title: OVCAR3, shNUF2,  replicate 3

city: Jinan

first: Ruobing

last: Leng

state: Shandong

address: 324 JingwuWeiqi Road

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

data_processing:
Paired-end libraries were prepared according to the manufacturer's protocols
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt ( 3' adapter and reads with an average quality that are lower than 20 removals)
The clean reads were mapped to the reference genome (GRCh38) via hierarchical indexing for spliced alignment of transcripts (HISAT)
Read counts were obtained using HTSeq, and gene counts were then normalized among samples using the FPKM normalization method.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes read count values and fpkm  values for each Sample

extract_protocol:
RNA was harvested using TRIzolTM reagent (Thermo Fisher). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq™ Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.

value: ovarian cancer cells

value: NUF2 knockdown

value: transfected with shNUF2


title: Sample59

status: Public on Jan 11 2023

type: SRA

city: los angeles

first: Shubhamoy

last: Ghosh

state: CA

address: 650 Charles E Young  Dr East

department: Pediatrics

country: USA

institute: University of California Los Angeles

library_source: other

data_processing:
Demultiplexed sequence data were imported to QIIME2 and quality filtering was performed using DADA2to ensure adequate sequence quality
A feature table along with a representative sequence table containing amplicon sequence variants (ASV) were generated and a rooted phylogenetic tree was constructed based on sequence similarity to infer the evolutionary relationship between microorganisms.
The outputs from QIIME2 (feature table, taxonomic classifications, phylogenetic tree) along with the corresponding metadata, were imported to R (version 4.2.1) and assembled into a phyloseq object using the phyloseq package (version 1.40.0)
all data visualization steps were performed using ggplot2 package in R

molecule: other

organism: Rattus norvegicus

source_name: Sprague Dawley

growth_protocol: Pregnant Sprague-Dawley rats (Charles River Laboratories, Hollister, CA) were housed in individual cages at 21-23C within 12h light/dark cycles.

extract_protocol:
fecal samples from within the intestines of Day2, Day21 and adult offspring (Day180) were collected and bacterial genomic DNA was extracted for 16S rDNA microbiota profiling
The V4 region of the 16S rRNA gene was amplified with individually barcoded universal primers. PCR amplified products were purified and pooled in equimolar concentrations and sequenced using the Illumina MiSeq platform and 2 X 250bp reagent kit for paired-end sequencing.

treatment_protocol: At gestational day 11  dams were randomized to either continue regular chow (CON group) or on a Western diet ad libitum (HFhf group)along with 25% fructose in their drinking water.The pregnant dams in the IUGR group were 50% calorie restricted beginning from gestation day (G) 10 in their access to regular chow diet until the birth of their pups.after birth, the maternal diet was switched to either regular chow accessed ad libitum forming the IUGR-RC (regular chow) group, or a HFhf diet creating the   IUGR-HFhf group

tag: Sex

value: F

tag: age (day)

tag: collection time

value: AM

tag: strain

value: Sprague Dawley

tag: specimen

value: feces

tag: group

value: HFhf

tag: molecule

value: 16S rDNA


title: pR_CTCF_IP_rep2

city: Napoli

first: Maria

middle: Rosaria

last: Matarazzo

address: Via Pietro Castellino 111

country: Italy

institute: Institute of Genetics and Biophysics "ABT"

library_source: genomic

data_processing:
The quality of the sequenced single-end (SE) reads from IP and input were assessed using FastQC. The low quality SE reads were filtered out and the Illumina adapters were trimmed using Cutadapt with the following settings: -q > 30; -m > 40. The reads were aligned to the hg38 reference genome using Bowtie2 with default parameters. Aligned SE reads with MAPQ score < 20 were filtered out and  the duplicates were removed using samtools markdup command.
Assembly: hg38
Supplementary files format and content: N/A

molecule: genomic DNA

organism: Homo sapiens

source_name: iPSCs

growth_protocol: The iPSC lines were cultured on Geltrex™ LDEV-Free Reduced Growth Factor Basement Membrane Matrix (A1413302, Gibco™) coated plates and maintained in StemMACS™ iPS-Brew XF, human medium (130-104-368, Miltenyi Biotec).

extract_protocol:
Decrosslinking from beads was performed in a 1% SDS solution containing Tris-HCl pH8 and 10 mM EDTA for 2 hours at 69°C with agitation. Decrosslinking of the DNA-protein complex was performed by adding Proteinase K (20 ng/mL) for 2 hours at 62°C with agitation. DNA was then purified using ExpinTM PCR SV (103-102, GeneAll®).
ChIP-Seq libraries were generated according to Illumina's instructions and single-end (SE) sequencing was performed on the Illumina Hi-Seq 2500 system at the Technion Genome Center (Haifa, Israel)

tag: cell type

value: iPSCs

tag: condition

tag: chip antibody

value: CTCF, Abcam


title: RNAseq-TCFL5Het-testis-rep1

city: Worcester

first: Tianxiong

last: Yu

state: MA

address: 364 Plantation St

institute: Umass Med

library_source: transcriptomic

data_processing:
For small RNA-seq data, after removing 3′ adaptor sequence from the reads, we filtered reads whose PHRED score was <5. Those reads that passed the quality check were then mapped to mouse genome (mm10) using piPipes that uses bowtie 2.2.5 allowing one mismatch.  For RNA-seq data, we first removed rRNA reads using bowtie 2.2.5 with default parameters and then the unaligned reads were further mapped to mouse genome (mm10) using STAR. Mapped results were generated as SAM format that was further transformed into duplication removed sorted BAM format using SAMtools 1.8 and Umitools. For ChIP-seq data, raw reads were mapped to mapped to mouse genome (mm10) using Bowtie 2.2.5 with parameter —very-sensitive —no-unal —no-mixed —no-discordant. We then removed duplicate reads using SAMtools. Normalized genome coverage files in bigWig format were generated using homemade script. For CUT&RUN data, Raw reads were mapped to mapped to mouse genome (mm10) using Bowtie 2.2.5 with parameter —very-sensitive —no-unal —no-mixed —no-discordant. We presented the data in bigWig file that was reported as unique mapping reads as read depth per million reads (rpm).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

molecule: total RNA

organism: Mus musculus

source_name: testis

extract_protocol: none provided by the submitter

tag: antibody

tag: Stage

value: adult


title: RNAseq-TCFL5Het-testis-rep3


title: OVCAR3, shNUF2,  replicate 1

country: China

tag: cell line

tag: genotype

tag: treatment


title: WT1_CTCF_IP_rep2


title: Sample57


title: OVCAR3, shNC,  replicate 3

value: WT

value: transfected with shNC


title: RNAseq-TCFL5Mut-testis-rep2


title: OVCAR3, shNC,  replicate 1


title: WT1_CTCF_IP_rep1


title: OVCAR3, shNUF2,  replicate 2


title: RNAseq-TCFL5Het-RST-rep3

source_name: round spermatid


title: Sample55

value: IUGR-HFhf


title: Huh7 cells, ASO_NEAT1, 24hpi [Sample 12]

city: Faridabad

first: Abhay

middle: Deep

last: Pandey

address: 3rd Milestone, Faridabad-Gurgaon Expressway

department: Virology

country: India

institute: Regional Centre for Biotechnology

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol: 1000 ng of total RNA sample was used for removal of ribosomal RNA using KAPA RNA HyperPrep Kit with RiboErase (HMR) as per manufacturer instructions (KR1351-v2.17). rRNA depleted total RNA was used for library preparation as per manufacturer’s instructions.

value: hepatoma cells

value: NEAT1 knockdown

value: Dengue Virus 2 infection

tag: time


title: RNAseq-TCFL5Het-RST-rep4


title: Huh7 cells, ASO_NEAT1, 24hpi [Sample 10]


title: Covid Patient 15 [A_88]

city: Tucson

first: Janko

middle: Nikolich

last: Zugich

address: 1656 E. Mabel St., MRB225, Tucson, AZ 85724

department: Immunobiology

institute: University of Arizona

description:
COVID_23June_refUMAP.rds
Mladenpaper.rds

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
After cleaning up of data using removal of doublets and other quality control measures, all the samples were integrated into one rds file named "Mladenpaper.rds" and after using reference based label transfer method the "COVID_23June_refUMAP.rds" file was generated.
Assembly: GRCh38
Supplementary files format and content: "Mladenpaper.rds" has unlabelled cells integrated from all the 15 samples where as "COVID_23June_refUMAP.rds" has labels marked using reference based label transfer.
Supplementary files format and content: Tab-separated values files and matrix files and rds files

source_name: blood

extract_protocol: Library preparation was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3’ GEM, v2 protocol (10x Genomics)). Briefly, cells were resuspended at a concentration of 1000 live cells/μL and loaded into the Chromium Next GEM Chip G along with reverse transcription reagents. Gel bead-in-emulsions (GEMs) were loaded with the 10x Chromium Controller (10x). mRNA was reverse transcribed into cDNA containing a flanking Unique Molecular Identifier and 10x barcode. Per manufacturer’s instructions, paired-end size-selected libraries were constructed from the barcoded cDNA with the further addition of Illumina P5 and P7 sequence sites as well as library specific Truseq (Illumina) R2 sample indices for subsequent library sequencing and demultiplexing.

tag: tissue

value: blood

tag: subject status

value: COVID patients

value: PBMC

tag: age

value: Mild


title: Huh7 cells, ASO_NEAT1, 24hpi [Sample 11]


title: Sample53

tag: Sex

value: F

tag: age (day)

tag: collection time

value: AM

value: Sprague Dawley


title: Covid Patient 14 [A_87]


title: Covid Patient 13 [A_86]


title: RNAseq-TCFL5Het-RST-rep1

tag: strain


title: RNAseq-TCFL5Het-RST-rep2


title: Sample51

tag: specimen

value: feces

tag: group

value: CON

tag: molecule

value: 16S rDNA


title: Huh7 cells, ASO_Control, 24hpi [Sample 8]

tag: cell type


title: Sample52


title: Sample56


title: RNAseq-TCFL5Mut-testis-rep1

tag: antibody

value: adult


title: Sample54


title: RNAseq-TCFL5Het-SPII-rep4

source_name: secondary spermatocyte

tag: Stage


title: Huh7 cells, ASO_Control, 24hpi [Sample 9]

tag: cell line

value: WT


title: Huh7 cells, AS0_Control, 24hpi [Sample 7]

tag: genotype


title: RNAseq-TCFL5Het-SPII-rep3


title: Sample50


title: OVCAR3, shNC,  replicate 2

value: ovarian cancer cells

tag: treatment

value: transfected with shNC


title: Sample49


title: cG50_RNAseq_rep2

data_processing:
Low-quality read filtering and adapter-trimming of the strand-specific PE reads were performed using Cutadapt by setting the following parameters: -q 30 -m 40. The trimmed reads were aligned to the hg38 reference genome using HISAT2 with options: --dta --rna-strandness RF.
The reads were quantified using featurecounts function from the Rsubread package with the settings (useMetaFeatures=TRUE, allowMultiOverlap=FALSE, strandSpecific=2, CountMultiMappingReads=FALSE). The raw count matrix were pre-processed to filter out zero count or low count genes (CPM < 0.5) using the Proportion Test Method from the NOIseq R package. The raw counts were normalized across the samples using the Upper Quartile (UQUA) method and a posterior probability cut-off was applied to subset the DE genes.
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

extract_protocol:
Total RNA extraction from iPSCs and LCLs was performed using TRI Reagent® (T9424, Sigma-Aldrich), according to the manufacturer's protocol. Extracted RNA was further purified from genomic DNA using the TURBO DNA-free™ Kit (AM1907, Invitrogen™).
Strand-specific libraries were prepared according to Illumina's instructions and the libraries were sequenced at the IGA (Udine, Italy) using the Illumina Hi-Seq 2500 platform.

