title: MCF7_rep1_single_nuclei

city: Manchester

first: Angela

last: Simeone

address: 200 Hathersage Rd

institute: Genomic Services QIAGEN

description: single nuclei CUT&Tag

data_processing:
Library strategy: CUT&TAG
After checking sequencing quality with FastQC, bases with quality score below 20 were trimmed from both reads using cutadapt (V, cutadapt -q 20). Resulting reads were aligned to hg38 with bwa mem and aligned reads that were not overlapping the ENCODE black list were saved into bam (samtools view -Sb -F780 -q 10). Duplicate reads were identified and removed using Picard (Picard MarkDuplicates) and de-duplicated bam were sorted and indexed. In order to find enrichment loci with SEACR, deduplicated bam files were transformed into bedpe files (bedtools bamtobed -bedpe) and then only fragments with size below 1000bp (awk '{if ($1==$4 && $6-$2 < 1000)) print $0}') were kept. Next, coverage of the <1000bp fragments across human genome was computed using bedtools genomecov and reported in bedgraph format.
SEACR was used to identify regions of local enrichments. Bedgraphs obtained from selecting only  fragments of maximym 1kb  were used as input files for SEACR   (SEACR_1.3 $bdg_1000 0.05 non stringent). Peaks with a minimum coverage of 8 reads have been kept for further analysis. Peaks from individual libraries were combined together if replicates were available. Regions observed in 2 technical replicates (n=2) were selected as representative of the biological sample (multi2.bed, supp. files). When multiple biological replicates (i.e. different passages) were available, multi2 regions observed in a minimum two of them were used to generate consensus regions (bio.bed, supp. files)
multi2.bed files represent consensus for the same biological replicate across 2 technical replicates; bio.bed is the list of consensus loci across the available biological replicates.
Genome_build: hg38
Supplementary_files_format_and_content: .bw: bigwig genomic track file obtained normalising signal in 10bp window by total library size (RPM)
Supplementary_files_format_and_content: .bed: peaks

growth_protocol: K-562 cells (RRID:CVCL_0004) were cultured in RPMI 1640 (Gibco, 21875034) supplemented with 10% heat-inactivated fetal bovine serum (Gibco, A3840401). U2OS cells (RRID:CVCL_0042) were cultured in DMEM (Gibco, 41966029) supplemented with 10% heat-inactivated fetal bovine serum. MCF-7 cells (RRID:CVCL_0031) were cultured in DMEM (Gibco, 41966029) supplemented with 10% heat-inactivated fetal bovine serum and 1% Penicillin-Streptomycin (Gibco, 15070063). All cell lines were maintained in incubator at 37 °C with 5% CO2.

extract_protocol: Single-nuclei G4 CUT&Tag: Harvested cells were fixed in 0.1% formaldehyde in PBS for 2min at room temperature and quenched with glycine at a final concentration of 0.075M. Nuclei were extracted by incubating the fixed cells in 1mL NE1 buffer (20mM HEPES pH7.5, 10mM KCl, 0.5mM spermidine, 0.1% Triton X-100 and 20% glycerol in nuclease-free water with a Roche Complete Protease Inhibitor EDTA-Free tablet) for 10min on ice, washed once with 1mL PBS and resuspended in 500µL 1% BSA antibody buffer (2mM EDTA, 1% BSA, 0.05% digitonin, 20mM HEPES pH7.5, 150mM KCl, 0.5mM spermidine in nuclease-free water with a Roche Complete Protease Inhibitor EDTA-free tablet). Following wash steps were performed through centrifugations at 4°C for 3min at 600×g in a swinging bucket rotor for the initial steps, and then at 4°C for 3min at 300×g after third antibody incubation step when the nuclei were in Dig-300 buffer. 500,000 fixed nuclei were transferred to 0.2mL Lo-retention tubes and washed twice with 200µL 1% BSA antibody buffer, resuspended in 50µL 1% BSA antibody buffer and incubated at 25°C for 1h at 600rpm. 2µL of 5.4µM BG4 scFv was added to each sample and incubated in cold room overnight at 600rpm. After that, cells were washed twice with 100µL dig-wash buffer and then incubated in 50µL dig-wash buffer with 2µL of anti-flag antibody (Cell Signaling Technology Cat# 2368, RRID:AB_2217020) at 25°C for 1h at 600rpm. Next, cells were washed twice with 100µL dig-wash buffer and then incubated in 50µL dig-wash buffer with 0.5µL of anti-rabbit antibody (Antibodies-Online Cat# ABIN101961, RRID:AB_10775589) at 25°C for 1h at 600rpm. Cells were washed three times with 100µL Dig-300 buffer (20mM HEPES pH7.5, 300mM KCl, 0.5mM spermidine, 0.01% digitonin in nuclease-free water with a Roche Complete Protease Inhibitor EDTA-free tablet) and then incubated in 1:250 dilution of pA-Tn5 in 50µL Dig-300 buffer at 25°C for 1h at 600rpm. To activate tagmentation, cells were washed three times with 100µL Dig-300 buffer and incubated in 100µL tagmentation buffer (10mM MgCl2 in Dig-300 buffer) at 37°C for 1h in thermocycler and mixed every 10min. After tagmentation, BSA was added to the samples to a final concentration of 1% and centrifuged at 4°C for 3min at 600×g. The nuclei were washed twice with 1X diluted nuclei buffer with 1% BSA by centrifugation at 4°C for 3min at 600×g and resuspended in 25µL 1X diluted nuclei buffer on ice. Then, the nuclei were checked and counted by staining with trypan blue and observed under microscope using hemocytometer. Chromium Next GEM Single Cell ATAC Reagents Kits v1.1 user guide was used with the following modifications. In step 1, 5µL of nuclei suspension in 1X diluted nuclei buffer (at 2500 nuclei/µL), 7ul of ATAC buffer (10X Genomics 2000193) and 3ul of low TE were mixed and isothermal incubation was omitted. All the remaining steps from step 2 were performed as the standard protocol. The libraries were sequenced on a NextSeq 500 sequencer (Illumina) with a paired-end format of 50 bp x 2 using the High Output kit (Illumina).

