title: LF1 Quiescence 1 Low Ox

description: Library name: TRNAQ1


title: Cry12DKO_NELF-E_CT24

status: Public on Jan 15 2026

type: SRA

city: Dallas

first: Noheon

last: Park

state: Texas

address: 5323 Harry Hines BLVD, NA4.124

department: Neuroscience

country: USA

institute: UT Southwestern Medical Center

description: Library name: Sample189

library_source: genomic

data_processing:
Illumina bcl2fastq version 2.17 for base calling and demultiplexing.
For ChIPseq, the adaptor and the reads with < 30bp were trimmed by CutAdapt v.1.18. Then, the data were mapped by BWA v0.7.16a-r1185-dirty with default options and the uniquely mapped reads were chosen by SAMtools v1.9. The PCR duplicates were removed by awk commands, and the final reads were extended to the MACS2 prediction sizes.
For mRNAseq, the adaptor, poly T sequences, and < 30bp reads of the raw data were trimmed by CutAdapt v.1.18 and mapped by STAR v2.5.3a. The uniquely mapped reads were chosen by SAMtools v1.9.
For PROseq, the adaptor sequences and < 16bp reads were removed by CutAdapt v.1.18 and the reverse complement (RC) sequences were made from FASTX-Toolkit. The RC was mapped by BWA v0.7.16a-r1185-dirty aln and the uniquely mapped reads were determined by SAMtools v1.9.
The normalized BigWig files are from BEDTools v2.27.1. The raw counts of the NGS data are retrieved from FeatureCounts v1.6.4.
Assembly: M14 from GENCODE
Supplementary files format and content: ChIP-seq BigWig files were made from Uniquely mapped duplicate-removed bed files. PRO-seq and mRNA-seq BigWig files were made from uniquely mapped STAR Bam files
Supplementary files format and content: Excel  file includes raw counts and RPKM values for the mRNA-seq results

molecule: genomic DNA

organism: Mus musculus

source_name: Liver

growth_protocol: At 6 weeks old, the animals were housed in the two light chambers with a 2hr shifted light:dark (LD)=12hrs:12hrs condition and fed ad libitum.

extract_protocol:
For ChIP-seq, , the fresh whole liver lobes were homogenized in 4 ml PBS containing 1% formaldehyde and kept for 8 min at room temperature (RT). For dual crosslinking, the fresh whole liver lobes were homogenized in 4 ml PBS containing 2mM EGS for 20 min at RT. After quencing and cell lysis, chromatin was sonicated by Covaris S2 with the options of 30 sec on/off, intensity 5, cycles/burst 200, duty 20% at 4°C. For PRO-seq, the largest mouse liver lobe was homogenized and the dissociated cells were filtered by 100mm mesh and centrifuged. The precipitated cells were re-suspended and lysed.  The extracted nucleus was re-suspended with the storage buffer and frozen till the next step. After the nuclear run-on, the RNA was extracted by Trizol LS (ThermoFisher). For mRNA-seq, the frozen liver samples were homogenized with Trizol (ThermoFisher) and RNA was extracted according to the manufacturer's instructions.
For ChIP-seq, the DNA fragments ranging from 125 to 175bp were size selected by AMPure magnetic beads (Beckman). Then, the DNA is adenylated, ligated to NEXTflex DNA barcode adaptors (PerkinElmer) and amplified (Enzymatics). For PRO-seq, the libraries were made with TruSeq small RNA Library primers nad the amplified libraries were size-separated by 8% PAGE gels and the DNA ranging from 140 bp to 200 bp was cut out and eluted by the crush/soak methods. For mRNA-seq, the mRNA was extracted from 10 mg of total RNA (RIN values > 8) pooled from three mice by NEXTflex Poly (A) Beads (PerkinElmer), fragmented by heat, reversely transcribed, ligated and amplified with NEXTflex DNA barcode adaptors (PerkinElmer). For all libraries, the size and quality of the libraries were validated by TapeStation (Agilent) and the amounts were measured by Qubit (ThermoFisher)

treatment_protocol: After 4 weeks of the entrainment(10 weeks old), a light/dark chamber was released to constant darkness (DD) condition 24hrs earlier than the other. The liver samples (N=3) were collected after 36 hours of DD condition beginning with the first point (CT00) and subsequent every 4hrs collections for each light chamber till CT44.

tag: tissue

value: Liver

tag: strain

tag: collectiontime

tag: genotype

tag: age

tag: chip antibody

value: anti NELF-E (Abcam Cat# ab170104)


title: PBMC, Other, pOI1

city: Farmington

first: Asa

last: Thibodeau

state: CT

address: 10 Discovery Drive

department: Genomic Medicine

institute: The Jackson Laboratory

description:
Library name: pOI1_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

library_source: transcriptomic single cell

data_processing:
Barcode processing and gene counting were performed using Cell Ranger software 6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/6.1/what-is-cell-ranger)
Ambient RNA decontamination was performed usin soupX software 1.6.2 (doi: 10.1093/gigascience/giaa151)
Assembly: GRCh38-2020-A
Supplementary files format and content: H5ad file includes scanpy object containing post-QC cell information for all samples.
Supplementary files format and content: H5ad file includes scanpy object containing cell information for all samples before manual cell filtering.
Supplementary files format and content: Tab separated value file includes raw barcode information.
Supplementary files format and content: Tab separated value file includes raw feature (gene) information.
Supplementary files format and content: Matrix file includes raw gene expression values
Supplementary files format and content: Tab separated value file includes filtered barcode information.
Supplementary files format and content: Tab separated value file includes filtered feature (gene) information.
Supplementary files format and content: Matrix file includes filtered gene expression values
Supplementary files format and content: Tab separated value file includes soupX corrected barcode information.
Supplementary files format and content: Tab separated value file includes soupX corrected feature (gene) information.
Supplementary files format and content: Matrix file includes soupX corrected gene expression values
Supplementary files format and content: Tab delimited text file includes soupX profile of ambient RNA.

molecule: polyA RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
PBMCs were thawed quickly at 37oC and into DMEM supplemented with 10% FBS. Cells were quickly spun down at 400 g, for 10 min. Cells were washed once with 1 x PBS supplemented with 0.04% BSA and finally re-suspended in 1 x PBS with 0.04% BSA. Viability was determined using trypan blue staining and measured on a Countess FLII. Briefly, 12,000 cells were loaded for capture onto the Chromium platform using the single cell 3’ gene expression reagent kit (v3 or v3.1) (10x Genomics).
Following capture and lysis via Chromium Chip G, cDNA was synthesized and amplified (12 cycles) as per manufacturer's protocol (10x Genomics, protocols CG000204; CG000315). Amplified cDNA and libraries were checked for quality on Agilent 4200 Tapestation, quantified by KAPA qPCR, and sequenced on an Illumina NovaSeq 6000 targeting 100,000 raw read pairs per cell.

value: Blood

tag: cell type

value: Peripheral blood mononuclear cells

tag: age (months)

tag: Sex

value: male

tag: race/ethnicity

value: Biracial

tag: disease state

value: Other


title: PBMC_bulk_Young_3

city: Tarrytown

first: Kun

last: Xiong

state: NY

address: 777 Old Saw Mill River Road

department: Molecular Profiling and Data Science

institute: Regeneron Pharmaceuticals

description:
Library name: 1528157
PBMC_bulk_Young_3

library_source: transcriptomic

data_processing:
For bulk RNAseq, raw fastq were processed by ArrayStudio (11.7.4) to obtain counts of gene expression. For scRNA, Cell Ranger Single Cell Software Suite (6.1.1) were used to de-muliplexing, alignment, filtering, and UMI counting.
Assembly: GRCm38
Supplementary files format and content: txt file of raw counts for bulk RNAseq. H5ad of processed cells for scRNA

molecule: total RNA

source_name: PBMC

extract_protocol:
For bulk RNAseq, ribosomal RNA-depleted RNA-seq libraries were generated using QIAseq® FastSelect −rRNA HMR (QIAGEN) with the KAPA® RNA HyperPrep Kit (Roche Sequencing). For scRNA, single cells suspended in PBS with 0.04% BSA were loaded, 10K cells per lane, on a Chromium Controller (10X Genomics).
For bulk RNAseq, starting material was 100 ng of RNA dependent on availability per tissue type. RNA fragmentation was done at 85°C for 6 minutes. cDNA was ligated with 1.5 µM or 300 nM xGen Dual Index UMI Adapters (Integrated DNA Technologies) respective to RNA input. Ligated cDNA libraries were amplified using 14 PCR cycles, also respective to RNA input. Sequencing of the resulting libraries was done on NovaSeq 6000 (Illumina) using a 2x76, paired-end sequencing recipe. For scRNA, libraries were prepared using Chromium Next GEM Single Cell 3’ Kit, v3.1 (10X Genomics) with single-index barcoding, according to the manufacturer’s guidelines.

value: PBMC

value: Young


title: Cry12DKO_NELF-E_CT16

description: Library name: Sample187


title: PBMC, Healthy, pHC17

description:
Library name: pHC17_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: female

value: White

value: Healthy


title: cell-free DNA from NMN treated sample 63.1 at BL

type: other

city: Renton

first: Dantong

last: Zhu

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: PBMC DNA from treated mice

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MouseMethylation array using standard Illumina protocol

scan_protocol: Arrays were imaged using HiScan and standard recommend Illumina scanner setting

data_processing: SeSame package in R environment (v. 4.4.2)

label: Cy3 and Cy5

molecule: other

label_protocol: Standard Illumina Protocol

extract_protocol: Red blood cells were removed with RBC lysis buffer (155 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA, pH 7.3), and then the remaining cells were digested overnight at 65°C with proteinase K (20 mg/mL) in TESR buffer (10 mM Tris-HCl, 25 mM EDTA, 0.5% SDS, 20 µg/mL RNase). DNA was washed and isolated using SPRI beads and eluted in 10 mM Tris-HCl pH8.

tag: treatment

value: NMN


title: cell-free DNA from NMN treated sample 62.3 at T4

description: PBMC DNA from treated mice


title: PBMC_bulk_Old_2

description:
Library name: 1528166
PBMC_bulk_Old_2

value: Old


title: PBMC_bulk_Young_2

description:
Library name: 1528156
PBMC_bulk_Young_2


title: Cry12DKO_NELF-E_CT12

description: Library name: Sample186


title: PBMC, Healthy, pHC16

description:
Library name: pHC16_scRNA
10x Genomics (mRNA 3' V3 Chemistry)


title: cell-free DNA from NMN treated sample 63.1 at T2

description: PBMC DNA from treated mice


title: PBMC, Healthy, pHC14

description:
Library name: pHC14_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Black


title: cell-free DNA from NMN treated sample 62.3 at T3

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 63.1 at T4

description: PBMC DNA from treated mice


title: PBMC_bulk_Young_1

description:
Library name: 1528155
PBMC_bulk_Young_1


title: Cry12DKO_NELF-E_CT08

description: Library name: Sample185


title: PBMC, Healthy, pHC15

description:
Library name: pHC15_scRNA
10x Genomics (mRNA 3' V3 Chemistry)


title: PBMC_bulk_Young_4

description:
Library name: 1528158
PBMC_bulk_Young_4


title: WT BMDMs treated with glucose for 18 hours rep3

city: Boston

first: Peter

middle: G

last: Kim

state: MA

address: 360 Longwood Ave, LC8202

department: Medical Oncology

institute: Dana Farber Cancer Institute

description:
Library name: W3_18G
Novogene
Glucose_RNAseqBMDM_counts.csv, resdraw_TetvsWT_G.csv

data_processing:
For single cell RNAseq, demultiplexing, barcode processing, gene counting and aggregation were made using Cell Ranger 9.0.1 (10x Genomics), and further analyzed using Seurat v3. For BMDM RNAseq, files were trimmed using Trimmomatic-0.39 for adapters, aligned to the mm10 genome using RSEM-1.3.1 and STAR-2.7.2b.
Assembly: Mouse mm10
Supplementary files format and content: counts.csv
Supplementary files format and content: tab separated value, barcode, and matrix files

source_name: blood

extract_protocol:
For single cell RNAseq, cells were sorted using the Sony MA900 sorter based on the expression of BFP or RFP expression, which measures sgRNA transduction. 15000 cells were isolated per sample. RNA was encapsulated using 10x Genomics 5' reagent kit. For BMDMs, bone marrow cells were crushed, filtered, and differentiated using 20ng/ml of MCSF in DMEM/10% FCS/PSG for 10 days. BMDM RNA was extracted using Qiagen RNEasy RNA extraction kit.
scRNA library was prepared using the single cell 5' reagent kit (10x Genomics) according to manufacturer's instructions. Library was sequenced on an Illumina Novaseq SP. BMDM RNAseq library was prepared using NEBNext Ultra II RNA Library Prep Kit according to manufacturer's instructions after poly(A) selection module or via Novogene.