value: iPSCs

tag: condition

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/ p.S780L)


title: Covid Patient 11 [A_27]

tag: tissue


title: cG50_RNAseq_rep1


title: ChIPseq-AMYB-testis-rep1

data_processing:
For small RNA-seq data, after removing 3′ adaptor sequence from the reads, we filtered reads whose PHRED score was <5. Those reads that passed the quality check were then mapped to mouse genome (mm10) using piPipes that uses bowtie 2.2.5 allowing one mismatch.  For RNA-seq data, we first removed rRNA reads using bowtie 2.2.5 with default parameters and then the unaligned reads were further mapped to mouse genome (mm10) using STAR. Mapped results were generated as SAM format that was further transformed into duplication removed sorted BAM format using SAMtools 1.8 and Umitools. For ChIP-seq data, raw reads were mapped to mapped to mouse genome (mm10) using Bowtie 2.2.5 with parameter —very-sensitive —no-unal —no-mixed —no-discordant. We then removed duplicate reads using SAMtools. Normalized genome coverage files in bigWig format were generated using homemade script. For CUT&RUN data, Raw reads were mapped to mapped to mouse genome (mm10) using Bowtie 2.2.5 with parameter —very-sensitive —no-unal —no-mixed —no-discordant. We presented the data in bigWig file that was reported as unique mapping reads as read depth per million reads (rpm).
Genome_build: mm10; rheMac8
Supplementary_files_format_and_content: bigWig

extract_protocol:
In brief, testis frozen tissues were cut into small pieces on dry ice and collected to 1.7 ml tubes containing cold PBS in which samples were cross-linked with 2% (w/v) formaldehyde at room temperature for 30 min using end-over-end tumbler. We then crushed fixed tissues in the presence of ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) by 40 strokes with a Dounce homogenizer pestle “B” (Kimble-Chase, Vineland, USA). To shear the chromatin into 150 to 200 bp, lysed samples were sonicated using Covaris ultrasonicator (Covaris, E220). Sonicated lysate was then diluted 1:10 with ChIP dilution buffer (0.01% SDS, 1.1% Triton X-1001.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.1, 167 mM NaCl) and we performed immunoprecipitation using 5.5 µg anti-A-MYB antibody (Sigma, HPA008791, lot # C105987). Following the immunoprecipitation of the chromatin, we extracted DNA by phenol:chloroform:isoamyl alcohol (25:24:1) (pH 8).
Library construction for anti-AMYB DNA was performed after DNA extraction as previously described (Zhang, Z., Theurkauf, W.E., Weng, Z., and Zamore, P.D. (2012). Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence 3, 9.).

value: rabbit anti AMYB antibody; Sigma, HPA008791

value: adult, three month


title: Sample48

value: M

value: PM

value: HFhf


title: cG13_RNAseq_rep2


title: RNAseq-TCFL5Het-SPII-rep1


title: Covid Patient 9 [A_17]

value: blood

tag: subject status

value: COVID patients

value: PBMC

value: Mild


title: RNAseq-TCFL5Het-SPII-rep2


title: Sample46

value: Sprague Dawley

value: feces


title: Covid Patient 12 [A_85]

tag: age


title: Sample47

tag: Sex

value: 16S rDNA


title: Covid Patient 8 [A_12]

value: Severe


title: RNAseq-TCFL5Het-SPI-rep3

source_name: pachytene spermatocyte

value: adult


title: cG13_RNAseq_rep1


title: RNAseq-TCFL5Het-SPI-rep4


title: pG_RNAseq_rep2

value: ICF1 patient (DNMT3B p. I41fsX42 / p.S780L)


title: Sample45

tag: age (day)


title: RNAseq-TCFL5Het-SPI-rep2


title: Sample44

tag: collection time

value: IUGR-HFhf


title: Covid Patient 10 [A_26]


title: pG_RNAseq_rep1

value: iPSCs


title: RNAseq-TCFL5Het-SPI-rep1

tag: strain


title: Covid Patient 6 [A_56]

description:
10x Genomics
COVID_23June_refUMAP.rds
Mladenpaper.rds


title: cR35_RNAseq_rep2

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/wt)


title: RNAseq-TCFL5Het-SPG-rep3

source_name: spermatogonia


title: Sample43

tag: specimen


title: Covid Patient 7 [A_04]


title: RNAseq-TCFL5Het-SPG-rep2


title: Covid Patient 3 [A_23]


title: cR7_RNAseq_rep1


title: cR7_RNAseq_rep2


title: pR_RNAseq_rep1

value: ICF1 patient (DNMT3B p. D817G / p. D817G)


title: ChIPseq-Input-testis-rep3

value: Input

value: adult, four month


title: Sample37

value: M

value: PM

tag: group

value: CON


title: Sample35

value: AM

value: HFhf

tag: molecule


title: Sample33

value: Sprague Dawley


title: CNTNAP4 KO, Rep2

city: Baltimore

first: Aaron

last: James

state: Maryland

address: 720 Rutland Avenue, Ross Bldg., Room 529

department: Pathology

institute: Johns Hopkins University

data_processing:
Illumina CASAVA performed base-calling of Illumina NovaSeq 5000, 75-base-single-end data producing FASTQ files
Mapping with STAR - 2.7.3a using default parameters
Count quantification in Partek Flow to annotation model (Partek E/M), GRCh38.p13_refseq_v99 transcript counts with default parameters
Partek Flow normalized to FPKM at default parameters
FPKMs log2 quantile normalzed with Partek GS v7.0 and 1-way two-tailed t-test run
Assembly: GRCh38.p13
Supplementary files format and content: Quantile normalized log2 FPKM, contains nulls for zero values

source_name: 143B osteosarcoma cell line

growth_protocol: The 143B cells were cultured Dulbecco's Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 100 U/ml penicillin and 100 µg/ml streptomycin in a humidified incubator with 5% CO2 at 37°C.

extract_protocol:
RNA extraction was performed using TRIzol reagent according to the manufacturer’s instructions
Illumina TruSeq Stranded mRNA kit with manufacturer's protocol

treatment_protocol: The transient plasmid DNA transfection was performed using TransIT®-LT1 Transfection Reagent according to manufacture's protocol

tag: cell type

value: osteosarcoma cell

value: 143B cells transfected with CNTNAP4 KO plasmid for 48 h

value: CNTNAP4 KO


title: Covid Patient 2 [A_22]

value: blood

value: COVID patients

value: PBMC

value: Severe


title: ChIPseq-TCFL5-testis-rep3

tag: antibody


title: pR_RNAseq_rep2

value: iPSCs


title: RNAseq-TCFL5Het-SPG-rep1

tag: Stage

value: adult


title: Sample38

value: feces

value: 16S rDNA


title: CNTNAP4 KO, Rep1

tag: cell line


title: WT1_RNAseq_rep2_run2

tag: genotype

value: healthy control (DNMT3B wt/wt)


title: ChIPseq-Input-testis-rep1

value: Input

value: adult, three month


title: Sample34

value: M

value: AM


title: Covid Patient 4 [A_45]


title: ChIPseq-Input-testis-rep2

value: adult, two month


title: Sample41

value: PM

value: Sprague Dawley

value: IUGR-HFhf


title: cR35_RNAseq_rep1

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/wt)


title: WT1_RNAseq_rep1_run2


title: CNTNAP4 KO, Rep3

value: osteosarcoma cell

tag: treatment

value: 143B cells transfected with CNTNAP4 KO plasmid for 48 h

value: CNTNAP4 KO


title: Covid Patient 1 [A_618]

value: blood

value: COVID patients

value: PBMC

tag: condition

value: Mild


title: Sample32

value: feces

value: 16S rDNA


title: ChIPseq-TCFL5-testis-rep2


title: WT1_RNAseq_rep2_run1

value: iPSCs

value: healthy control (DNMT3B wt/wt)


title: Sample30

value: M

value: AM


title: Vector Control, Rep3

value: 143B cells transfected with vector plasmid for 48 h

value: control


title: ChIPseq-TCFL5-testis-rep1

value: adult, three month


title: Vector Control, Rep2


title: Sample29

value: Sprague Dawley

value: IUGR-HFhf


title: WT1_RNAseq_rep1_run1


title: CUTRUN-NEG-pachyteneCell-rep1

source_name: pachytene spermatocytes

value: Input

value: adult


title: Vector Control, Rep1

value: osteosarcoma cell


title: 4d_rep2

city: Shanghai

first: Chen

last: Min

address: 800 Dong Chuan Rd

institute: Shanghai Jiao Tong University

data_processing:
Sequence reads were trimmed for low-quality sequence Trimmomatic , and short reads  were removed( parameters- SLIDINGWINDOW:3:10 LEADING:10 TRAILING:10 MINLEN:100 )
rRNA reads were removed by SortMeRNA
The clean reads were mapped to the human genome (GRCh37) with the HISAT2 (parameters- rna-strandness: RF)
Gene expression levels were calculated using all protein_coding RNA by StringTie
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Human monocyte-derived macrophages

growth_protocol: Monocytes were at first suspended in serum-free RPMI1640 medium supplemented with 1% Pen/Strep in T25 flasks for 1.5 hours in a humidified incubator to allow cell adhesion and activation. Adherent cells were further cultured for 7 days in RPMI1640 medium containing 10% heat-inactivated serum(normal human serum, NHS) and 1 % Pen/Strep. Half of the culture medium was removed at day 4 and replaced by fresh medium.

extract_protocol:
RNA was extracted using Trizol reagent and NEB Next PolyA mRNA Magnetic Isolation Module (New England Biolabs) accroding to the manufacturer’s protocol.
The RNA-Seq libraries were prepared with KAPA Stranded mRNA-Seq Kit (KAPA Biosystems) accroding to the manufacturer’s protocol.

treatment_protocol: trans-differentiation of human monocytes activated by surface-adsorption into macrophages via serum addition

value: Human monocyte-derived macrophages

tag: time


title: Sample28

value: CON


title: CUTRUN-TCFL5-pachyteneCell-rep2


title: CUTRUN-NEG-pachyteneCell-rep2


title: 3d_rep3


title: 7d_rep1


title: cG50_histone_input

data_processing:
The quality of the sequenced single-end (SE) reads from IP and input were assessed using FastQC. The low quality SE reads were filtered out and the Illumina adapters were trimmed using Cutadapt with the following settings: -q > 30; -m > 40. The reads were aligned to the hg38 reference genome using Bowtie2 with default parameters. Aligned SE reads with MAPQ score < 20 were filtered out and  the duplicates were removed using samtools markdup command.
The peaks and DERs were called using sicer_df command from SICER2 tool. The setting for each ChIP-seq is as follows: i) DNMT3B: -f 200; -fdr 0.0001; -fdr_df 0.0001; -egf 0.88; -w 200; -g 1400 2) H3K4me3: -f 200; -fdr 0.00001; -fdr_df 0.01; -egf 0.88; -w 200; -g 200 3) hH3K36me3: -f 200; -fdr 0.00001; -fdr_df 0.01; -egf 0.88; -w 200; -g 1400
Genome_build: hg38
Supplementary_files_format_and_content: peaks

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/ p.S780L)

tag: chipseq antibody


title: Sample27

value: feces


title: Sample25

value: 16S rDNA


title: pG_histone_input

value: iPSCs

value: ICF1 patient (DNMT3B p. I41fsX42 / p.S780L)


title: cG13_histone_input


title: Sample22

value: M

value: PM

value: HFhf


title: CUTRUN-TCFL5-pachyteneCell-rep1

extract_protocol:
Briefly, small pieces of frozen testis tissue were cross-linked with 2% (w/v) formaldehyde at room temperature for 30 min using end-over-end tumbler. We next crushed fixed tissues in the presence of ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8.1) by 40 strokes with a “B” pestle of Dounce homogenizer (Kimble-Chase, Vineland, USA). Thereafter, lysate was sonicated using Covaris ultrasonicator (Covaris, E220) to shear the chromatin to 150–200 bp. Lysate was then diluted 1:10 with ChIP dilution buffer (0.01% SDS, 1.1% Triton X-1001.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, 167 mM NaCl).  We performed immunoprecipitation using 6 µg rabbit polyclonal anti-H3K27Ac antibody (Abcam, ab4729). Following the immunoprecipitation, we extracted DNA with phenol:chloroform:isoamyl alcohol.
Libraries construction for anti-H3K27Ac, and input DNA were performed after DNA extraction as previously described (Zhang, Z., Theurkauf, W.E., Weng, Z., and Zamore, P.D. (2012). Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence 3, 9.).
none provided by the submitter


title: Sample26

value: AM


title: cR35_histone_input

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/wt)


title: cR7_histone_input


title: RNAseq-TCFL5Het-testis-rep4


title: H3K27me3_shControl_rep2 (lane 1)

city: Copenhagen

first: Bo

last: Porse

address: Ole Maaløes Vej 5, 4

department: Finsen Laboratory and BRIC

country: Denmark

institute: University of Copenhagen

data_processing:
Reads were mapped to mouse genome assembly (mm9) using bowtie2
IDR was used to identify reproducible set of H3K4me1 and H3K27ac enriched region between the two replicates of WT and KD conditions.
Next, we defined 46,594 enhancer regions enriched for either of H3K4me1 and/or H3K27ac peaks in WT or KD conditions.
For H3K27me3 ChIP-data, we also made spikeIn (hg19) and input controls, and we there made a combined genome index of mm9 and hg19 to map the raw reads using Bowtie29. Additionally, uniquely mapped and PCR duplicate collapsed reads mapping to mm9 and hg19 were separated, and total reads mapping to hg19 were used to scale the reads counts in mm9 as in Orlando et al. 2014 (scale factor = 1000000/total mapped reads in hg19). Read counts were further subtracted from corresponding counts derived from input control.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated using bedtools. Signal is normalized to TPM. Identical reads are counted once. bedGraph files were converted to bigWig format using bedGraphToBigWig tool.

