title: D02_DAC_220331, RNA


title: Lymphnode Metastisis Sample 14

status: Public on Jul 21 2025

type: SRA

city: Philadelphia

first: Joshua

middle: Hunter

last: Rhoades

state: PA

address: 3800 Spruce St

department: Vet School

country: USA

institute: University of Pennsylvania

library_source: other

data_processing:
library strategy: CRISPR screen
Processed with Mageck software
Assembly: N/A
Supplementary files format and content: txt

molecule: other

organism: Mus musculus

source_name: Lymphnode Metastasis

extract_protocol:
DNeasy blood and tissue kit/ Qiagen DNA microkit
Takara Extaq targeted amplification

tag: tissue

value: Metastasis

tag: cell type

value: Colorectal adenocarcinoma

tag: genotype

value: APC KO, TRP53 KO, KRASG12D mutant


title: Lymphnode Metastisis Sample 20


title: C10_DAC_220331, RNA

city: Newcastle

first: Heather

last: Lee

state: NSW

address: University Drive, Callaghan

country: Australia

institute: The University of Newcastle

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.

molecule: polyA RNA

organism: Homo sapiens

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: Peripheral blood

tag: cell line

value: promyeloblast

tag: disease/cancer type

value: Acute promyelocytic leukemia

tag: Sex

value: Female

tag: age

tag: batch

tag: treatment

value: decitabine


title: Lymphnode Metastisis Sample 18


title: D10_DAC_220331, RNA


title: C12_Unt_220331, RNA

value: untreated


title: Liver Metastisis Sample 11

source_name: Liver Metastasis


title: C09_DAC_220331, RNA


title: Primary Tumor Sample 9 [mouse7_primary_i701F1]

source_name: Primary Tumor

value: Tumor


title: C08_DAC_220331, RNA


title: Liver Metastisis Sample 13


title: Primary Tumor Sample 10 [mouse8_primary_i701F3]


title: C07_DAC_220331, RNA


title: Primary Tumor Sample 7 [mouse5_primary_i701F7]


title: Primary Tumor Sample 8 [mouse6_primary_i701F8]


title: Primary Tumor Sample 6 [mouse4_primary_i701F6]


title: C06_DAC_220331, RNA


title: Primary Tumor Sample 5 [mouse3_primary_i701F5]


title: C01_Unt_220331, RNA


title: C04_DAC_220331, RNA


title: C02_DAC_220331, RNA


title: C03_DAC_220331, RNA


title: C05_DAC_220331, RNA


title: B12_Unt_220331, RNA


title: C11_DAC_220331, RNA


title: Primary Tumor Sample 3 [mouse1_primary_i701F2]


title: Primary Tumor Sample 4 [mouse2_primary_i701F4]


title: Primary Tumor Sample 1 [baseline_i709F1]


title: Primary tumor  [Zvi_lib2_CMO]

description: CMO index data for library 2

data_processing:
Demultiplexed with cellranger multi
Processed with Seurat package in R.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: fastq.gz files are raw fastq data. Cellranger multi output for both libraries in the form of barcode, feature and matrix tsv.gz files, which are used as input to Seurat pipeline.

source_name: Colorectal primary tumor from mouse cecum

growth_protocol: Organoids were implanted into ceca

extract_protocol:
Viable single cells were isolated using FACS and captured using Chromium Next GEM Single Cell 3’ Reagent Kit v3.1
All libraries were prepared for sequencing using standard Illumina protocols.

value: C57BL/6 colorectal adenocarcinoma

value: APC, TRP53, KRASG12D mutant


title: B11_DAC_220331, RNA


title: Primary tumor  [Zvi_lib2_scRNA-seq]

description: Single cell sequencing


title: B09_DAC_220331, RNA


title: B10_DAC_220331, RNA


title: B08_DAC_220331, RNA


title: Primary tumor  [Zvi_lib1_CMO]

description: CMO index data for library 1


title: B07_DAC_220331, RNA


title: B06_DAC_220331, RNA


title: iNSC3.Input

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

country: China

institute: Shanghai Jiao Tong University

library_source: transcriptomic

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
Clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts.
Assembly: mm9
Supplementary files format and content: excel

source_name: iNSCs

growth_protocol: SSCs were cultured on mitotically inactivated STO (SIM mouse embryo-derived thioguanine- and ouabain-resistant) cell feeders in minimum essential medium alpha (MEMa; Invitrogen) supplemented with 10% fetal bovine serum (FBS) (Life Technologies), 10 ng/mL mouse leukemia inhibitory factor (LIF) (Santa Cruz Biotechnology), 20 ng/mL mouse epidermal growth factor (EGF) (PeproTech), 10 ng/mL basic fibroblast growth factor (bFGF) (PeproTech), 20 ng/mL mouse glial cell line-derived neurotrophic factor (GDNF) (PeproTech), 1mM non-essential amino acids (NEAA) (Gibco), 2 mM L-glutamine (Sigma), 1 mM sodium pyruvate (Amresco), 25 μg/mL insulin (Sigma), 100 μg/mL human transferrin (Sigma), 1x vitamin (Sigma), 60 μM putrescine (Sigma), 60 ng/mL progesterone (Sigma), 100 IU/mL penicillin (Gibco), 100 μg/mL streptomycin (Gibco),  and 0.1 mM β-mercaptoethanol (Sigma).

extract_protocol:
Total RNA was extracted from SSCs and iNSCs with TRIzol reagent (Invitrogen, 15596026), and then mRNA was purified using a Dynabeads mRNA Purification Kit (Invitrogen, 61006) according to the manufacturer’s instructions and fragmented into ~200 nt fragments using the RNA Fragmentation Reagents (Invitrogen, AM8740). Subsequently, the fragments were incubated with an m6A antibody-Pierce protein A/G beads mixture (Abcam, ab151230; Thermo Fisher Scientific, 88802), and then the eluted m6A mRNA was further purified using an RNA cleanup kit (Zymo Research, R1013).
The purified m6A mRNA was used for library construction with the NEBNext Ultra II Directional RNA Library Prep Kit. The mRNA was sequenced with Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: Two days before transdifferentiation, SSCs were digested with 0.05% trypsin. After 2 h of differential plating, the supernatant was collected and about 10,000 SSCs were inoculated into 24-well plates coated with laminin. After 24 h of culture, the medium was changed to transdifferentiation medium A (SSCs medium + 1 μM retinoic acid) for 24 h, followed by transdifferentiation medium B (MEM/F12 medium and neurobasal medium 1:1 mixture, 0.5% N2, 1% B27, 25 μg/mL bovine serum albumin (BSA), 25 μg/mL insulin, 2 mM L-glutamine, 0.1 mM β-mercaptoethanol, 10 μM SB431542, 1% FBS + 20 ng/mL bFGF), and the medium was changed every 2 days.

value: spermatogonial stem cells (SSCs)

tag: antibody


title: B05_DAC_220331, RNA


title: iNSC3.IP

value: anti-m6A (ab151230, Abcam)


title: iNSC2.IP


title: iNSC1.Input


title: B03_DAC_220331, RNA


title: B01_Unt_220331, RNA


title: iNSC2.Input


title: B02_DAC_220331, RNA


title: SSC3.IP

source_name: SSCs

value: testis

value: neural stem cell-like cells (iNSCs)


title: A10_DAC_220331, RNA


title: SSC2.Input


title: A12_Unt_220331, RNA


title: A09_DAC_220331, RNA


title: SSC3.Input


title: COVID-19,Convalescent,individual148,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-R148-V1
sample_age:28,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

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.

value: Whole blood

value: M

tag: severity scale

tag: severity class

tag: visit number


title: A08_DAC_220331, RNA


title: Primary tumor  [Zvi_lib1_scRNA-seq]

description: Single cell sequencing


title: SSC1.IP


title: SSC1.Input


title: A07_DAC_220331, RNA


title: A06_DAC_220331, RNA


title: A05_DAC_220331, RNA


title: iNSC1.IP


title: COVID-19,Convalescent,individual147,Visit1

description:
Library name: C19-R147-V1
sample_age:56,sample_sex:M,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual144,Visit1

description:
Library name: C19-R144-V1
sample_age:55,sample_sex:M,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual146,Visit1

description:
Library name: C19-R146-V1
sample_age:54,sample_sex:M,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual145,Visit1

description:
Library name: C19-R145-V1
sample_age:51,sample_sex:M,severity_scale:0,severity_class:NA


title: A04_DAC_220331, RNA


title: B04_DAC_220331, RNA


title: A11_DAC_220331, RNA


title: SSC2.IP


title: COVID-19,Convalescent,individual142,Visit1

description:
Library name: C19-R142-V1
sample_age:54,sample_sex:M,severity_scale:0,severity_class:NA


title: H11_AZA_220331, NOMe

library_source: genomic

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

molecule: genomic DNA

value: azacytidine


title: COVID-19,Convalescent,individual140,Visit1

description:
Library name: C19-R140-V1
sample_age:51,sample_sex:M,severity_scale:0,severity_class:NA


