,Visit1

description:
Library name: C19-R006-V1
sample_age:58,sample_sex:F,severity_scale:0,severity_class:NA


title: ChIP_CTCF_H295R_rep1

description: CTCF ChIP-seq in H295R cells

value: Anti-CTCF, Millipore #07-729


title: Pluri_cnl_rep1


title: 3F_AZA_250620, NOMe

value: Peripheral blood


title: COVID-19,Convalescent,individual004,Visit1

description:
Library name: C19-R004-V1
sample_age:53,sample_sex:F,severity_scale:0,severity_class:NA


title: ChIP_SMARCA4_H295R_rep1

description: SMARCA4 ChIP-seq in H295R cells

value: Anti-SMARCA4, Proteintech #21634-1AP


title: 3G_AZA_250620, NOMe


title: 3E_AZA_250620, NOMe


title: COVID-19,Convalescent,individual003,Visit1

description:
Library name: C19-R003-V1
sample_age:59,sample_sex:F,severity_scale:0,severity_class:NA


title: 3D_DAC_250620, NOMe


title: ChIP_PBRM1_H295R_rep1

description: PBRM1 ChIP-seq in H295R cells

value: Anti-PBRM1, Bethyl Laboratories #A301591A


title: ChIP_BRD9_H295R_rep1

description: BRD9 ChIP-seq in H295R cells

value: Anti-BRD9, Abcam #ab137245


title: COVID-19,Convalescent,individual002,Visit1

description:
Library name: C19-R002-V1
sample_age:63,sample_sex:M,severity_scale:0,severity_class:NA


title: ChIP_ARID1A_H295R_rep1

description: ARID1A ChIP-seq in H295R cells

value: Anti-ARID1A, Cell Signaling Technology #12354S


title: COVID-19,Convalescent,individual001,Visit1

description:
Library name: C19-R001-V1
sample_age:65,sample_sex:F,severity_scale:0,severity_class:NA

value: Whole blood


title: ChIP_Bcat_H295R_BRM014_rep2

description: β-catenin ChIP-seq in H295R cells treated with BRM014

value: Anti-β-catenin ,Invitrogen #71-2700


title: ChIP_H3K27ac_H295R_rep1

description: H3K27ac ChIP-seq in H295R cells

value: Anti-H3K27ac, Abcam #ab4729


title: ChIP_Bcat_H295R_DMSO_rep2

description: β-catenin ChIP-seq in H295R cells treated with DMSO

value: DMSO


title: ChIP_Bcat_H295R_DMSO_rep1


title: COVID-19,Convalescent,individual001,Visit5

description:
Library name: C19-R001-L1
sample_age:66,sample_sex:F,severity_scale:0,severity_class:NA

value: Female


title: 3B_DAC_250620, NOMe

value: promyeloblast

value: Acute promyelocytic leukemia


title: ChIP_SF1_H295R_BRM014_rep2

description: SF-1 ChIP-seq in H295R cells treated with BRM014

value: Anti-SF-1, R&D Systems #PPN16650C


title: 3C_DAC_250620, NOMe

value: decitabine


title: COVID-19,Hospitalized,patient061,Visit3

description:
Library name: C19-C061-V3
sample_age:25,sample_sex:F,severity_scale:0,severity_class:NA


title: ChIP_H3K4me1_H295R_rep1

description: H3K4me1 ChIP-seq in H295R cells

value: Anti-H3K4me1, Abcam #ab8895


title: ChIP_H3K4me3_H295R_rep1

description: H3K4me3 ChIP-seq in H295R cells

value: Anti-H3K4me3, EMD Millipore #05-745-R

value: WT


title: 3A_DAC_250620, NOMe

value: Peripheral blood


title: ChIP_SF1_H295R_BRM014_rep1


title: ChIP_Bcat_H295R_BRM014_rep1


title: 2H_AZA_250620, NOMe

value: azacytidine


title: ATAC_H295R_BRM014_rep2

description: ATAC-seq in H295R cells treated with BRM014

data_processing:
ATAC-seq reads were aligned to the hg38 genome assembly using Bowtie v2.4.1.
Fragments with read qualities greater than 10 were considered for further analysis. 200 bp pseudofragments were created at the positions corresponding to the transposition sites, and peak calls were made using MACS 2.1.2 without modeling of fragment size. Reads within peaks were counted using bedtools.
The table of all counts was processed using DESeq2, using default parameters.
Bigwig files were created based on 200 bp pseudofragments, with intermediate files created using bedtools 2.28.0. All bigWig files are unscaled and require scaling before comparison across samples.
Assembly: hg38
Supplementary files format and content: Unscaled bigWig files of genome-wide coverage

extract_protocol:
Nuclei were permeabilized and transposed according to the Omni-ATAC protocol.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with either 1 µM BRM014 or an equivalent volume of DMSO for 1 hour prior to library construction.


title: ATAC_H295R_DMSO_rep2

description: ATAC-seq in H295R cells treated with DMSO


title: ChIP_SF1_H295R_DMSO_rep2

description: SF-1 ChIP-seq in H295R cells treated with DMSO


title: COVID-19,Hospitalized,patient061,Visit2

description:
Library name: C19-C061-V2
sample_age:25,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Hospitalized,patient060,Visit2

description:
Library name: C19-C060-V2
sample_age:26,sample_sex:F,severity_scale:0,severity_class:NA


title: ChIP_SF1_H295R_DMSO_rep1


title: ATAC_H295R_BRM014_rep1


title: COVID-19,Hospitalized,patient060,Visit3

description:
Library name: C19-C060-V3
sample_age:26,sample_sex:F,severity_scale:0,severity_class:NA


title: H12_HL60_colonies_rep3, RNA

data_processing:
bisulfite libraries were processed using Bismark (v0.22.3) and as previously described [Hunt, K. V. et al. sTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs. Scientific Reports (2022)] [Hunt, K. V. et al.  Protocol for targeted analysis of transposable element methylation levels and transcriptome in single cells using scTEM-seq. Protocol Exchange  (2022)].
After initial demultiplexing of primary Illumina indexes, Cutadapt (v2.10) [18] was used to demultiplex pools based on custom secondary indexes
Commands –g and -G were used to pass named forward and reverse index lists as a .fasta file to Cutadapt for demultiplexing
Bisulfite reads were trimmed using Trim Galore (v0.6.5). 10bp was trimmed from both the 5’ and 3’ ends to remove oligo sequences from reads.
Reads were mapped to Bowtie2 (v 2.4.1) indexed human genome (GRCh38) non-directionally and as paired end using Bismark (v0.22.3)
The methylation extraction module from Bismark was then used to produce coverage files (.cov) for methylation analysis.
Assembly: GRCh38
Supplementary files format and content: Bismark output file: genome-wide CpG methylation reports (CpG.cov.gz) are tab-delimited, use 1-based genomic coordinates and are in the following format: <chromosome> <position> <methylation rate>
Following demultiplexing, squencing runs with multiple sequencing lanes per read were concatenated into single R1 and R2 fastq files, per sample using zcat and gzip.
Raw reads were trimmed in pair-end mode using Trim Galore (v0.6.5) and Cutadapt (v2.10), retaining unpaired reads.
Hisat2 (v2.1.0) was used to map and align trimmed and unpaired reads using default parameters (--phred33) to the human reference genome build (GRCh38), and samtools (v1.10) was used to sort by coordinate and generate bam files.
TEtranscripts (v2.2.1) was used to obtain raw gene and transposable element countreateds from unique and ambiguously aligned reads (bam files) using TEcountreated with the flags '--sortByPos --mode multi’. The GTF files used were generated as follows: 1) TEs (http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/rmsk.txt.gz; USCS repeating element Repeat Masker; hg38; 2021-09-03) and 2) genes (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_30/gencode.v30.annotation.gtf.gz; gencode Release 30; GRCh38.p12; 2019-04-08). To ensure the GTF files worked with TEtranscripts the gene GTF (from gencode) was updated by converting ‘M’ to ‘MT’ for mitochondrial genes in the chromosome column and removal of ‘Chr’ preceding each chromosome number. The TE GTF was generated from the repeat mask file  using the conversion tool from the TEtranscripts developers (http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/makeTEgtf.pl.gz) ‘perl makeTEgtf.pl -c 6 -s 7 -e 8 -o 10 -t 11 -n hg38_rmsk -f 13 -C 12 -S 2 rmsk.txt >> hg38_rmsk_TE.gtf’ and removing ‘chr’ from chromosome names ‘sed 's/chr//' hg38_rmsk_TE.gtf > hg38_rmsk_TE_NoChr.gtf’.    TEtranscripts the gene GTF (from gencode) was updated by converting ‘M’ to ‘MT’ for mitochondrial
Individual sample counts from TEtranscripts were collated into a single countreated table (tab-deliminated) and updated with relevant gene information from the gene GTF file.
Assembly: GRCh38
Supplementary files format and content: Count table (tab-deliminated) compiled from TEtranscripts results. First column contains gene (ensembl ID) and transposable element (TE) ID and column two contains hgnc symbol equiavelnt (gene IDs). Columns 3-7 contains TE information and columns 7-13  contains gene informations. Countreateds for individual samples are contained in column 14 onwards.