treatment_protocol: For single cell RNAseq, Cas9 WT or Tet2 HSPCs were transduced with control, Ogt, Acly gRNAs and myeloid cells including Ly6C monocytes were sorted 4-weeks post-transplantation from two mice per arm. For ZPugNAc treatments, after differentiation, BMDMs were treated with DMSO or ZPugNAc (50uM) for 8 hours in DMEM/10%FCS/PSG with 20ng/ml of MCSF. For glucose treatments, BMDMs were differentiated in DMEM/10%FCS/PSG with 20ng/ml of MCSF, grown in serum free defined media consisting of DMEM without glucose or glutamine (Thermo A1443001), supplemented with ITS-X (Thermo), 20ng/ml M-CSF, HEPES (10mM), and glucose 5.5mM for 24 hours, then challenged with vehicle or glucose (55mM) for 18 hours.

value: blood

value: bone marrow derived macrophages

value: WT

value: glucose 55mM for 18 hours


title: cell-free DNA from NMN treated sample 62.3 at T2

description: PBMC DNA from treated mice


title: Cry12DKO_NELF-E_CT00

description: Library name: Sample183

value: Liver

value: anti NELF-E (Abcam Cat# ab170104)


title: Cry12DKO_NELF-E_CT20

description: Library name: Sample188


title: Alb_Cre_Bmal1fxfx_RNAP_II_CT44

description: Library name: Sample181

value: anti Pan Pol II (SantaCruz, Cat#SC55492)


title: Cry12DKO_NELF-E_CT04

description: Library name: Sample184


title: WT BMDMs treated with glucose for 18 hours rep1

description:
Library name: W1_18G
Novogene
Glucose_RNAseqBMDM_counts.csv, resdraw_TetvsWT_G.csv


title: PBMC, Healthy, pHC13

description:
Library name: pHC13_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Blood

value: Peripheral blood mononuclear cells

value: Biracial


title: Alb_Cre_Bmal1fxfx_NELF-E_CT12

description: Library name: Sample212


title: WT BMDMs treated with glucose for 18 hours rep2

description:
Library name: W2_18G
Novogene
Glucose_RNAseqBMDM_counts.csv, resdraw_TetvsWT_G.csv


title: Alb_Cre_Bmal1fxfx_RNAP_II_CT40

description: Library name: Sample180


title: Alb_Cre_Bmal1fxfx_RNAP_II_INPUT

description: Library name: Sample182

value: input mix(00-44)


title: WT BMDMs treated with vehicle for 18 hours rep1

description:
Library name: W1_18B
Novogene
Glucose_RNAseqBMDM_counts.csv, resdraw_TetvsWT_G.csv

value: vehicle for 18 hours


title: PBMC, Healthy, pHC10

description:
Library name: pHC10_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: male


title: WT BMDMs treated with vehicle for 18 hours rep2

description:
Library name: W2_18B
Novogene
Glucose_RNAseqBMDM_counts.csv, resdraw_TetvsWT_G.csv


title: cell-free DNA from NMN treated sample 62.1 at T2

description: PBMC DNA from treated mice

value: PBMC


title: Tet2 KO BMDMs treated with glucose for 18 hours rep3

description:
Library name: T3_18G
Novogene
Glucose_RNAseqBMDM_counts.csv, resdraw_TetvsWT_G.csv

value: Tet2 KO


title: cell-free DNA from NMN treated sample 62.3 at BL

description: PBMC DNA from treated mice

value: NMN


title: WT BMDMs treated with vehicle for 18 hours rep3

description:
Library name: W3_18B
Novogene
Glucose_RNAseqBMDM_counts.csv, resdraw_TetvsWT_G.csv


title: PBMC, Healthy, pHC11

description:
Library name: pHC11_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: female

value: White

value: Healthy


title: Tet2 KO BMDMs treated with glucose for 18 hours rep2

description:
Library name: T2_18G
Novogene
Glucose_RNAseqBMDM_counts.csv, resdraw_TetvsWT_G.csv

value: blood

value: bone marrow derived macrophages


title: Alb_Cre_Bmal1fxfx_RNAP_II_CT28

description: Library name: Sample177

value: Liver


title: cell-free DNA from NMN treated sample 62.1 at BL

description: PBMC DNA from treated mice


title: Alb_Cre_Bmal1fxfx_RNAP_II_CT32

description: Library name: Sample178


title: Alb_Cre_Bmal1fxfx_RNAP_II_CT36

description: Library name: Sample179


title: cell-free DNA from NMN treated sample 59.4 at T5

description: PBMC DNA from treated mice


title: Tet2 KO BMDMs treated with glucose for 18 hours rep1

description:
Library name: T1_18G
Novogene
Glucose_RNAseqBMDM_counts.csv, resdraw_TetvsWT_G.csv

value: glucose 55mM for 18 hours


title: cell-free DNA from NMN treated sample 59.4 at T4

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 62.1 at T3

description: PBMC DNA from treated mice


title: PBMC, Healthy, pHC7

description:
Library name: pHC7_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Black


title: cell-free DNA from NMN treated sample 65.2 at T4

description: PBMC DNA from treated mice


title: Alb_Cre_Bmal1fxfx_RNAP_II_CT20

description: Library name: Sample175

value: anti Pan Pol II (SantaCruz, Cat#SC55492)


title: cell-free DNA from NMN treated sample 59.4 at T3

description: PBMC DNA from treated mice


title: PBMC, Healthy, pHC12

description:
Library name: pHC12_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Blood

value: Peripheral blood mononuclear cells


title: Alb_Cre_Bmal1fxfx_RNAP_II_CT24

description: Library name: Sample176


title: PBMC, Healthy, pHC8

description:
Library name: pHC8_scRNA
10x Genomics (mRNA 3' V3 Chemistry)


title: Alb_Cre_Bmal1fxfx_RNAP_II_CT12

description: Library name: Sample173


title: PBMC, Healthy, pHC5

description:
Library name: pHC5_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Biracial


title: cell-free DNA from NMN treated sample 59.4 at BL

description: PBMC DNA from treated mice


title: PBMC, Healthy, pHC3

description:
Library name: pHC3_scRNA
10x Genomics (mRNA 3' V3 Chemistry)


title: PBMC, Healthy, pHC6

description:
Library name: pHC6_scRNA
10x Genomics (mRNA 3' V3 Chemistry)


title: Tet2 KO BMDMs treated with vehicle for 18 hours rep1

description:
Library name: T1_18B
Novogene
Glucose_RNAseqBMDM_counts.csv, resdraw_TetvsWT_G.csv

value: vehicle for 18 hours


title: PBMC, Healthy, pHC9

description:
Library name: pHC9_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: male


title: PBMC, Healthy, pHC4

description:
Library name: pHC4_scRNA
10x Genomics (mRNA 3' V3 Chemistry)


title: Tet2 KO BMDMs treated with vehicle for 18 hours rep3

description:
Library name: T3_18B
Novogene
Glucose_RNAseqBMDM_counts.csv, resdraw_TetvsWT_G.csv


title: Alb_Cre_Bmal1fxfx_RNAP_II_CT16

description: Library name: Sample174


title: Tet2 KO BMDMs treated with vehicle for 18 hours rep2

description:
Library name: T2_18B
Novogene
Glucose_RNAseqBMDM_counts.csv, resdraw_TetvsWT_G.csv


title: Alb_Cre_Bmal1fxfx_RNAP_II_CT08

description: Library name: Sample172


title: cell-free DNA from NMN treated sample 59.3 at T4

description: PBMC DNA from treated mice

value: PBMC


title: cell-free DNA from NMN treated sample 59.4 at T2

description: PBMC DNA from treated mice


title: PBMC, Healthy, pHC2

description:
Library name: pHC2_scRNA
10x Genomics (mRNA 3' V3 Chemistry)


title: Alb_Cre_Bmal1fxfx_RNAP_II_CT04

description: Library name: Sample171


title: PBMC, Severe RSV, pRSV19

description:
Library name: pRSV19_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Severe RSV


title: cell-free DNA from NMN treated sample 59.3 at T3

description: PBMC DNA from treated mice

value: NMN


title: cell-free DNA from NMN treated sample 59.3 at BL

description: PBMC DNA from treated mice


title: Cas9 LSK Tet2 KO HSPCs transduced with Acly gRNAs

description:
Library name: T_sgAcly
10x Genomics

value: mature myeloid cells (e.g. monocytes)

value: Tet2 KO

value: Acly gRNA


title: Alb_Cre_Bmal1fxfx_RNAP_II_CT00

description: Library name: Sample170


title: cell-free DNA from NMN treated sample 59.2 at T4

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 59.3 at T2

description: PBMC DNA from treated mice


title: PBMC, Healthy, pHC1

description:
Library name: pHC1_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: female

value: White

value: Healthy


title: PBMC, Moderate RSV, pRSV18

description:
Library name: pRSV18_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Moderate RSV


title: No_Cre_Bmal1fxfx_RNAP_II_CT44

description: Library name: Sample168

value: Liver


title: No_Cre_Bmal1fxfx_RNAP_II_INPUT

description: Library name: Sample169

value: input mix(00-44)


title: Cas9 LSK WT HSPCs transduced with non-targeting control gRNAs

description:
Library name: W_sgCtrl
10x Genomics

value: blood

value: WT

value: Control gRNA


title: Cas9 LSK WT HSPCs transduced with Acly gRNAs

description:
Library name: W_sgAcly
10x Genomics


title: PBMC, Severe RSV, pRSV17

description:
Library name: pRSV17_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Blood

value: Peripheral blood mononuclear cells


title: cell-free DNA from NMN treated sample 59.2 at T3

description: PBMC DNA from treated mice

value: PBMC


title: Cas9 LSK Tet2 KO HSPCs transduced with non-targeting control gRNAs

description:
Library name: T_sgCtrl
10x Genomics


title: No_Cre_Bmal1fxfx_RNAP_II_CT36

description: Library name: Sample166

value: anti Pan Pol II (SantaCruz, Cat#SC55492)


title: cell-free DNA from NMN treated sample 59.2 at T2

description: PBMC DNA from treated mice

value: NMN


title: Cas9 LSK Tet2 KO HSPCs transduced with Ogt gRNAs

description:
Library name: T_sgOgt
10x Genomics

value: mature myeloid cells (e.g. monocytes)

value: Ogt gRNA


title: cell-free DNA from NMN treated sample 59.2 at BL

description: PBMC DNA from treated mice


title: PBMC, Severe RSV, pRSV16

description:
Library name: pRSV16_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: male

value: Severe RSV


title: P_WT4

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

description: Library name: P_WT4

data_processing:
sequenced libraries were processed with deepTools (11) v_2.0, using STAR (4) v_2.7.10, for trimming and mapping, and feature Counts (12) v_2.0.3 to quantify mapped reads. Raw mapped reads were processed in R (Lucent Technologies) (5) with DESeq2 (13) v_1.36 to generate normalized read counts to visualize as heatmaps using Morpheus (Broad Institute) and determine differentially expressed genes with greater than 1.4-fold change and lower than 0.01 adjusted P-value. Gene ontology analysis was performed with DAVID (10) (v_2016 and v_2021)
Assembly: mm10
Supplementary files format and content: matrix of raw gene counts per sample

source_name: Peritoneal cavity

extract_protocol:
Lungs and liver harvesting were performed after perfusion with ice-cold PBS through the heart, organs were placed into 5 ml tubes containing 2 ml digestion solution with 2mg/ml Collagenase IV (ThermoFisher) and 0.1mg/ml DNAse I (Sigma) and cut into small pieces with scissors. The solution was incubated in a shaker at 37°C for 1 hour. Tissues were further homogenized using a 20G x 1” needle and a 5 ml syringe, and homogenates were filtered through a 100μm cell strainer. Red blood cells (RBC) from lungs and liver were lysed with ACK for 2 min, washed with PBS 1% FCS, 2mM EDTA (FACS buffer), and kept on ice until flow cytometry staining.  Peritoneal macrophages were obtained by peritoneal lavage and kept on ice until flow cytometry staining FACS was performed on a BD FACS Aria III (BD Biosciences) to achieve > 95% purity. Dead cells were excluded by live/dead viability dye (Thermo) staining. RNAseq was obtained by sorting 5000–100000 cells from each population directly into RLT buffer (Qiagen) containing 1% 2-ME and submitted to the Emory Integrated Genomics Core at Emory University (Atlanta, GA).Total RNA was isolated using the Quick-RNA Microprep Kit (Zymo Research).
The cDNA was generated using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio), and sequencing libraries were generated from the cDNA using the Nextera XT kit (Illumina). Libraries were pooled at equimolar ratios and sequenced on a Novaseq 6000 at approximately 100M reads per sample using 100PE reads.