title: H12_Neg_220331, NOMe

value: control


title: A02_DAC_220331, RNA

value: Peripheral blood


title: A01_Neg_220331, RNA

value: promyeloblast


title: H10_AZA_220331, NOMe

value: Acute promyelocytic leukemia


title: COVID-19,Convalescent,individual138,Visit1

description:
Library name: C19-R138-V1
sample_age:50,sample_sex:M,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual139,Visit1

description:
Library name: C19-R139-V1
sample_age:53,sample_sex:M,severity_scale:0,severity_class:NA


title: H09_AZA_220331, NOMe

value: Female


title: COVID-19,Convalescent,individual137,Visit1

description:
Library name: C19-R137-V1
sample_age:41,sample_sex:M,severity_scale:0,severity_class:NA


title: A03_DAC_220331, RNA

value: decitabine


title: H08_AZA_220331, NOMe


title: H07_AZA_220331, NOMe


title: COVID-19,Convalescent,individual134,Visit1

description:
Library name: C19-R134-V1
sample_age:54,sample_sex:M,severity_scale:0,severity_class:NA


title: H03_AZA_220331, NOMe


title: H02_AZA_220331, NOMe


title: H05_AZA_220331, NOMe


title: H06_AZA_220331, NOMe


title: COVID-19,Convalescent,individual133,Visit1

description:
Library name: C19-R133-V1
sample_age:27,sample_sex:M,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual131,Visit1

description:
Library name: C19-R131-V1
sample_age:37,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual136,Visit1

description:
Library name: C19-R136-V1
sample_age:55,sample_sex:M,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual130,Visit1

description:
Library name: C19-R130-V1
sample_age:29,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual135,Visit1

description:
Library name: C19-R135-V1
sample_age:51,sample_sex:M,severity_scale:0,severity_class:NA


title: H01_Unt_220331, NOMe

value: untreated


title: COVID-19,Convalescent,individual141,Visit1

description:
Library name: C19-R141-V1
sample_age:55,sample_sex:M,severity_scale:0,severity_class:NA


title: H04_AZA_220331, NOMe


title: COVID-19,Convalescent,individual143,Visit1

description:
Library name: C19-R143-V1
sample_age:55,sample_sex:M,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual132,Visit1

description:
Library name: C19-R132-V1
sample_age:30,sample_sex:F,severity_scale:0,severity_class:NA


title: G12_Unt_220331, NOMe


title: COVID-19,Convalescent,individual129,Visit1

description:
Library name: C19-R129-V1
sample_age:51,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual128,Visit1

description:
Library name: C19-R128-V1
sample_age:44,sample_sex:F,severity_scale:0,severity_class:NA


title: G11_AZA_220331, NOMe


title: COVID-19,Convalescent,individual127,Visit1

description:
Library name: C19-R127-V1
sample_age:37,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual125,Visit1

description:
Library name: C19-R125-V1
sample_age:37,sample_sex:F,severity_scale:0,severity_class:NA


title: G10_AZA_220331, NOMe


title: G08_AZA_220331, NOMe


title: G07_AZA_220331, NOMe


title: COVID-19,Convalescent,individual123,Visit1

description:
Library name: C19-R123-V1
sample_age:42,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual126,Visit1

description:
Library name: C19-R126-V1
sample_age:34,sample_sex:F,severity_scale:0,severity_class:NA


title: G06_AZA_220331, NOMe


title: G05_AZA_220331, NOMe


title: COVID-19,Convalescent,individual121,Visit1

description:
Library name: C19-R121-V1
sample_age:41,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual122,Visit1

description:
Library name: C19-R122-V1
sample_age:41,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual119,Visit1

description:
Library name: C19-R119-V1
sample_age:41,sample_sex:F,severity_scale:0,severity_class:NA


title: G04_AZA_220331, NOMe


title: G03_AZA_220331, NOMe


title: COVID-19,Convalescent,individual120,Visit1

description:
Library name: C19-R120-V1
sample_age:44,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual117,Visit1

description:
Library name: C19-R117-V1
sample_age:36,sample_sex:F,severity_scale:0,severity_class:NA


title: F12_Unt_220331, NOMe


title: G02_AZA_220331, NOMe


title: F11_AZA_220331, NOMe


title: G01_Unt_220331, NOMe


title: COVID-19,Convalescent,individual118,Visit1

description:
Library name: C19-R118-V1
sample_age:40,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual116,Visit1

description:
Library name: C19-R116-V1
sample_age:39,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual115,Visit1

description:
Library name: C19-R115-V1
sample_age:39,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual114,Visit1

description:
Library name: C19-R114-V1
sample_age:35,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual113,Visit1

description:
Library name: C19-R113-V1
sample_age:39,sample_sex:F,severity_scale:0,severity_class:NA


title: G09_AZA_220331, NOMe


title: F08_AZA_220331, NOMe


title: F09_AZA_220331, NOMe


title: F10_AZA_220331, NOMe


title: COVID-19,Convalescent,individual124,Visit1

description:
Library name: C19-R124-V1
sample_age:37,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual112,Visit1

description:
Library name: C19-R112-V1
sample_age:52,sample_sex:F,severity_scale:0,severity_class:NA


title: F06_AZA_220331, NOMe


title: F07_AZA_220331, NOMe


title: COVID-19,Convalescent,individual111,Visit1

description:
Library name: C19-R111-V1
sample_age:34,sample_sex:F,severity_scale:0,severity_class:NA


title: F03_AZA_220331, NOMe


title: F05_AZA_220331, NOMe


title: COVID-19,Convalescent,individual110,Visit1

description:
Library name: C19-R110-V1
sample_age:39,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual109,Visit1

description:
Library name: C19-R109-V1
sample_age:44,sample_sex:M,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual106,Visit1

description:
Library name: C19-R106-V1
sample_age:42,sample_sex:M,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual107,Visit1

description:
Library name: C19-R107-V1
sample_age:45,sample_sex:F,severity_scale:0,severity_class:NA


title: F01_Unt_220331, NOMe


title: IFNAR^flox/flox; CD11c-Cre, CD11blo, Nippo, rep2

city: Wellington

first: Franca

last: Ronchese

state: Wellington

address: Gate 7 University of Wellington Central Services Building

department: FR

country: New Zealand

institute: Malaghan Institute of Medical Research

data_processing:
Sequences trimmed using cutadapt 4.9 (-j 40 -u 14), first 14 nt of read 2 trimmed as reccomended by Otago Genomics when not using Cogent NGS pipeline
Trimmed reads mapped to GENCODE GRCm39 M35 mus musculus genome, STAR 2.7.11b (--runMode genomeGenerate --genomeFastaFiles /mnt/GRCm39.primary_assembly.genome.fa --sjdbGTFfile /mnt/gencode.vM35.annotation.gtf --sjdbOverhang 100) / (--outSAMtype BAM SortedByCoordinate )
Read counting performed using Rsubread::featureCounts(primaryOnly = FALSE,isPairedEnd = TRUE,requireBothEndsMapped = TRUE,checkFragLength = FALSE,GTF.featureType = "exon",allowMultiOverlap = FALSE,countMultiMappingReads = TRUE)
Normalisation performed using DESeq2, including p-values, and l2fc. Also performed additional vst normalisation, and (log1p) per kilobase normalisation from gtf file based upon longest transcript length (aka VSTpk).
Assembly: GRCm39 M35 mm39
Supplementary files format and content: comma-separated variables file includes non-normalised exon counts from Rsubread::featureCounts
Supplementary files format and content: comma-separated variables file includes normalised exon counts from DESeq2 (not VST or per kilobase)

molecule: total RNA

source_name: Lymph Node

growth_protocol: CD11c-cre IFNAR fl/fl (IFNAR∆CD11c) mice and IFNAR fl/fl (IFNARWT) cagemates were housed under specific pathogen free conditions.

extract_protocol:
Using QIAzol miRNeasy kit (QIAgen)
Done by Otago Genomics, using SMARTer ® Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian (Takara).

treatment_protocol: Mice were injected intradermally with 300 inactivated N. brasiliensis larvae labelled with CellTracker Orange (CTO).