growth_protocol:
Cell lines were maintained in tissue culture flasks (Greiner Bio-One) at 37°C, 5% CO2, and sub-cultured at 500,000 cells/mL every 2-3 days with fresh medium.  HL-60 cells were maintained in Iscove's Modified Dulbecco's media supplemented with 4mM GlutaMAX and 10% Fetal Bovine Serum (FBS). MOLM-13 and MV-4-11 cells were maintained in Roswell Park Memorial Institute 1640 media supplemented with 2mM GlutaMAX and 10% FBS.
Treated cells were seeded in MethoCult Optimum (H4034; STEMCELL Technologies Inc.) at 500 cells/well in 6-well plates. Cells were then cultured at 37°C, 5% CO2 for 14 days to allow colony formation. Wells containing colonies were imaged using Cytation3 (Biotek). Individual colonies were manually plucked using a 20µL pipette tip into 100µL of media, centrifuged at 200xg for 5 mins, and then resuspended in 20µL of RLT PLUS buffer before storage at −80°C.

extract_protocol:
Individual colonies were manually plucked using a 20µL pipette tip into 100µL of media, centrifuged at 200xg for 5 mins, and then resuspended in 20µL of RLT PLUS buffer before storage at −80°C. Lysates from single colonies (HL-60: 7.5µL; MOLM-13 and MV-4-11: 2.5µL) were used to separate genomic DNA and mRNA by G&T separation and as previously described following 'scTEM-seq for low-input samples' [Hunt, K. V. et al. sTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs. Scientific Reports (2022)] [Hunt, K. V. et al.  Protocol for targeted analysis of transposable element methylation levels and transcriptome in single cells using scTEM-seq. Protocol Exchange  (2022)].
Single colony TEM-seq and parallel RNA-seq analysis was performed as described, with minor modifications. During single colony TEM-seq library preparation, the number of SINE Alu amplification cycles was reduced to 29. For RNA-seq analysis, 15 cycles of cDNA amplification were used. [Hunt, K. V. et al.  Protocol for targeted analysis of transposable element methylation levels and transcriptome in single cells using scTEM-seq. Protocol Exchange  (2022)]

treatment_protocol: Cell lines were treated with HMAs at various doses in suspension culture, every 24h for 72h total. All cell lines were treated with 100nM decitabine (DAC; Selleckchem #S1200), HL-60 cells were treated with 2000nM azacytidine (AZA; Selleckchem # S1782), and MOLM-13 and MV-4-11 cells were treated with 500nM AZA. Untreated cells (UNT) were given an equal volume of 0.1% DMSO in UltraPure™ DNase/RNase-Free Distilled Water (Thermo Fisher Scientific) and served as a control.

tag: paired sample_id

tag: processing protocol

value: RNA-Seq

value: untreated


title: H11_HL60_colonies_rep3, RNA


title: 2E_AZA_250620, NOMe


title: H9_HL60_colonies_rep3, RNA


title: ATAC_H295R_DMSO_rep1


title: 2G_AZA_250620, NOMe


title: H10_HL60_colonies_rep3, RNA


title: H8_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient059,Visit3

description:
Library name: C19-C059-V3
sample_age:52,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate

value: Male

value: Mild-Moderate


title: COVID-19,Hospitalized,patient058,Visit2

description:
Library name: C19-C058-V2
sample_age:42,sample_sex:M,severity_scale:4,severity_class:Severe-Critical

value: Whole blood

value: Severe-Critical


title: 2B_DAC_250620, NOMe


title: 2D_DAC_250620, NOMe


title: COVID-19,Hospitalized,patient059,Visit1

description:
Library name: C19-C059-V1
sample_age:52,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient058,Visit3

description:
Library name: C19-C058-V3
sample_age:42,sample_sex:M,severity_scale:4,severity_class:Severe-Critical


title: H6_HL60_colonies_rep3, RNA


title: 2C_DAC_250620, NOMe


title: H4_HL60_colonies_rep3, RNA


title: 2A_DAC_250620, NOMe


title: 1H_Unt_250620, NOMe


title: G12_HL60_colonies_rep3, RNA


title: G11_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient058,Visit1

description:
Library name: C19-C058-V1
sample_age:42,sample_sex:M,severity_scale:4,severity_class:Severe-Critical


title: H3_HL60_colonies_rep3, RNA


title: H2_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient057,Visit3

description:
Library name: C19-C057-V3
sample_age:47,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient057,Visit2

description:
Library name: C19-C057-V2
sample_age:47,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: H1_HL60_colonies_rep3, RNA


title: 2F_AZA_250620, NOMe


title: 1G_Unt_250620, NOMe


title: G9_HL60_colonies_rep3, RNA


title: 1F_Unt_250620, NOMe


title: G10_HL60_colonies_rep3, RNA


title: G8_HL60_colonies_rep3, RNA


title: G5_HL60_colonies_rep3, RNA


title: 1E_Unt_250620, NOMe


title: 1D_Unt_250620, NOMe


title: G4_HL60_colonies_rep3, RNA


title: G6_HL60_colonies_rep3, RNA


title: G7_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient056,Visit2

description:
Library name: C19-C056-V2
sample_age:40,sample_sex:F,severity_scale:0,severity_class:NA


title: G3_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient056,Visit3

description:
Library name: C19-C056-V3
sample_age:40,sample_sex:F,severity_scale:0,severity_class:NA


title: 1B_Unt_250620, NOMe


title: G2_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient055,Visit3

description:
Library name: C19-C055-V3
sample_age:49,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Hospitalized,patient055,Visit2

description:
Library name: C19-C055-V2
sample_age:49,sample_sex:F,severity_scale:0,severity_class:NA


title: 1C_Unt_250620, NOMe


title: H5_HL60_colonies_rep3, RNA


title: F12_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient054,Visit3

description:
Library name: C19-C054-V3
sample_age:24,sample_sex:F,severity_scale:3,severity_class:Severe-Critical


title: F10_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient054,Visit2

description:
Library name: C19-C054-V2
sample_age:24,sample_sex:F,severity_scale:3,severity_class:Severe-Critical