value: Peritoneal cavity

value: Macrophage


title: Cas9 LSK WT HSPCs transduced with Ogt gRNAs

description:
Library name: W_sgOgt
10x Genomics


title: No_Cre_Bmal1fxfx_RNAP_II_CT32

description: Library name: Sample165


title: cell-free DNA from NMN treated sample 59.1 at T5

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 59.1 at T4

description: PBMC DNA from treated mice


title: PBMC, Severe RSV, pRSV15

description:
Library name: pRSV15_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: female

value: White


title: No_Cre_Bmal1fxfx_RNAP_II_CT28

description: Library name: Sample164

value: Liver


title: PBMC, Severe RSV, pRSV14

description:
Library name: pRSV14_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Multiracial


title: No_Cre_Bmal1fxfx_RNAP_II_CT24

description: Library name: Sample163


title: PBMC, Mild RSV, pRSV13

description:
Library name: pRSV13_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Mild RSV


title: cell-free DNA from NMN treated sample 59.1 at T3

description: PBMC DNA from treated mice


title: P_WT1

description: Library name: P_WT1

value: WT


title: No_Cre_Bmal1fxfx_RNAP_II_CT40

description: Library name: Sample167


title: PBMC, Mild RSV, pRSV12

description:
Library name: pRSV12_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Blood


title: P_KO4

description: Library name: P_KO4

value: KO


title: cell-free DNA from NMN treated sample 59.1 at T2

description: PBMC DNA from treated mice

value: PBMC


title: No_Cre_Bmal1fxfx_RNAP_II_CT16

description: Library name: Sample161

value: anti Pan Pol II (SantaCruz, Cat#SC55492)


title: P_KO2

description: Library name: P_KO2


title: No_Cre_Bmal1fxfx_RNAP_II_CT20

description: Library name: Sample162


title: cell-free DNA from NMN treated sample 59.1 at BL

description: PBMC DNA from treated mice

value: NMN


title: P_WT2

description: Library name: P_WT2


title: cell-free DNA from NMN treated sample 58.3 at T4

description: PBMC DNA from treated mice


title: PBMC, Moderate RSV, pRSV11

description:
Library name: pRSV11_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Peripheral blood mononuclear cells

value: Moderate RSV


title: P_KO1

description: Library name: P_KO1


title: PBMC, Mild RSV, pRSV8

description:
Library name: pRSV8_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: male

value: Black


title: PBMC, Moderate RSV, pRSV10

description:
Library name: pRSV10_scRNA
10x Genomics (mRNA 3' V3 Chemistry)


title: P_KO3

description: Library name: P_KO3

value: Peritoneal cavity


title: No_Cre_Bmal1fxfx_RNAP_II_CT12

description: Library name: Sample160


title: PBMC, Mild RSV, pRSV9

description:
Library name: pRSV9_scRNA
10x Genomics (mRNA 3' V3 Chemistry)


title: cell-free DNA from NMN treated sample 58.3 at T2

description: PBMC DNA from treated mice


title: No_Cre_Bmal1fxfx_RNAP_II_CT08

description: Library name: Sample159


title: cell-free DNA from NMN treated sample 58.3 at T3

description: PBMC DNA from treated mice


title: P_WT3

description: Library name: P_WT3

value: Macrophage


title: No_Cre_Bmal1fxfx_RNAP_II_CT00

description: Library name: Sample157


title: PBMC, Moderate RSV, pRSV6

description:
Library name: pRSV6_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: female

value: Biracial


title: cell-free DNA from NMN treated sample 58.3 at BL

description: PBMC DNA from treated mice


title: No_Cre_Bmal1fxfx_RNAP_II_CT04

description: Library name: Sample158

value: Liver


title: Cry12DKO_RNAP_II_INPUT

description: Library name: Sample156

value: input mix(00-44)


title: Lung_WT2

description: Library name: Lung_WT2

source_name: Lung

value: Lung


title: PBMC, Mild RSV, pRSV7

description:
Library name: pRSV7_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: White

value: Mild RSV


title: Lung_WT4

description: Library name: Lung_WT4

value: WT


title: Lung_WT3

description: Library name: Lung_WT3


title: cell-free DNA from NMN treated sample 58.1 at T3

description: PBMC DNA from treated mice

value: PBMC


title: PBMC, Moderate RSV, pRSV5

description:
Library name: pRSV5_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Blood


title: Lung_WT1

description: Library name: Lung_WT1


title: Cry12DKO_RNAP_II_CT44

description: Library name: Sample155

value: anti Pan Pol II (SantaCruz, Cat#SC55492)


title: PBMC, Moderate RSV, pRSV4

description:
Library name: pRSV4_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Peripheral blood mononuclear cells


title: Lung_KO4

description: Library name: Lung_KO4

value: KO


title: PBMC, Moderate RSV, pRSV3

description:
Library name: pRSV3_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: male

value: Moderate RSV


title: Cry12DKO_RNAP_II_CT40

description: Library name: Sample154


title: cell-free DNA from NMN treated sample 58.1 at BL

description: PBMC DNA from treated mice

value: NMN


title: cell-free DNA from NMN treated sample 58.1 at T2

description: PBMC DNA from treated mice


title: Lung_KO3

description: Library name: Lung_KO3

value: Macrophage


title: cell-free DNA from NMN treated sample 56.4 at T3

description: PBMC DNA from treated mice


title: Cry12DKO_RNAP_II_CT28

description: Library name: Sample151


title: Lung_KO1

description: Library name: Lung_KO1


title: cell-free DNA from NMN treated sample 56.4 at T4

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 56.4 at T2

description: PBMC DNA from treated mice


title: PBMC, Severe RSV, pRSV2

description:
Library name: pRSV2_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Severe RSV


title: PBMC, Severe Steroid Treated COVID-19, pCoV31

description:
Library name: pCoV31_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Severe Steroid Treated COVID-19


title: Cry12DKO_RNAP_II_CT32

description: Library name: Sample152

value: Liver


title: Cry12DKO_RNAP_II_CT24

description: Library name: Sample150


title: Cry12DKO_RNAP_II_CT36

description: Library name: Sample153


title: cell-free DNA from NMN treated sample 56.4 at BL

description: PBMC DNA from treated mice


title: Cry12DKO_RNAP_II_CT20

description: Library name: Sample149


title: PBMC, Severe COVID-19, pCoV29

description:
Library name: pCoV29_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: female

value: Black

value: Severe COVID-19


title: Liver_WT3

description: Library name: Liver_WT3


title: cell-free DNA from NMN treated sample 56.3 at T4

description: PBMC DNA from treated mice


title: PBMC, Severe COVID-19, pCoV30

description:
Library name: pCoV30_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: White


title: Lung_KO2

description: Library name: Lung_KO2

value: Lung


title: Liver_WT2

description: Library name: Liver_WT2

value: WT


title: Liver_WT4

description: Library name: Liver_WT4


title: Cry12DKO_RNAP_II_CT16

description: Library name: Sample148


title: cell-free DNA from NMN treated sample 56.3 at T3

description: PBMC DNA from treated mice

value: PBMC


title: PBMC, Moderate COVID-19, pCoV28

description:
Library name: pCoV28_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Blood

value: Moderate COVID-19


title: cell-free DNA from NMN treated sample 56.3 at T2

description: PBMC DNA from treated mice


title: Liver_WT1

description: Library name: Liver_WT1


title: PBMC, Moderate COVID-19, pCoV26

description:
Library name: pCoV26_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Peripheral blood mononuclear cells


title: PBMC, Severe Steroid Treated COVID-19, pCoV27

description:
Library name: pCoV27_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: male


title: Cry12DKO_RNAP_II_CT08

description: Library name: Sample146

value: anti Pan Pol II (SantaCruz, Cat#SC55492)


title: cell-free DNA from NMN treated sample 56.3 at BL

description: PBMC DNA from treated mice

value: NMN


title: Liver_KO2

description: Library name: Liver_KO2

value: KO

value: Macrophage


title: cell-free DNA from NMN treated sample 56.2 at T4

description: PBMC DNA from treated mice


title: Liver_KO3

description: Library name: Liver_KO3


title: Liver_KO4

description: Library name: Liver_KO4


title: cell-free DNA from NMN treated sample 56.2 at T5

description: PBMC DNA from treated mice


title: PBMC, Convalescent COVID-19, pCoV25

description:
Library name: pCoV25_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Hispanic

value: Convalescent COVID-19


title: Cry12DKO_RNAP_II_CT04

description: Library name: Sample145

value: Liver


title: PBMC, Severe RSV, pRSV1

description:
Library name: pRSV1_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: female

value: Biracial

value: Severe RSV


title: Cry12DKO_RNAP_II_CT00

description: Library name: Sample144


title: PBMC, Moderate COVID-19, pCoV24

description:
Library name: pCoV24_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Black


title: WT_mRNA-seq_CT44

description: Library name: Sample142

value: WT


title: cell-free DNA from NMN treated sample 56.2 at T2

description: PBMC DNA from treated mice

value: PBMC


title: WT_DHPS_Plavage_3

description: Library name: WT_DHPS_Plavage_3

data_processing:
Samples were demultiplexed, quality checked, filtered and aligned genome build GRCm38 using pre-established pipelines implemented via snakePipes (3) with STARsolo v. (4), deeptools v3.3.2, seqtk v1.3, pigz v2.3.4, snpsplit v0.3.4, samtools v1.10, fastqc v0.11.9, cutadapt v2.8, trim-galore v0.6.5, multiqc v1.8, fastp v0.20.0, umi_tools v1.0.1 and star v2.7.4a. Resulting raw read count matrix of barcodes corresponding to cells and features corresponding to detected genes were processed, analyzed and visualized in R v. 4.3.1 (5) using Seurat v.4 (6) with default parameters in all functions, unless specified. Poor quality cells, with low total unique molecular identifier (UMI) counts and high percent mitochondrial gene expression, were excluded. Filtered samples were normalized using a regularized negative binomial regression (SCTransform) (6) and integrated with the reciprocal principal component analysis (rpca) approach followed by mutual nearest neighbors, using 50 principal components. Integrated gene expression matrices were visualized with a UMAP (7) as a dimensionality reduction approach. Resolution for cell clustering was determined by evaluating hierarchical clustering trees at a range of resolutions (0 - 1.2) with Clustree (8), selecting a value inducing minimal cluster instability. Datasets were subsetted to include only macrophages, based on the expression of key macrophage markers (Adgre1, Csf1r, H2-Ab1, Cd68, Lyz2, Itgam, Mertk). Macrophage only datasets were then split along conditions, and processed anew as described above. Differentially expressed genes between clusters were identified as those expressed in at least 25% of cells with a greater than +1 log fold change and an adjusted p value of less than 0.01, using the FindMarkers function in Seurat v.4 with all other parameters set to default. Ribosomal protein genes were excluded from results. Cluster specific genes were explored for pathway enrichment using StringDB (9). Differential expressed genes (pdj value<0.05, Log2Fold>0.5) across clusters were used to perform pathway enrichment analysis by Gene ontology analysis using DAVID (10) (v_2016 and v_2021).
Assembly: mm10
Supplementary files format and content: Raw and filtered counts as Seurat Objects in "rds" format

source_name: peritoneal cavity

extract_protocol:
Single cells were isolated from the peritoneal cavity of indicated animals with 3-4 biological replicates per genotype (KO and DHPS) and prepared for single cell RNA sequencing using the GemCode Single Cell Platform with GemCode Gel Beads, Chip and Library Kits (v3) and 10X Genomics Chromium Controller following the manufacturer’s protocol.
Libraries were sequenced on NovaSeq 6000 (Illumina).