value: Lymph Node

value: Dendritic Cells

value: IFNAR^flox/flox; CD11c-Cre (C57BL/6)

value: Nippostrongylus brasiliensis


title: IFNAR^flox/flox; CD11c-Cre, CD11bhi, Nippo, rep3


title: IFNAR^flox/flox; CD11c-Cre, CD11blo, PBS, rep1

value: PBS


title: IFNAR^flox/flox; CD11c-Cre, CD11blo, PBS, rep3


title: E10_AZA_220331, NOMe


title: COVID-19,Convalescent,individual104,Visit1

description:
Library name: C19-R104-V1
sample_age:49,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual103,Visit1

description:
Library name: C19-R103-V1
sample_age:46,sample_sex:F,severity_scale:0,severity_class:NA


title: IFNAR^flox/flox; CD11c-Cre, CD11bhi, PBS, rep1


title: E09_AZA_220331, NOMe


title: E11_AZA_220331, NOMe


title: IFNAR^flox/flox; CD11c-Cre, CD11bhi, PBS, rep3


title: F02_AZA_220331, NOMe


title: COVID-19,Convalescent,individual108,Visit1

description:
Library name: C19-R108-V1
sample_age:52,sample_sex:F,severity_scale:0,severity_class:NA


title: F04_AZA_220331, NOMe


title: E12_Unt_220331, NOMe


title: COVID-19,Convalescent,individual102,Visit1

description:
Library name: C19-R102-V1
sample_age:52,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual101,Visit1

description:
Library name: C19-R101-V1
sample_age:46,sample_sex:F,severity_scale:0,severity_class:NA


title: Wildtype, CD11blo, PBS, rep2

value: WT


title: Wildtype, CD11blo, PBS, rep3


title: E08_AZA_220331, NOMe


title: Wildtype, CD11blo, PBS, rep1


title: IFNAR^flox/flox; CD11c-Cre, CD11blo, Nippo, rep3


title: COVID-19,Convalescent,individual100,Visit1

description:
Library name: C19-R100-V1
sample_age:57,sample_sex:F,severity_scale:0,severity_class:NA


title: IFNAR^flox/flox; CD11c-Cre, CD11bhi, PBS, rep2


title: Wildtype, CD11bhi, PBS, rep3


title: Wildtype, CD11bhi, PBS, rep1


title: E06_AZA_220331, NOMe


title: IFNAR^flox/flox; CD11c-Cre, CD11bhi, Nippo, rep2


title: E05_AZA_220331, NOMe


title: IFNAR^flox/flox; CD11c-Cre, CD11bhi, Nippo, rep1


title: Wildtype, CD11blo, Nippo, rep3


title: Wildtype, CD11bhi, PBS, rep2


title: COVID-19,Convalescent,individual097,Visit1

description:
Library name: C19-R097-V1
sample_age:38,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual099,Visit1

description:
Library name: C19-R099-V1
sample_age:48,sample_sex:F,severity_scale:0,severity_class:NA


title: IFNAR^flox/flox; CD11c-Cre, CD11blo, Nippo, rep1


title: E03_AZA_220331, NOMe


title: Wildtype, CD11blo, Nippo, rep1


title: COVID-19,Convalescent,individual098,Visit1

description:
Library name: C19-R098-V1
sample_age:50,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual096,Visit1

description:
Library name: C19-R096-V1
sample_age:52,sample_sex:M,severity_scale:0,severity_class:NA


title: E04_AZA_220331, NOMe


title: E07_AZA_220331, NOMe


title: E02_AZA_220331, NOMe


title: Wildtype, CD11blo, Nippo, rep2


title: COVID-19,Convalescent,individual096,Visit5

description:
Library name: C19-R096-L1
sample_age:53,sample_sex:M,severity_scale:0,severity_class:NA


title: Mitotic chr, PBK KO, rep4

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
Reads were trimmed using fastp (v0.23.3)
Reads were mapped to GRCm39 with bwa-mem (v0.7.17)
Reads were filtered using samtools (v1.17) to retain only properly paired alignments with a quality score ≥3, PCR duplicates were marked using sambamba (v1.0.1)
MACS2 callpeak (version 2.2.8) with the parameters “--nomodel --shift -100 --extsize 200 -g mm” to call accessible regions
Coverage tracks created with deeptools bamCoverage (v3.5.1)
Assembly: GRCm39
Supplementary files format and content: .narrowPeak files contain accessible peak locations for each sample
Supplementary files format and content: .bw (bigwig) files contain coverage tracks for each sample

source_name: preB

growth_protocol: Abelson-transformed WT and PBK KO mouse preB cells were cultured in suspension in IMDM medium supplemented with 12% FCS, 2 mM L-glutamine, 2X non-essential amino acids, antibiotics and 50 µM 2-mercaptoethanol. Cells were maintained at 37 °C with 5% CO2 and split every 2–3 days.

extract_protocol:
Mitotic chromosomes were extracted and purified by flow cytometry. Briefly, arrested preB cells (~108) were incubated for 20 min at RT in 10 ml of hypotonic solution (75 mM KCl, 10 mM MgSO4, 0.5 mM spermidine trihydrochloride (Sigma-Aldrich, S2501), 0.2 mM spermine tetrahydrochloride (Sigma-Aldrich, S2876), pH 8.0), followed by 15 min on ice in 3 ml of polyamine buffer (80 mM KCl, 15 mM Tris-HCl, 2 mM EDTA, 0.5 mM EGTA, 3 mM DTT, 0.25% Triton X-100, 0.5 mM spermidine trihydrochloride, 0.2 mM spermine tetrahydrochloride, pH 7.7). Samples were vortexed for 30 s at maximum speed, passed several times through a 21-gauge needle, centrifuged at 200 g for 2 min, filtered through a 20 μm CellTrics filter (Sysmex) and stored at 4 °C overnight. Next day, chromosomes were stained on ice by adding 5 μg/ml Hoechst 33258 (Sigma-Aldrich, 94403), 25 μg/ml Chromomycin A3 (Sigma-Aldrich, C2659) and MgSO4 (10 mM final) for 45 min, followed by addition of sodium citrate (10 mM final) and sodium sulfite (25 mM final) for 1 h.  Stained chromosomes were purified using a Becton Dickinson Influx with BD FACS Sortware (v1.2.0.142), using a 70 μm nozzle tip, a drop-drive frequency of 96 kHz and a sheath pressure of 448 kPa. Forward scatter was measured with a 488 nm laser (Coherent Sapphire, 200 mW); Hoechst 33258 was analysed with a 355 nm air-cooled laser (Spectra Physics Vanguard, 350 mW) and 400 nm (long-pass)/500 nm (short-pass) filters; Chromomycin A3 was analysed with a water-cooled 460 nm laser (Coherent Genesis, 500 mW) and 500 nm (long-pass)/600 nm (short-pass) filters.
2 x 106 flow-sorted chromosomes were pelleted at 10,000 g for 10 min at 4 °C before tagmentation in a 50 μl reaction (2.5 μl Tagmentase (loaded Tn5 transposase, Diagenode, C01070012), 25 μl 2X Tagmentation buffer (Diagenode, C01019043), 22.5 μl H2O) at 37 °C for 30 min with 1,000 rpm shaking.
DNA was purified (Qiagen MinElute PCR purification kit) and PCR amplified (7 cycles; NEBNext High Fidelity master mix) with primers containing sequencing adapters. Amplified libraries were purified using 1.8X volume Ampure XP beads (Beckman Coulter), firstly using 0.5X beads to remove large fragments, before using the remaining volume of beads to capture and purify libraries.

treatment_protocol: Cells were arrested in metaphase by diluting preB cells to approximately 106 cells/ml and additing 0.1 μg/ml demecolcine (Sigma-Aldrich, D1925) for 5 h.

value: preB

value: Pbk-/-


title: Wildtype, CD11bhi, Nippo, rep2


title: Wildtype, CD11bhi, Nippo, rep1


title: E01_Unt_220331, NOMe


title: COVID-19,Convalescent,individual105,Visit1

description:
Library name: C19-R105-V1
sample_age:48,sample_sex:F,severity_scale:0,severity_class:NA

value: Whole blood


title: Wildtype, CD11bhi, Nippo, rep3


title: D12_Unt_220331, NOMe


title: D10_DAC_220331, NOMe


title: Mitotic chr, PBK KO, rep2


title: COVID-19,Convalescent,individual095,Visit1

description:
Library name: C19-R095-V1
sample_age:54,sample_sex:M,severity_scale:0,severity_class:NA

value: M


title: COVID-19,Convalescent,individual094,Visit1

description:
Library name: C19-R094-V1
sample_age:30,sample_sex:F,severity_scale:0,severity_class:NA


title: Mitotic chr, WT, rep1

value: Pbk+/+


title: D11_DAC_220331, NOMe

value: Peripheral blood


title: COVID-19,Convalescent,individual093,Visit1

description:
Library name: C19-R093-V1
sample_age:51,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual092,Visit1

description:
Library name: C19-R092-V1
sample_age:51,sample_sex:F,severity_scale:0,severity_class:NA


title: Mitotic chr, WT, rep2


title: Mitotic chr, WT, rep3


title: Unstimulated Donot 86

city: Mountain View

first: Kitt

middle: D

last: Paraiso

state: CA

address: 320 Logue Ave.

department: Bioinformatics

institute: Cellecta, Inc.

description:
Library name: 86-UN
FC17_clonotype_counts.xlsx

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

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).