source_name: Lp30 cells

growth_protocol: Cells sorted from freshly harvested murine bone marrow

extract_protocol:
GFP+ Lp30 cells were FACS-sorted fresh from murine bone marrow. Chromatin from 500,000 cells per sample was crosslinked with 1% formaldehyde (Sigma).  Samples were spiked with 25,000 HEK-293 cells, lysed and fragmented using the Diagenode Bioruptor Plus (15 cycles, 30sec on/30 sec off at high setting) to 200-700bp length following the small-cell-number protocol (PMC4328043). Chromatin  was incubated with antibodies overnight rotating at 4 degrees Celcius. The antibody-bound chromatin was captured with Protein-A sepharose beads (Sigma), washed, de-cross-linked with protease K at 65 degrees Celcius overnight as previously described (PMC4328043).
Washing procedures were optimized for the individual antibodies as follows:
H3K4me3-ChIP: 2x rinse and 2x wash in with RIPA-low (140 mM NaCl, 10 mM Tris-HCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, 1 mM PMSF), followed by 2x wash in RIPA with 0.5 M NaCl (RIPA-high), 1x wash in LiCl buffer (250 mM LiCl, 10 mM Tris-HCl, 1 mM EDTA, 0.5% Tergitol, and 0.1% sodium deoxycholate),and 2x wash in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH=8). H3K4me1/H3K27ac/IgG-ChIP: 2x rinse in RIPA-low, followed by 4x wash in RIPA-low, 1x wash in LiCl buffer, and 2x wash in TE buffer.
DNA libraries were prepared following NEBNext Ultra II DNA Library Kit for Illumina (New England Biolabs) guidelines and sequenced on Illumina NextSeq500.

value: GFP+ Lp30 cells

tag: chip-antibody

value: C36B11, Cell Signaling


title: H3K27me3_shControl_rep2 (lane 2)


title: 3d_rep2


title: Sample21

tag: Sex

value: Sprague Dawley


title: pR_histone_input

value: ICF1 patient (DNMT3B p. D817G / p. D817G)


title: 4d_rep1


title: Input_shControl_rep2 (lane 1)


title: 3d_rep1


title: WT1_histone_input

value: healthy control (DNMT3B wt/wt)


title: Sample19

tag: age (day)

value: IUGR-HFhf


title: Input_shControl_rep2 (lane 2)


title: 2d_rep3

value: Human monocyte-derived macrophages


title: Sample18

tag: collection time


title: cG50_H3K36me3_IP_rep2

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/ p.S780L)

value: H3K36me3, Abcam


title: 2d_rep1


title: cG13_H3K36me3_IP_rep2


title: 1d_rep3


title: H3K27me3_shControl_rep1 (lane 2)

tag: strain


title: cG50_H3K36me3_IP_rep1


title: Input_shControl_rep1 (lane 1)


title: H3K27me3_shControl_rep1 (lane 1)


title: Sample17

tag: specimen

value: feces

value: 16S rDNA


title: Sample15

tag: group

value: CON


title: pG_H3K36me3_IP_rep2

value: iPSCs


title: Sample16

value: M

value: PM

tag: molecule


title: cG13_H3K36me3_IP_rep1

tag: cell type


title: H3K27me3_shKdm5c_rep3 (lane 2)


title: Input_shControl_rep1 (lane 2)


title: Sample14


title: 1d_rep2


title: 1d_rep1


title: pG_H3K36me3_IP_rep1


title: Sample13


title: 12h_rep2


title: cR35_H3K36me3_IP_rep2


title: Sample12

value: AM

value: HFhf


title: 2d_rep2


title: Input_shKdm5c_rep3 (lane 1)

value: GFP+ Lp30 cells


title: 12h_rep1


title: cR35_H3K36me3_IP_rep1


title: H3K27me3_shKdm5c_rep2 (lane 1)

value: C36B11, Cell Signaling


title: Sample11

value: Sprague Dawley


title: Input_shKdm5c_rep2 (lane 1)


title: cR7_H3K36me3_IP_rep2


title: 4h_rep2


title: H3K27me3_shKdm5c_rep1 (lane 1)


title: Sample10


title: pR_H3K36me3_IP_rep2

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/wt)


title: Sample8


title: 4h_rep1


title: pR_H3K36me3_IP_rep1


title: Input_shKdm5c_rep1 (lane 1)


title: Input_shKdm5c_rep1 (lane 2)


title: Sample7


title: WT1_H3K36me3_IP_rep2

value: ICF1 patient (DNMT3B p. D817G / p. D817G)


title: Sample5

value: IUGR-HFhf


title: 2h_rep2

value: Human monocyte-derived macrophages


title: WT1_H3K36me3_IP_rep1

value: healthy control (DNMT3B wt/wt)


title: Covid Patient 5 [A_53]

tag: tissue

value: blood

tag: subject status

value: COVID patients

value: PBMC

tag: age

value: Severe


title: expr_Lp30_shKdm5c_II_Rep3

data_processing:
Reads were mapped to mouse genome assembly (mm9) using STAR, and gene expression levels were quantified using featureCounts (GTF.featureType=exon, countMultiMappingReads=Y, fraction=T) on Gencode gene annotation (release M1).
Total 17,815 genes having >5 reads in at least two samples are selected for differential expression analysis using RUVSeq R-package (RUVg function)
Differentially expressed genes were determined separately for each of the two shRNAs (WT vs shRNA1 and WT vs shRNA2) and factors of unwanted variation between samples was determined using 568 non-differentially expressed genes (FDR>0.95 in both shRNA comparisons).
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated using bedtools. Signal is normalized to TPM. bedGraph files were converted to bigWig format using bedGraphToBigWig tool.

growth_protocol: GFP+ cells were FACS sorted from freshly harvested murine bone marrow

extract_protocol:
RNA from 500,000 sorted Lp30 GFP+ cells from each transplanted mouse was purified using the RNeasy Micro kit (Qiagen). Before purification, 5 ul 100x diluted ERCC Spike-in Mix (Thermo Fischer Scientific) was added to each cell lysate.
Indexed cDNA libraries were made from 250 ng of each RNA sample using the TruSeq V2 protocol (Illumina). The libraries were pooled in an equimolar ratio, PhiX Spike-in was added to 1:100 ratio, and single-ended 75 bp sequencing was done on a NextSeq 500 (Illumina) using the High Output Flow Cell Cartridge V2.

value: GFP+


title: 2h_rep1


title: 0h_rep4

source_name: human primary monocytes activated by surface-adsorption


title: expr_Lp30_shKdm5c_II_Rep4


title: cG50_H3K4me3_IP_rep2

value: iPSCs

tag: genotype

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/ p.S780L)

value: H3K4me3, Abcam


title: Sample4

value: M

value: AM

value: feces

value: CON

value: 16S rDNA


title: 8h_rep2


title: 0h_rep3

value: human primary monocytes activated by surface-adsorption


title: cR7_H3K36me3_IP_rep1

value: ICF1 patient (DNMT3B p. I41fsX42 / p.S780L)

value: H3K36me3, Abcam


title: 8h_rep1

value: Human monocyte-derived macrophages


title: H3K27me3_shKdm5c_rep1 (lane 2)

value: GFP+ Lp30 cells

value: C36B11, Cell Signaling


title: Sample1

value: Sprague Dawley


title: Sample9

value: HFhf


title: cG50_H3K4me3_IP_rep1


title: expr_Lp30_shKdm5c_II_Rep1

value: GFP+


title: expr_Lp30_shKdm5c_I_Rep3


title: SampleML-R8

value: F


title: 0h_rep1


title: SampleML-R9


title: cG13_H3K4me3_IP_rep1

value: iPSCs

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/wt)


title: cG13_H3K4me3_IP_rep2

value: H3K4me3, Abcam


title: 0h_rep2


title: mono_rep5

source_name: human primary monocytes

value: human primary monocytes

value: mono


title: expr_Lp30_shKdm5c_I_Rep2


title: pG_H3K4me3_IP_rep2


title: expr_Lp30_shKdm5c_I_Rep1


title: mono_rep4


title: SampleML-R5

value: feces


title: expr_Lp30_shKdm5c_II_Rep2


title: pG_H3K4me3_IP_rep1

value: ICF1 patient (DNMT3B p. D817G / p. D817G)


title: SampleML-R4

value: 16S rDNA


title: expr_Lp30_shControl_Rep3


title: expr_Lp30_shControl_Rep2


title: expr_Lp30_shControl_Rep1


title: mono_rep2


title: cR35_H3K4me3_IP_rep1

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/ p.S780L)


title: mono_rep1


title: SampleML-R3


title: SampleML-R2


title: cR7_H3K4me3_IP_rep2


title: Subject 4 Palm Epidermis

city: Irvine

first: Julie

last: Wiedemann

state: California

address: Sprague Hall

institute: UCI

data_processing:
Raw sequencing data were demultiplexed and processed using Cellranger (10× Genomics version 3.0.2) using hg19 reference provided by 10× Genomics
Preliminary analysis and visualization of the single cell datasets were performed using Seurat. We performed integrated analysis of the 12 datasets from 3 sites, normalizing separately for each dataset, selected 2000 informative features, and performed integration using the FindIntegrationAnchors function.
Assembly: hg19
Supplementary files format and content: TAR file containing Cell Ranger outputs for each dataset. Contains filtered feature-barcode matrix in MEX format and tsv files of cell barcodes and features

source_name: palm

extract_protocol:
Generation of single-cell suspensions for scRNA-seq was performed as previously described (Gudjonsson et. al. (2020), JCI insight). Dermal and epidermal fractions were either combined or sequenced independently.
Libraries were constructed by the University of Michigan Advanced Genomics Core on the 10× Genomics Chromium system and sequenced on the Illumina NovaSeq 6000 sequencer to generate 150 bp paired-end reads.

value: epidermis

tag: subject id

value: Subject 4


title: h3k4me3_shControl_Rep2

data_processing:
Reads were mapped to mouse genome assembly (mm9) using bowtie2
IDR was used to identify reproducible set of H3K4me1 and H3K27ac enriched region between the two replicates of shRNA-control and Kdm5c-KD conditions.
Next, we defined 46,594 peak regions enriched for either of H3K4me1 and/or H3K27ac peaks in shRNA-control and Kdm5c-KD conditions.
Peak regions not overlapping with promoter regions (1000 bp region up-stream to TSS) are annotated as Enhancers (N=38,596).
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated using bedtools. Signal is normalized to TPM. Identical reads are counted once. bedGraph files were converted to bigWig format using bedGraphToBigWig tool.

extract_protocol:
GFP+ Lp30 cells were FACS-sorted fresh from murine bone marrow. Chromatin from 500,000 cells per sample was crosslinked with 1% formaldehyde (Sigma), lysed and fragmented using the Diagenode Bioruptor Plus (15 cycles, 30sec on/30 sec off at high setting) to 150-300bp length following the small-cell-number protocol (PMC4328043). Chromatin  was incubated with antibodies overnight rotating at 4 degrees Celcius. The antibody-bound chromatin was captured with Protein-A sepharose beads (Sigma), washed, de-cross-linked with protease K at 65 degrees Celcius overnight as previously described (PMC4328043).  Washing procedures were optimized for the individual antibodies as follows:   H3K4me3-ChIP: 2x rinse and 2x wash in with RIPA-low (140 mM NaCl, 10 mM Tris-HCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, 1 mM PMSF), followed by 2x wash in RIPA with 0.5 M NaCl (RIPA-high), 1x wash in LiCl buffer (250 mM LiCl, 10 mM Tris-HCl, 1 mM EDTA, 0.5% Tergitol, and 0.1% sodium deoxycholate),and 2x wash in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH=8). H3K4me1/H3K27ac/IgG-ChIP: 2x rinse in RIPA-low, followed by 4x wash in RIPA-low, 1x wash in LiCl buffer, and 2x wash in TE buffer.
DNA libraries were prepared following NEBNext Ultra II DNA Library Kit for Illumina (New England Biolabs) guidelines and sequenced on Illumina NextSeq500.