value: peritoneal cavity


title: cell-free DNA from NMN treated sample 56.2 at T3

description: PBMC DNA from treated mice


title: Cry12DKO_RNAP_II_CT12

description: Library name: Sample147


title: PBMC, Moderate COVID-19, pCoV22

description:
Library name: pCoV22_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Blood

value: Moderate COVID-19


title: cell-free DNA from NMN treated sample 56.1 at T4

description: PBMC DNA from treated mice


title: PBMC, Moderate COVID-19, pCoV20

description:
Library name: pCoV20_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Peripheral blood mononuclear cells

value: male


title: PBMC, Convalescent COVID-19, pCoV18

description:
Library name: pCoV18_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: White


title: PBMC, Moderate COVID-19, pCoV23

description:
Library name: pCoV23_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Asian


title: cell-free DNA from NMN treated sample 56.1 at T3

description: PBMC DNA from treated mice

value: NMN


title: cell-free DNA from NMN treated sample 56.1 at T2

description: PBMC DNA from treated mice


title: WT_mRNA-seq_CT40

description: Library name: Sample141


title: PBMC, Convalescent COVID-19, pCoV19

description:
Library name: pCoV19_scRNA
10x Genomics (mRNA 3' V3 Chemistry)


title: cell-free DNA from NMN treated sample 56.1 at BL

description: PBMC DNA from treated mice


title: WT_mRNA-seq_CT20

description: Library name: Sample136


title: PBMC, Severe Steroid Treated COVID-19, pCoV21

description:
Library name: pCoV21_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Severe Steroid Treated COVID-19


title: KO_DHPS_Plavage_1

description: Library name: KO_DHPS_Plavage_1

value: KO


title: WT_mRNA-seq_CT36

description: Library name: Sample140

value: Liver


title: KO_DHPS_Plavage_2

description: Library name: KO_DHPS_Plavage_2


title: cell-free DNA from NMN treated sample 56.2 at BL

description: PBMC DNA from treated mice


title: PBMC, Severe Steroid Treated COVID-19, pCoV17

description:
Library name: pCoV17_scRNA
10x Genomics (mRNA 3' V3 Chemistry)


title: cell-free DNA from healthy control sample 81.4 at T4

description: PBMC DNA from healthy control mice

value: control


title: Liver_KO1

description: Library name: Liver_KO1

value: Macrophage


title: WT_mRNA-seq_CT32

description: Library name: Sample139


title: WT_DHPS_Plavage_2

description: Library name: WT_DHPS_Plavage_2


title: Ribo_DHPS_WT_2

description: Library name: Ribo_DHPS_WT_2

extract_protocol:
Freshly isolated cells from total peritoneal lavage were processed with the following modifications. 1ml of homogenization buffer was used per mouse, DTT was removed from washing buffer to avoid uncoupling of conjugated anti-HA antibodies from magnetic beads. Total lysate (100 μL) was used as input. The remaining lysate was used for IP of polysomes. 25 μL of anti-HA.11 (Pierce) were used per lysate with rotation at 4°C for 4 h. Beads were then washed three times with 500 μL of wash buffer. RNA was extracted from magnetic beads with TRIzol reagent (Invitrogen), and total RNA isolated with Direct-zol RNA Microprep Kit (Zymo Research) according to the manufacturer’s instructions.
Total RNA was submitted to Admera Health, LLC (South Plainsfield, NJ) RNA sequencing. For RNA sequencing, isolated RNA sample quality was assessed by RNA Tapestation (Agilent Technologies Inc., California, USA) and quantified by AccuBlue® Broad Range RNA Quantitation assay (Biotium, California, USA). Paramagnetic beads coupled with oligo d(T)25 are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual (New England BioLabs Inc., Massachusetts, USA). Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendations. The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period, approximately 40 minutes at 42°C. All remaining steps for library construction were used according to the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA). Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation D1000 ScreenTape (Agilent Technologies Inc., California, USA). Final library size was about 430bp with an insert size of about 300bp. Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaseqX plus platform (Illumina, California, USA) with a read length configuration of 150 PE for 40M PE reads per sample (20M in each direction).

value: Peritoneal cavity

tag: antibody


title: cell-free DNA from healthy control sample 81.4 at T3

description: PBMC DNA from healthy control mice


title: WT_mRNA-seq_CT24

description: Library name: Sample137


title: WT_mRNA-seq_CT16

description: Library name: Sample135


title: WT_DHPS_Plavage_1

description: Library name: WT_DHPS_Plavage_1


title: WT_mRNA-seq_CT12

description: Library name: Sample134


title: PBMC, Convalescent COVID-19, pCoV14

description:
Library name: pCoV14_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: female

value: Black

value: Convalescent COVID-19


title: cell-free DNA from healthy control sample 81.4 at T2

description: PBMC DNA from healthy control mice

value: PBMC


title: Ribo_DHPS_KO_3

description: Library name: Ribo_DHPS_KO_3


title: WT_mRNA-seq_CT28

description: Library name: Sample138

value: WT


title: WT_mRNA-seq_CT08

description: Library name: Sample133


title: PBMC, Convalescent COVID-19, pCoV16

description:
Library name: pCoV16_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Blood


title: cell-free DNA from healthy control sample 81.4 at BL

description: PBMC DNA from healthy control mice


title: PBMC, Convalescent COVID-19, pCoV15

description:
Library name: pCoV15_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Peripheral blood mononuclear cells


title: WT_mRNA-seq_CT04

description: Library name: Sample132


title: Ribo_DHPS_KO_2

description: Library name: Ribo_DHPS_KO_2


title: Ribo_DHPS_KO_1

description: Library name: Ribo_DHPS_KO_1


title: cell-free DNA from healthy control sample 81.3 at T2

description: PBMC DNA from healthy control mice


title: WT_mRNA-seq_CT00

description: Library name: Sample131


title: PBMC, Moderate COVID-19, pCoV12

description:
Library name: pCoV12_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: male

value: Hispanic

value: Moderate COVID-19


title: WT_PRO-seq_CT44

description: Library name: Sample129

data_processing:
Illumina bcl2fastq version 2.17 for base calling and demultiplexing.
For ChIPseq, the adaptor and the reads with < 30bp were trimmed by CutAdapt v.1.18. Then, the data were mapped by BWA v0.7.16a-r1185-dirty with default options and the uniquely mapped reads were chosen by SAMtools v1.9. The PCR duplicates were removed by awk commands, and the final reads were extended to the MACS2 prediction sizes.
For mRNAseq, the adaptor, poly T sequences, and < 30bp reads of the raw data were trimmed by CutAdapt v.1.18 and mapped by STAR v2.5.3a. The uniquely mapped reads were chosen by SAMtools v1.9.
For PROseq, the adaptor sequences and < 16bp reads were removed by CutAdapt v.1.18 and the reverse complement (RC) sequences were made from FASTX-Toolkit. The RC was mapped by BWA v0.7.16a-r1185-dirty aln and the uniquely mapped reads were determined by SAMtools v1.9.
The normalized BigWig files are from BEDTools v2.27.1. The raw counts of the NGS data are retrieved from FeatureCounts v1.6.4.
Assembly: M14 from GENCODE
Supplementary files format and content: ChIP-seq BigWig files were made from Uniquely mapped duplicate-removed bed files. PRO-seq and mRNA-seq BigWig files were made from uniquely mapped STAR Bam files
Supplementary files format and content: Excel  file includes raw counts and RPKM values for the mRNA-seq results
Library strategy: PRO-Seq


title: Input_DHPS_WT_3

description: Library name: Input_DHPS_WT_3

value: Input


title: cell-free DNA from healthy control sample 81.3 at BL

description: PBMC DNA from healthy control mice


title: PBMC, Severe COVID-19, pCoV11

description:
Library name: pCoV11_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: White

value: Severe COVID-19


title: PBMC, Convalescent COVID-19, pCoV13

description:
Library name: pCoV13_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Biracial


title: Input_DHPS_WT_1

description: Library name: Input_DHPS_WT_1


title: Ribo_DHPS_WT_3

description: Library name: Ribo_DHPS_WT_3


title: WT_PRO-seq_CT36

description: Library name: Sample127

value: Liver


title: PBMC, Moderate COVID-19, pCoV9

description:
Library name: pCoV9_scRNA
10x Genomics (mRNA 3' V3 Chemistry)


title: Input_DHPS_WT_2

description: Library name: Input_DHPS_WT_2


title: WT_PRO-seq_CT32

description: Library name: Sample126


title: cell-free DNA from healthy control sample 81.2 at T2

description: PBMC DNA from healthy control mice

value: control


title: cell-free DNA from healthy control sample 81.2 at T3

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 81.2 at T4

description: PBMC DNA from healthy control mice


title: PBMC, Convalescent COVID-19, pCoV10

description:
Library name: pCoV10_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Asian


title: WT_PRO-seq_CT28

description: Library name: Sample125


title: PBMC, Moderate COVID-19, pCoV8

description:
Library name: pCoV8_scRNA
10x Genomics (mRNA 3' V3 Chemistry)


title: Input_DHPS_KO_3

description: Library name: Input_DHPS_KO_3

value: Peritoneal cavity

value: KO


title: Input_DHPS_KO_1

description: Library name: Input_DHPS_KO_1


title: Input_DHPS_KO_2

description: Library name: Input_DHPS_KO_2


title: cell-free DNA from healthy control sample 81.2 at BL

description: PBMC DNA from healthy control mice


title: PBMC, Severe COVID-19, pCoV7

description:
Library name: pCoV7_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: female


title: WT_PRO-seq_CT24

description: Library name: Sample124


title: WT_PRO-seq_CT40

description: Library name: Sample128


title: WT_PRO-seq_CT20

description: Library name: Sample123


title: cell-free DNA from healthy control sample 81.1 at T3

description: PBMC DNA from healthy control mice

value: PBMC


title: PBMC, Moderate COVID-19, pCoV5

description:
Library name: pCoV5_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Black


title: Young

city: Guangzhou

first: Meng

last: Zhao

address: Zhongshan 2nd Road

country: China

institute: Sun Yat-sen University

description:
Library name: Young
GEXSCOPE Single Cell RNA Library Kits (Singleron)

data_processing:
The Seurat R package (v.4.2.3) was used for data normalization, generating uniform manifold approximation and projection plots, and performing differential expression analysis. Wilcoxon rank-sum tests were used to identify differentially expressed genes in each cluster compared with others. The ClusterProfiler R package (v.4.0), including GSEA and enricher functions, was used for pathway enrichment analysis. The gene sets were adapted from the Molecular Signatures Database MSigDB (https://www.gseamsigdb.org/gsea/downloads.jsp). Gene set variation analysis was performed using the GSVA R package (v.1.46.0) with z scores calculated over the samples. Pathways with P < 0.05 were selected for visualization.
Assembly: GRCm38
Supplementary files format and content: Young_matrix.tar.gz
Supplementary files format and content: Old_matrix.tar.gz

source_name: bone marrow

extract_protocol:
In brief, intact bone marrows from mice at the age of 2-4 months or 20-24 months were flushed from mouse femora and tibiae. Bone marrow cells by pipetting with 1 mL syringe, and then underwent red blood cell lysis using 0.16 M ammonium chloride solution.
Single-cell suspensions with PBS were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron) (Ref). Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: bone marrow

value: Hematopoietic Stem Cell

value: Wild type

value: 2-4 months


title: PBMC, Moderate COVID-19, pCoV6

description:
Library name: pCoV6_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Blood

value: Peripheral blood mononuclear cells

value: Hispanic

value: Moderate COVID-19


title: PAMs, ASFV, NIM811, rep3

city: Harbin

first: Liqin

last: Yang

address: haping road 678

department: Harbin Veterinary Research Institute

institute: Chinese Academy of Agricultural Sciences

description:
Library name: Sample 12
Column name in Counts_all_Samples.txt: ASFV_NIM811_3

data_processing:
Illumina Bcltofastq 1.8.4 ver software used for basecalling.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp with default parameters.
Trimmed sequence reads were mapped to Sscrofa11.1 and ASM433821v1 using HISAT2 (version-2.2.1).
Read count extraction and normalization were performed using featureCounts(version-1.5.3).
Assembly: Sscrofa11.1 and ASM433821v1
Supplementary files format and content: tab-delimited text file includes raw counts for each Samples

organism: Sus scrofa

source_name: porcine alveolar macrophages

growth_protocol: PAMs were collected from 5-week-old healthy specificpathogen-free (SPF) piglets and were maintained in RPMI-1640 medium supplemented with 20% porcine serum , 100 U/mL penicillin and 100 μg/mL streptomycin, and 2 mmol/mL glutamine at 37 °C with 5% CO2 in a humidified incubator.