value: Naive CD8+ T cell

value: Unstimulated Donot 86


title: Unstimulated Donor 55

description:
Library name: 55-UN
FC17_clonotype_counts.xlsx

value: Unstimulated Donor 55


title: SL9-IST-Stimulated Donor 55

description:
Library name: 55-SL9
FC17_clonotype_counts.xlsx

value: SL9-IST Donor 55


title: COVID-19,Convalescent,individual091,Visit5

description:
Library name: C19-R091-L1
sample_age:25,sample_sex:F,severity_scale:0,severity_class:NA

value: Female


title: D09_DAC_220331, NOMe

value: promyeloblast

value: Acute promyelocytic leukemia

value: decitabine


title: Mitotic chr, PBK KO, rep3


title: SL9-IST-Stimulated Donor 86

description:
Library name: 86-SL9
FC17_clonotype_counts.xlsx

value: SL9-IST Donor 86


title: COVID-19,Convalescent,individual091,Visit1

description:
Library name: C19-R091-V1
sample_age:24,sample_sex:F,severity_scale:0,severity_class:NA


title: D08_DAC_220331, NOMe


title: Mitotic chr, PBK KO, rep1


title: WT_2

city: Fuzhou

first: Long-Bin

last: zhang

state: Fujian

address: Jianping Road

department: College of Biological Science and Engineering

institute: Fuzhou University

description:
Library name: SAMPLE17
No more information

data_processing:
Basecalls performed using Illumina CASAVA1.7 software
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
The mapped reads of each sample were assembled by StringTie (v1.3.3b)
featureCounts v1.5.0-p3 was used to count the reads numbers mapped toeach gene
Differential expression analysis oftwo conditions/groups (two biological replicates per condition) was performedusing the DESeq2 R package (1.20.0)
Assembly: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/280/675/GCF_000280675.1_ASM28067v1/GCF_000280675.1_ASM28067v1_genomic.fna.gz
Supplementary files format and content: The data was filed with FPKM of each detected genes and formed excel file
Supplementary files format and content: raw counts

organism: Beauveria bassiana

source_name: submerged hyphae

growth_protocol: Aliquots of 50 mL 10^6 conidia/mL cuticle broth (CB) supplemented with 1% cuticle powder of Locusta migratoria exoskeleton were incubated by shaking at 150 rpm for 5 days at 25 degree centigrade

extract_protocol:
After 5-day CB incubation, total RNA was extracted from three replicating cultures of Ngs1-deletion mutants and wild-type strain under the action of an RNAisoTM Plus Reagent (TaKaRa, Dalian, China), respectively
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-Toligo-attached magnetic beads. Fragmentation was carried out usingdivalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragmentsof preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers andIndex (X) Primer. At last, PCR products were purified (AMPure XPsystem) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: No specific treatment for each strain

value: submerged hyphae

value: hyphal body

value: Wild type

value: Cultivated in cuticle broth (CB) supplemented with 1% cuticle powder of Locusta migratoria exoskeleton, followed by shaking at 150 rpm for 5 days at 25 degree centigrade

value: Day 5


title: IFNAR^flox/flox; CD11c-Cre, CD11blo, PBS, rep2

value: Lymph Node

value: Dendritic Cells

value: IFNAR^flox/flox; CD11c-Cre (C57BL/6)

value: PBS


title: Mitotic chr, WT, rep4

value: preB

value: Pbk+/+


title: COVID-19,Convalescent,individual092,Visit5

description:
Library name: C19-R092-L1
sample_age:52,sample_sex:F,severity_scale:0,severity_class:NA

value: Whole blood


title: COVID-19,Convalescent,individual089,Visit1

description:
Library name: C19-R089-V1
sample_age:33,sample_sex:M,severity_scale:0,severity_class:NA

value: M


title: Hxk1_1

description:
Library name: SAMPLE13
No more information

value: Hxk1 deletion


title: D07_DAC_220331, NOMe

value: Peripheral blood

value: promyeloblast

value: Acute promyelocytic leukemia

value: Female


title: Hex2_3

description:
Library name: SAMPLE12
No more information

value: submerged hyphae

value: hyphal body

value: Hex2 deletion


title: Hex2_1

description:
Library name: SAMPLE10
No more information

value: Cultivated in cuticle broth (CB) supplemented with 1% cuticle powder of Locusta migratoria exoskeleton, followed by shaking at 150 rpm for 5 days at 25 degree centigrade

value: Day 5


title: WT_3

description:
Library name: SAMPLE18
No more information

value: Wild type


title: Hxk1_3

description:
Library name: SAMPLE15
No more information


title: Hxk1_2

description:
Library name: SAMPLE14
No more information


title: WT_1

description:
Library name: SAMPLE16
No more information


title: D04_DAC_220331, NOMe

value: decitabine


title: COVID-19,Convalescent,individual090,Visit1

description:
Library name: C19-R090-V1
sample_age:42,sample_sex:M,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual088,Visit1

description:
Library name: C19-R088-V1
sample_age:21,sample_sex:M,severity_scale:0,severity_class:NA


title: Hex1_2

description:
Library name: SAMPLE8
No more information

value: Hex1 deletion


title: D03_DAC_220331, NOMe


title: Hex1_1

description:
Library name: SAMPLE7
No more information


title: COVID-19,Convalescent,individual087,Visit1

description:
Library name: C19-R087-V1
sample_age:48,sample_sex:M,severity_scale:0,severity_class:NA


title: D06_DAC_220331, NOMe


title: Hex1_3

description:
Library name: SAMPLE9
No more information


title: D01_Unt_220331, NOMe

value: untreated


title: Hex2_2

description:
Library name: SAMPLE11
No more information


title: GPI1_2

description:
Library name: SAMPLE5
No more information

value: GPI1 deletion


title: GPI1_1

description:
Library name: SAMPLE4
No more information


title: Alg14_3

description:
Library name: SAMPLE3
No more information

value: Alg14 deletion


title: COVID-19,Convalescent,individual086,Visit1

description:
Library name: C19-R086-V1
sample_age:32,sample_sex:F,severity_scale:0,severity_class:NA

value: Whole blood


title: GPI1_3

description:
Library name: SAMPLE6
No more information


title: D02_DAC_220331, NOMe


title: COVID-19,Convalescent,individual083,Visit1

description:
Library name: C19-R083-V1
sample_age:40,sample_sex:F,severity_scale:0,severity_class:NA


title: D05_DAC_220331, NOMe


title: COVID-19,Convalescent,individual085,Visit1

description:
Library name: C19-R085-V1
sample_age:28,sample_sex:M,severity_scale:0,severity_class:NA

value: M


title: Alg14_2

description:
Library name: SAMPLE2
No more information


title: C11_DAC_220331, NOMe

value: Peripheral blood


title: COVID-19,Convalescent,individual084,Visit1

description:
Library name: C19-R084-V1
sample_age:48,sample_sex:M,severity_scale:0,severity_class:NA


title: C10_DAC_220331, NOMe

value: promyeloblast


title: COVID-19,Convalescent,individual081,Visit1

description:
Library name: C19-R081-V1
sample_age:37,sample_sex:F,severity_scale:0,severity_class:NA


title: C09_DAC_220331, NOMe

value: Acute promyelocytic leukemia


title: DU145-RCC2-KO rep1

city: Birmingham

first: Lizhong

last: Wang

address: 740 20th St S

institute: UAB

data_processing:
In our project, we sequenced 6 samples on BGISEQ-500 Platform in total
After reads filtering, we map clean reads to reference genome using HISAT
IGV(Integrative Genomics Viewer) tool can be used to review the mapping result.
we use StringTie to reconstruct transcripts, and with genome annotation information we identify novel transcripts by using Cuffcompare(a tool of Cufflinks ) and predict the coding ability of those new transcripts using CPC
After genome mapping, we use GATK to call  SNP  and  INDEL  variant for each sample.
Assembly: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: RCC2 KO  DU145 cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: prostate

value: prostate cancer cells

value: RCC2 KO


title: DU145-RCC2-KO rep2


title: COVID-19,Convalescent,individual081,Visit5

description:
Library name: C19-R081-L1
sample_age:38,sample_sex:F,severity_scale:0,severity_class:NA

value: Female


title: DU145-Scr rep2

source_name: Scramble DU145 cells

value: Scramble


title: DU145-Scr rep1


title: C07_DAC_220331, NOMe


title: C08_DAC_220331, NOMe


title: COVID-19,Convalescent,individual082,Visit1

description:
Library name: C19-R082-V1
sample_age:41,sample_sex:M,severity_scale:0,severity_class:NA


title: C06_DAC_220331, NOMe


title: C12_Unt_220331, NOMe


title: WT_f_REP4

city: Munich

first: Felix

middle: L

last: Struebing

address: Feodor-Lynen-Str. 23

department: Center for Neuropathology

country: Germany

institute: University of Munich

description: Library name: OBMG14

data_processing:
Alignment to mm39 using STAR, export of raw count matrix
Assembly: GRCm39
Supplementary files format and content: tab-delimited text of raw count matrix

source_name: olfactory bulb

extract_protocol:
MACS (CD11b) bead isolation of olfactory bulb microglia
Takara SMART-Seq Stranded (634444)

value: olfactory bulb

value: WT


title: COVID-19,Convalescent,individual079,Visit1

description:
Library name: C19-R079-V1
sample_age:26,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual080,Visit1

description:
Library name: C19-R080-V1
sample_age:51,sample_sex:F,severity_scale:0,severity_class:NA


title: DU145-CD24-KO rep2

source_name: CD24 KO  DU145 cells

value: CD24 KO


title: KI_f_REP3

description: Library name: OBMG11

value: KI


title: Alg14_1

description:
Library name: SAMPLE1
No more information

value: submerged hyphae

value: hyphal body

value: Cultivated in cuticle broth (CB) supplemented with 1% cuticle powder of Locusta migratoria exoskeleton, followed by shaking at 150 rpm for 5 days at 25 degree centigrade