value: 9751S, Cell Signaling


title: SampleML-R7


title: h3k4me3_shControl_Rep1


title: cR7_H3K4me3_IP_rep1

tag: condition

value: ICF1 patient (DNMT3B p. I41fsX42 / p.S780L)


title: pR_H3K4me3_IP_rep2


title: SampleML-R16

value: Sprague Dawley


title: Subject 4 Hip Epidermis

source_name: hip


title: SampleML-R6


title: SampleML-R15


title: mono_rep3

tag: time


title: pR_H3K4me3_IP_rep1

tag: chipseq antibody


title: h3k4me3_shKdm5c_Rep2

tag: chip-antibody


title: cR35_H3K4me3_IP_rep2

value: healthy control (DNMT3B wt/wt)


title: WT1_H3K4me3_IP_rep2


title: h3k4me3_shKdm5c_Rep1

value: GFP+


title: WT1_H3K4me3_IP_rep1


title: SampleML-R14

tag: Sex

value: F


title: SampleML-R13

tag: age (day)


title: Subject 4 Hip Dermis

value: dermis


title: h3k4me1_shControl_Rep2

value: ab8895, Abcam


title: Subject 4 Palm Dermis


title: Subject 3 Palm Epidermis

value: Subject 3


title: h3k4me1_shKdm5c_Rep2


title: SampleML-R12

tag: collection time


title: h3k4me1_shControl_Rep1

tag: strain


title: Subject 3 Hip Epidermis


title: cG50_DNMT3B_input

value: iPSCs

value: DNMT3, Diagenode


title: SampleML-R10

tag: specimen

value: feces


title: Subject 3 Palm Dermis


title: Subject 3 Hip Dermis


title: SampleML-R1

tag: group


title: cG13_DNMT3B_input


title: SampleML-130

value: PM

value: HFhf

tag: molecule


title: h3k4me1_shKdm5c_Rep1

tag: cell type


title: h3k27ac_shControl_Rep2

value: ab4729, Abcam


title: Subject 2 Sole

source_name: sole

tag: tissue

value: recombined epidermis + dermis

value: Subject 2


title: SampleML-129

source_name: Sprague Dawley

value: 16S rDNA


title: SampleML-128


title: cR35_DNMT3B_input

source_name: iPSCs

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/wt)


title: pR_DNMT3B_input

value: ICF1 patient (DNMT3B p. D817G / p. D817G)


title: WT1_DNMT3B_input

value: healthy control (DNMT3B wt/wt)


title: pG_DNMT3B_input

value: ICF1 patient (DNMT3B p. I41fsX42 / p.S780L)


title: h3k27ac_shControl_Rep1

value: GFP+


title: Subject 2 Hip


title: cR7_DNMT3B_input


title: 7 dpa, replicate 31, scRNAseq

city: Boston

first: Isaac

middle: M

last: Oderberg

state: Massachusetts

address: 77 Avenue Louis Pasteur 4th Floor, Room 458

department: Division of Genetics

institute: Brigham and Women's Hospital

description: Drop-seq

data_processing:
Fastq files were processed as described using the 2.4.0 version of the Drop-seq tools, mapping the reads to GRCz11 with the default parameters.
For the DigitalExpression command we set NUM_CORE_BARCODES=5000.
We used STAR version 2.5.3 and fastqc version 0.11.2.
Assembly: GRCz11
Supplementary files format and content: *.txt.gz
Supplementary files format and content: Digital Gene Expression Matrix

organism: Danio rerio

source_name: liver

extract_protocol:
Adult zebrafish livers were enyzmatically dissociated and live, nucleated cells were enriched using FACS. The resultant single-cell suspension was subjected to the Drop-seq protocol.
Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit, with the goal of capturing 1000 cells per library.
Libraries were sequenced on an Illumina NextSeq 500 using the Single-End 75bp kit with the following parameters: Read 1: 20 bp, Read 2: 50 bp, Read 1 Index: 8 bp, Custom Read 1 primer, GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.

value: liver

value: mCherry+ cells

tag: treatment

value: 7 dpa


title: h3k27ac_shKdm5c_Rep2


title: SampleML-124

value: M

value: Sprague Dawley


title: SampleML-123

value: feces


title: SampleML-127

value: F

value: PM


title: 2 dpa, replicate 3, scRNAseq

description: Drop-seq

value: 2 dpa


title: HUVEC_ANRIL_1

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped
After that, clean reads were aligned to the GRch38 genome by tophat2 (Kim, Pertea et al. 2013) allowing 4 mismatches.
The R Bioconductor package edgeR was utilized to screen out the differentially expressed genes (DEGs). A false discovery rate <0.05 and fold change>2 or < 0.5 were set as the cut-off criteria for identifying DEGs
The ABLas pipeline was applied to define and quantify the alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples according to previously described methods
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

molecule: polyA RNA

source_name: ANRIL overexpression in HUVEC cell

growth_protocol: HUVEC cells (8000, Sciencell) were cultured at 37 ℃ with 5% CO 2 in ECM with 5% fetal bovine serum (FBS), 100 µg/mL streptomycin, 100 U/mL penicillin and 1% growth factors. Plasmid  transfection of HUVEC cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 24h for  RT-qPCR analysis.

extract_protocol:
Total RNA was extracted with TRIZOL (Ambion). Total RNA was treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were  determined by measuring the absorbance at 260nm/280nm (A260/A280) using Nanodrop One (Thermo). RNA integrity was further verified by 1.5% agarose gel electrophoresis
For each sample, 1 μg of total RNA was used for RNA-seq library preparation by KAPA Stranded mRNA-Seq Kit for Illumina® Platforms (#KK8544). Polyadenylated mRNAs  were purified by VAHTS mRNA capture Beads (N401-01) and fragmented mRNAs were converted into double strand cDNA. Following end repair and A tailing, the DNAs  were ligated to Diluted Roche Adaptor (KK8726). Products corresponding to 300- 500bps were amplified, purified, quantified, and stored at -80 ℃ before sequencing.  The strand marked with dUTP (the 2nd cDNA strand) was not amplified, allowing  strand-specific sequencing.For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina Novaseq 6000 system for 150 nt  paired-end sequencing

treatment_protocol: GAPDH is used as a control gene to evaluate the over-expression effect of ANRIL. cDNA was synthesized according to standard procedures. Bio-Rad S1000 was subjected to reverse transcription-polymerase chain reaction (RT-PCR) with Bestar SYBR green RT-PCR master mixture (DBI Bioscience, Shanghai, China). The concentration of each transcript was then standardized to GAPDH mRNA level through the 2- ΔΔCT  method.   Graphpad prism software (San Diego, California) was used for paired Student’s t-test comparison.

tag: cell line background

value: HUVEC

tag: genotype/variation

value: ANRIL overexpression


title: cG13_DNMT3B_IP_rep2

value: iPSCs

tag: genotype

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/ p.S780L)

value: DNMT3, Diagenode


title: h3k27ac_shKdm5c_Rep1

value: ab4729, Abcam


title: 3 dpa, replicate 3, scRNAseq

description: Drop-seq

value: 3 dpa


title: HUVEC_NC_3

source_name: HUVEC  cell (control plasmid)

value: control plasmid


title: HUVEC_ANRIL_3


title: Subject 1 Sole

value: recombined epidermis + dermis

tag: subject id

value: Subject 1


title: IgG_shControl

value: GFP+

value: I8140, Sigma


title: Subject 1 Hip


title: cG50_DNMT3B_IP_rep1

tag: condition


title: SampleML-126

value: Sprague Dawley

value: HFhf

value: 16S rDNA


title: cG50_DNMT3B_IP_rep2

tag: chipseq antibody


title: 1 dpa, replicate 3, scRNAseq

description: Drop-seq

value: liver

value: mCherry+ cells

value: 1 dpa


title: HUVEC_NC_2

value: HUVEC


title: SampleML-122

value: M

value: PM

value: feces


title: pG_DNMT3B_IP_rep2

value: iPSCs

value: ICF1 patient (DNMT3B p. I41fsX42 / p.S780L)

value: DNMT3, Diagenode


title: 0 dpa, replicate 3, scRNAseq

description: Drop-seq

value: 0 dpa


title: cG13_DNMT3B_IP_rep1

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/ p.S780L)


title: SampleML-121


title: HUVEC_NC_1

value: control plasmid


title: pG_DNMT3B_IP_rep1


title: SampleML-125


title: SampleML-120

value: F

value: AM


title: HUVEC_ANRIL_2

value: ANRIL overexpression


title: mock, replicate 3, scRNAseq

description: Drop-seq

value: mock


title: scTCR seq of PBMC from ICU Adult_7 at Convalescent stage

city: Darlinghurst

first: Peter

last: Croucher

state: New South Wales

address: 384 Victoria St

department: Bone

country: Australia

institute: Garvan Insititute of Medical Research

data_processing:
Library strategy: TCR-seq
Single-cell sequencing data was demultiplexed, aligned and quantified using Cell Ranger (10x Genomics) against the human reference genome (10x Genomics, July 7, 2020 release) with default parameters.
Filtering and quality control was performed using Seurat (Stuart et al., 2019) on raw data containing 522,926 cells where 433,301 cells were retained satisfying thresholds of both <10% mitochondria content and number of genes between 200 and 5000. ‘SCTransform’ was used for normalization with regression of batch, gender and cell mitochrondria content covariates (Hafemeister and Satija, 2019).
Cell annotation was performed using ‘reference-based mapping’ pipeline implemented in Azimuth algorithm in Seurat (Hao et al., 2021). Azimuth annotated T cells were re-clustered and T cell sub-populations were manually annotated based on UMAP clustering and markers defined by ‘FindAllMarkers’ function in Seurat.
Genome_build: Human GRCh38 (July 7 2020 release)
Supplementary_files_format_and_content: Seurat object saved as Rdata format

source_name: PBMC

growth_protocol: PBMCs were diluted 1:1 with PBS and the mix overlaid in a 2:1 ratio with Ficoll-Paque in 50ml Falcon tube. Cells were centrifuged at 1700 rpm for 30 minutes with brake off at room temperature (18-21˚C). Mononuclear cells at the interface were collected and transferred to a new Falcon tube and washed 2 with ice-cold PBS/0.5% FBS by centrifugation at 1300 rpm for 8 minutes with brake on. Cells were resuspended in 5ml culture media (RPMI/1% HEPES) for counting with a haemocytometer and Trypan blue. Cells were then resuspended in 500ul culture media at a concentration of 2 x 10^7/ml and 500ul freezing media (200ml culture media, 200ml FBS and 100ml DMSO) and cryovials transferred to the -80˚C freezer in a Styrofoam box for 24-48 hours before storage in liquid nitrogen. Frozen PBMCs were thawed and centrifuged at 400g for 5 minutes. Samples were washed with twice with 4% FBS/PBS and stained with DAPI (0.1 ug/ml) for 5 minutes at room temperature prior sorting of live DAPI— cells on the AriaIII (BD Biosciences)

extract_protocol:
Single cell transcriptomic libraries were generated using the 5’v2 Gene expression and immune profiling kit (10x Genomics). Viable PBMCs were sorted into 2% FBS/PBS and cell counts were performed using a haemocytometer. Up to 40,000 cells were loaded into each lane of Chromium Next GEM Chip K Single Cell Kit (10x Genomics) to achieve a recovery cell number of approximately 20,000 cells.
cDNA and TCR libraries were generated according to manufacturer’s instructions (10x Genomics).
Generated libraries were sequenced on the NovaSeq S4 flow cell (Illumina) at Read 1 = 28, i7 index = 10, i5 index = 10 and Read 2: 90 cycles according to manufacturer’s instructions.

value: PBMC

tag: disease state

tag: status

value: Convalescent

tag: age group

tag: library type

value: TCR


title: SampleML-119

data_processing:
Demultiplexed sequence data were imported to QIIME2 and quality filtering was performed using DADA2to ensure adequate sequence quality
A feature table along with a representative sequence table containing amplicon sequence variants (ASV) were generated and a rooted phylogenetic tree was constructed based on sequence similarity to infer the evolutionary relationship between microorganisms.
The outputs from QIIME2 (feature table, taxonomic classifications, phylogenetic tree) along with the corresponding metadata, were imported to R (version 4.2.1) and assembled into a phyloseq object using the phyloseq package (version 1.40.0)
all data visualization steps were performed using ggplot2 package in R

extract_protocol:
fecal samples from within the intestines of Day2, Day21 and adult offspring (Day180) were collected and bacterial genomic DNA was extracted for 16S rDNA microbiota profiling
The V4 region of the 16S rRNA gene was amplified with individually barcoded universal primers. PCR amplified products were purified and pooled in equimolar concentrations and sequenced using the Illumina MiSeq platform and 2 X 250bp reagent kit for paired-end sequencing.