extract_protocol:
RNA was harvested using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PAMs were infected with or without ASFV (MOI = 0.1) for 72 h, with or without NIM811 treatment.

value: porcine alveolar macrophages


title: WT_PRO-seq_CT16

description: Library name: Sample122

value: Liver

value: WT


title: PBMC, Convalescent COVID-19, pCoV4

description:
Library name: pCoV4_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Convalescent COVID-19


title: Old

description:
Library name: Old
GEXSCOPE Single Cell RNA Library Kits (Singleron)

value: 20-24 months


title: oHSC-ABC-3

description: Library name: Old_HSC_ABC_3

data_processing:
RNA-seq reads were aligned to mouse genome mm10 and gene annotation from the Ensembl database. For read alignment and expression quantification, low-quality reads were removed and the adaptor sequences were trimmed by Trim Galore (v0.6.2). Then, the remaining pair-end reads were mapped to the reference genome by STAR version 2.6.1d with ENCODE options. The uniquely mapped reads were counted by HTSeq version 0.10.0, and normalized by trimmed mean of M values (TMM), and transformed to reads per kilobases per million mapped reads (RPKM) by edgeR version 3.24.3. Low abundant genes were removed with an expression cutoff of RPKM ≥1 in at least one sample.
Assembly: mm10
Supplementary files format and content: counts_bulk_yHSC.oHSC.ABC.csv.gz

extract_protocol:
In brief, intact bone marrows from mice at the age of 2-4 months or 20-24 months were flushed from mouse femora and tibiae. Bone marrow cells by pipetting with 1 mL syringe, and then underwent red blood cell lysis using 0.16 M ammonium chloride solution.
Low input RNA seq was performed according to published scRNA seq protocols with modifications (Picelli et al., 2014). Briefly, FACS-sorted 1500 HSCs in 3-5 μl PBS were transferred into 40 μl cell lysis buffer prepared by adding 2 μl of RNase inhibitor to 38 μl of a 0.25% (vol/vol) Triton X-100 solution. Quickly vortex the tube to mix, and then purify RNA using 80 μl VAHTS RNA Clean Beads (N412, Vayzme), following reverse transcription with 5 μl purified RNA and 15 μl RT mix. cDNAs were purified by VAHTS DNA Clean Beads (N411, Vazyme) for PCR enrichment with 12 cycles. Enriched cDNA was quantified using Qubit dsDNA HS Assay Kit after purification. TruePrepTM DNA library Prep Kit V2 (TD503, Vazyme) was used to prepare RNA seq library following the manufacturer's protocol. Individual libraries were sequenced as NovaSeq 6000 PE150 platform. At least three replicates were included.

tag: group

value: old HSC treated with ABC294640


title: oHSC-ABC-1

description: Library name: Old_HSC_ABC_1


title: PAMs, ASFV, DMSO, rep3

description:
Library name: Sample 9
Column name in Counts_all_Samples.txt: ASFV_DMSO_3

value: DMSO


title: oHSC-3

description: Library name: Old_HSC_3

value: old HSC


title: PAMs, ASFV, NIM811, rep2

description:
Library name: Sample 11
Column name in Counts_all_Samples.txt: ASFV_NIM811_2


title: oHSC-ABC-2

description: Library name: Old_HSC_ABC_2


title: PAMs, ASFV, NIM811, rep1

description:
Library name: Sample 10
Column name in Counts_all_Samples.txt: ASFV_NIM811_1


title: cell-free DNA from healthy control sample 81.1 at T4

description: PBMC DNA from healthy control mice

value: PBMC

value: control


title: PBMC, Severe COVID-19, pCoV2

description:
Library name: pCoV2_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: female

value: Black

value: Severe COVID-19


title: WT_PRO-seq_CT04

description: Library name: Sample119


title: WT_PRO-seq_CT08

description: Library name: Sample120


title: WT_PRO-seq_CT00

description: Library name: Sample118


title: PAMs, ASFV, DMSO, rep2

description:
Library name: Sample 8
Column name in Counts_all_Samples.txt: ASFV_DMSO_2


title: oHSC-2

description: Library name: Old_HSC_2

value: bone marrow

value: Hematopoietic Stem Cell

value: Wild type


title: PBMC, Moderate COVID-19, pCoV3

description:
Library name: pCoV3_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: Blood

value: Peripheral blood mononuclear cells

value: male

value: Asian

value: Moderate COVID-19


title: PBMC, Healthy, pHC17

description:
Library name: pHC17_snATAC
10x Genomics (scATAC-seq)

library_source: genomic single cell

data_processing:
Data processing was performed using Cell Ranger-ATAC software 2.1.0 (https://support.10xgenomics.com/single-cell-atac/software/overview/welcome)
Assembly: GRCh38-2020-A
Supplementary files format and content: H5ad file includes scanpy object containing gene activity scores for all PBMCs.
Supplementary files format and content: H5ad file includes scanpy object containing gene activity scores and chromVAR deviations for CD4+ T Cells.
Supplementary files format and content: H5ad file includes scanpy object containing gene activity scores and chromVAR deviations for B cells.
Supplementary files format and content: H5ad file includes scanpy object containing gene activity scores and chromVAR deviations for CD8+ T, cytotoxic T and NK cells.
Supplementary files format and content: H5ad file includes scanpy object containing gene activity scores and chromVAR deviations for myeloid cells.
Supplementary files format and content: Comma separated value file includes single cell read metrics.
Supplementary files format and content: Tab separated value file includes high quality fragment positions on the reference genome with cell barcode and read support information.
Supplementary files format and content: Tab separated value file includes raw cell barcodes.
Supplementary files format and content: Tab separated value file includes raw peak calls.
Supplementary files format and content: Matrix file includes raw read counts for raw peaks and barcodes.
Supplementary files format and content: Tab separated value file includes filtered cell barcodes.
Supplementary files format and content: Tab separated value file includes filtered peak calls.
Supplementary files format and content: Matrix file includes raw read counts for filtered peaks and barcodes.

extract_protocol:
Viable single cell suspensions from each sample were used to generate snATAC-seq data using the 10x Chromium platform according to the manufacturer’s protocols (10x Genomics, protocols CG000169; CG000168). Briefly, >100,000 cells from each sample were centrifuged and the supernatant was removed without disrupting the cell pellet. Lysis Buffer was added for 5 minutes on ice to generate isolated and permeabilized nuclei, and the lysis reaction was quenched by dilution with Wash Buffer. After centrifugation to collect the washed nuclei, diluted Nuclei Buffer was used to re-suspend nuclei at the desired nuclei concentration as determined using a Countess II FL Automated Cell Counter and combined with ATAC Buffer and ATAC Enzyme to form a Transposition Mix.
Transposed nuclei were immediately combined with Barcoding Reagent, Reducing Agent B and Barcoding Enzyme and loaded onto a 10x Chromium Chip H for droplet generation followed by library construction. The barcoded sequencing libraries were subjected to bead clean-up and checked for quality on an Agilent 4200 TapeStation, quantified by KAPA qPCR, and pooled for sequencing on an Illumina NovaSeq 6000 (2x50bp libraries).

value: White

value: Healthy


title: WT_PRO-seq_CT12

description: Library name: Sample121

value: Liver

value: WT


title: PAMs, ASFV, DMSO, rep1

description:
Library name: Sample 7
Column name in Counts_all_Samples.txt: ASFV_DMSO_1

value: porcine alveolar macrophages

value: DMSO


title: oHSC-1

description: Library name: Old_HSC_1

value: old HSC


title: PAMs, uninfected, NIM811, rep3

description:
Library name: Sample 6
Column name in Counts_all_Samples.txt: NO_NIM811_3


title: WT_BMAL1_CT44

description: Library name: Sample116

value: anti BMAL1 (Yoo et al 2013)


title: WT_BMAL1_INPUT

description: Library name: Sample117

value: input mix(00-44)


title: PBMC, Convalescent COVID-19, pCoV1

description:
Library name: pCoV1_scRNA
10x Genomics (mRNA 3' V3 Chemistry)

value: female

value: Black

value: Convalescent COVID-19


title: PBMC, Healthy, pHC16

description:
Library name: pHC16_snATAC
10x Genomics (scATAC-seq)

value: Blood


title: WT_BMAL1_CT40

description: Library name: Sample115


title: PBMC, Other, pOI1

description:
Library name: pOI1_snATAC
10x Genomics (scATAC-seq)

value: Peripheral blood mononuclear cells

value: Biracial

value: Other


title: yHSC-2

description: Library name: Young_HSC_2

value: bone marrow

value: Hematopoietic Stem Cell

value: Wild type

value: young HSC


title: PAMs, uninfected, NIM811, rep2

description:
Library name: Sample 5
Column name in Counts_all_Samples.txt: NO_NIM811_2


title: WT_BMAL1_CT36

description: Library name: Sample114

value: Liver

value: WT


title: PBMC, Healthy, pHC14

description:
Library name: pHC14_snATAC
10x Genomics (scATAC-seq)

value: Healthy


title: PBMC, Healthy, pHC15

description:
Library name: pHC15_snATAC
10x Genomics (scATAC-seq)

value: male


title: PBMC, Healthy, pHC13

description:
Library name: pHC13_snATAC
10x Genomics (scATAC-seq)


title: WT_BMAL1_CT32

description: Library name: Sample113

value: anti BMAL1 (Yoo et al 2013)


title: PAMs, uninfected, NIM811, rep1

description:
Library name: Sample 4
Column name in Counts_all_Samples.txt: NO_NIM811_1

value: porcine alveolar macrophages


title: Old_HSC_Sphk2_KO_3

description:
Library name: Old_HSC_Sphk2_KO_3
Old_SK2_HSC_3

data_processing:
RNA-seq reads were aligned to mouse genome mm10 and gene annotation from the Ensembl database. For read alignment and expression quantification, low-quality reads were removed and the adaptor sequences were trimmed by Trim Galore (v0.6.2). Then, the remaining pair-end reads were mapped to the reference genome by STAR version 2.6.1d with ENCODE options. The uniquely mapped reads were counted by HTSeq version 0.10.0, and normalized by trimmed mean of M values (TMM), and transformed to reads per kilobases per million mapped reads (RPKM) by edgeR version 3.24.3. Low abundant genes were removed with an expression cutoff of RPKM ≥1 in at least one sample.
Assembly: mm10
Supplementary files format and content: yHSC_oHSC_Sphk2_Raw_Counts.txt.gz with raw counts matrices

extract_protocol:
In brief, intact bone marrows from mice at the age of 2 months or 22-24 months were flushed from mouse femora and tibiae. Bone marrow cells by pipetting with 1 mL syringe, and then underwent red blood cell lysis using 0.16 M ammonium chloride solution.
Low input RNA-seq was performed according to published single-cell RNA-seq protocols with modifications (Tang et al., 2010). Briefly, FACS-sorted 1000 Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC) (2-3 µL) of each sample were transferred into 25 μL cell lysis buffer prepared as follows: 0.9x PCR buffer II, 1.35 mM MgCl2, 0.45% NP40, 4.5 mM DTT, 0.36 U μL–1 RNase inhibitor (ThermoFisher, EN0581), 12.5 nM UP1 primer, 0.045 mM dNTP), following reverse transcription with RT mix prepared as follows: 14.4 U μL–1 Superscript III reverse transcriptase (Invitrogen, 18080-044), 0.48U μL–1 RNase inhibitor, 0.07 U μL–1 T4 gene 32 protein (NEB, #M0300L). cDNA purified with AMPure XP beads (Beckman Coulter, A63881) were used to perform poly A tailing, then one round of PCR enrichment with 13 cycles of amplification was performed. Enriched cDNA was quantified using Qubit dsDNA HS Assay Kit after purification. TruePrepTM DNA library Prep Kit V2 (Vazyme, TD503) was used to prepare RNA seq library following the manufacturer’s protocol. Libraries were sequenced as pair-end 150 bp using HiSeq X10. Three technical replicates were included for each type.