value: Day 5


title: KI_f_REP4

description: Library name: OBMG13


title: KI_m_REP4

description: Library name: OBMG16


title: COVID-19,Convalescent,individual078,Visit5

description:
Library name: C19-R078-L1
sample_age:52,sample_sex:F,severity_scale:0,severity_class:NA

value: Whole blood


title: WT_f_REP2

description: Library name: OBMG8


title: COVID-19,Convalescent,individual077,Visit1

description:
Library name: C19-R077-V1
sample_age:30,sample_sex:M,severity_scale:0,severity_class:NA

value: M


title: C04_DAC_220331, NOMe

value: Peripheral blood

value: promyeloblast

value: decitabine


title: WT_m_REP4

description: Library name: OBMG10


title: WT_f_REP3

description: Library name: OBMG12


title: WT_m_REP3

description: Library name: OBMG9


title: KI_f_REP2

description: Library name: OBMG5


title: C03_DAC_220331, NOMe

value: Acute promyelocytic leukemia


title: KI_m_REP2

description: Library name: OBMG7


title: COVID-19,Convalescent,individual075,Visit1

description:
Library name: C19-R075-V1
sample_age:49,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual076,Visit1

description:
Library name: C19-R076-V1
sample_age:46,sample_sex:M,severity_scale:0,severity_class:NA


title: KI_f_REP1

description: Library name: OBMG3


title: KI_m_REP1

description: Library name: OBMG6


title: C02_DAC_220331, NOMe


title: C05_DAC_220331, NOMe


title: WT_m_REP2

description: Library name: OBMG2


title: KI_m_REP3

description: Library name: OBMG15


title: WT_m_REP1

description: Library name: OBMG1


title: BCAA 5+3 AML cells biol rep3

city: Boston

first: Christina

last: Mayerhofer

state: MA

address: 185 Cambridge St.

department: Center for Regenerative Medicine

institute: MGH, Simches building

data_processing:
Sequencing data was demultiplexed using Cell Ranger (10x Genomics).
Reads were aligned to the mouse genome mm10 release 102 using Rsubread
R featureCounts was used to detect exons summarized to gene counts.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: bone marrow

growth_protocol: The MLL-AF9 leukemia cells express GFP under the control of the ubiquitin transporter and luciferase under the control of the β-actin promoter.  Leukemic cells from a terminally ill mouse were harvested and expanded ex vivo in RPMI1640 medium (Lonza) supplemented with 10% fetal bovine serum (FBS; Gibco), 100 U/ml penicillin, 100 μg/ml streptomycin, 2mM L-glutamine (all from Corning), 20 ng/ml recombinant mouse SCF (rmSCF), 10 ng/ml recombinant mouse interleukin 3 (rmIL-3) and 10 ng/ml rmIL-6 (all from R&D Systems).

extract_protocol:
Mice were euthanized at the point of maximum response of chemotherapy and femurs, tibias, pelvis and humeri were isolated and cleaned to remove muscle. Bones were then crushed using a pre-cooled mortar and pestle in ice-cold flow buffer (PBS containing 2% FBS), and the obtained BM cell suspension was passed through a 70 μm cell strainer. Red blood cells were removed by incubating cells for 5 minutes in ACK lysing buffer (Gibco) on ice, the remaining BM cells were washed and resuspended in ice-cold flow buffer containing the viability dye 7-aminoactinomycin D (7AAD; BD Biosciences). Viable cells (AML cells GFP+7AAD-) were sorted on a BD FACSAria II (BD Biosciences) with the sample collector cooled to 4°C. RNA was extracted with Trizole (Life Technologies, 15596018). RNA-seq libraries were generated using the Roche Kapa mRNA HyperPrep protocol according to the users’ manual. Libraries were pooled and sequenced on the Illumina platform with 2x 38bp reads.
RNA-seq libraries were generated using the Roche Kapa mRNA HyperPrep protocol according to the users’ manual. Libraries were pooled and sequenced on the Illumina platform with 2x 38bp reads.

treatment_protocol: Recipient male mice (age 8-10 weeks) were injected intravenously (retro-orbital) with 1 million leukemia cells in 200 μl PBS without preconditioning. Disease progression was tracked in luciferase-expressing AML using bioluminescence imaging. When reaching a critical AML burden, mice were treated with 5+3 (cytarabine, 100 mg/kg, once daily for 5 days and doxorubicin, 3 mg/kg, once daily for the first 3 days) or vehicle (PBS) delivered via i.p. injection.

value: bone marrow

value: MLL-AF9 AML

value: Acute myeloid leukemia

value: BCAA 5+3


title: BCAA 5+3 AML cells biol rep2

value: WT


title: B10_DAC_220331, NOMe

value: Female


title: C01_Unt_220331, NOMe

value: untreated


title: COVID-19,Convalescent,individual078,Visit1

description:
Library name: C19-R078-V1
sample_age:51,sample_sex:F,severity_scale:0,severity_class:NA


title: WT_f_REP1

description: Library name: OBMG4

value: olfactory bulb


title: COVID-19,Convalescent,individual074,Visit1

description:
Library name: C19-R074-V1
sample_age:31,sample_sex:F,severity_scale:0,severity_class:NA


title: BCAA 5+3 AML cells biol rep1


title: COVID-19,Convalescent,individual073,Visit1

description:
Library name: C19-R073-V1
sample_age:32,sample_sex:F,severity_scale:0,severity_class:NA


title: B12_Unt_220331, NOMe


title: COVID-19,Convalescent,individual072,Visit1

description:
Library name: C19-R072-V1
sample_age:25,sample_sex:M,severity_scale:0,severity_class:NA


title: AA 5+3 AML cells biol rep5


title: B09_DAC_220331, NOMe


title: COVID-19,Convalescent,individual071,Visit1

description:
Library name: C19-R071-V1
sample_age:25,sample_sex:F,severity_scale:0,severity_class:NA


title: AA 5+3 AML cells biol rep3


title: AA 5+3 AML cells biol rep4


title: AA 5+3 AML cells biol rep2


title: B08_DAC_220331, NOMe


title: COVID-19,Convalescent,individual070,Visit1

description:
Library name: C19-R070-V1
sample_age:27,sample_sex:M,severity_scale:0,severity_class:NA


title: ATAC_293T_KO_DMSO_rep3

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:
Library name: ATAC_293T_KO_DMSO_rep3
ATAC-seq in β-catenin KO HEK 293T cells

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

source_name: HEK 293T

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). HEK 293T cells were cultured in DMEM supplemented with 5% FBS and 1% PS

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.

value: HEK 293T

value: Beta-catenin KO

value: DMSO


title: B07_DAC_220331, NOMe

source_name: Peripheral blood


title: Donor1 CAIS

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

description: Library name: Donor1_CAIS

data_processing:
FASTQ files were demultiplexed from the raw base call (BCL) files using 10x Genomics 'cellranger demux' (CellRanger v3.0.2).
The whitelist of cell barcodes was identified with 'umi_tools whitelist --set-cell-number N --bc-pattern=CCCCCCCCCCCCCCCCNNNNNNNNNNNN' (umi_tools v1.0.0); with N = 2000 for donor1 and donor2, 5000 for donor3 and 1500 for donorOA.
Reads of the whitelisted cells were extracted with 'umi_tools extract --bc-pattern=CCCCCCCCCCCCCCCCNNNNNNNNNNNN --filter-cell-barcode --whitelist=whitelist.txt' (umi_tools v1.0.0).
Extracted reads were aligned with STAR aligner (v2.5.3a) to the primary assembly of human genome (GRCh38) with parameter '--outFilterMultimapNmax 1' (to exclude multi-mapping reads).
Mapped reads were assigned to gene_name attributes from GENCODE basic annotation for GRCh38 (version 31) using Subread featureCounts (v1.6.4). Results were save in BAM files with option 'featureCounts -R BAM' and succesively sorted and indexed with samtools (v1.9).
Per gene counts were summarized for each cell using 'umi_tools count --per-gene --gene-tag=XT --assigned-status-tag=XS --per-cell' (umi_tools v1.0.0).
Assembly: hg38 (GRCh38 - v31)
Supplementary files format and content: Tab separated files of raw counts;  table with three columns: the gene_id, the cell barcode and the count of deduplicated UMIs. One file per sample, gzipped (.gz).

source_name: testis

extract_protocol:
Fresh testes parenchyma was washed twice in PBS and subjected to enzymatic digestion (collagenase type I, collagenase type IV, hyaluronidase, trypsin, Deoxyribonuclease I; all enzymes at 1 mg/ml in DMEM-F12 without serum) for 10 minutes at 37°C with gentle agitation, repeated twice (1ml of digestion medium each time). The cell suspension was filtered through strainers with mesh size 70µm, washed twice with 0.4% BSA/PBS and filtered through a 40µm cell strainer to obtain single cell.
Chromium Single Cell 3′ Library & Gel Bead Kit v2 kit (10xGenomics).