title: 12H_Neg_250620, NOMe

value: control


title: F9_HL60_colonies_rep3, RNA

value: Female


title: F8_HL60_colonies_rep3, RNA

value: promyeloblast


title: F7_HL60_colonies_rep3, RNA

value: Acute promyelocytic leukemia


title: COVID-19,Hospitalized,patient054,Visit1

description:
Library name: C19-C054-V1
sample_age:24,sample_sex:F,severity_scale:3,severity_class:Severe-Critical


title: F6_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient053,Visit3

description:
Library name: C19-C053-V3
sample_age:68,sample_sex:F,severity_scale:0,severity_class:NA


title: 12F_Unt_250620, NOMe


title: F5_HL60_colonies_rep3, RNA


title: 12E_Unt_250620, NOMe


title: COVID-19,Hospitalized,patient053,Visit2

description:
Library name: C19-C053-V2
sample_age:68,sample_sex:F,severity_scale:0,severity_class:NA


title: F3_HL60_colonies_rep3, RNA


title: F4_HL60_colonies_rep3, RNA


title: F2_HL60_colonies_rep3, RNA


title: G1_HL60_colonies_rep3, RNA


title: 12D_Unt_250620, NOMe


title: COVID-19,Hospitalized,patient052,Visit3

description:
Library name: C19-C052-V3
sample_age:28,sample_sex:M,severity_scale:0,severity_class:NA


title: COVID-19,Hospitalized,patient057,Visit1

description:
Library name: C19-C057-V1
sample_age:47,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: F11_HL60_colonies_rep3, RNA


title: F1_HL60_colonies_rep3, RNA


title: 1A_Neg_250620, NOMe


title: COVID-19,Hospitalized,patient052,Visit2

description:
Library name: C19-C052-V2
sample_age:28,sample_sex:M,severity_scale:0,severity_class:NA


title: E10_HL60_colonies_rep3, RNA


title: 12C_Unt_250620, NOMe


title: COVID-19,Hospitalized,patient051,Visit3

description:
Library name: C19-C051-V3
sample_age:28,sample_sex:M,severity_scale:0,severity_class:NA


title: E12_HL60_colonies_rep3, RNA


title: 12G_Unt_250620, NOMe


title: E11_HL60_colonies_rep3, RNA


title: E8_HL60_colonies_rep3, RNA


title: E9_HL60_colonies_rep3, RNA


title: 12B_Unt_250620, NOMe


title: E7_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient051,Visit2

description:
Library name: C19-C051-V2
sample_age:28,sample_sex:M,severity_scale:0,severity_class:NA


title: E6_HL60_colonies_rep3, RNA


title: E5_HL60_colonies_rep3, RNA


title: 11H_AZA_250620, NOMe


title: COVID-19,Hospitalized,patient050,Visit3

description:
Library name: C19-C050-V3
sample_age:30,sample_sex:M,severity_scale:0,severity_class:NA


title: E4_HL60_colonies_rep3, RNA


title: E2_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient050,Visit2

description:
Library name: C19-C050-V2
sample_age:30,sample_sex:M,severity_scale:0,severity_class:NA


title: E3_HL60_colonies_rep3, RNA


title: 11G_AZA_250620, NOMe


title: 11F_AZA_250620, NOMe


title: E1_HL60_colonies_rep3, RNA


title: D12_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient049,Visit3

description:
Library name: C19-C049-V3
sample_age:53,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient049,Visit2

description:
Library name: C19-C049-V2
sample_age:53,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: D10_HL60_colonies_rep3, RNA


title: D11_HL60_colonies_rep3, RNA


title: 11D_DAC_250620, NOMe


title: 12A_Unt_250620, NOMe


title: 11E_AZA_250620, NOMe


title: D8_HL60_colonies_rep3, RNA


title: 11C_DAC_250620, NOMe


title: D7_HL60_colonies_rep3, RNA


title: D9_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient049,Visit1

description:
Library name: C19-C049-V1
sample_age:53,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient048,Visit3

description:
Library name: C19-C048-V3
sample_age:64,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: D6_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient048,Visit2

description:
Library name: C19-C048-V2
sample_age:64,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: 11B_DAC_250620, NOMe


title: D4_HL60_colonies_rep3, RNA


title: D2_HL60_colonies_rep3, RNA


title: D3_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient048,Visit1

description:
Library name: C19-C048-V1
sample_age:64,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient047,Visit3

description:
Library name: C19-C047-V3
sample_age:29,sample_sex:M,severity_scale:0,severity_class:NA


title: C12_HL60_colonies_rep3, RNA


title: 10H_AZA_250620, NOMe


title: 10G_AZA_250620, NOMe


title: COVID-19,Hospitalized,patient047,Visit2

description:
Library name: C19-C047-V2
sample_age:29,sample_sex:M,severity_scale:0,severity_class:NA


title: H7_HL60_colonies_rep3, RNA


title: C10_HL60_colonies_rep3, RNA


title: C9_HL60_colonies_rep3, RNA


title: 10F_AZA_250620, NOMe


title: C11_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient046,Visit2

description:
Library name: C19-C046-V2
sample_age:60,sample_sex:M,severity_scale:4,severity_class:Severe-Critical


title: C8_HL60_colonies_rep3, RNA


title: C5_HL60_colonies_rep3, RNA


title: 10D_DAC_250620, NOMe


title: 10E_AZA_250620, NOMe


title: C4_HL60_colonies_rep3, RNA


title: C6_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient046,Visit3

description:
Library name: C19-C046-V3
sample_age:60,sample_sex:M,severity_scale:4,severity_class:Severe-Critical


title: COVID-19,Hospitalized,patient046,Visit1

description:
Library name: C19-C046-V1
sample_age:60,sample_sex:M,severity_scale:4,severity_class:Severe-Critical


title: 10C_DAC_250620, NOMe


title: 11A_DAC_250620, NOMe


title: C7_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient045,Visit3

description:
Library name: C19-C045-V3
sample_age:28,sample_sex:M,severity_scale:0,severity_class:NA


title: D5_HL60_colonies_rep3, RNA


title: D1_HL60_colonies_rep3, RNA


title: C2_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient045,Visit2

description:
Library name: C19-C045-V2
sample_age:28,sample_sex:M,severity_scale:0,severity_class:NA


title: 10B_DAC_250620, NOMe


title: B11_HL60_colonies_rep3, RNA


title: 10A_DAC_250620, NOMe


title: COVID-19,Hospitalized,patient044,Visit3

description:
Library name: C19-C044-V3
sample_age:62,sample_sex:F,severity_scale:2,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient044,Visit2

description:
Library name: C19-C044-V2
sample_age:62,sample_sex:F,severity_scale:2,severity_class:Mild-Moderate


title: B10_HL60_colonies_rep3, RNA


title: B9_HL60_colonies_rep3, RNA


title: 9H_AZA_060320, NOMe


title: 9G_AZA_060320, NOMe


title: B8_HL60_colonies_rep3, RNA


title: C3_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient044,Visit1

description:
Library name: C19-C044-V1
sample_age:62,sample_sex:F,severity_scale:2,severity_class:Mild-Moderate


title: B6_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient043,Visit3

description:
Library name: C19-C043-V3
sample_age:24,sample_sex:F,severity_scale:2,severity_class:Mild-Moderate


title: B7_HL60_colonies_rep3, RNA


title: 9F_AZA_060320, NOMe


title: B4_HL60_colonies_rep3, RNA


title: B5_HL60_colonies_rep3, RNA


title: 9E_AZA_060320, NOMe


title: B2_HL60_colonies_rep3, RNA


title: B1_HL60_colonies_rep3, RNA


title: C1_HL60_colonies_rep3, RNA


title: 9D_DAC_060320, NOMe


title: B3_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient043,Visit1

description:
Library name: C19-C043-V1
sample_age:23,sample_sex:F,severity_scale:2,severity_class:Mild-Moderate