value: B6N.129S6-Sphk2tm1Rlp/J (Sphk2 cKO)


title: PAMs, uninfected, DMSO, rep3

description:
Library name: Sample 3
Column name in Counts_all_Samples.txt: NO_DMSO_3

value: DMSO


title: PAMs, uninfected, DMSO, rep2

description:
Library name: Sample 2
Column name in Counts_all_Samples.txt: NO_DMSO_2


title: PBMC, Healthy, pHC12

description:
Library name: pHC12_snATAC
10x Genomics (scATAC-seq)

value: Black


title: Old_HSC_Sphk2_KO_2

description:
Library name: Old_HSC_Sphk2_KO_2
Old_SK2_HSC_2


title: WT_BMAL1_CT28

description: Library name: Sample112


title: WT_BMAL1_CT24

description: Library name: Sample111


title: yHSC-3

description: Library name: Young_HSC_3


title: PAMs, uninfected, DMSO, rep1

description:
Library name: Sample 1
Column name in Counts_all_Samples.txt: NO_DMSO_1


title: Old_HSC_Sphk2_KO_1

description:
Library name: Old_HSC_Sphk2_KO_1
Old_SK2_HSC_1


title: PBMC, Healthy, pHC11

description:
Library name: pHC11_snATAC
10x Genomics (scATAC-seq)

value: Blood

value: female

value: White


title: WT_BMAL1_CT20

description: Library name: Sample110


title: PBMC, Healthy, pHC9

description:
Library name: pHC9_snATAC
10x Genomics (scATAC-seq)

value: Peripheral blood mononuclear cells


title: AB5075_DMSO_rep2

city: London

first: Kavita

last: Gadar

address: Kingston Lane

country: United Kingdom

institute: Brunel University

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl2fastq (2.20.0.422)
Read mapping was performed with HISAT
Differential expression analysis was performed using edgeR’s exact test for differences between two groups of negative-binomial counts with an estimated dispersion value of .1.
Read quantification was performed using Subread’s featureCounts functionality.
Read counts loaded into R and were normalized using edgeR’s Trimmed Mean of M values algorithm.  Subsequent values were then converted to counts per million (cpm).
Assembly: NZ_CP008706.1
Supplementary files format and content: Matrix table (tab-delimited file) with raw gene counts for every gene and every sample
Supplementary files format and content: Individual tab-delimited files with normalize counts (cpm) for every sample.

organism: Acinetobacter baumannii AB5075

source_name: Acinetobacter baumannii AB5075

growth_protocol: A. baumannii AB5075 (12 independent replicates) was inoculated from stock and incubated overnight in LB (37 C, 180 rpm). Then, cultures were diluted in LB (suplemented with 50 μM agrimoniin, 2.3 μM ellagic acid, 0.05 mg/mL of Wicklow tormentil root extract or with a mock treatment of DMSO) to OD600 0.05 and incubated at 37 C, 180 rpm until reaching mid-exponential phase (OD600 0.6 approx.).

extract_protocol:
Cultures were harvested by centrifugation and washed in RNAlater to preserve RNA integrity. RNA was isolated using athe Qiagen RNAeasy Kit with on-column DNAase digestion (Qiagen). RNA quality was assessed using a Bioanalyzer.
Samples were additionally treated with RNAse-free DNAse (Invitrogen). cDNA library was prepared with Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices.

treatment_protocol: The treatment (50 μM agrimoniin, 2.3 μM ellagic acid, 0.05 mg/mL of Wicklow tormentil root extract or a DMSO control) was applied as a supplement in the LB medium and was present since the beginning of the growth.

value: Acinetobacter baumannii AB5075

value: DMSO Control


title: WT_BMAL1_CT16

description: Library name: Sample109


title: AB5075_DMSO_rep3


title: Old_HSC_3

description:
Library name: Old_HSC_3
Old_WT_HSC_3

value: bone marrow

value: Hematopoietic Stem Cell

value: Wild type


title: yHSC-1

description: Library name: Young_HSC_1

value: young HSC


title: Old_HSC_2

description:
Library name: Old_HSC_2
Old_WT_HSC_2


title: WT_BMAL1_CT12

description: Library name: Sample108

value: Liver

value: WT


title: AB5075_DMSO_rep1


title: AB5075_Wicklow_rep3

value: 0.05 mg/mL of Wicklow tormentil root extract


title: PBMC, Healthy, pHC8

description:
Library name: pHC8_snATAC
10x Genomics (scATAC-seq)

value: Healthy


title: WT_BMAL1_CT08

description: Library name: Sample107

value: anti BMAL1 (Yoo et al 2013)


title: Young_HSC_3

description:
Library name: Young_HSC_3
Young_WT_HSC_3


title: AB5075_Wicklow_rep2


title: PBMC, Severe RSV, pRSV17

description:
Library name: pRSV17_snATAC
10x Genomics (scATAC-seq)

value: male

value: Severe RSV


title: Old_HSC_1

description:
Library name: Old_HSC_1
Old_WT_HSC_1


title: WT_BMAL1_CT00

description: Library name: Sample105


title: AB5075_Wicklow_rep1


title: PBMC, Severe RSV, pRSV15

description:
Library name: pRSV15_snATAC
10x Genomics (scATAC-seq)

value: Blood


title: WT_PAF1_CT44

description: Library name: Sample103

value: anti PAF1 (Bethyl Laboratories Cat# A300-173A)


title: PBMC, Severe RSV, pRSV14

description:
Library name: pRSV14_snATAC
10x Genomics (scATAC-seq)

value: Multiracial


title: Young_HSC_1

description:
Library name: Young_HSC_1
Young_WT_HSC_1


title: PBMC, Healthy, pHC10

description:
Library name: pHC10_snATAC
10x Genomics (scATAC-seq)

value: Peripheral blood mononuclear cells

value: Black


title: AB5075_Ellagic_Acid_rep3

value: Acinetobacter baumannii AB5075

value: 2.3 microM ellagic acid


title: AB5075_Ellagic_Acid_rep2


title: PBMC, Severe RSV, pRSV16

description:
Library name: pRSV16_snATAC
10x Genomics (scATAC-seq)

value: White


title: oHSC_H3K9ac

description: Library name: oHSC_H3K9ac

data_processing:
Pair-end reads were mapped to the mm10 reference genome using the bwa mem. The duplicated reads were removed using the Picard Toolkit (https://broadinstitute.github.io/picard/), whereas the reads with a quality lower than 20 were filtered. The ChIP-seq peaks were called using the default (narrow) setting in MACS2. The promoter regions were defined as +/- 1.5Kb around the TSSs regions. Differential peak analysis was performed using the edgeR with a cutoff FDR < 0.05 and Fold change > 1.
Assembly: mm10
Supplementary files format and content: yHSC-H3K9ac_summits.bed.txt.gz
Supplementary files format and content: oHSC-H3K9ac_summits.bed.txt.gz
Supplementary files format and content: oHSC-ABC-H3K9ac_summits.bed.txt.gz
Library strategy: CUT&Tag

extract_protocol:
In brief, intact bone marrows from mice at the age of 2-4 months or 18-24 months were flushed from mouse femora and tibiae. Bone marrow cells by pipetting with 1 mL syringe, and then underwent red blood cell lysis using 0.16 M ammonium chloride solution.
Genomic DNA extraction, library preparation, and sequencing were performed by using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (TD904, Vazyme). 5×104 sorted HSCs were collected at room temperature and incubated overnight with canavalin A beads and Acetyl-Histone H3K9ac antibody (9649, CST) at 4 ℃. Genomic DNA was fragmented using pA/pG-Tn5 transposons and extracted using DNA Extract Beads. Using DNA as a template for PCR, sequencing libraries were generated by adding Illumina sequencing adapters with custom primers. The resulting library DNA was purified using VAHTS DNA Clean Beads (N411, Vazyme).

value: bone marrow

value: Hematopoietic Stem Cell

value: Wild type


title: WT_PAF1_CT40

description: Library name: Sample102

value: Liver

value: WT


title: PBMC, Mild RSV, pRSV13

description:
Library name: pRSV13_snATAC
10x Genomics (scATAC-seq)

value: female

value: Mild RSV


title: WT_PAF1_CT36

description: Library name: Sample101


title: WT_BMAL1_CT04

description: Library name: Sample106

value: anti BMAL1 (Yoo et al 2013)


title: yHSC_H3K9ac

description: Library name: yHSC_H3K9ac


title: AB5075_Ellagic_Acid_rep1


title: PBMC, Moderate RSV, pRSV18

description:
Library name: pRSV18_snATAC
10x Genomics (scATAC-seq)

value: male

value: Moderate RSV


title: Young_HSC_2

description:
Library name: Young_HSC_2
Young_WT_HSC_2


title: oHSC_ABC_H3K9ac

description: Library name: oHSC_ABC_H3K9ac


title: WT_PAF1_INPUT

description: Library name: Sample104

value: input mix(00-44)


title: intestine, ND3

city: Nanjing

first: Yue

address: 1 WenYuan Road

institute: Nanjing Normal University

description: Library name: N-3

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: intestine

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: intestine


title: WT_PAF1_CT32

description: Library name: Sample100

value: anti PAF1 (Bethyl Laboratories Cat# A300-173A)


title: AB5075_Agrimoniin_rep2

value: 50 microM agrimoniin


title: PBMC, Mild RSV, pRSV12

description:
Library name: pRSV12_snATAC
10x Genomics (scATAC-seq)

value: Blood

value: Peripheral blood mononuclear cells


title: intestine, ND1

description: Library name: N-1


title: WT_PAF1_CT24

description: Library name: Sample98


title: intestine, ND2

description: Library name: N-2


title: PBMC, Moderate RSV, pRSV10

description:
Library name: pRSV10_snATAC
10x Genomics (scATAC-seq)

value: White


title: WT_PAF1_CT28

description: Library name: Sample99


title: WT_PAF1_CT16

description: Library name: Sample96


title: WT_Veh_4

type: RNA

first: Supriyo

last: De

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: WT

hyb_protocol: Once the hybridization reactions have been removed from the thermal cycler, proceed immediately to an nCounter Prep Station. This step can process up to 12 samples per run in approximately 2.5 to 3 hours.

scan_protocol: Next, the nCounter Digital Analyzer which is a multi-channel epifluorescence scanner collects raw data by taking images of the immobilized fluorescent reporters in the sample cartridge with a CCD camera through a microscope objective lens. Images are processed internally and the results are exported as a.csv file.

data_processing: RCC format files containing the raw data  were analyzed via the NanoString nCounter nSolver 4.0 software (MAN-C0019-08) with the NanoString Advanced Analysis 2.0 plugin (MAN-10,030-03) following the NanoString Gene Expression Data Analysis Guidelines (MAN-C0011-04). Both positive control and housekeeping normalization were used to normalize all sources of variation associated with the platform. Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes and p-values were calculated using criteria provided by Nanostring. ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library1. Abundance of various cell populations is calculated on ROSALIND using the Nanostring Cell Type Profiling Module. ROSALIND performs a filtering of Cell Type Profiling results to include results that have scores with a p-Value greater than or equal to 0.05. Fold changes and pValues are calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual. P-value adjustment is performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR).

label: NanoString barcodes

organism: Mus

source_name: prefrontal cortex

label_protocol: Per NanoString protocol. Label a 12-tube PCR hybridization strip. The purified RNA is diluted in nuclease-free water to 20 ng/uL. Recommended total RNA samples are 20 ng to 100 ng for hybridization assay. The prepared samples are used as input into nCounter hybridization reactions containing NanoString Reporter and Capture probes. First, remove Reporter CodeSet and Capture ProbeSet tubes from the freezer and thaw at room temperature. Second, after it has thawed, inspect the tube of Reporter CodeSet to make sure no colored precipitate is present. Third, If you see a colored precipitate, heat the entire tube to 75°C for 10 minutes and cool at room temperature before using .The purified RNA was hybridized at thermal cycler at 65°C for 16 to 24 hours into nCounter 15 µL of hybridization buffer containing NanoString Reporter and Capture probes. Add 8 μL of Master Mix to each well of a strip tube. Add 5 µL of sample to each tube containing Master Mix. Add 2 µL of Capture ProbeSet to each tube. Maximum hybridization time should not exceed 48 hours.