tag: Sex

tag: age (day)

tag: collection time

tag: strain

value: Sprague Dawley

value: HFhf

value: 16S rDNA


title: scTCR seq of PBMC from ICU Adult_6 at Acute stage

tag: cell type

value: Acute


title: cR35_DNMT3B_IP_rep1

extract_protocol:
Decrosslinking from beads was performed in a 1% SDS solution containing Tris-HCl pH8 and 10 mM EDTA for 2 hours at 69°C with agitation. Decrosslinking of the DNA-protein complex was performed by adding Proteinase K (20 ng/mL) for 2 hours at 62°C with agitation. DNA was then purified using ExpinTM PCR SV (103-102, GeneAll®).
ChIP-Seq libraries were generated according to Illumina's instructions and single-end (SE) sequencing was performed on the Illumina Hi-Seq 2500 system at the Technion Genome Center (Haifa, Israel)

value: iPSCs

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/wt)


title: SampleML-118

tag: specimen

value: feces

tag: group

tag: molecule


title: cR35_DNMT3B_IP_rep2

value: DNMT3, Diagenode


title: 7 dpa, replicate 2, scRNAseq

description: Drop-seq

tag: tissue

value: liver

value: mCherry+ cells

tag: treatment

value: 7 dpa


title: cR7_DNMT3B_IP_rep1

tag: genotype


title: SampleML-117

value: F

value: AM


title: 3 dpa, replicate 2, scRNAseq

description: Drop-seq

value: 3 dpa


title: scTCR seq of PBMC from ICU Adult_6 at Convalescent stage

value: PBMC


title: 2 dpa, replicate 2, scRNAseq

description: Drop-seq

value: 2 dpa


title: SampleML-116


title: 1 dpa, replicate 2, scRNAseq

description: Drop-seq

value: 1 dpa


title: scTCR seq of PBMC from Non-ICU Adult_5 at Convalescent stage

value: Convalescent

value: TCR


title: scTCR seq of PBMC from ICU Adult_7 at Acute stage


title: SampleML-115

value: M

value: Sprague Dawley

value: HFhf

value: 16S rDNA


title: WT1_DNMT3B_IP_rep2

value: iPSCs

tag: condition

value: healthy control (DNMT3B wt/wt)


title: mock, replicate 2, scRNAseq

description: Drop-seq

value: liver

value: mock


title: SampleML-113

value: feces


title: pR_DNMT3B_IP_rep2

value: ICF1 patient (DNMT3B p. D817G / p. D817G)

tag: chipseq antibody

value: DNMT3, Diagenode


title: pR_DNMT3B_IP_rep1


title: scTCR seq of PBMC from Non-ICU Adult_5 at Acute stage

tag: disease state

value: Acute


title: scTCR seq of PBMC from Non-ICU Adult_4 at Acute stage

value: PBMC

tag: status


title: scTCR seq of PBMC from Non-ICU Adult_4 at Convalescent stage

tag: age group


title: 0 dpa, replicate 2, scRNAseq

description: Drop-seq

value: mCherry+ cells

value: 0 dpa


title: SampleML-112

value: AM


title: WT1_DNMT3B_IP_rep1


title: scTCR seq of PBMC from Non-ICU Adult_3 at Convalescent stage

value: Convalescent

tag: library type

value: TCR


title: cR7_DNMT3B_IP_rep2

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/wt)


title: SampleML-111

tag: Sex

value: M

value: Sprague Dawley

value: HFhf


title: 2 dpa, replicate 1, scRNAseq

description: Drop-seq

value: 2 dpa


title: SampleML-114

tag: age (day)

value: 16S rDNA


title: 3 dpa, replicate 1, scRNAseq

description: Drop-seq

value: liver

value: 3 dpa


title: scTCR seq of PBMC from Non-ICU Adult_3 at Acute stage


title: 7 dpa, replicate 1, scRNAseq

description: Drop-seq

value: 7 dpa


title: SampleML-110

value: F

tag: collection time

value: PM

value: feces

value: CON


title: U937 cells treated with NEL-replicate 2

city: Arcadia

first: WEI

last: CHEN

address: 655 e huntington dr

department: Shared Resource

institute: City of Hope National Medical Center

data_processing:
Base calling was done using Illumina RTA and bcl2fastq v2.18.0.12
Sequences were aligned to hg19 using Tophat2 with default settings
Gene expression level of Ensembl GRCh37 coding genes were quantified using HTSeq v0.11.2
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file gene expression counts

source_name: AML cell line

growth_protocol: RPMI 1640 supplemented with 10% dialyzed FBS (Cytiva) and 1% streptomycin/penicillin

extract_protocol:
Total RNA was isolated using Trizol Reagent (Life technologies) and purified by spin column using Direct-zol™ RNA MicroPrep (Zymo Research)
RNA libraries were prepared for sequencing using Kapa mRNA HyperPrep kit (Cat:KK8581) with 200ng of total RNA
stranded polyA RNA-Seq

treatment_protocol: Cells were treated with 10 µM of NEL or vehicle control (DMSO)

value: NEL (10 uM)


title: U937 cells treated with NEL-replicate 4


title: SampleML-109

tag: strain


title: 1 dpa, replicate 1, scRNAseq

description: Drop-seq

tag: cell type

value: mCherry+ cells

value: 1 dpa


title: scTCR seq of PBMC from Non-ICU Adult_2 at Acute stage

value: PBMC

value: Acute

value: TCR


title: SampleML-108

value: Sprague Dawley

tag: specimen


title: mock, replicate 1, scRNAseq

description: Drop-seq

value: mock


title: U937 cells treated with DMSO-replicate 3

value: DMSO


title: scTCR seq of PBMC from Non-ICU Adult_1 at Acute stage


title: U937 cells treated with DMSO-replicate 4


title: uninjured GFP+ cells, replicate 1, scRNAseq

description: Drop-seq

value: GFP+ cells

value: Uninjured


title: SampleML-106

tag: group

value: 16S rDNA


title: SampleML-107

tag: molecule


title: U937 cells treated with DMSO-replicate 2


title: scTCR seq of PBMC from Child_7 at Convalescent stage

value: Convalescent

value: Child


title: SampleML-105

value: M

value: PM


title: U937 cells treated with NEL-replicate 3


title: scTCR seq of PBMC from Non-ICU Adult_1 at Convalescent stage


title: scTCR seq of PBMC from Non-ICU Adult_2 at Convalescent stage


title: uninjured mCherry+ cells, replicate 2, scRNAseq

description: Drop-seq

tag: tissue

value: liver


title: U937 cells treated with DMSO-replicate 1

tag: treatment


title: 0 dpa, replicate 1, scRNAseq

description: Drop-seq

tag: genotype

value: 0 dpa


title: uninjured mCherry+ cells, replicate 1, scRNAseq

description: Drop-seq

value: mCherry+ cells


title: U937 cells treated with NEL-replicate 1

value: NEL (10 uM)


title: SampleML-104

value: feces

value: CON


title: KG1A cells treated with NEL-replicate 3


title: SampleML-102


title: uninjured, replicate 5, scRNAseq

description: Drop-seq

value: all cells

value: TU


title: SampleML-103

value: Sprague Dawley


title: uninjured mCherry+ cells, replicate 3, scRNAseq

description: Drop-seq


title: scTCR seq of PBMC from Child_5 at Convalescent stage

value: PBMC

value: TCR


title: SampleML-101


title: uninjured, replicate 4, scRNAseq

description: Drop-seq

value: Uninjured


title: KG1A cells treated with NEL-replicate 2


title: SampleML-100

value: F

value: AM

value: 16S rDNA


title: KG1A cells treated with NEL-replicate 1


title: scTCR seq of PBMC from Child_5 at Acute stage

value: Acute

value: Child


title: scTCR seq of PBMC from Child_4 at Convalescent stage

value: Convalescent


title: SampleML-099


title: KG1A cells treated with DMSO-replicate 3

value: DMSO


title: scTCR seq of PBMC from Child_7 at Acute stage


title: scTCR seq of PBMC from Child_6 at Convalescent stage


title: SampleML-098


title: KG1A cells treated with NEL-replicate 4


title: scTCR seq of PBMC from Child_4 at Acute stage


title: uninjured, replicate 1, scRNAseq

description: Drop-seq

value: liver


title: uninjured, replicate 2, scRNAseq

description: Drop-seq


title: KG1A cells treated with DMSO-replicate 2


title: scTCR seq of PBMC from Child_3 at Convalescent stage


title: uninjured, replicate 6, scRNAseq

description: Drop-seq


title: uninjured, replicate 3, scRNAseq

description: Drop-seq


title: scTCR seq of PBMC from Child_3 at Acute stage


title: MM-seq_lambda_293_shMettl4_SYSY

city: Guangzhou

first: Zhang

last: Zhang

state: Guangdong

address: Xingangxi Roda 135#

institute: Sun Yat-sen University

data_processing:
Raw reads were firsly removed sequencing adaptors by cutadapt (v. 1.15). Clean reads were mapped to reference genome using bowtie2 (v 2.3.3) with default parameters except one mismatch. The sorted bam file was generated using samtools (v1.6; ref). Integrative Genomics Viewer (IGV) was used for data visualization. Picard (v1.129) MarkDuplicates was used to mark and remove duplicates.
For MM-seq data using T7E1/MBN endonuclease, we discarded single-end mapping results and counted both 5’ and 3’ terminals of each fragment as potential T7E1 digest sites. For MM-seq data using lambda exonuclease, only 5’ terminal of sequenced fragments were calculated. A binominal distribution model was assumed that each fragment could be randomly sheared or cleavage by structure-sensitive enzymes. The P-values were further corrected by Bonferroni correction, and FDR≤0.01 was set as the cutoff.
Assembly: human (hg19), mouse (mm10), Chlamydomonas reinhardtii (v5.5), Escherichia coli (ensembl release-45)
Supplementary files format and content: genomic positions of 6mA
Library strategy: MM-seq (Modification-induced Mismatch Sequencing)

source_name: human HEK293T cell line

growth_protocol: Chlamydomonas reinhardtii was cultured in Tris Acetate Phosphate (TAP) medium with modified trace element solution (pH 7.5) at 110 rpm at 22 ℃. Human cell lines were cultured in 10% (v/v)  FBS (Gibco) containing DMEM (Corning) at 37 °C under 5 % CO2 and passed mycoplasma contamination test.

extract_protocol:
Chlamydomonas reinhardtii: cells were treated with lysis buffer (50mM Tris-HCl(pH8.0), 200mM NaCl, 20mM EDTA, 2% SDS, 1mg/ml Proteinase K) and CTAB buffer (50mM Tris-HCl (pH8.0), 20mM EDTA, 1.4M NaCl, 2% CTAB, 1% PVP4000) at 65℃ for 30 min. Total RNA was digested using 100 µg/ml RNase A for 20 min at room temperature. Genomic DNA was isolated by phenol-chloroform extraction and ethanol precipitation. E. coli: Genomic DNA was extracted using FastPure Bacteria DNA Isolation Mini Kit (Vazyme, DC103). Cell lines: Cells were collected and then lysed by lysis buffer (0.1% TritonX-100, 0.1% Tween-20 diluted in 1× PBS) supplemented with 5 μg Proteinase K (Sangon) and 2 μl RNase A (Takara) under the condition of shaking (~1000 rpm) at 37 ℃ for 30 min. E. coli: MinElute PCR Purification Kit (QIAGEN, 28006) was used to isolate genomic DNA.
During MM-seq with endonuclease digestion, 6mA immunoprecipitation reaction was conducted in total volume of 500μL with 4μg fragmented gDNA, 5μL (0.5mg/mL) anti-m6A monoclonal antibody (CST), 100μL 5×IP Buffer, 30μL pre-block protein-A magnetic beads. The mixture was transferred to head-over-tail rotating wheel to incubate at 4 °C overnight and placed on a magnetic rack until beads are captured. The supernatant was discarded and the beads was washed with 500 μL ice-cold 1×IP Buffer by gentle vortex. The beads were re-suspended in the T7E1 or MBN digestion system (M0302S or M0250S, NEB) and incubated for 30 min at 37 °C. After washed with 500 μL ice-cold 1×IP Buffer, 5μL Proteinase K was added to the beads and incubated for 2h at 65 °C with 1,000 rpm. The products were purified by Zymo Research oligo Clean & Concentrator and eluted in 12 μL ddH2O. NGS libraries were constructed for products from genomic DNA using NEBNext Ultra II DNA Library Prep Kit (E7645S).  Same procedure about 6mA immunoprecipitation reaction was applied when using exonuclease cleavage in MM-seq. The beads with IP products were conducted primer extension, end-repair, adaptor ligation and primer extension steps using T4 DNA polymerase (M0203S, NEB), T4PNK (T4 Polynucleotide Kinase, M0201S, NEB), T4 DNA ligase (M0202S, NEB) and Phi29 DNA polymerase (M0264S, NEB), respectively. The beads were washed by 500 μL ice-cold 1×IP Buffer after each treatment. The beads were resuspended in the lambda exonuclease (M0262S, NEB) digestion system incubating for 30 min at 37 °C. After washed by 1×IP Buffer, the beads were treated by 5μL Proteinase K to digest antibody. The mixture were incubated for 2h at 65 °C with 1,000 rpm speed. Then the beads were spin down briefly and placed the tube on magnetic rack for 30s until beads were captured and transferred the supernatant in a new tube. The products were purified by Zymo Research oligo Clean & Concentrator and elute in 12 μL ddH2O. After primer extension by Phi29 DNA polymerase, the products were added into R2 Adapter ligation reaction. Then, the products were clean up by using 52 μL well-mixed AMPure beads and eluted dsDNA fragment in 30 μL ddH2O. After the PCR amplification, the library was purified using 50 μL well mixed AMPure beads or agarose gel size selection.