title: B12_HL60_colonies_rep3, RNA


title: 9C_DAC_060320, NOMe


title: A11_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient042,Visit3

description:
Library name: C19-C042-V3
sample_age:49,sample_sex:F,severity_scale:4,severity_class:Severe-Critical


title: A12_HL60_colonies_rep3, RNA


title: 9B_DAC_060320, NOMe


title: A10_HL60_colonies_rep3, RNA


title: A9_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient042,Visit2

description:
Library name: C19-C042-V2
sample_age:49,sample_sex:F,severity_scale:4,severity_class:Severe-Critical


title: A8_HL60_colonies_rep3, RNA


title: A7_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient042,Visit1

description:
Library name: C19-C042-V1
sample_age:49,sample_sex:F,severity_scale:4,severity_class:Severe-Critical


title: A4_HL60_colonies_rep3, RNA


title: A6_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient041,Visit3

description:
Library name: C19-C041-V3
sample_age:59,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: 8G_AZA_060320, NOMe


title: 8H_AZA_060320, NOMe


title: A3_HL60_colonies_rep3, RNA


title: COVID-19,Hospitalized,patient041,Visit2

description:
Library name: C19-C041-V2
sample_age:59,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: 8F_AZA_060320, NOMe


title: COVID-19,Hospitalized,patient041,Visit1

description:
Library name: C19-C041-V1
sample_age:59,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: H12_HL60_colonies_rep2, RNA


title: 8E_AZA_060320, NOMe


title: A2_HL60_colonies_rep3, RNA


title: A1_HL60_colonies_rep3, RNA


title: H11_HL60_colonies_rep2, RNA


title: H10_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient040,Visit3

description:
Library name: C19-C040-V3
sample_age:71,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: H9_HL60_colonies_rep2, RNA


title: H8_HL60_colonies_rep2, RNA


title: 8D_DAC_060320, NOMe


title: COVID-19,Hospitalized,patient040,Visit2

description:
Library name: C19-C040-V2
sample_age:71,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient043,Visit2

description:
Library name: C19-C043-V2
sample_age:23,sample_sex:F,severity_scale:2,severity_class:Mild-Moderate


title: 9A_DAC_060320, NOMe


title: COVID-19,Hospitalized,patient040,Visit1

description:
Library name: C19-C040-V1
sample_age:71,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: A5_HL60_colonies_rep3, RNA


title: H5_HL60_colonies_rep2, RNA


title: H4_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient039,Visit2

description:
Library name: C19-C039-V2
sample_age:27,sample_sex:F,severity_scale:2,severity_class:Mild-Moderate


title: 8A_DAC_060320, NOMe


title: H3_HL60_colonies_rep2, RNA


title: H1_HL60_colonies_rep2, RNA


title: 7H_AZA_060320, NOMe


title: H2_HL60_colonies_rep2, RNA


title: 7G_AZA_060320, NOMe


title: G10_HL60_colonies_rep2, RNA


title: G9_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient038,Visit2

description:
Library name: C19-C038-V2
sample_age:60,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient038,Visit3

description:
Library name: C19-C038-V3
sample_age:60,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: G11_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient038,Visit1

description:
Library name: C19-C038-V1
sample_age:60,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: 8C_DAC_060320, NOMe


title: 7F_AZA_060320, NOMe


title: G8_HL60_colonies_rep2, RNA


title: 7E_AZA_060320, NOMe


title: G6_HL60_colonies_rep2, RNA


title: G7_HL60_colonies_rep2, RNA


title: H6_HL60_colonies_rep2, RNA


title: H7_HL60_colonies_rep2, RNA


title: 7D_DAC_060320, NOMe


title: G5_HL60_colonies_rep2, RNA


title: 8B_DAC_060320, NOMe


title: COVID-19,Hospitalized,patient037,Visit3

description:
Library name: C19-C037-V3
sample_age:39,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient039,Visit3

description:
Library name: C19-C039-V3
sample_age:27,sample_sex:F,severity_scale:2,severity_class:Mild-Moderate


title: G4_HL60_colonies_rep2, RNA


title: 7C_DAC_060320, NOMe


title: COVID-19,Hospitalized,patient037,Visit2

description:
Library name: C19-C037-V2
sample_age:39,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: G12_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient039,Visit1

description:
Library name: C19-C039-V1
sample_age:26,sample_sex:F,severity_scale:2,severity_class:Mild-Moderate


title: 7B_DAC_060320, NOMe


title: COVID-19,Hospitalized,patient037,Visit1

description:
Library name: C19-C037-V1
sample_age:39,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: G1_HL60_colonies_rep2, RNA


title: F12_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient036,Visit3

description:
Library name: C19-C036-V3
sample_age:57,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: F11_HL60_colonies_rep2, RNA


title: F10_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient036,Visit2

description:
Library name: C19-C036-V2
sample_age:57,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: 6H_AZA_060320, NOMe


title: COVID-19,Hospitalized,patient036,Visit1

description:
Library name: C19-C036-V1
sample_age:57,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: 7A_DAC_060320, NOMe


title: 6G_AZA_060320, NOMe


title: F7_HL60_colonies_rep2, RNA


title: F6_HL60_colonies_rep2, RNA


title: F8_HL60_colonies_rep2, RNA


title: F5_HL60_colonies_rep2, RNA


title: 6F_AZA_060320, NOMe


title: F3_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient035,Visit2

description:
Library name: C19-C035-V2
sample_age:33,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: G3_HL60_colonies_rep2, RNA


title: 6E_AZA_060320, NOMe


title: COVID-19,Hospitalized,patient035,Visit3

description:
Library name: C19-C035-V3
sample_age:33,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: G2_HL60_colonies_rep2, RNA


title: 6D_DAC_060320, NOMe


title: COVID-19,Hospitalized,patient035,Visit1

description:
Library name: C19-C035-V1
sample_age:33,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: F1_HL60_colonies_rep2, RNA


title: E12_HL60_colonies_rep2, RNA


title: 6C_DAC_060320, NOMe


title: E11_HL60_colonies_rep2, RNA


title: F9_HL60_colonies_rep2, RNA


title: E10_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient034,Visit2

description:
Library name: C19-C034-V2
sample_age:30,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient034,Visit3

description:
Library name: C19-C034-V3
sample_age:30,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: 6B_DAC_060320, NOMe


title: E9_HL60_colonies_rep2, RNA


title: E8_HL60_colonies_rep2, RNA


title: 6A_DAC_060320, NOMe


title: E7_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient034,Visit1

description:
Library name: C19-C034-V1
sample_age:30,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: F4_HL60_colonies_rep2, RNA


title: E4_HL60_colonies_rep2, RNA


title: 5H_AZA_060320, NOMe


title: 5G_AZA_060320, NOMe


title: E3_HL60_colonies_rep2, RNA


title: F2_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient033,Visit2

description:
Library name: C19-C033-V2
sample_age:36,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: E2_HL60_colonies_rep2, RNA


title: 5F_AZA_060320, NOMe


title: E1_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient033,Visit1

description:
Library name: C19-C033-V1
sample_age:36,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: D12_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient032,Visit3

description:
Library name: C19-C032-V3
sample_age:27,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: D11_HL60_colonies_rep2, RNA


title: 5E_AZA_060320, NOMe


title: D9_HL60_colonies_rep2, RNA


title: 5D_DAC_060320, NOMe


title: D8_HL60_colonies_rep2, RNA


title: D10_HL60_colonies_rep2, RNA


title: D6_HL60_colonies_rep2, RNA


title: 5C_DAC_060320, NOMe


title: D7_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient032,Visit2

description:
Library name: C19-C032-V2
sample_age:27,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: 5B_DAC_060320, NOMe