extract_protocol: Prefrontal cortexl tissue (10 mg) from the mice were prepared for the extraction of total RNA using a Nucleospin RNA isolation kit (Macherey-Nagel, #740955.250) as per the manufacturer’s protocol.

treatment_protocol: WT (C57BL6/J), RecQ1, WRN, RecQ4 deficient mice were maintained on a 12h light-dark schedule and fed standard NIH chow. Mice were exposed the whole body with γ-irradiation (IR, 6 Gy).

value: Vehicle

value: F

value: prefrontal cortex


title: AB5075_Agrimoniin_rep1

value: Acinetobacter baumannii AB5075


title: AB5075_Agrimoniin_rep3


title: intestine, HLJDD4

description: Library name: H2-4


title: PBMC, Mild RSV, pRSV7

description:
Library name: pRSV7_snATAC
10x Genomics (scATAC-seq)


title: WT_PAF1_CT20

description: Library name: Sample97

data_processing:
Illumina bcl2fastq version 2.17 for base calling and demultiplexing.
For ChIPseq, the adaptor and the reads with < 30bp were trimmed by CutAdapt v.1.18. Then, the data were mapped by BWA v0.7.16a-r1185-dirty with default options and the uniquely mapped reads were chosen by SAMtools v1.9. The PCR duplicates were removed by awk commands, and the final reads were extended to the MACS2 prediction sizes.
For mRNAseq, the adaptor, poly T sequences, and < 30bp reads of the raw data were trimmed by CutAdapt v.1.18 and mapped by STAR v2.5.3a. The uniquely mapped reads were chosen by SAMtools v1.9.
For PROseq, the adaptor sequences and < 16bp reads were removed by CutAdapt v.1.18 and the reverse complement (RC) sequences were made from FASTX-Toolkit. The RC was mapped by BWA v0.7.16a-r1185-dirty aln and the uniquely mapped reads were determined by SAMtools v1.9.
The normalized BigWig files are from BEDTools v2.27.1. The raw counts of the NGS data are retrieved from FeatureCounts v1.6.4.
Assembly: M14 from GENCODE
Supplementary files format and content: ChIP-seq BigWig files were made from Uniquely mapped duplicate-removed bed files. PRO-seq and mRNA-seq BigWig files were made from uniquely mapped STAR Bam files
Supplementary files format and content: Excel  file includes raw counts and RPKM values for the mRNA-seq results

extract_protocol:
For ChIP-seq, , the fresh whole liver lobes were homogenized in 4 ml PBS containing 1% formaldehyde and kept for 8 min at room temperature (RT). For dual crosslinking, the fresh whole liver lobes were homogenized in 4 ml PBS containing 2mM EGS for 20 min at RT. After quencing and cell lysis, chromatin was sonicated by Covaris S2 with the options of 30 sec on/off, intensity 5, cycles/burst 200, duty 20% at 4°C. For PRO-seq, the largest mouse liver lobe was homogenized and the dissociated cells were filtered by 100mm mesh and centrifuged. The precipitated cells were re-suspended and lysed.  The extracted nucleus was re-suspended with the storage buffer and frozen till the next step. After the nuclear run-on, the RNA was extracted by Trizol LS (ThermoFisher). For mRNA-seq, the frozen liver samples were homogenized with Trizol (ThermoFisher) and RNA was extracted according to the manufacturer's instructions.
For ChIP-seq, the DNA fragments ranging from 125 to 175bp were size selected by AMPure magnetic beads (Beckman). Then, the DNA is adenylated, ligated to NEXTflex DNA barcode adaptors (PerkinElmer) and amplified (Enzymatics). For PRO-seq, the libraries were made with TruSeq small RNA Library primers nad the amplified libraries were size-separated by 8% PAGE gels and the DNA ranging from 140 bp to 200 bp was cut out and eluted by the crush/soak methods. For mRNA-seq, the mRNA was extracted from 10 mg of total RNA (RIN values > 8) pooled from three mice by NEXTflex Poly (A) Beads (PerkinElmer), fragmented by heat, reversely transcribed, ligated and amplified with NEXTflex DNA barcode adaptors (PerkinElmer). For all libraries, the size and quality of the libraries were validated by TapeStation (Agilent) and the amounts were measured by Qubit (ThermoFisher)

value: Liver

value: WT


title: PBMC, Mild RSV, pRSV8

description:
Library name: pRSV8_snATAC
10x Genomics (scATAC-seq)

value: Black

value: Mild RSV


title: PBMC, Moderate RSV, pRSV6

description:
Library name: pRSV6_snATAC
10x Genomics (scATAC-seq)

value: female

value: Biracial


title: intestine, HLJDD2

description: Library name: H2-2


title: intestine, HLJDD1

description: Library name: H2-1


title: WT_PAF1_CT12

description: Library name: Sample95


title: intestine, HLJDD3

description: Library name: H2-3


title: WT_Veh_2

description: WT

value: M


title: PBMC, Moderate RSV, pRSV5

description:
Library name: pRSV5_snATAC
10x Genomics (scATAC-seq)

value: male

value: Moderate RSV


title: WT_Veh_1

description: WT


title: PBMC, Moderate RSV, pRSV11

description:
Library name: pRSV11_snATAC
10x Genomics (scATAC-seq)


title: WT_Veh_3

description: WT


title: WT_PAF1_CT08

description: Library name: Sample94

value: anti PAF1 (Bethyl Laboratories Cat# A300-173A)


title: PBMC, Moderate RSV, pRSV4

description:
Library name: pRSV4_snATAC
10x Genomics (scATAC-seq)

value: Blood


title: intestine, HFD4

description: Library name: H-4

value: intestine


title: intestine, HFD3

description: Library name: H-3


title: WT_PAF1_CT04

description: Library name: Sample93


title: PBMC, Moderate RSV, pRSV3

description:
Library name: pRSV3_snATAC
10x Genomics (scATAC-seq)

value: Peripheral blood mononuclear cells

value: White


title: WT_IR_5

description: WT

value: 6 Gy γ-irradiation

value: F


title: WT_PAF1_CT00

description: Library name: Sample92


title: WT_IR_4

description: WT

value: prefrontal cortex


title: intestine, HFD2

description: Library name: H-2


title: IL33_neg_Irisin#3

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: Library name: IL33_neg_Irisin#3

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Additional quality control after normalization included removal of biological replicates with a poor Pearson’s correlation (<0.9) and/or poor congregation by principal component analysis of the top 1000 variable genes. Genes with fewer than 15 reads across samples or a high coefficient of variation (>0.30) were removed in Multiplot Studio (GenePattern; Broad Institute).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: VAT

extract_protocol:
For cultured cells in 96-well plate, 20ul TCL buffer containing 1% 2-mercaptoethanol was used to lyse cells and 5ul of that was submitted to RNA-seq.
Library construction and sequencing and data processing were performed according to the standard Immunological Genome Project protocols (https://www.immgen.org/img/Protocols/ImmGenULI_RNAseq_methods.pdf).

value: VAT

value: Stromal Cell


title: WT_IR_3

description: WT

value: WT


title: intestine, HFD1

description: Library name: H-1


title: PBMC, Severe RSV, pRSV2

description:
Library name: pRSV2_snATAC
10x Genomics (scATAC-seq)

value: Severe RSV


title: LMMP 17-month female 1

first: Loyal

last: Goff

state: MD

address: 733 N Broadway

description:
Library name: 17mo-F-1
sample_P30-M-2

data_processing:
Base calls and demultiplexing were performed with Illumina’s bcl2fastq
Isoform abundances were generated via pseudoalignment with kallisto quant (v 0.48.0) to Ensembl release 90.
Median fragment length (estimated): 168.7 bp
Median reads/sample: 46,756,241
Mean read pseudoalignment: 94.2%
Assembly: Ensembl 90
Supplementary files format and content: *_abundance.tsv: Estimated isoform abundances from pseudoalignment with kallisto. Includes isoform id, gene length, est_counts, and TPM
Supplementary files format and content: isoform_estimated_counts_all_samples.csv: Sample x isoform matrix of est_counts

source_name: longitudinal muscle and myenteric plexus (ileum)

extract_protocol:
Frozen tissue samples each in 1.5mL tubes were submerged in 375 uL of RLT buffer with β-mercaptoethanol. Tissue and buffer were transferred to a ice-cold 2 mL Qiagen sample tube with a 5mm stainless steel bead and  lysed in a TissueLyzer at full speed for 3 minutes. RNA isolation was completed with the Qiagen RNeasy Mini, Animal Tissue and Cells with DNA Digest protocol.
Standard Illumina stranded mRNA prep ligation kit was used with 100ng total RNA input per sample. 2x50 bp paired-end reads were sequenced.

value: 17 month

value: Female

value: WT (C57BL/6J)

tag: batch


title: WT_IR_2

description: WT


title: IL33_neg_Irisin#2

description: Library name: IL33_neg_Irisin#2


title: LMMP 17-month female 2

description:
Library name: 17mo-F-2
sample_P30-M-3

value: longitudinal muscle and myenteric plexus (ileum)


title: WT_IR_1

description: WT


title: PBMC, Severe RSV, pRSV1

description:
Library name: pRSV1_snATAC
10x Genomics (scATAC-seq)

value: female

value: Biracial


title: PBMC, Severe Steroid Treated COVID-19, pCoV31

description:
Library name: pCoV31_snATAC
10x Genomics (scATAC-seq)

value: Blood

value: male

value: Severe Steroid Treated COVID-19


title: PBMC, Moderate COVID-19, pCoV26

description:
Library name: pCoV26_snATAC
10x Genomics (scATAC-seq)

value: Peripheral blood mononuclear cells

value: Black

value: Moderate COVID-19


title: PBMC, Severe COVID-19, pCoV30

description:
Library name: pCoV30_snATAC
10x Genomics (scATAC-seq)

value: White

value: Severe COVID-19


title: IL33_neg_PBS#2

description: Library name: IL33_neg_PBS#2

value: VAT

value: Stromal Cell

value: PBS


title: IL33_neg_PBS#3

description: Library name: IL33_neg_PBS#3


title: LMMP 17-month male 2

description:
Library name: 17mo-M-2
sample_P30-F-3

value: 17 month

value: Male


title: LMMP 17-month male 3

description:
Library name: 17mo-M-3
sample_P30-M-1

value: WT (C57BL/6J)


title: LMMP 17-month male 1

description:
Library name: 17mo-M-1
sample_P30-F-2

value: longitudinal muscle and myenteric plexus (ileum)


title: RQ4_Veh_2

description: HO

value: Vehicle

value: F

value: RECQL4 KO

value: prefrontal cortex


title: IL33_neg_PBS#1

description: Library name: IL33_neg_PBS#1


title: RQ4_Veh_1

description: HO

value: M


title: PBMC, Severe Steroid Treated COVID-19, pCoV27

description:
Library name: pCoV27_snATAC
10x Genomics (scATAC-seq)

value: Blood

value: Peripheral blood mononuclear cells

value: male

value: Severe Steroid Treated COVID-19


title: ME_CnT_IgG_replicate3

city: Cambridge

first: Somdutta

last: Dhir

address: Robinson Way

department: CRUK-CI

institute: University of Cambridge

description: Library name: Sample17

data_processing:
Fastq files from tagmentation-based duet evoC were processed through a modified version of biomodal’s duet analysis pipeline. 9nt scar sequences, AAGAGATAG and AAAAAACAA were trimmed from the 5`-ends of Reads 1 and 2. Read pairs that lacked either scar sequence were discarded. Adapters containing the full 19nt Tn5 ME sequence and 2 Uracils (ME2U) hairpin were trimmed from the 3`-ends of Reads 1 and 2. A further 9nt were trimmed from the 3`-ends of Read 1 and 2.The trimmed read pairs were then resolved using the bespoke resolution algorithm described in Füllgrabe et al. (2023). The resolved, single-end reads were aligned against a GRCm38 reference (gencode vM25) that contained additional sequences for pUC19, bacteriophage lambda and short spike-in oligonucleotides using bwa-mem2 (v2.2.1).
For Mosaic end CUT&Tag, raw fastq files were trimed with cutadapt version 1.18 to remove adaptors and bases with quality lower than 20 (-q 20) mapped with bwa-mem 0.7.17-r2188 to mm10 genome, and only the reads within the whitelist have been retained.
Bigwig files were created using bamCoverage with counts per milion normalisation (CPM) after extending the paired-end reads.
Assembly: mm10 and GRCm38(gencode vM25)
Supplementary files format and content: CG_quant reports , BigWigs
Library strategy: CUT&Tag

source_name: Embryonic stem cells

growth_protocol: E14TG2A mouse embryonic stem cells were cultured in serum/LIF conditions on gelatin-coated plates. Serum/LIF medium was prepared with high-glucose DMEM (Sigma, D6546-500mL) supplemented with 10% FBS (Gibco, 16141079), 1X GlutaMax-I (Gibco, 35050-038), 1X NEAA (Gibco, 11140-035), 0.1 mM β-mercaptoethanol (Sigma, M3148) and 1,000 U/mL LIF (PeproTech, murine LIF, 250-02-25UG).