tag: cell line or tissue

tag: sequence type

value: MM-seq by lambda exonucleases


title: KG1A cells treated with DMSO-replicate 1


title: MM-seq_lambda_293_shNC_SYSY

value: shNC


title: scTCR seq of PBMC from Child_6 at Acute stage

tag: disease state


title: SampleML-096

value: feces

value: CON


title: SampleML-095

value: M


title: SampleML-097

value: Sprague Dawley


title: MM-seq_lambda_293_WT_CST

value: wild type


title: MM-seq_lambda_293_WT_SYSY


title: SampleML-094


title: THP1 cells engineered with iRxI/AxA mutant-replicate 2

city: Duarte

first: wei

last: chen

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

description: THP1-RRM2 OE_rep2

growth_protocol: RPMI 1640 supplemented with 10% Tet-system approved FBS and 1% streptomycin/penicillin

treatment_protocol: Cells were treated with Doxycycine (2 µg/mL)

value: engineered with iRxI/AxA mutant

value: AML cell line

value: Doxycycline (2 µg/mL)

tag: cell line


title: scTCR seq of PBMC from Child_2 at Acute stage

value: PBMC

tag: status

tag: age group

value: TCR


title: scTCR seq of PBMC from Child_1 at Convalescent stage

tag: library type


title: THP1 cells engineered with iRxI/AxA mutant-replicate 3

description: THP1-RRM2 OE_rep3


title: SampleML-093

tag: Sex

tag: age (day)

value: AM

value: 16S rDNA


title: scTCR seq of PBMC from Child_1 at Acute stage

value: Acute

value: Child


title: THP1 cells engineered with iRxI/AxA mutant-replicate 4

description: THP1-RRM2 OE_rep4


title: THP1 cells engineered with iRxI/AxA mutant-replicate 1

description: THP1-RRM2 OE_rep1


title: SampleML-092

tag: collection time

tag: strain


title: scRNA seq of PBMC from ICU Adult_7 at Convalescent stage

data_processing:
Single-cell sequencing data was demultiplexed, aligned and quantified using Cell Ranger (10x Genomics) against the human reference genome (10x Genomics, July 7, 2020 release) with default parameters.
Filtering and quality control was performed using Seurat (Stuart et al., 2019) on raw data containing 522,926 cells where 433,301 cells were retained satisfying thresholds of both <10% mitochondria content and number of genes between 200 and 5000. ‘SCTransform’ was used for normalization with regression of batch, gender and cell mitochrondria content covariates (Hafemeister and Satija, 2019).
Cell annotation was performed using ‘reference-based mapping’ pipeline implemented in Azimuth algorithm in Seurat (Hao et al., 2021). Azimuth annotated T cells were re-clustered and T cell sub-populations were manually annotated based on UMAP clustering and markers defined by ‘FindAllMarkers’ function in Seurat.
Genome_build: Human GRCh38 (July 7 2020 release)
Supplementary_files_format_and_content: Seurat object saved as Rdata format

tag: cell type

value: Convalescent


title: SampleML-091

tag: specimen

tag: group


title: THP1 cells engineered with empty vector-replicate 3

value: engineered with empty vector


title: scRNA seq of PBMC from ICU Adult_6 at Acute stage


title: Primary T cells, cytokine-derived cDNA

city: Singapore

first: Tongjin

last: WU

address: MD6, 14 Medical Drive

department: Institute for Health Innovation and Technology

country: Singapore

institute: National University of Singapore

description: Cytokine-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains cytokine-targeted antibody derived tag reads

data_processing:
Raw mRNA-derived cDNA FASTQ data was processed for cell barcodes calling and UMI counting of mRNA library using Cell Ranger v4.0 (10x Genomics) with default parameters. The generated cell barcodes were used to find individual cell barcode-matched expression profile of sample hashtags, surface proteins and cytokines using CITE-seq-Count with a Hamming distance of 1 for both cell barcodes calling and UMI counting.
Further processing was done with Seurat package (v4.0). Dead cells were removed by filtering out cells expressing > 5% mitochondrial transcript counts.
For the analysis of cytokine secretion, where indicated, sparse dots above 99 quantiles of the background-counts distribution at “0 hr” and apparently discrete dots within data of other time points were removed.
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz; CITE-seq-Count output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz.

growth_protocol: Cryopreserved PBMC were recovered overnight before experiments

extract_protocol:
For end-timepoint measurement of cytokine secretion by TRAPS-seq, human lymphocytes with depletion of CD19+ cells were enriched using Moflo Astrios cell sorter (Beckman Coulter) and kept in incubator overnight before stimulation. Cells were activated by anti-CD3/CD28 Dynabeads (Gibco, 11161D) at 2:1 bead-to-cell ratio for indicated time periods (0 hour, 1 hours, 6 hours and 16 hours) in 96-well U-bottom plate. Post beads removal, cells were stained with saturated cytokine-capturing antibodies for 15 min at 4oC and resuspended in full medium at 40,000 cells per 10 ml medium in 15 ml Falcon tube. The cytokine capture was carried out at 37oC for 45 min with gentle rotation. Cells that are stimulated for different duration (0, 1, 6, 16 hours) were individually labelled with β2M-targeting hashtags (0.5 µg each Ab-Oligo) and Fc-blocking agents. While indicated, control cells without CapAb modification were labelled with CD45-targeting hashtags instead, which was used to verify potential perturbation of gene expression in cell groups modified with CD45-anchored CapAb. The barcoded cell samples were pooled together and stained with Ab-Oligo cocktail (CD3, CD4, CD8, CD45RA, CCR7, CD27, CD28, CD95, CD69, CD107a, IFN-γ, IL-2 and TNF-α) for 45 min at 4oC. Cells were washed with cold PBS containing 2% FBS for 4 times and re-suspended in PBS before run on the Chromium Controller (10x Genomics). For secretion tracing, total T cells were enriched by immunomagnetic negative selection (STEMCELL Technologies, 19051) and loaded onto the nanowell array dropwise at 40,000 cells per array. The unloaded cells were gently rinsed off and 20 µl anti-CD3/CD28 Dynabeads (Gibco, 11161D) were loaded. The cells were activated in open array for 10 hours before subjected to TRAPS-seq-powered on-array secretion tracing. Briefly, for 1st-round SCA, buffer exchange was performed on the cells within the array before the cells are labelled with unsaturated concentration of CapAbs and Fc-blocking agent for 20 min at 4oC. After buffer exchange, the array was reversibly sealed by glass slide and incubated at 37oC for 45 min. The glass slide was then removed and on-array cell washing was performed. Captured cytokines were stained by the 1st-set of detection antibodies (2 µg per Ab-Oligo against IFN-γ, IL-2 or TNF-α) with further blocking of unbound cytokines with purified unconjugated antibodies. The steps of CapAbs labelling and cytokine capture were repeated one more time. Cells were recovered and stained with pooled 2nd-set of detection antibodies (0.4 µg per cytokine Ab-Oligo against IFN-γ, IL-2 or TNF-α and 0.5 µg per surface marker Ab-Oligo against CD3, CD4, CD8, CD45RA, CCR7, CD27, CD28, CD95, CD69, CD107a). Cells were washed with cold PBS containing 2% FBS for 4 times and re-suspended in PBS before run on the Chromium Controller (10x Genomics).
The 10x Genomics single cell 3' reagent kits (v3.1 Chemistry) was used to generate single-cell barcoded sequencing libraries following reverse transcription. The recovered material includes complementary DNA (cDNA) of mRNA and protein libraries representative of cytokines, surface markers and sample-indicating hashtags. After sample cleanup using silane beads, 35 µl of the eluted DNA sample was pre-amplified following the standard protocol with the addition of two additional primers for surface protein and hashtag and cycled as follows: as follows: 98oC 3 min, 12 cycles of: 98oC 15 s, 63oC 20 s, and 72oC 1 min; Then an extension step of 1 min at 72oC. The 1st-round PCR product was cleaned up and followed by a double size selection step using SPRIselect reagent (Beckman Coulter) to separate protein library from cDNA library. The amplified cDNA product was subjected to final gene expression library construction according to the instructions with the kit. Part of the protein library product (5 µl) was used for the preparation of sequencing libraries corresponding to surface marker and cytokine while additional part (5 µl) was used for the construction of sequencing library of sample hashtags using KAPA HiFi Master Mix (Roche). The 2nd-round P7/read 2 PCR primers used for protein library preparation (the P5/read 1 primer is similar to what was used in cDNA library). The size range and concentration of final library constructions was verified by Agilent 2100 Bioanalyzer. The libraries for cDNA and sample hashtag were pooled and sequenced in Illumina HiSeq platform. The protein libraries for surface protein and cytokine were sequenced in MiSeq platform using MiSeq Reagent Kit v3 and customized sequencing primers.
OTHER: TRAPS-seq

treatment_protocol: PBMC were stimulated with anti-CD3/CD28 Dynabeads for different duration as indicated.

tag: tissue

value: Total T cells


title: THP1 cells engineered with empty vector-replicate 4

tag: treatment


title: Primary T cells, surface protein marker-derived cDNA

description: Surface protein marker-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains surface protein-targeted antibody derived tag reads


title: Primary T cells, HTO-derived cDNA

description: Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag (HTO) reads


title: SampleML-088

value: F

value: feces

value: HFhf

tag: molecule


title: scTCR seq of PBMC from Child_2 at Convalescent stage


title: scRNA seq of PBMC from ICU Adult_6 at Convalescent stage


title: THP1 cells engineered with empty vector-replicate 1

tag: genotype


title: scRNA seq of PBMC from ICU Adult_7 at Acute stage


title: THP1 cells engineered with empty vector-replicate 2


title: scRNA seq of PBMC from Non-ICU Adult_5 at Acute stage


title: SampleML-086

value: Sprague Dawley


title: scRNA seq of PBMC from Non-ICU Adult_5 at Convalescent stage


title: CD19+ cells-depleted primary lymphocytes, cytokine-derived cDNA

value: CD19+ cells-depleted total lymphocytes


title: U937 cells treated with dG-replicate 2

description:
counts_KG1A_U937_VEH vs. dG.txt
RPKM_KG1A_U937_VEH vs. dG.txt

data_processing:
Base calling was done using Illumina RTA and bcl2fastq v2.18.0.12
Sequences were aligned to hg38 using Tophat2 with default settings
Gene expression level of Ensembl GRCh38 coding genes were quantified using HTSeq v0.11.2
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text file gene expression counts

extract_protocol:
Total RNA was isolated using Trizol Reagent (Life technologies) and purified by spin column using Direct-zol™ RNA MicroPrep (Zymo Research)
RNA libraries were prepared for sequencing using Kapa mRNA HyperPrep kit (Cat:KK8581) with 200ng of total RNA

treatment_protocol: Cells were treated with 10 mM of dG or vehicle control (PBS)

value: dG (10 mM)


title: CD19+ cells-depleted primary lymphocytes, HTO-derived cDNA


title: CD19+ cells-depleted primary lymphocytes, surface protein marker-derived cDNA