title: D5_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient032,Visit1

description:
Library name: C19-C032-V1
sample_age:27,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: D4_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient031,Visit3

description:
Library name: C19-C031-V3
sample_age:22,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: E6_HL60_colonies_rep2, RNA


title: E5_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient031,Visit2

description:
Library name: C19-C031-V2
sample_age:22,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient033,Visit3

description:
Library name: C19-C033-V3
sample_age:36,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: D3_HL60_colonies_rep2, RNA


title: 4H_AZA_060320, NOMe


title: 5A_DAC_060320, NOMe


title: D2_HL60_colonies_rep2, RNA


title: D1_HL60_colonies_rep2, RNA


title: C12_HL60_colonies_rep2, RNA


title: C11_HL60_colonies_rep2, RNA


title: 4G_AZA_060320, NOMe


title: C10_HL60_colonies_rep2, RNA


title: C9_HL60_colonies_rep2, RNA


title: 4F_AZA_060320, NOMe


title: C8_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient030,Visit2

description:
Library name: C19-C030-V2
sample_age:57,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: 4E_AZA_060320, NOMe


title: COVID-19,Hospitalized,patient030,Visit1

description:
Library name: C19-C030-V1
sample_age:57,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: C7_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient029,Visit3

description:
Library name: C19-C029-V3
sample_age:54,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: 4D_DAC_060320, NOMe


title: C4_HL60_colonies_rep2, RNA


title: 4C_DAC_060320, NOMe


title: COVID-19,Hospitalized,patient029,Visit2

description:
Library name: C19-C029-V2
sample_age:54,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: C2_HL60_colonies_rep2, RNA


title: 4B_DAC_060320, NOMe


title: C5_HL60_colonies_rep2, RNA


title: C3_HL60_colonies_rep2, RNA


title: C1_HL60_colonies_rep2, RNA


title: B10_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient028,Visit3

description:
Library name: C19-C028-V3
sample_age:55,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: B12_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient029,Visit1

description:
Library name: C19-C029-V1
sample_age:54,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient030,Visit3

description:
Library name: C19-C030-V3
sample_age:57,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: B11_HL60_colonies_rep2, RNA


title: B9_HL60_colonies_rep2, RNA


title: 4A_DAC_060320, NOMe


title: COVID-19,Hospitalized,patient028,Visit2

description:
Library name: C19-C028-V2
sample_age:55,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient031,Visit1

description:
Library name: C19-C031-V1
sample_age:22,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: B7_HL60_colonies_rep2, RNA


title: 3G_AZA_060320, NOMe


title: B8_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient028,Visit1

description:
Library name: C19-C028-V1
sample_age:55,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: 3H_AZA_060320, NOMe


title: B6_HL60_colonies_rep2, RNA


title: C6_HL60_colonies_rep2, RNA


title: 3F_AZA_060320, NOMe


title: B5_HL60_colonies_rep2, RNA


title: B4_HL60_colonies_rep2, RNA


title: B3_HL60_colonies_rep2, RNA


title: 3E_AZA_060320, NOMe


title: B1_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient027,Visit2

description:
Library name: C19-C027-V2
sample_age:38,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: 3D_DAC_060320, NOMe


title: A12_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient027,Visit3

description:
Library name: C19-C027-V3
sample_age:38,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: B2_HL60_colonies_rep2, RNA


title: 3C_DAC_060320, NOMe


title: COVID-19,Hospitalized,patient027,Visit1

description:
Library name: C19-C027-V1
sample_age:38,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: A9_HL60_colonies_rep2, RNA


title: COVID-19,Hospitalized,patient026,Visit2

description:
Library name: C19-C026-V2
sample_age:40,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient026,Visit3

description:
Library name: C19-C026-V3
sample_age:40,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: A10_HL60_colonies_rep2, RNA


title: A11_HL60_colonies_rep2, RNA


title: 3B_DAC_060320, NOMe


title: A7_HL60_colonies_rep2, RNA


title: A8_HL60_colonies_rep2, RNA


title: 3A_DAC_060320, NOMe


title: COVID-19,Hospitalized,patient026,Visit1

description:
Library name: C19-C026-V1
sample_age:40,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: 2H_AZA_060320, NOMe


title: COVID-19,Hospitalized,patient025,Visit3

description:
Library name: C19-C025-V3
sample_age:48,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: A3_HL60_colonies_rep2, RNA


title: A5_HL60_colonies_rep2, RNA


title: A4_HL60_colonies_rep2, RNA


title: 2G_AZA_060320, NOMe


title: COVID-19,Hospitalized,patient025,Visit2

description:
Library name: C19-C025-V2
sample_age:48,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: A2_HL60_colonies_rep2, RNA


title: H12_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient025,Visit1

description:
Library name: C19-C025-V1
sample_age:48,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: 2E_AZA_060320, NOMe


title: COVID-19,Hospitalized,patient024,Visit2

description:
Library name: C19-C024-V2
sample_age:36,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: 2D_DAC_060320, NOMe


title: H9_HL60_colonies_rep1, RNA


title: H11_HL60_colonies_rep1, RNA


title: H8_HL60_colonies_rep1, RNA


title: A1_HL60_colonies_rep2, RNA


title: H7_HL60_colonies_rep1, RNA


title: H6_HL60_colonies_rep1, RNA


title: 2C_DAC_060320, NOMe


title: A6_HL60_colonies_rep2, RNA


title: 2B_DAC_060320, NOMe


title: H4_HL60_colonies_rep1, RNA


title: H5_HL60_colonies_rep1, RNA


title: 2A_DAC_060320, NOMe


title: COVID-19,Hospitalized,patient023,Visit4

description:
Library name: C19-C023-V4
sample_age:57,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient023,Visit3

description:
Library name: C19-C023-V3
sample_age:57,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: H2_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient023,Visit2

description:
Library name: C19-C023-V2
sample_age:57,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: H1_HL60_colonies_rep1, RNA


title: H3_HL60_colonies_rep1, RNA


title: 1H_Unt_060320, NOMe


title: 2F_AZA_060320, NOMe


title: 1G_Unt_060320, NOMe


title: COVID-19,Hospitalized,patient024,Visit3

description:
Library name: C19-C024-V3
sample_age:36,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: H10_HL60_colonies_rep1, RNA


title: G11_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient023,Visit1

description:
Library name: C19-C023-V1
sample_age:57,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: G10_HL60_colonies_rep1, RNA


title: G9_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient022,Visit2

description:
Library name: C19-C022-V2
sample_age:62,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: G8_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient024,Visit1

description:
Library name: C19-C024-V1
sample_age:36,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: 1F_Unt_060320, NOMe


title: 1E_Unt_060320, NOMe


title: G5_HL60_colonies_rep1, RNA


title: G7_HL60_colonies_rep1, RNA


title: 1D_Unt_060320, NOMe


title: G4_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient022,Visit1

description:
Library name: C19-C022-V1
sample_age:62,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: 1C_Unt_060320, NOMe


title: COVID-19,Hospitalized,patient021,Visit2

description:
Library name: C19-C021-V2
sample_age:65,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: G12_HL60_colonies_rep1, RNA


title: G3_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient021,Visit1

description:
Library name: C19-C021-V1
sample_age:65,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: G1_HL60_colonies_rep1, RNA


title: G6_HL60_colonies_rep1, RNA


title: G2_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient022,Visit5

description:
Library name: C19-C022-L1
sample_age:63,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: F12_HL60_colonies_rep1, RNA