value: testis

value: CAIS

value: total RNA


title: B06_DAC_220331, NOMe

value: Peripheral blood

value: promyeloblast


title: AA 5+3 AML cells biol rep1


title: COVID-19,Convalescent,individual069,Visit1

description:
Library name: C19-R069-V1
sample_age:44,sample_sex:F,severity_scale:0,severity_class:NA

value: Whole blood


title: ATAC_293T_KO_DMSO_rep2

description:
Library name: ATAC_293T_KO_DMSO_rep2
ATAC-seq in β-catenin KO HEK 293T cells


title: ATAC_293T_KO_DMSO_rep1

description:
Library name: ATAC_293T_KO_DMSO_rep1
ATAC-seq in β-catenin KO HEK 293T cells


title: ATAC_293T_WT_BRM014_rep3

description:
Library name: ATAC_293T_WT_BRM014_rep3
ATAC-seq in HEK 293T cells treated with BRM014


title: COVID-19,Convalescent,individual068,Visit1

description:
Library name: C19-R068-V1
sample_age:48,sample_sex:M,severity_scale:0,severity_class:NA

value: M


title: COVID-19,Convalescent,individual067,Visit1

description:
Library name: C19-R067-V1
sample_age:45,sample_sex:F,severity_scale:0,severity_class:NA


title: B04_DAC_220331, NOMe

value: Acute promyelocytic leukemia

value: decitabine


title: B05_DAC_220331, NOMe


title: ATAC_293T_WT_BRM014_rep1

description:
Library name: ATAC_293T_WT_BRM014_rep1
ATAC-seq in HEK 293T cells treated with BRM014


title: ATAC_293T_WT_BRM014_rep2

description:
Library name: ATAC_293T_WT_BRM014_rep2
ATAC-seq in HEK 293T cells treated with BRM014


title: COVID-19,Convalescent,individual066,Visit1

description:
Library name: C19-R066-V1
sample_age:36,sample_sex:F,severity_scale:0,severity_class:NA


title: ATAC_293T_WT_DMSO_rep3

description:
Library name: ATAC_293T_WT_DMSO_rep3
ATAC-seq in HEK 293T cells treated with DMSO


title: B03_DAC_220331, NOMe


title: ATAC_293T_WT_DMSO_rep2

description:
Library name: ATAC_293T_WT_DMSO_rep2
ATAC-seq in HEK 293T cells treated with DMSO


title: B11_DAC_220331, NOMe


title: ATAC_293T_WT_DMSO_rep1

description:
Library name: ATAC_293T_WT_DMSO_rep1
ATAC-seq in HEK 293T cells treated with DMSO


title: COVID-19,Convalescent,individual065,Visit1

description:
Library name: C19-R065-V1
sample_age:56,sample_sex:F,severity_scale:0,severity_class:NA


title: B02_DAC_220331, NOMe


title: COVID-19,Convalescent,individual064,Visit1

description:
Library name: C19-R064-V1
sample_age:20,sample_sex:F,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual063,Visit1

description:
Library name: C19-R063-V1
sample_age:24,sample_sex:F,severity_scale:0,severity_class:NA


title: B01_Unt_220331, NOMe


title: ChIP_p300_H295R_BRM014_rep1

description:
Library name: ChIP_p300_H295R_BRM014_rep1
CBP/p300 ChIP-seq in H295R cells treated with BRM014

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

extract_protocol:
Lysates were obtained from sonicated nuclei crosslinked with either 1% formaldehyde and 2 mM disuccinimidyl glutarate (double cross-linking) for BAF subunits, β-catenin and CBP/p300, 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-CBP/p300, Abcam #ab14990


title: ChIP_p300_H295R_DMSO_rep2

description:
Library name: ChIP_p300_H295R_DMSO_rep2
CBP/p300 ChIP-seq in H295R cells treated with DMSO

value: Anti-CBP/p300, Abcam #ab14989

value: WT


title: ChIP_p300_H295R_BRM014_rep2

description:
Library name: ChIP_p300_H295R_BRM014_rep2
CBP/p300 ChIP-seq in H295R cells treated with BRM014

value: Anti-CBP/p300, Abcam #ab14991


title: ChIP_p300_H295R_DMSO_rep1

description:
Library name: ChIP_p300_H295R_DMSO_rep1
CBP/p300 ChIP-seq in H295R cells treated with DMSO

value: Anti-CBP/p300, Abcam #ab14988


title: A12_Unt_220331, NOMe

value: Female

value: untreated


title: COVID-19,Convalescent,individual061,Visit1

description:
Library name: C19-R061-V1
sample_age:20,sample_sex:F,severity_scale:0,severity_class:NA


title: ChIP_p300_293T_DMSO_rep2

description:
Library name: ChIP_p300_293T_DMSO_rep2
CBP/p300 ChIP-seq in HEK 293T cells treated with DMSO

value: HEK 293T

value: Anti-CBP/p300, Abcam #ab14985

value: DMSO


title: COVID-19,Convalescent,individual062,Visit1

description:
Library name: C19-R062-V1
sample_age:47,sample_sex:M,severity_scale:0,severity_class:NA


title: ChIP_p300_293T_BRM014_rep1

description:
Library name: ChIP_p300_293T_BRM014_rep1
CBP/p300 ChIP-seq in HEK 293T cells treated with BRM014

value: Anti-CBP/p300, Abcam #ab14986


title: A11_DAC_220331, NOMe

value: Peripheral blood


title: ChIP_p300_293T_BRM014_rep2

description:
Library name: ChIP_p300_293T_BRM014_rep2
CBP/p300 ChIP-seq in HEK 293T cells treated with BRM014

value: Anti-CBP/p300, Abcam #ab14987


title: ChIP_p300_293T_DMSO_rep1

description:
Library name: ChIP_p300_293T_DMSO_rep1
CBP/p300 ChIP-seq in HEK 293T cells treated with DMSO

value: Anti-CBP/p300, Abcam #ab14984


title: COVID-19,Convalescent,individual060,Visit1

description:
Library name: C19-R060-V1
sample_age:34,sample_sex:M,severity_scale:0,severity_class:NA

value: Whole blood

value: M


title: HCC15_N2_DOXI

city: Madrid

first: Rafael

last: Torres

state: Madrid

address: Darwin 3

department: Bioinformatics for Genomics and Proteomics (BioinfoGP)

country: Spain

institute: CNB

description: Library name: N2_DOXI

data_processing:
Quality analysis performed with FASTQC v0.11.5
Primers and barcodes removed keeping only 20-nt sequences to be matched to SAM v1 reference gRNA sequences. We used cutadapt v 1.15 with -g CGAAACACCG -e 0.05 -m 20 -M 20 -O 10 -l 20
gRNA quantification with MAGeCK v4.6.7 using mageck count –trim-5 0 (no trimming) and –normmethod median in miniconda environment
Multiple comparison of conditions (as DOXI vs NODOXI samples) were done using mageck test. For each comparison, the command mageck test was run with parameters -k (test_vs_control_comparison_name).count.txt -t (condition_ considered_as_test) -c (condition_considered_as_control) -n (test_vs _control_comparison_name) –pdf-report –norm-method median (median normalization, default option). As SAM V1 library lacks control guides, no - -control-sgrna parameter is used. The results were combined with those obtained by CRISPhierRmix (Bodapati et al) , which provides a greater spectrum of possible hits with statistical significance whilst MAGeCK provides information about the direction and magnitude of the change between conditions (in the form of Log Fold Change) and the normalized count values for the sgRNAs that support these calculations.
Assembly: SAM v1 human library
Supplementary files format and content: all_samples.count.xlsx: Excel format. Raw counts for all the genes in the samples
Supplementary files format and content: md5sum_fastq_files.txt: Text file with the MD5 code for the FASTQ files
Supplementary files format and content: sam_human_library_annotated.xlsx: Excel format. SAM v1 human library data
Library strategy: CRISPR Screen

growth_protocol: The following LUSC cell lines were purchased from the American Type Culture Collection: SK-MES-1 (HTB-58), NCI-H520 (HTB182), and NCI-H226 (CRL-5826).  HCC-15 (ACC-496) was obtained from the DSMZ collection. Normal airway epithelial cells (HSAEC1/KT) were acquired from ATCC.Cells were maintained in DMEM, RPMI-1640, or MEM (Gibco)containing 10% fetal bovine serum (TicoEurope), 2 mM L-glutamine, 10 mM HEPES, 100 IU/ml penicillin, 100ug/ml streptomycin, 1 mM sodium pyruvate, 100× MEM non-essential amino acids (Biowest), and 50 μg/ml gentamicin (Sigma). Cells were maintained at 37 °C, 5% CO2, and 95% humidity. HSAEK1/KT cells were cultured in SABMTM small airway epithelial cell growth basal medium supplemented with SAGMTM Medium SingleQuotsTM (Lonza).