title: SampleML-085

value: CON


title: SampleML-089


title: CD19+ cells-depleted primary lymphocytes, mRNA-derived cDNA

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: U937 cells treated with dG-replicate 1


title: scRNA seq of PBMC from Non-ICU Adult_4 at Convalescent stage


title: U937 cells treated with PBS-replicate 2

value: PBS


title: MM-seq_lambda_293_WT

data_processing:
library strategy: MM-seq (Modification-induced Mismatch Sequencing)
Raw reads were firsly removed sequencing adaptors by cutadapt (v. 1.15). Clean reads were mapped to reference genome using bowtie2 (v 2.3.3) with default parameters except one mismatch. The sorted bam file was generated using samtools (v1.6; ref). Integrative Genomics Viewer (IGV) was used for data visualization. Picard (v1.129) MarkDuplicates was used to mark and remove duplicates.
For MM-seq data using T7E1/MBN endonuclease, we discarded single-end mapping results and counted both 5’ and 3’ terminals of each fragment as potential T7E1 digest sites. For MM-seq data using lambda exonuclease, only 5’ terminal of sequenced fragments were calculated. A binominal distribution model was assumed that each fragment could be randomly sheared or cleavage by structure-sensitive enzymes. The P-values were further corrected by Bonferroni correction, and FDR≤0.01 was set as the cutoff.
Genome_build: human (hg19), mouse (mm10), Chlamydomonas reinhardtii (v5.5), Escherichia coli (ensembl release-45)
Supplementary_files_format_and_content: genomic positions of 6mA

extract_protocol:
Chlamydomonas reinhardtii: cells were treated with lysis buffer (50mM Tris-HCl(pH8.0), 200mM NaCl, 20mM EDTA, 2% SDS, 1mg/ml Proteinase K) and CTAB buffer (50mM Tris-HCl (pH8.0), 20mM EDTA, 1.4M NaCl, 2% CTAB, 1% PVP4000) at 65℃ for 30 min. Total RNA was digested using 100 µg/ml RNase A for 20 min at room temperature. Genomic DNA was isolated by phenol-chloroform extraction and ethanol precipitation. E. coli: Genomic DNA was extracted using FastPure Bacteria DNA Isolation Mini Kit (Vazyme, DC103). Cell lines: Cells were collected and then lysed by lysis buffer (0.1% TritonX-100, 0.1% Tween-20 diluted in 1× PBS) supplemented with 5 μg Proteinase K (Sangon) and 2 μl RNase A (Takara) under the condition of shaking (~1000 rpm) at 37 ℃ for 30 min. E. coli: MinElute PCR Purification Kit (QIAGEN, 28006) was used to isolate genomic DNA.
During MM-seq with endonuclease digestion, 6mA immunoprecipitation reaction was conducted in total volume of 500μL with 4μg fragmented gDNA, 5μL (0.5mg/mL) anti-m6A monoclonal antibody (CST), 100μL 5×IP Buffer, 30μL pre-block protein-A magnetic beads. The mixture was transferred to head-over-tail rotating wheel to incubate at 4 °C overnight and placed on a magnetic rack until beads are captured. The supernatant was discarded and the beads was washed with 500 μL ice-cold 1×IP Buffer by gentle vortex. The beads were re-suspended in the T7E1 or MBN digestion system (M0302S or M0250S, NEB) and incubated for 30 min at 37 °C. After washed with 500 μL ice-cold 1×IP Buffer, 5μL Proteinase K was added to the beads and incubated for 2h at 65 °C with 1,000 rpm. The products were purified by Zymo Research oligo Clean & Concentrator and eluted in 12 μL ddH2O. NGS libraries were constructed for products from genomic DNA using NEBNext Ultra II DNA Library Prep Kit (E7645S). Same procedure about 6mA immunoprecipitation reaction was applied when using exonuclease cleavage in MM-seq. The beads with IP products were conducted primer extension, end-repair, adaptor ligation and primer extension steps using T4 DNA polymerase (M0203S, NEB), T4PNK (T4 Polynucleotide Kinase, M0201S, NEB), T4 DNA ligase (M0202S, NEB) and Phi29 DNA polymerase (M0264S, NEB), respectively. The beads were washed by 500 μL ice-cold 1×IP Buffer after each treatment. The beads were resuspended in the lambda exonuclease (M0262S, NEB) digestion system incubating for 30 min at 37 °C. After washed by 1×IP Buffer, the beads were treated by 5μL Proteinase K to digest antibody. The mixture were incubated for 2h at 65 °C with 1,000 rpm speed. Then the beads were spin down briefly and placed the tube on magnetic rack for 30s until beads were captured and transferred the supernatant in a new tube. The products were purified by Zymo Research oligo Clean & Concentrator and elute in 12 μL ddH2O. After primer extension by Phi29 DNA polymerase, the products were added into R2 Adapter ligation reaction. Then, the products were clean up by using 52 μL well-mixed AMPure beads and eluted dsDNA fragment in 30 μL ddH2O. After the PCR amplification, the library was purified using 50 μL well mixed AMPure beads or agarose gel size selection.

tag: cell line or tissue

tag: sequence type

value: MM-seq by lambda exonucleases

value: wide type


title: Primary T cells, mRNA-derived cDNA

value: PBMC


title: scRNA seq of PBMC from Non-ICU Adult_4 at Acute stage

tag: disease state


title: SampleML-084

value: AM

value: 16S rDNA


title: scRNA seq of PBMC from Non-ICU Adult_3 at Convalescent stage

tag: status


title: U937 cells treated with PBS-replicate 1


title: MM-seq_lambda_293_WGA

value: whole genome amplification


title: SampleML-082


title: SampleML-083


title: Raly_overexpression_2nd

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 16 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2, Qvalue <= 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample.

source_name: RALY overexpression in HeLa cell

growth_protocol: The human HeLa cell line was purchased from the Institute of Biochemistry and Cell Biology (Chinese Academy of Sciences, Shanghai, China). The cells were seeded into a petri dish (100 mm) at a density of 1× 10e5 cells/mL per well, and cultured at 37 °C with 5% CO2 in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10% fetal bovine serum (FBS) (Hyclone), penicillin (100U/ mL), and streptomycin (100 g/mL).

extract_protocol:
The HeLa cells were ground into fine powder before RNA extraction. Total RNA was extracted with TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1μg of the total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80°C before sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

treatment_protocol: The transfection of HeLa cells with an RALY-overexpressing plasmid was performed using Lipofectamine 2000 (Invitrogen, Carls-bad, CA, USA) according to the manufacturer’s instructions. The transfected cells were harvested after 48 h.

tag: cell line

value: HeLa

tag: genotype/variation

value: RALY overexpression


title: KG1A cells treated with dG-replicate 2


title: KG1A cells treated with dG-replicate 1


title: scRNA seq of PBMC from Non-ICU Adult_3 at Acute stage

value: Acute

tag: age group

tag: library type


title: SampleML-087

tag: Sex

value: F

tag: age (day)

tag: collection time


title: SampleML-081

tag: strain

tag: specimen

value: feces


title: scRNA seq of PBMC from Non-ICU Adult_2 at Convalescent stage

tag: cell type

value: Convalescent


title: KG1A cells treated with PBS-replicate 1

tag: treatment


title: scRNA seq of PBMC from Non-ICU Adult_2 at Acute stage


title: KG1A cells treated with PBS-replicate 2


title: scRNA seq of PBMC from Non-ICU Adult_1 at Convalescent stage


title: SampleML-080

value: Sprague Dawley

tag: group

tag: molecule


title: Ctrl_plasmid_1st

source_name: HeLa cell (control plasmid)

value: control


title: Ctrl_plasmid_2nd


title: SampleML-079


title: scRNA seq of PBMC from Non-ICU Adult_1 at Acute stage


title: SampleML-078

value: M

value: HFhf


title: Y9816

city: Edmonton

first: Graham

last: Plastow

state: Alberta

address: 1400 College Plaza, 8215 - 112 Street

department: Agricultural, Food & Nutritional Science

country: Canada

institute: University of Alberta

data_processing:
The raw reads were concatenated as there were two files for each read (run on seperate lanes), then trimmed so those samples with quality scores < 20 were filtered, and  mapped to bovine genome (ARS-UCD1.2.98;https://bovinegenome.elsiklab.missouri.edu/downloads/ARS-UCD1.2 ) using the STAR software. The number of reads uniquely aligned to each gene was calculated using FeatureCounts.
Assembly: ARS-UCD1.2
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Bos taurus

source_name: Blood

extract_protocol:
Total RNA was extracted from Tempus tubes using a Preserved Blood RNA Purification Kit (Norgen Biotek Corp.,Thorlord ON, ), and the Nanodrop 1000 (Thermo Scientifc, Willmingotn, DE, USA) and 2200 RNA Screentape Tapestation System (Agilent Technologies Inc, Cedar Creek, TX) were used respectively to quantify and measure the RNA integrity Number for each sample.
All samples had RIN values above 8,0 and were all used for library construction and RNA-seq was performed on the Novaseq platform running 50 samples per lane on 2 lanes.
cDNA libraries were prepared for sequencing for each individual animal from the high-quality RNA using the TruSeq RNA Library Preparation kit v2 (Illumina, San Diego, CA, United States) and the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs Ltd., Whitby, ON, Canada).

tag: disease status

value: BRD


title: scRNA seq of PBMC from Child_7 at Convalescent stage

value: Child


title: R98

value: Control (pen-matched)


title: SampleML-077

city: los angeles

first: Shubhamoy

last: Ghosh

address: 650 Charles E Young  Dr East


title: SampleML-076


title: Y9747


title: YTL1584B2, GAL, rapa, MNase, 3

city: Amsterdam

first: Ineke

last: Brouwer

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Paired-end 2x75 bp reads were aligned to the reference genome SacCer3 (January 2015) using bowtie2 (Langmead and Salzberg, 2012) with the settings --sensitive --end-to-end -3 15 -5 5 -X 1980 --no-contain --no-discordant -p 40 -x.
aligned reads were filtered for length and only reads between 95 and 225 bp were retained for analysis
read coverage was determined on a chromosome-by-chromosome basis by counting the number of reads covering each base, and the normalized coverage was determined by normalizing the read coverage to the total coverage on the chromosome
Genome_build: sacCer3
Supplementary_files_format_and_content: paired-end sequencing reads aligned to reference sequence and filtered for length to retain reads between 95-225 bp

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae BY4743

growth_protocol: Cultures were inoculated and grown overnight (O/N) in Synthetic Complete (SC) medium with 2% of indicated sugar (raffinose or galactose). The following day O/N cultures were used to inoculate 250 ml cultures of SC media at OD595=0.30 and were grown until OD 0.75 at which point the culture was split into 2 seperate 100 ml cultures, of which was one was treated for 60 minutes with 7.5 uM rapamycin and the other with the same volume of DMSO.

extract_protocol:
Preparation and analysis of mono-nucleosomal DNA was performed as described previously (Donovan et al., 2019; Jonge et al., 2017) with minor modifications. Briefly, cells were grown in SC + 2% raffinose or SC + 2% galactose from OD 0.3 to OD 0.75 and then treated with 7.5 mM rapamycin or DMSO for 60 min. Then, cells were fixed in 1% PFA, washed with 1 M sorbitol, treated with spheroplasting buffer (1M sorbitol, 1 mM β-mercaptoethanol, 10 mg/ml zymolyase 100T (US biological, Z1004.250)) and washed twice with 1 M sorbitol. Spheroplasted cells were treated with 0.01171875 U (low MNase) or 0.1875 U (high MNase) micrococcal nuclease (Sigma-Aldrich, N5386-200UN) in digestion buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris pH7.4, 5 mM MgCl2, 0.075% NP-40, 1 mM β-mercaptoethanol, 0.5 mM spermidine) at 37°C. After 45 min, reactions were terminated on ice with 25 mM EDTA and 0.5% SDS. Samples were treated with proteinase K for 1 h at 37°C and decrosslinked overnight at 65°C. Digested DNA was extracted with phenol/chloroform (PCI 15:14:1), precipitated with NH4-Ac, and treated with 0.1 mg/ml RNaseA/T1. The extent of digestion was checked on a 3% agarose gel.
Sequencing libraries were prepared using the KAPA HTP Library Preparation Kit (07961901001, KAPA Biosystems) using 1 ug of input DNA, 5 uL of 10 uM adapter, double-sided size selection before and after amplification using 10 cycles. Libraries were checked on Bioanalyzer High Sensitivity DNA kit (agilent).