title: 1A_Neg_060320, NOMe


title: COVID-19,Hospitalized,patient020,Visit4

description:
Library name: C19-C020-V4
sample_age:66,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: F10_HL60_colonies_rep1, RNA


title: 1B_Unt_060320, NOMe


title: F11_HL60_colonies_rep1, RNA


title: F9_HL60_colonies_rep1, RNA


title: F8_HL60_colonies_rep1, RNA


title: 12H_Neg_060320, NOMe


title: COVID-19,Hospitalized,patient020,Visit2

description:
Library name: C19-C020-V2
sample_age:66,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: F7_HL60_colonies_rep1, RNA


title: F6_HL60_colonies_rep1, RNA


title: 12F_Unt_060320, NOMe


title: F5_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient020,Visit1

description:
Library name: C19-C020-V1
sample_age:66,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: F4_HL60_colonies_rep1, RNA


title: 12E_Unt_060320, NOMe


title: F3_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient019,Visit4

description:
Library name: C19-C019-V4
sample_age:18,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: F2_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient019,Visit3

description:
Library name: C19-C019-V3
sample_age:18,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: 12D_Unt_060320, NOMe


title: F1_HL60_colonies_rep1, RNA


title: E12_HL60_colonies_rep1, RNA


title: E11_HL60_colonies_rep1, RNA


title: 12C_Unt_060320, NOMe


title: 12B_Unt_060320, NOMe


title: COVID-19,Hospitalized,patient020,Visit3

description:
Library name: C19-C020-V3
sample_age:66,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: E10_HL60_colonies_rep1, RNA


title: E9_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient019,Visit1

description:
Library name: C19-C019-V1
sample_age:18,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: E8_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient018,Visit4

description:
Library name: C19-C018-V4
sample_age:53,sample_sex:M,severity_scale:3,severity_class:Severe-Critical


title: E7_HL60_colonies_rep1, RNA


title: 12A_Unt_060320, NOMe


title: 12G_Unt_060320, NOMe


title: E5_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient018,Visit3

description:
Library name: C19-C018-V3
sample_age:53,sample_sex:M,severity_scale:3,severity_class:Severe-Critical


title: 11H_AZA_060320, NOMe


title: E3_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient018,Visit2

description:
Library name: C19-C018-V2
sample_age:53,sample_sex:M,severity_scale:3,severity_class:Severe-Critical


title: E2_HL60_colonies_rep1, RNA


title: 11F_AZA_060320, NOMe


title: COVID-19,Hospitalized,patient018,Visit1

description:
Library name: C19-C018-V1
sample_age:53,sample_sex:M,severity_scale:3,severity_class:Severe-Critical


title: E1_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient019,Visit2

description:
Library name: C19-C019-V2
sample_age:18,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: D12_HL60_colonies_rep1, RNA


title: 11E_AZA_060320, NOMe


title: D10_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient017,Visit4

description:
Library name: C19-C017-V4
sample_age:46,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: D11_HL60_colonies_rep1, RNA


title: 11D_DAC_060320, NOMe


title: D9_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient017,Visit3

description:
Library name: C19-C017-V3
sample_age:46,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: D8_HL60_colonies_rep1, RNA


title: E6_HL60_colonies_rep1, RNA


title: D7_HL60_colonies_rep1, RNA


title: 11C_DAC_060320, NOMe


title: 11B_DAC_060320, NOMe


title: COVID-19,Hospitalized,patient017,Visit2

description:
Library name: C19-C017-V2
sample_age:46,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient017,Visit1

description:
Library name: C19-C017-V1
sample_age:46,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: E4_HL60_colonies_rep1, RNA


title: D6_HL60_colonies_rep1, RNA


title: 11G_AZA_060320, NOMe


title: D5_HL60_colonies_rep1, RNA


title: D3_HL60_colonies_rep1, RNA


title: D4_HL60_colonies_rep1, RNA


title: 11A_DAC_060320, NOMe


title: COVID-19,Hospitalized,patient017,Visit5

description:
Library name: C19-C017-L1
sample_age:47,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: 10H_AZA_060320, NOMe


title: COVID-19,Hospitalized,patient016,Visit2

description:
Library name: C19-C016-V2
sample_age:53,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: 10G_AZA_060320, NOMe


title: D2_HL60_colonies_rep1, RNA


title: C10_HL60_colonies_rep1, RNA


title: C9_HL60_colonies_rep1, RNA


title: C11_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient015,Visit4

description:
Library name: C19-C015-V4
sample_age:31,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: 10F_AZA_060320, NOMe


title: C8_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient015,Visit3

description:
Library name: C19-C015-V3
sample_age:31,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: C7_HL60_colonies_rep1, RNA


title: 10E_AZA_060320, NOMe


title: C6_HL60_colonies_rep1, RNA


title: 10D_DAC_060320, NOMe


title: C5_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient015,Visit2

description:
Library name: C19-C015-V2
sample_age:31,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: 10C_DAC_060320, NOMe


title: C3_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient015,Visit1

description:
Library name: C19-C015-V1
sample_age:31,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: C2_HL60_colonies_rep1, RNA


title: B12_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient014,Visit4

description:
Library name: C19-C014-V4
sample_age:65,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: 10B_DAC_060320, NOMe


title: 10A_DAC_060320, NOMe


title: B11_HL60_colonies_rep1, RNA


title: C12_HL60_colonies_rep1, RNA


title: D1_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient016,Visit1

description:
Library name: C19-C016-V1
sample_age:53,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: ZNF217 Prog siRNA 49

city: Stanford

first: Douglas

last: Porter

address: 269 Campus Drive

department: Dermatology

institute: Stanford

data_processing:
Lexogen reads were processed according to the manufacturer’s recommendation, mapped with STAR (v. 2.7) to hg38 using “basic” tagged Gencode v.39 transcripts, and genes quantified with FeatureCounts (from Rsubread v.2.10.5). Quantifications were analyzed with DESeq2 (v.1.38.3), with apeGLM shrinkage.
Assembly: hg38
Supplementary files format and content: Featurecounts estimated raw reads per gene.

source_name: Primary keratinocytes

growth_protocol: Primary human keratinocytes were isolated from fresh surgically discarded newborn foreskin, and progenitor cells cultured in complete Keratinocyte-SFM (Life Technologies, #17005-142) and Medium 154 (Life Technologies #M-154-500). Cells were induced to differentiate by the addition of 1.2 mM calcium for 3 days at full confluence. Biological replicates were performed in all cases using primary cells from at least 2 independent, unrelated donors.