extract_protocol:
Cells were harvested by Accutase dissociation and used in CUT&Tag (Kaya-Okur et al. 2020, PMID: 32913232) assays for different histone mark antibodies and a non-specific IgG control (H3K27ac, H3K4me1, H3K4me3, H3K27me3, total rabbit IgG). Genomic DNA was extracted from cells after CUT&Tag using proteinase K digestion and Zymo DNA clean and concentrator clean-up.
Genomic DNA isolated from each CUT&Tag cell sample replicate was subjected to end repair and 6-base-seq library construction (Fullgrabe and Gosal et al. 2023, PMIID: 36747096).

treatment_protocol: No treatment

value: Embryonic stem cells

tag: cell line


title: IL33_neg_Irisin#1

description: Library name: IL33_neg_Irisin#1

value: VAT


title: RQ4_Veh_3

description: HO


title: PBMC, Convalescent COVID-19, pCoV25

description:
Library name: pCoV25_snATAC
10x Genomics (scATAC-seq)

value: female

value: Hispanic

value: Convalescent COVID-19


title: PBMC, Severe COVID-19, pCoV29

description:
Library name: pCoV29_snATAC
10x Genomics (scATAC-seq)

value: Black

value: Severe COVID-19


title: LMMP 6-month female 3

description:
Library name: 6mo-F-3
sample_P30-F-1

value: longitudinal muscle and myenteric plexus (ileum)

value: 6 month

value: Female

value: WT (C57BL/6J)


title: ME_CnT_IgG_replicate2

description: Library name: Sample16


title: ME_CnT_IgG_replicate1

description: Library name: Sample15


title: RQ4_IR_4

description: HO

value: 6 Gy γ-irradiation

value: F

value: RECQL4 KO

value: prefrontal cortex


title: PBMC, Moderate COVID-19, pCoV23

description:
Library name: pCoV23_snATAC
10x Genomics (scATAC-seq)

value: Blood

value: Peripheral blood mononuclear cells

value: male

value: Asian

value: Moderate COVID-19


title: RQ4_IR_3

description: HO


title: LMMP 6-month female 2

description:
Library name: 6mo-F-2
sample_6mo-M-3


title: 6B_CnT_IgG_replicate3

description: Library name: Sample14

data_processing:
Fastq files from tagmentation-based duet evoC were processed through a modified version of biomodal’s duet analysis pipeline. 9nt scar sequences, AAGAGATAG and AAAAAACAA were trimmed from the 5`-ends of Reads 1 and 2. Read pairs that lacked either scar sequence were discarded. Adapters containing the full 19nt Tn5 ME sequence and 2 Uracils (ME2U) hairpin were trimmed from the 3`-ends of Reads 1 and 2. A further 9nt were trimmed from the 3`-ends of Read 1 and 2.The trimmed read pairs were then resolved using the bespoke resolution algorithm described in Füllgrabe et al. (2023). The resolved, single-end reads were aligned against a GRCm38 reference (gencode vM25) that contained additional sequences for pUC19, bacteriophage lambda and short spike-in oligonucleotides using bwa-mem2 (v2.2.1).
For Mosaic end CUT&Tag, raw fastq files were trimed with cutadapt version 1.18 to remove adaptors and bases with quality lower than 20 (-q 20) mapped with bwa-mem 0.7.17-r2188 to mm10 genome, and only the reads within the whitelist have been retained.
Bigwig files were created using bamCoverage with counts per milion normalisation (CPM) after extending the paired-end reads.
Assembly: mm10 and GRCm38(gencode vM25)
Supplementary files format and content: CG_quant reports , BigWigs

value: Embryonic stem cells


title: LMMP 6-month female 1

description:
Library name: 6mo-F-1
sample_6mo-M-2


title: PBMC, Moderate COVID-19, pCoV22

description:
Library name: pCoV22_snATAC
10x Genomics (scATAC-seq)


title: LMMP 6-month male 3

description:
Library name: 6mo-M-3
sample_6mo-M-1

value: Male


title: LMMP 6-month male 1

description:
Library name: 6mo-M-1
sample_6mo-F-2


title: PBMC, Severe Steroid Treated COVID-19, pCoV21

description:
Library name: pCoV21_snATAC
10x Genomics (scATAC-seq)

value: White

value: Severe Steroid Treated COVID-19


title: LMMP 1-month female 3

description:
Library name: P30-F-3
sample_6mo-F-1

value: longitudinal muscle and myenteric plexus (ileum)

value: 1 month


title: 6B_CnT_H3K27ac_replicate3

description: Library name: Sample11


title: RQ4_IR_2

description: HO

value: M


title: WRN_Veh_3

description: HO

value: Vehicle

value: WRN

value: WRN KO


title: 6B_CnT_IgG_replicate1

description: Library name: Sample12


title: WRN_Veh_2

description: HO


title: PBMC, Moderate COVID-19, pCoV24

description:
Library name: pCoV24_snATAC
10x Genomics (scATAC-seq)

value: female

value: Black


title: LMMP 6-month male 2

description:
Library name: 6mo-M-2
sample_6mo-F-3

value: 6 month

value: WT (C57BL/6J)


title: PBMC, Convalescent COVID-19, pCoV19

description:
Library name: pCoV19_snATAC
10x Genomics (scATAC-seq)

value: Blood

value: Peripheral blood mononuclear cells

value: male

value: Convalescent COVID-19


title: 6B_CnT_IgG_replicate2

description: Library name: Sample13

value: Embryonic stem cells


title: PBMC, Moderate COVID-19, pCoV20

description:
Library name: pCoV20_snATAC
10x Genomics (scATAC-seq)

value: Biracial

value: Moderate COVID-19


title: WRN_Veh_1

description: HO

value: F

value: prefrontal cortex


title: PBMC, Convalescent COVID-19, pCoV18

description:
Library name: pCoV18_snATAC
10x Genomics (scATAC-seq)

value: White


title: 6B_CnT_H3K27ac_replicate2

description: Library name: Sample10


title: RQ4_IR_1

description: HO

value: 6 Gy γ-irradiation

value: M

value: RECQL4 KO


title: RQ4_IR_5

description: HO


title: LMMP 1-month female 2

description:
Library name: P30-F-2
sample_17mo-M-3

value: longitudinal muscle and myenteric plexus (ileum)

value: 1 month

value: Female


description:
Library name: pCoV17_snATAC
10x Genomics (scATAC-seq)

value: Black

value: Severe Steroid Treated COVID-19


title: LMMP 1-month male 3

description:
Library name: P30-M-3
sample_17mo-M-1

value: Male

value: WT (C57BL/6J)


title: LMMP 1-month female 1

description:
Library name: P30-F-1
sample_17mo-M-2


title: PBMC, Convalescent COVID-19, pCoV16

description:
Library name: pCoV16_snATAC
10x Genomics (scATAC-seq)

value: Blood

value: Peripheral blood mononuclear cells

value: male

value: Convalescent COVID-19


title: 6B_CnT_H3K27ac_replicate1

description: Library name: Sample9

value: Embryonic stem cells


title: WRN_IR_2

description: HO

value: F

value: WRN

value: WRN KO

value: prefrontal cortex


title: PBMC, Convalescent COVID-19, pCoV15

description:
Library name: pCoV15_snATAC
10x Genomics (scATAC-seq)

value: White


title: WRN_IR_3

description: HO

value: 6 Gy γ-irradiation

value: M


title: 6B_CnT_H3K27Me3_replicate1

description: Library name: Sample7


title: WRN_IR_1

description: HO


title: LMMP 1-month male 2

description:
Library name: P30-M-2
sample_17mo-F-2

value: longitudinal muscle and myenteric plexus (ileum)

value: 1 month


title: 6B_CnT_H3K27Me3_replicate2

description: Library name: Sample8


title: 6B_CnT_H3K4Me3_replicate3

description: Library name: Sample6


title: 6B_CnT_H3K4Me3_replicate2

description: Library name: Sample5


title: PBMC, Convalescent COVID-19, pCoV14

description:
Library name: pCoV14_snATAC
10x Genomics (scATAC-seq)

value: female

value: Black


title: KC2+cre (Group8)

city: Jinan

first: xiaochen

last: liu

address: Wenhua West Road No.44

institute: shandong university

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: lung

growth_protocol: Cells were cultured in RPMI-1640 medium (Gibco, #11875093) supplemented with 10% fetal bovine serum, 1% penicillin and streptomycin and 10 μM ROCK inhibitor (146986-50-7, MedChemExpress).

extract_protocol:
RNA was harvested using Trizol (Sigma)
RNA libraries for RNA-seq were prepared by NOVOGENE.

treatment_protocol: After culture for 72 hours, adherent cells were subcultured after detachment using 0.25% trypsin (25200-072, Gibco). For activation of KRASG12D and deletion of CUL4B, K and KC cells were cultured to 70% confluence and were then infected with 1×107 PFU/mL Ad-Cre. After 12 hours, the culture medium was changed.

value: lung

value: lung epithelial cells

value: primary culture cells

value: KRASG12D and CUL4B knockout

value: Ad-Cre treated


title: RQ1_Veh_2

description: HO

value: Vehicle

value: RECQL KO


title: PBMC, Convalescent COVID-19, pCoV13

description:
Library name: pCoV13_snATAC
10x Genomics (scATAC-seq)

value: Blood

value: Peripheral blood mononuclear cells

value: male

value: Biracial

value: Convalescent COVID-19


title: 6B_CnT_H3K4Me3_replicate1

description: Library name: Sample4

value: Embryonic stem cells


title: RQ1_Veh_4

description: HO

value: F

value: prefrontal cortex


title: 6B_CnT_H3K4Me1_replicate3

description: Library name: Sample3


title: RQ1_Veh_3

description: HO


title: PBMC, Convalescent COVID-19, pCoV10

description:
Library name: pCoV10_snATAC
10x Genomics (scATAC-seq)

value: female

value: Asian


title: LMMP 1-month male 1

description:
Library name: P30-M-1
sample_17mo-F-1

value: longitudinal muscle and myenteric plexus (ileum)

value: 1 month

value: Male

value: WT (C57BL/6J)


title: PBMC, Moderate COVID-19, pCoV8

description:
Library name: pCoV8_snATAC
10x Genomics (scATAC-seq)

value: Moderate COVID-19


title: 6B_CnT_H3K4Me1_replicate2

description: Library name: Sample2


title: PBMC, Severe COVID-19, pCoV7

description:
Library name: pCoV7_snATAC
10x Genomics (scATAC-seq)

value: White

value: Severe COVID-19


title: K1+cre (Group3)

value: lung

value: lung epithelial cells

value: primary culture cells

value: Ad-Cre treated


title: K2+cre (Group7)


title: 6B_CnT_H3K4Me1_replicate1

description: Library name: Sample1


title: RQ1_Veh_1

description: HO

value: Vehicle

value: M

value: RECQL KO


title: PBMC, Moderate COVID-19, pCoV5

description:
Library name: pCoV5_snATAC
10x Genomics (scATAC-seq)

value: Blood

value: Peripheral blood mononuclear cells

value: male

value: Black