treatment_protocol: 60 min treatment with 7.5 uM rapamycin or same volume of DMSO

value: YTL1584; Sth1-FRB/Sth1-FRB and Spt15/Spt15-FRB

tag: treatment 1

value: galactose, 60 min 7.5 uM rapamycin

tag: treatment 2

value: 0.1875U Mnase

tag: replicate


title: R9265


title: YTL1584B2, GAL, rapa, MNase, 1


title: Raly_overexpression_1st

tag: cell line


title: YTL1584B2, GAL, -rapa, MNase, 3

value: galactose, 60 min DMSO


title: SampleML-075

institute: University of California Los Angeles

value: AM

value: 16S rDNA


title: YTL1584B2, GAL, -rapa, MNase, 1


title: SampleML-074


title: scRNA seq of PBMC from Child_6 at Convalescent stage

value: PBMC

tag: disease state

tag: status


title: YTL1584A1-1, GAL, rapa, MNase, 1


title: R8953


title: U5523


title: YTL1584A1-1, GAL, rapa, MNase, 3


title: scRNA seq of PBMC from Child_6 at Acute stage

value: Acute

tag: age group

tag: library type


title: scRNA seq of PBMC from Child_5 at Convalescent stage


title: SampleML-073

tag: Sex

tag: age (day)

value: feces


title: U5476


title: scRNA seq of PBMC from Child_5 at Acute stage


title: YTL1584A1-1, GAL, -rapa, MNase, 3

tag: strain


title: R545


title: scRNA seq of PBMC from Child_4 at Convalescent stage

value: Convalescent


title: scRNA seq of PBMC from Child_7 at Acute stage


title: SampleML-071

tag: collection time

value: Sprague Dawley

tag: specimen

value: CON


title: YTL525B, RAF, -rapa, MNase, 3

source_name: S. cerevisiae BY4742

value: YTL525; Sth1-FRB

value: raffinose, 60 min DMSO

value: B


title: SampleML-070

value: M


title: YTL525B, RAF, -rapa, MNase, 1


title: SampleML-069


title: scRNA seq of PBMC from Child_4 at Acute stage

tag: cell type

value: Child


title: scRNA seq of PBMC from Child_3 at Convalescent stage


title: SampleML-068

tag: group


title: scRNA seq of PBMC from Child_3 at Acute stage


title: U5416

value: Control (pen-matched)


title: YTL525A, RAF, -rapa, MNase, 1

value: A


title: SampleML-067

tag: molecule


title: YTL525A, RAF, -rapa, MNase, 3

value: 0.1875U Mnase


title: scRNA seq of PBMC from Child_2 at Convalescent stage


title: YTL1584A1-1, GAL, -rapa, MNase, 1

value: YTL1584; Sth1-FRB/Sth1-FRB and Spt15/Spt15-FRB

value: galactose, 60 min DMSO


title: SampleML-072

value: AM

value: HFhf

value: 16S rDNA


title: scRNA seq of PBMC from Child_2 at Acute stage

value: PBMC

value: Acute


title: YTL1306B1, GAL, rapa, MNase, 3

value: YTL1306; Sth1-FRB and Swi2-FRB

value: galactose, 60 min 7.5 uM rapamycin


title: YTL1306B1, GAL, rapa, MNase, 1


title: U5250

tag: disease status


title: SampleML-066

value: Sprague Dawley

value: feces

value: CON


title: YTL1306B1, GAL, -rapa, MNase, 3

tag: treatment 1


title: U5452


title: scRNA seq of PBMC from Child_1 at Acute stage


title: U5080


title: U5420


title: SampleML-065

value: M


title: SampleML-064

value: PM

value: IUGR-HFhf


title: SampleML-063

value: IUGR-RC


title: O5084

value: Control (pen-matched)


title: O5074


title: R502


title: SampleML-062


title: PTID6_W7_Male_scATAC

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

description: The FASTQs are from human subjects going into dbGAP so they are not listed here

data_processing:
Binary Base Call (BCL) files were demultiplexed into FASTQ files was performed using 10x cellranger mkfastq (10x Genomics v.3.1.0)/cellranger-atac mkfastq (10x Genomics v.1.2.0).
10x cellranger/cellranger-atac count was used to process sequencing reads by performing adapter trimming and sequence alignment to the GRCh38 (hg38) reference genome (refdata-cellranger-atacGRCh38-1.1.0). The output files for rna: atac: fragments.tsv.gz and singlecell.csv were utilized for downstream processing and quality control analysis.
Hash Tag Oligo Counting: BarCounter v1.0 ; Default Parameters
HDF5 files (filtered) were then uploaded into R statistical programming language using the Seurat package (version 4.0) where normalization, scaling, integration and reference based label transfer was performed.
scATAC based fragments were submitted to ArchR package to create ArchR object for qulity analysis and downstram analysis
Flow Raw data were compensated and curated to remove unrepresentative events due to instrument fluidics variability (time gating), doublets (by FSC-H and FSC-W), and cells exhibiting membrane permeability (live/dead gating) prior to quantification using BD FlowJo software.
For Olink data, quality assessment, limited detection, and normalization were performed by using the plate bridging control, two positive controls, and three background controls.
Genome_build: Ensembl GRCh38-3.0.0
Supplementary_files_format_and_content: Fragment TSVs (Tab separated), Single cell CSVs (Commas separated),  HDF5 file (Hierarchical Data Format), RDS (R Object Data), Rda (R Data).

source_name: peripheral blood mononuclear cells

extract_protocol:
30 mL of blood was drawn into BD NaHeparin vacutainer tubes (for PBMC; BD #367874) or K2-EDTA vacutainer tubes (for plasma; BD #367863). Upon arrival at the processing lab all NaHeparin tubes for each donor were pooled into a sterile plastic receptacle to establish one common pool for all time points and stored at room temperature until processing (4 hours or less from draw). PBMC were isolated by Ficoll density gradient separation and cryopreserved by a team of operators, as previously described (https://doi.org/10.1016/j.isci.2021.102404). Thawed PBMC were assayed by cytometry and single-cell RNA sequencing in two batches (donors 5206BW and 7626BW, donors 1178BW and 2216BW) by a team of operators. Plasma was isolated and cryopreserved by a team of operators, as previously described (https://doi.org/10.1016/j.isci.2021.102404).
Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium 3’ Single Cell Gene Expression assay (#1000121) and Chromium Controller Instrument according to the manufacturer’s published protocol with modifications for cell hashing21. To block off-target antibody binding, Blocking Solution (5 µL of Human Trustain FcX (BioLegend #422302), and 13.7 µL of a 10% Bovine Serum Albumin (BSA)) was added to 500,000 cells suspended in 50 µL Dulbecco’s Phosphate Buffered Saline (DPBS; Corning Life Sciences #21-031-CM) and incubated for 10 minutes on ice. To stain samples, 0.5 µg (1 µL) of a TotalSeq™-A anti-human Hashtag Antibody was suspended in 31.3 µL DPBS/2% BSA, then added to each sample. For each batch of samples, 100,000 cells from 12 hashed samples with a distinct Hashtag Antibody were pooled into the hashed poolPool 1; 8 additional samples were pooled into hashed pool. Roughly 20,000 cells from a Leukopak healthy control were also labeled with a distinct TotalSeq™-A Hashtag Antibody and were spiked into each pool to serve as a batch control. scATAC-seq libraries were prepared according to the Chromium Single Cell ATAC v1.1 Reagent Kits User Guide (CG000209 Rev B) with several modifications. 195,000 cells were loaded into each tagmentation reaction. Permeabilized cells were brought up to a volume of 129 µl in TD1 buffer (Illumina, 15027866) and mixed with 36 µl of Illumina TDE1 Tn5 transposase (Illumina, 15027916). Transposition was performed by incubating the prepared reactions on a C1000 Touch thermal cycler with 96–Deep Well Reaction Module (Bio-Rad, 1851197) at 37°C for 60 minutes, followed by a brief hold at 4°C. A Chromium NextGEM Chip H (10x Genomics, 2000180) was placed in a Chromium Next GEM Secondary Holder (10x Genomics, 3000332) and 50% Glycerol (Teknova, G1798) was dispensed into all unused wells. A master mix composed of Barcoding Reagent B (10x Genomics, 2000194), Reducing Agent B (10x Genomics, 2000087), and Barcoding Enzyme (10x Genomics, 2000125) was then added to each sample well, pipette-mixed, and loaded into row 1 of the chip. Chromium Single Cell ATAC Gel Beads v1.1 (10x Genomics, 2000210) were vortexed for 30 seconds and loaded into row 2 of the chip, along with Partitioning Oil (10x Genomics, 2000190) in row 3. A 10x Gasket (10x Genomics, 370017) was placed over the chip and attached to the Secondary Holder. The chip was loaded into a Chromium Single Cell Controller instrument (10x Genomics, 120270) for GEM generation. At the completion of the run, GEMs were collected, and linear amplification was performed on a C1000 Touch thermal cycler with 96–Deep Well Reaction Module: 72°C for 5 min, 98°C for 30 sec, 12 cycles of: 98°C for 10 sec, 59°C for 30 sec and 72°C for 1 min. Flow cytometry was performed as previously described (https://doi.org/10.1016/j.isci.2021.102404). In brief, cryopreserved PBMC were thawed, washed, and counted. 1-2 x106 cells were incubated with Human TruStain FcX (BioLegend #422302) and Fixable Viability Stain 510 (BD #564406) prior to staining with a 25-color cell surface panel (Key Resources Table) on ice for 25 minutes. Cells were washed and fixed with 4% paraformaldehyde (Electron Microscopy Sciences #15713) prior to acquisition on a BD Symphony cytometer. Plasma samples were submitted to Olink (Uppsala, Sweden) for assay using the Olink Proximity Extension assay, run on the Fluidigm Biomark system. Patient samples were distributed evenly across two plates, and all time points per patient were run on the same plate, with randomized well locations. Samples were assayed using the Olink Discovery Assay which encompasses all proteins across 13 panels (Cardiometabolic [V.3603], Cardiovascular II [V.5006], Cardiovascular III [V.6113], Cell Regulation [V.3701], Development [V.3512], Immune Response [V.3202], Inflammation [V.3021], Metabolism [V.3402], Neuro Exploratory [V.3901], Neurology [V.8012], Oncology II [V.7004], Oncology III [V.4001], Organ Damage [V.3311]).
Other: scRNA-seq, scATAC-seq, FlowCytometry, Olink, CBC

value: Male


title: YTL1306A, GAL, rapa, MNase, 3

tag: treatment 2

value: 0.1875U Mnase

value: A


title: YTL1306A, GAL, rapa, MNase, 1

tag: replicate


title: PTID6_W4_Male_scATAC


title: U5378


title: SampleML-061


title: PTID6_W2_Male_scATAC


title: SampleML-060


title: scRNA seq of PBMC from Child_1 at Convalescent stage

value: Convalescent

value: Child


title: YTL1306A, GAL, -rapa, MNase, 1

value: galactose, 60 min DMSO


title: O4906


title: YTL1306A, GAL, -rapa, MNase, 3


title: PTID5_W7_Female_scATAC

value: Female


title: O4946


title: PTID5_W4_Female_scATAC


title: P4772


title: SampleML-058

value: 16S rDNA


title: YTL1306B1, GAL, -rapa, MNase, 1

value: YTL1306; Sth1-FRB and Swi2-FRB


title: P4746


title: SampleML-057

value: Sprague Dawley


title: PTID5_W2_Female_scATAC


title: PTID4_W7_Male_scATAC


title: YTL525B, GAL, rapa, MNase, 3

value: YTL525; Sth1-FRB

value: galactose, 60 min 7.5 uM rapamycin

value: B


title: YTL525B, GAL, -rapa, MNase, 3


title: YTL525B, GAL, -rapa, MNase, 1


title: SampleML-056

value: M

value: PM

value: feces


title: P4647

value: Control (pen-matched)


title: PTID4_W6_Male_scATAC

value: Male


title: YTL524B, GAL, rapa, MNase, 3

value: YTL524; Swi2-FRB

value: 0.1875U Mnase


title: SampleML-055

value: IUGR-RC


title: O4875


title: SampleML-054

value: F

value: IUGR-HFhf


title: PTID4_W5_Male_scATAC


title: PTID4_W4_Male_scATAC


title: YTL524A, GAL, rapa, MNase, 3

value: A


title: SampleML-053

value: 16S rDNA


title: SampleML-052


title: YTL525B, GAL, rapa, MNase, 1


title: YTL524B, GAL, -rapa, MNase, 3

value: galactose, 60 min DMSO


title: SampleML-059

value: Sprague Dawley


title: PTID4_W2_Male_scATAC


title: SampleML-051