extract_protocol:
Total RNA was extracted using the RNeasy Plus kit (QIAGEN, 74136).
QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI (Lexogen, 191.96) following manufacturer’s protocol with UMI Second Strand Synthesis Module for QuantSeq FWD (Lexogen, 018.96)

value: Primary keratinocytes

value: Progenitor


title: B10_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient014,Visit2

description:
Library name: C19-C014-V2
sample_age:65,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: B8_HL60_colonies_rep1, RNA


title: B9_HL60_colonies_rep1, RNA


title: ZNF217 Prog siRNA 34


title: B6_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient013,Visit3

description:
Library name: C19-C013-V3
sample_age:62,sample_sex:F,severity_scale:4,severity_class:Severe-Critical


title: C4_HL60_colonies_rep1, RNA

value: decitabine


title: ZNF217 Day4 siRNA 44

value: Differentiated


title: B5_HL60_colonies_rep1, RNA


title: C1_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient013,Visit2

description:
Library name: C19-C013-V2
sample_age:62,sample_sex:F,severity_scale:4,severity_class:Severe-Critical


title: B2_HL60_colonies_rep1, RNA


title: B3_HL60_colonies_rep1, RNA


title: ZNF217 Day4 siRNA 17


title: B1_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient013,Visit1

description:
Library name: C19-C013-V1
sample_age:62,sample_sex:F,severity_scale:4,severity_class:Severe-Critical


title: ZNF217 Day4 siRNA 40


title: A11_HL60_colonies_rep1, RNA


title: A12_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient014,Visit3

description:
Library name: C19-C014-V3
sample_age:65,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: SP1 Prog siRNA 50


title: A10_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient012,Visit4

description:
Library name: C19-C012-V4
sample_age:42,sample_sex:M,severity_scale:3,severity_class:Severe-Critical


title: COVID-19,Hospitalized,patient012,Visit3

description:
Library name: C19-C012-V3
sample_age:42,sample_sex:M,severity_scale:3,severity_class:Severe-Critical


title: SP1 Prog siRNA 33


title: A8_HL60_colonies_rep1, RNA


title: A9_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient012,Visit2

description:
Library name: C19-C012-V2
sample_age:42,sample_sex:M,severity_scale:3,severity_class:Severe-Critical


title: COVID-19,Hospitalized,patient013,Visit4

description:
Library name: C19-C013-V4
sample_age:62,sample_sex:F,severity_scale:4,severity_class:Severe-Critical


title: ZNF217 Prog siRNA 25


title: B7_HL60_colonies_rep1, RNA


title: A7_HL60_colonies_rep1, RNA


title: SP1 Prog siRNA 28


title: B4_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient012,Visit1

description:
Library name: C19-C012-V1
sample_age:42,sample_sex:M,severity_scale:3,severity_class:Severe-Critical


title: A5_HL60_colonies_rep1, RNA


title: A3_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient011,Visit2

description:
Library name: C19-C011-V2
sample_age:51,sample_sex:F,severity_scale:4,severity_class:Severe-Critical


title: A4_HL60_colonies_rep1, RNA


title: SP1 Day4 siRNA 39


title: A2_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient011,Visit1

description:
Library name: C19-C011-V1
sample_age:51,sample_sex:F,severity_scale:4,severity_class:Severe-Critical


title: SP1 Day4 siRNA 20


title: 9G_AZA_250620, RNA

library_source: transcriptomic single cell

data_processing:
Following demultiplexing, multiple sequencing lanes per read were concatenated into single R1 and R2 fastq files, per sample using zcat and gzip.
Raw reads were trimmed in pair-end mode using Trim Galore (v0.6.5) and Cutadapt (v2.10), retaining unpaired reads.
Hisat2 (v2.1.0) was used to map and align trimmed and unpaired reads using default parameters (--phred33) to the human reference genome build (GRCh38), and samtools (v1.10) was used to sort by coordinate and generate bam files.
TEtranscripts (v2.2.1) was used to obtain raw gene and transposable element counts from unique and ambiguously aligned reads (bam files) using TEcount with the flags '--sortByPos --mode multi’. The GTF files used were generated as follows: 1) TEs (http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/rmsk.txt.gz; USCS repeating element Repeat Masker; hg38; 2021-09-03) and 2) genes (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_30/gencode.v30.annotation.gtf.gz; gencode Release 30; GRCh38.p12; 2019-04-08). To ensure the GTF files worked with TEtranscripts the gene GTF (from gencode) was updated by converting ‘M’ to ‘MT’ for mitochondrial genes in the chromosome column and removal of ‘Chr’ preceding each chromosome number. The TE GTF was generated from the repeat mask file  using the conversion tool from the TEtranscripts developers (http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/makeTEgtf.pl.gz) ‘perl makeTEgtf.pl -c 6 -s 7 -e 8 -o 10 -t 11 -n hg38_rmsk -f 13 -C 12 -S 2 rmsk.txt >> hg38_rmsk_TE.gtf’ and removing ‘chr’ from chromosome names ‘sed 's/chr//' hg38_rmsk_TE.gtf > hg38_rmsk_TE_NoChr.gtf’.    TEtranscripts the gene GTF (from gencode) was updated by converting ‘M’ to ‘MT’ for mitochondrial
Individual sample counts from TEtranscripts were collated into a single count table (tab-deliminated) and updated with relevant gene information from the gene GTF file.
Assembly: GRCh38
Supplementary files format and content: Bismark output file: genome-wide CpG methylation reports (CpG.cov.gz) are tab-delimited, use 1-based genomic coordinates and are in the following format: <chromosome> <position> <methylation rate>
Supplementary files format and content: Bismark output file: genome-wide GpC methylation reports (GpC.cov.gz) are tab-delimited, use 1-based genomic coordinates and are in the following format: <chromosome> <position> <methylation rate>
Supplementary files format and content: Count table (tab-deliminated) compiled from TEtranscripts results. First column contains gene (ensembl ID) and transposable element (TE) ID and column two contains hgnc symbol equiavelnt (gene IDs). Columns 3-7 contains TE information and columns 7-13  contains gene informations. Counts for individual samples are contained in column 14 onwards.


title: A1_HL60_colonies_rep1, RNA


title: 9H_AZA_250620, RNA


title: COVID-19,Hospitalized,patient010,Visit4

description:
Library name: C19-C010-V4
sample_age:35,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: 9F_AZA_250620, RNA


title: COVID-19,Hospitalized,patient010,Visit3

description:
Library name: C19-C010-V3
sample_age:35,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: Prog NRF1 rs62


title: 9D_DAC_250620, RNA


title: otherControl Prog siRNA 55


title: A6_HL60_colonies_rep1, RNA


title: COVID-19,Hospitalized,patient010,Visit2

description:
Library name: C19-C010-V2
sample_age:35,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: 9A_DAC_250620, RNA


title: otherControl Day4 siRNA 60


title: 8H_AZA_250620, RNA


title: Prog control rs61


title: 9E_AZA_250620, RNA


title: SP1 Day4 siRNA 45


title: 8G_AZA_250620, RNA


title: COVID-19,Hospitalized,patient010,Visit5

description:
Library name: C19-C010-L1
sample_age:36,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: 8F_AZA_250620, RNA


title: NRF1 Prog siRNA 52


title: COVID-19,Hospitalized,patient010,Visit1

description:
Library name: C19-C010-V1
sample_age:35,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: 8E_AZA_250620, RNA


title: NRF1 Day4 siRNA 57


title: COVID-19,Hospitalized,patient009,Visit2

description:
Library name: C19-C009-V2
sample_age:44,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient009,Visit1

description:
Library name: C19-C009-V1
sample_age:44,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: 8C_DAC_250620, RNA


title: COVID-19,Hospitalized,patient008,Visit4

description:
Library name: C19-C008-V4
sample_age:44,sample_sex:F,severity_scale:3,severity_class:Severe-Critical


title: 9C_DAC_250620, RNA


title: IRX2 Prog siRNA 48


title: 8B_DAC_250620, RNA


title: 7H_AZA_250620, RNA


title: 9B_DAC_250620, RNA


title: 7G_AZA_250620, RNA


title: IRX2 Prog siRNA 32


title: 7F_AZA_250620, RNA


title: IRX2 Prog siRNA 26


title: COVID-19,Hospitalized,patient008,Visit3

description:
Library name: C19-C008-V3
sample_age:44,sample_sex:F,severity_scale:3,severity_class:Severe-Critical


title: 7E_AZA_250620, RNA


title: COVID-19,Hospitalized,patient008,Visit2

description:
Library name: C19-C008-V2
sample_age:44,sample_sex:F,severity_scale:3,severity_class:Severe-Critical