extract_protocol:
The inducible NFE2L2 silencing vector was previously designed following the instructions in the pLKO-Tet-On User Manual (Novartis, Addgene).For infection, HEK-293T cells were transfected with jetPEI DNA reagent (Polyplus) and 150 mM NaCl solution, using the Tet-pLKO-neo shNFE2L2 vector, along with the pCM-V-VSV-G and psPAX2 plasmids (Addgene) following the manufacturer’s instructions. In parallel, target cells were seeded (150,000 cells/well in a 6-well plate). At 48 and 72 h, supernatants containing viral particles were filtered (0.45 µm; Millipore), supplemented with polybrene (8 µg/ml, Sigma), and added to the target cells. Plates were centrifuged for 90 min at 530 × g. After 5-6 h of incubation, the medium was replaced with the standard culture medium of the target cells. The following day, geneticin (G418, 0.3 mg/ml) was added to the culture medium for selection, and cells were maintained under selection for 15 days. Doxycycline (2 μg/ml, 96 h) was added. For the experiments with oxidative stress, the ROS inducer RSL3 (4.5 µM) or its vehicle was added for the last 24 h.In the case of PIK3CA overexpression, infection was performed as described above, except that HEK-293T cells were transfected with pLV-SFFV-PIK3CA-WPRE-Ubc-Emerald (Addgene 203797).CRISPRa library experiment workflow is as follows. To achieve sufficient representation of the sgRNA library, at least 35×106 cells were required at the final time point. HCC15 target cells (3×106 cells/well in a 6-well plate) were seeded, infected at an MOI of 0.3, and selected with puromycin (1 μg/ml, 96 hours). After one week of cell culture recovery in normal medium, 1.3 million cells/p150 plate were seeded per condition (or 0.6 million for the negative controls cells). Then, doxycycline was added (2 μg/ml;96 h) with RSL3 (4.5 μM) or DMSO vehicle for the last 24 hours. p150 plates were collected to extract genomic DNA. Extra plates were used to check NFE2L2 silencing and RSL3 treatment by qRT-PCR and PI assay. A control cell plate infected with the library but without treatment was used to check the different sgRNA representation.  The detailes of the different steps are described in Joung J, Konermann S, etal. Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. Nat Protoc. 2017 Apr;12(4):828-863. doi: 10.1038/nprot.2017.016.
the CRISPRa library (SAM LIBRARY) is well described in Joung J, Konermann S, etal. Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. Nat Protoc. 2017 Apr;12(4):828-863. doi: 10.1038/nprot.2017.016.

treatment_protocol: Vectors of the CRISPRa SAM system. Vector 1 includes dead (d)Cas9 bound to VP64, vector 2 encodes MS2 sequence and P65-HSF1 transcriptional activators;vector 3 is the sgRNA vector with RNA loops for binding to MS2. Vector1 and 2 were infected in HCC15 cells.

value: non-small cell lung carcinoma

value: N2 no NRF2 in ROS stress conditions, doxycycline selection

tag: index

value: REVERSE 7


title: HCC15_N5_DOXI

description: Library name: N5_DOXI

value: N5 no NRF2 in ROS stress conditions, doxycycline selection

value: REVERSE 5


title: HCC15_N7_DOXI

description: Library name: N7_DOXI

value: N7 no NRF2 in ROS stress conditions, doxycycline selection

value: REVERSE 3


title: COVID-19,Convalescent,individual059,Visit1

description:
Library name: C19-R059-V1
sample_age:33,sample_sex:F,severity_scale:0,severity_class:NA

value: Female


title: HCC15_N5_NODOXI

description: Library name: N5_NODOXI

value: N5 NRF2 activated, ROS stress, no Doxycycline selection

value: REVERSE 4


title: HCC15_N5b_NODOXI

description: Library name: N5b_NODOXI

value: N5b NRF2 activated, ROS stress, no Doxycycline selection

value: REVERSE 6


title: COVID-19,Convalescent,individual058,Visit1

description:
Library name: C19-R058-V1
sample_age:42,sample_sex:M,severity_scale:0,severity_class:NA


title: A08_DAC_220331, NOMe

value: Peripheral blood

value: promyeloblast

value: Acute promyelocytic leukemia

value: decitabine


title: COVID-19,Convalescent,individual057,Visit1

description:
Library name: C19-R057-V1
sample_age:48,sample_sex:M,severity_scale:0,severity_class:NA

value: Whole blood

value: M


title: HCC15_UNTREATED

description: Library name: UNTREATED

value: non-small cell lung carcinoma

value: sg-library infection but with no additional treatment

value: REVERSE 1


title: A07_DAC_220331, NOMe


title: HCC15_N7_NODOXI

description: Library name: N7_NODOXI

value: N7 NRF2 activated, ROS stress, no Doxycycline selection

value: REVERSE 2


title: A06_DAC_220331, NOMe


title: COVID-19,Convalescent,individual056,Visit1

description:
Library name: C19-R056-V1
sample_age:26,sample_sex:M,severity_scale:0,severity_class:NA


title: RUCAPARIB_RNA_rep4

first: Steven

last: McMahon

address: 233 S 10th St

department: Biochemistry and Molecular Biology

institute: Thomas Jefferson University

description: Library name: MC021_RUCAPARIB_RNA_rep4

data_processing:
RNA-seq data were quantified from reads mapping to transcripts, to abundance using the latest version of Kallisto. Differential gene expression was determined via DESeq2 after converting to raw gene counts.
Assembly: hg19 (homo sapiens)
Supplementary files format and content: Kallisto quantified abundance files as tsv

extract_protocol:
RNA was extracted and purified using Trizol Reagent per the manufacturer’s instructions.
A directional library was prepared for sequencing on an Illumina platform by Novogene following their company policies and procedures.

value: human prostate cancer cell line

value: RUCAPARIB


title: DMSO_RNA_rep4

description: Library name: MC019_DMSO_RNA_rep4

value: DMSO


title: COVID-19,Convalescent,individual055,Visit1

description:
Library name: C19-R055-V1
sample_age:56,sample_sex:M,severity_scale:0,severity_class:NA


title: NIRAPARIB_RNA_rep3

description: Library name: MC017_NIRAPARIB_RNA_rep3

value: NIRAPARIB


title: A05_DAC_220331, NOMe

value: Female


title: A04_DAC_220331, NOMe


title: COVID-19,Convalescent,individual054,Visit1

description:
Library name: C19-R054-V1
sample_age:37,sample_sex:F,severity_scale:0,severity_class:NA


title: A10_DAC_220331, NOMe


title: OLAPARIB_RNA_rep3

description: Library name: MC016_OLAPARIB_RNA_rep3

value: OLAPARIB


title: RUCAPARIB_RNA_rep3

description: Library name: MC015_RUCAPARIB_RNA_rep3


title: A09_DAC_220331, NOMe

value: Peripheral blood


title: A03_DAC_220331, NOMe

value: promyeloblast


title: VELIPARIB_RNA_rep3

description: Library name: MC014_VELIPARIB_RNA_rep3

value: VELIPARIB


title: COVID-19,Convalescent,individual053,Visit1

description:
Library name: C19-R053-V1
sample_age:47,sample_sex:M,severity_scale:0,severity_class:NA


title: TALAZOPARIB_RNA_rep2

description: Library name: MC012_TALAZOPARIB_RNA_rep2

value: TALAZOPARIB


title: A02_DAC_220331, NOMe

value: Acute promyelocytic leukemia

value: decitabine


title: DMSO_RNA_rep3

description: Library name: MC013_DMSO_RNA_rep3


title: NIRAPARIB_RNA_rep2

description: Library name: MC011_NIRAPARIB_RNA_rep2


title: COVID-19,Convalescent,individual052,Visit1

description:
Library name: C19-R052-V1
sample_age:59,sample_sex:M,severity_scale:0,severity_class:NA

value: Whole blood

value: M


title: COVID-19,Convalescent,individual051,Visit1

description:
Library name: C19-R051-V1
sample_age:36,sample_sex:F,severity_scale:0,severity_class:NA


title: DMSO_RNA_rep2

description: Library name: MC007_DMSO_RNA_rep2


title: VELIPARIB_RNA_rep4

description: Library name: MC020_VELIPARIB_RNA_rep4


title: A01_Neg_220331, NOMe

value: control


title: OLAPARIB_RNA_rep2

description: Library name: MC010_OLAPARIB_RNA_rep2


title: 9H_AZA_250620, NOMe

value: azacytidine


title: TALAZOPARIB_RNA_rep3

description: Library name: MC018_TALAZOPARIB_RNA_rep3


title: TALAZOPARIB_RNA_rep1

description: Library name: MC006_TALAZOPARIB_RNA_rep1


title: NIRAPARIB_RNA_rep1

description: Library name: MC005_NIRAPARIB_RNA_rep1


title: OLAPARIB_RNA_rep1

description: Library name: MC004_OLAPARIB_RNA_rep1


title: COVID-19,Convalescent,individual049,Visit1

description:
Library name: C19-R049-V1
sample_age:59,sample_sex:M,severity_scale:0,severity_class:NA


title: RUCAPARIB_RNA_rep1

description: Library name: MC003_RUCAPARIB_RNA_rep1


title: 9F_AZA_250620, NOMe


title: COVID-19,Convalescent,individual048,Visit1

description:
Library name: C19-R048-V1
sample_age:23,sample_sex:M,severity_scale:0,severity_class:NA


title: Input UL3 dH1 cloneA Rep2

city: Research Triangle Park

first: Nolan

middle: Garrity

last: Gokey

state: North Carolina

address: 111 TW Alexander Dr, Building 101 Room C432

department: DIR

institute: NIEHS

description:
Library name: Sample 16
ChIP-seq

data_processing:
The BBMap suite was used to trim adapter sequences, remove low quality reads and map ChIP-seq reads
to the human reference genome (T2Tv2) using default paramters.
Assembly: T2Tv2
Supplementary files format and content: bigwig files

source_name: human osteosarcoma cell line

growth_protocol: All cell lines were cultured in DMEM medium (Gibco, Grand Island, NY, USA), supplemented with 10% fetal bovine serum (Atlanta Biologicals, Atlanta, GA, USA), and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
ChIP-seq was performed as described in Hoffman 2018).
Libraries were generated using either the Nextera Tn5 kit (Illumina) or the Swift Biosciences DNA kit according to manufacturer's instructions.