title: 7D_DAC_250620, RNA


title: IRX2 Day4 siRNA 38


title: 7C_DAC_250620, RNA


title: IRX2 Day4 siRNA 42


title: 7B_DAC_250620, RNA


title: COVID-19,Hospitalized,patient008,Visit1

description:
Library name: C19-C008-V1
sample_age:44,sample_sex:F,severity_scale:3,severity_class:Severe-Critical


title: 7A_DAC_250620, RNA


title: IRX2 Day4 siRNA 18


title: COVID-19,Hospitalized,patient007,Visit4

description:
Library name: C19-C007-V4
sample_age:52,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: 8D_DAC_250620, RNA


title: 6H_AZA_250620, RNA


title: 6G_AZA_250620, RNA


title: 8A_DAC_250620, RNA


title: COVID-19,Hospitalized,patient007,Visit3

description:
Library name: C19-C007-V3
sample_age:52,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: FOXJ2 Prog siRNA 53


title: COVID-19,Hospitalized,patient007,Visit2

description:
Library name: C19-C007-V2
sample_age:52,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: 6E_AZA_250620, RNA


title: FOXJ2 Prog siRNA 22


title: 6D_DAC_250620, RNA


title: COVID-19,Hospitalized,patient007,Visit1

description:
Library name: C19-C007-V1
sample_age:52,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: 6C_DAC_250620, RNA


title: FOXJ2 Day4 siRNA 58


title: 6B_DAC_250620, RNA


title: 5H_AZA_250620, RNA


title: 6A_DAC_250620, RNA


title: 5G_AZA_250620, RNA


title: COVID-19,Hospitalized,patient006,Visit3

description:
Library name: C19-C006-V3
sample_age:28,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient006,Visit4

description:
Library name: C19-C006-V4
sample_age:28,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient006,Visit2

description:
Library name: C19-C006-V2
sample_age:28,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: ETV3 Prog siRNA 54


title: 5F_AZA_250620, RNA


title: ETV3 Prog siRNA 23


title: 5D_DAC_250620, RNA


title: 5E_AZA_250620, RNA


title: 5C_DAC_250620, RNA


title: 5B_DAC_250620, RNA


title: 5A_DAC_250620, RNA


title: COVID-19,Hospitalized,patient006,Visit1

description:
Library name: C19-C006-V1
sample_age:28,sample_sex:M,severity_scale:2,severity_class:Mild-Moderate


title: 4H_AZA_250620, RNA


title: 6F_AZA_250620, RNA


title: ETV3 Day4 siRNA 59


title: ETV3 Day4 siRNA 15


title: 4G_AZA_250620, RNA


title: Day4 NRF1 rs64


title: COVID-19,Hospitalized,patient005,Visit2

description:
Library name: C19-C005-V2
sample_age:69,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient005,Visit3

description:
Library name: C19-C005-V3
sample_age:69,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: 4F_AZA_250620, RNA


title: 4E_AZA_250620, RNA


title: FOXJ2 Day4 siRNA 14


title: 4D_DAC_250620, RNA


title: Day4 control rs63


title: 4C_DAC_250620, RNA


title: CXXC1 Prog siRNA 47


title: 4A_DAC_250620, RNA


title: COVID-19,Hospitalized,patient005,Visit1

description:
Library name: C19-C005-V1
sample_age:69,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: 4B_DAC_250620, RNA


title: COVID-19,Hospitalized,patient004,Visit4

description:
Library name: C19-C004-V4
sample_age:51,sample_sex:F,severity_scale:2,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient004,Visit3

description:
Library name: C19-C004-V3
sample_age:51,sample_sex:F,severity_scale:2,severity_class:Mild-Moderate


title: 3H_AZA_250620, RNA


title: 3G_AZA_250620, RNA


title: CXXC1 Prog siRNA 24


title: COVID-19,Hospitalized,patient005,Visit4

description:
Library name: C19-C005-V4
sample_age:69,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: CXXC1 Prog siRNA 31


title: 3F_AZA_250620, RNA


title: 3E_AZA_250620, RNA


title: COVID-19,Hospitalized,patient004,Visit2

description:
Library name: C19-C004-V2
sample_age:51,sample_sex:F,severity_scale:2,severity_class:Mild-Moderate


title: CXXC1 Day4 siRNA 43


title: 3D_DAC_250620, RNA


title: COVID-19,Hospitalized,patient004,Visit1

description:
Library name: C19-C004-V1
sample_age:51,sample_sex:F,severity_scale:2,severity_class:Mild-Moderate


title: CXXC1 Day4 siRNA 37


title: 3C_DAC_250620, RNA


title: 3B_DAC_250620, RNA


title: CXXC1 Day4 siRNA 16


title: COVID-19,Hospitalized,patient003,Visit3

description:
Library name: C19-C003-V3
sample_age:44,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient003,Visit4

description:
Library name: C19-C003-V4
sample_age:45,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: 2G_AZA_250620, RNA


title: 2F_AZA_250620, RNA


title: COVID-19,Hospitalized,patient003,Visit2

description:
Library name: C19-C003-V2
sample_age:44,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: 2H_AZA_250620, RNA


title: 3A_DAC_250620, RNA


title: control Prog siRNA 51


title: 2D_DAC_250620, RNA


title: 2E_AZA_250620, RNA


title: control Prog siRNA 46


title: 2C_DAC_250620, RNA


title: control Prog siRNA 30


title: 2B_DAC_250620, RNA


title: COVID-19,Hospitalized,patient002,Visit4

description:
Library name: C19-C002-V4
sample_age:39,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: 2A_DAC_250620, RNA


title: 1H_Unt_250620, RNA


title: control Prog siRNA 29


title: 1G_Unt_250620, RNA


title: control Prog siRNA 27


title: COVID-19,Hospitalized,patient002,Visit3

description:
Library name: C19-C002-V3
sample_age:39,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: 1F_Unt_250620, RNA


title: 1E_Unt_250620, RNA


title: COVID-19,Hospitalized,patient002,Visit2

description:
Library name: C19-C002-V2
sample_age:66,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: 1C_Unt_250620, RNA


title: 1D_Unt_250620, RNA


title: COVID-19,Hospitalized,patient002,Visit1

description:
Library name: C19-C002-V1
sample_age:39,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: control Prog siRNA 21


title: control Day4 siRNA 56


title: control Day4 siRNA 41


title: 12H_Neg_250620, RNA


title: COVID-19,Hospitalized,patient002,Visit5

description:
Library name: C19-C002-L1
sample_age:40,sample_sex:F,severity_scale:1,severity_class:Mild-Moderate


title: 12G_Unt_250620, RNA


title: 1B_Unt_250620, RNA


title: COVID-19,Hospitalized,patient003,Visit1

description:
Library name: C19-C003-V1
sample_age:44,sample_sex:M,severity_scale:1,severity_class:Mild-Moderate


title: COVID-19,Hospitalized,patient001,Visit3

description:
Library name: C19-C001-V3
sample_age:66,sample_sex:F,severity_scale:3,severity_class:Severe-Critical


title: control Day4 siRNA 36


title: control Day4 siRNA 35


title: 12D_Unt_250620, RNA


title: COVID-19,Hospitalized,patient001,Visit2

description:
Library name: C19-C001-V2
sample_age:66,sample_sex:F,severity_scale:3,severity_class:Severe-Critical


title: 12E_Unt_250620, RNA


title: 12B_Unt_250620, RNA


title: 12C_Unt_250620, RNA


title: COVID-19,Hospitalized,patient001,Visit1

description:
Library name: C19-C001-V1
sample_age:66,sample_sex:F,severity_scale:3,severity_class:Severe-Critical


title: 12A_Unt_250620, RNA


title: 11H_AZA_250620, RNA