value: human osteosarcoma cell line

value: UL3 cells

value: osteosarcoma

value: vehicle


title: COVID-19,Convalescent,individual047,Visit1

description:
Library name: C19-R047-V1
sample_age:44,sample_sex:M,severity_scale:0,severity_class:NA


title: Input UL3 dH1 cloneA Rep1

description:
Library name: Sample 15
ChIP-seq


title: VELIPARIB_RNA_rep1

description: Library name: MC002_VELIPARIB_RNA_rep1

value: human prostate cancer cell line


title: H3K4me1 UL3 dH1 cloneA Rep2

description:
Library name: Sample 10
ChIP-seq


title: H3K4me1 UL3 dH1 cloneA Rep1

description:
Library name: Sample 9
ChIP-seq


title: 9D_DAC_250620, NOMe

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.

value: Female


title: COVID-19,Convalescent,individual046,Visit1

description:
Library name: C19-R046-V1
sample_age:26,sample_sex:M,severity_scale:0,severity_class:NA


title: H3K27ac UL3 dH1 cloneA Rep2

description:
Library name: Sample 4
ChIP-seq


title: 9C_DAC_250620, NOMe


title: COVID-19,Convalescent,individual045,Visit1

description:
Library name: C19-R045-V1
sample_age:25,sample_sex:F,severity_scale:0,severity_class:NA


title: H3K27ac UL3 dH1 cloneA Rep1

description:
Library name: Sample 3
ChIP-seq


title: ATACseq UL3 dH1 cloneB Rep8

description:
Library name: Sample 15
ATAC-seq

data_processing:
The BBMap suite was used to trim adapter sequences, remove low quality reads and map ATAC-seq reads
to the human reference genome (T2Tv2) using default paramters.
Peaks were called using MACS2 (Zhang 2008), merged and analyzed as described.
Assembly: T2Tv2
Supplementary files format and content: bigwig files
Supplementary files format and content: text files

extract_protocol:
Nuclei were purified as in (Williams et al., 2015) and ATAC seq performed as in (Buenrostro et al., 2015).
Libraries were generated using the Nextera kit according to manufacturer's instructions (Illumina).


title: COVID-19,Convalescent,individual050,Visit1

description:
Library name: C19-R050-V1
sample_age:58,sample_sex:M,severity_scale:0,severity_class:NA


title: 9B_DAC_250620, NOMe


title: COVID-19,Convalescent,individual044,Visit1

description:
Library name: C19-R044-V1
sample_age:64,sample_sex:F,severity_scale:0,severity_class:NA


title: ATACseq UL3 dH1 cloneB Rep7

description:
Library name: Sample 14
ATAC-seq


title: ATACseq UL3 dH1 cloneA Rep5

description:
Library name: Sample 9
ATAC-seq


title: 9A_DAC_250620, NOMe


title: 9G_AZA_250620, NOMe


title: ATACseq UL3 dH1 cloneA Rep4

description:
Library name: Sample 8
ATAC-seq


title: COVID-19,Convalescent,individual043,Visit1

description:
Library name: C19-R043-V1
sample_age:25,sample_sex:M,severity_scale:0,severity_class:NA

value: Male


title: DU145-CD24-KO rep1

value: prostate

value: prostate cancer cells

value: CD24 KO


title: ATACseq UL3 Rep3

description:
Library name: Sample 3
ATAC-seq

value: wild-type


title: 9E_AZA_250620, NOMe

value: Peripheral blood

value: promyeloblast

value: Acute promyelocytic leukemia


title: ATACseq UL3 Rep4

description:
Library name: Sample 4
ATAC-seq


title: 8G_AZA_250620, NOMe


title: MART-1 IST-Stimulated Donor 122 Replicate 2

description:
Library name: IST-2
FC348_clonotype_counts.xlsx

value: Naive CD8+ T cell

value: WT

value: MART-1 IST Donor 122


title: MART-1 IST-Stimulated Donor 122 Replicate 3

description:
Library name: IST-3
FC348_clonotype_counts.xlsx


title: 8H_AZA_250620, NOMe

value: azacytidine


title: MART-1 IST-Stimulated Donor 122 Replicate 1

description:
Library name: IST-1
FC348_clonotype_counts.xlsx


title: COVID-19,Convalescent,individual041,Visit1

description:
Library name: C19-R041-V1
sample_age:52,sample_sex:F,severity_scale:0,severity_class:NA

value: Whole blood


title: MART-1 DC-Stimulated Donor 122 Replicate 2

description:
Library name: DC-2
FC348_clonotype_counts.xlsx

value: MART-1-DC Donor 122


title: 8F_AZA_250620, NOMe


title: MART-1 DC-Stimulated Donor 122 Replicate 1

description:
Library name: DC-1
FC348_clonotype_counts.xlsx


title: 8E_AZA_250620, NOMe


title: COVID-19,Convalescent,individual039,Visit1

description:
Library name: C19-R039-V1
sample_age:66,sample_sex:M,severity_scale:0,severity_class:NA


title: Unstimulated Donor 122 Replicate 3

description:
Library name: UN-3
FC348_clonotype_counts.xlsx

value: Unstimulated Donor 122


title: MART-1 DC-Stimulated Donor 122 Replicate 3

description:
Library name: DC-3
FC348_clonotype_counts.xlsx


title: 8D_DAC_250620, NOMe

value: decitabine


title: MART-1 IST-Stimulated Donor 86 Replicate 3

description:
Library name: SYN_3_S89
FC345_clonotype_counts.xlsx

value: Mart-1 IST Donor 86


title: Unstimulated Donor 122 Replicate 2

description:
Library name: UN-2
FC348_clonotype_counts.xlsx


title: COVID-19,Convalescent,individual038,Visit1

description:
Library name: C19-R038-V1
sample_age:62,sample_sex:F,severity_scale:0,severity_class:NA

value: Female


title: 8C_DAC_250620, NOMe


title: COVID-19,Convalescent,individual037,Visit1

description:
Library name: C19-R037-V1
sample_age:63,sample_sex:M,severity_scale:0,severity_class:NA

value: Male


title: 8B_DAC_250620, NOMe


title: MART-1 IST-Stimulated Donor 86 Replicate 1

description:
Library name: SYN_1_S23
FC345_clonotype_counts.xlsx


title: MART-1 IST-Stimulated Donor 86 Replicate 2

description:
Library name: SYN2_S56
FC345_clonotype_counts.xlsx


title: COVID-19,Convalescent,individual042,Visit1

description:
Library name: C19-R042-V1
sample_age:65,sample_sex:M,severity_scale:0,severity_class:NA


title: MART-1 DC-Stimulated Donor 86 Replicate 3

description:
Library name: DC_3_S78
FC345_clonotype_counts.xlsx

value: MART-1 DC Donor 86


title: MART-1 DC-Stimulated Donor 86 Replicate 2

description:
Library name: DC_2_S45
FC345_clonotype_counts.xlsx


title: 7H_AZA_250620, NOMe


title: COVID-19,Convalescent,individual040,Visit1

description:
Library name: C19-R040-V1
sample_age:33,sample_sex:M,severity_scale:0,severity_class:NA


title: COVID-19,Convalescent,individual034,Visit1

description:
Library name: C19-R034-V1
sample_age:49,sample_sex:F,severity_scale:0,severity_class:NA


title: MART-1 DC-Stimulated Donor 86 Replicate 1

description:
Library name: DC_1_S12
FC345_clonotype_counts.xlsx


title: Unstimulated Donor 86 Replicate 2

description:
Library name: UN_2_S34
FC345_clonotype_counts.xlsx

value: Unstimulated Donor 86


title: Unstimulated Donor 86 Replicate 1

description:
Library name: UN_1_S11
FC345_clonotype_counts.xlsx


title: COVID-19,Convalescent,individual033,Visit1

description:
Library name: C19-R033-V1
sample_age:52,sample_sex:F,severity_scale:0,severity_class:NA


title: 7F_AZA_250620, NOMe


title: Comp5min_rep2

city: Münster

first: Sara

middle: A

last: Wickström

address: Röntgenstraße 20

department: Cell & Tissue Dynamics

institute: Max Planck Institute for Molecular Biomedicine

description: scRNAseq and scATACseq

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

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).

value: iPS


title: Comp5min_rep1

description: scRNAseq and scATACseq


title: COVID-19,Convalescent,individual032,Visit1

description:
Library name: C19-R032-V1
sample_age:53,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

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.