treatment_protocol: CUT&Tag using BG4 antibody

tag: cell number

tag: antibody

value: BG4 single-chain antibody

tag: input type

value: 10X single nuclei


title: Aged HSC

status: Public on Dec 08 2021

type: SRA

city: Minato-ku

first: Atsushi

last: Iwama

state: Tokyo

address: 4-6-1, Shirokanedai

department: Center for Stem Cell Biology and Regenerative Medicine

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

library_source: genomic

data_processing:
Base call files were demultiplexed into fastq files by "cell ranger-atac mkfastq"
We used "cellranger-atac count" for Read alignment, barcode counting and peak calling
With "filtered_peak_bc_matrix.h5", "fragments.tsv.gz" and "singlecell.csv" generated from cellranger-atac, We used Signac to perform subsequent analysis
Genome_build: mm10
Supplementary_files_format_and_content: filtered_peak_bc_matrix.h5, fragments.tsv.gz, fragments.tsv.gz.tbi, singlecell.csv

molecule: genomic DNA

organism: Mus musculus

source_name: 20 month hematopoietic stem cells

extract_protocol:
After FACS sorting and purification of HCSs, nuclei are isolated using Chromium Next GEM Single Cell ATAC Reagent Kits v1.1
Libraries were then generated using Chromium Next GEM Single Cell ATAC Reagent Kits v1.1

tag: cell type

value: Murine bone marrow derived HSCs

tag: surface markers

value: IL-7- Lin- Sca-1+ c-kit+  CD34- CD150+ CD48- Flt3-

tag: age

tag: strain


title: T6_TCP2

city: DIJON

first: François

last: Ghiringhelli

address: 1 rue du Professeur Marion

country: France

institute: UMR INSERM 1231

library_source: transcriptomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Pseudo alignment and quantification were performed using kallisto 0.45
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed data file is a csv file containing TPM expression values

molecule: polyA RNA

source_name: LLC1 cells

extract_protocol: RNA-Seq libraries were generated from 600 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: cell line

value: LLC1 cells

tag: treatment

value: Cisplatin-Pemetrexed + Trametinib

tag: time

value: 6 hours


title: non-stimulated PBMCs of HC, biological rep2

type: RNA

city: Xindu district, Chengdu city

first: Mao

last: Lu

state: Sichuan

address: Baoguang Road middle segment

department: Department of Dermatovenereology,

country: China

institute: The First Affiliated Hospital, Chengdu Medical College, Chengdu, China

description: gene expression in non-stimulated PBMCs of healthy control 2

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human PrimeView Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) was used to analyze array images to get raw data. Next, Genespring software (version 13.1; Agilent Technologies) was employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the RMA algorithm.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: non-stimulated PBMCs of healthy control patient 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: PBMCs were extracted from 5 ml venous blood of each participant at room temperature (RT) by density gradient centrifugation.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The PBMCs suspension in each well of 6-well plate was equally divided into two wells. One was added with 0.6 ml M. globosa suspension and the other was added with an equal volume of culture solution. After cultured at 37 ˚C in 5% CO2 and saturated humidity for 48 h, the cell suspension was centrifuged at 1000 rpm for 10 min. Finally, the cell precipitation was added with 1 ml Trizol lysate preserving at -80 ˚C.

tag: tissue

value: PBMCs

tag: gender

value: Male

value: 9 years old

tag: agent


title: non-stimulated PBMCs of HC, biological rep1

description: gene expression in non-stimulated PBMCs of healthy control 1

source_name: non-stimulated PBMCs of healthy control patient 1

value: 8 years old


title: T6_TCP1


title: non-stimulated PBMCs of AD, biological rep1

description: gene expression in non-stimulated PBMCs of AD patient 1

source_name: non-stimulated PBMCs of AD patient 1


title: MCF7_rep2_single_nuclei

country: United Kingdom

description: single nuclei CUT&Tag


title: COVID_11_day_10_COVID_12_day_1_PBMC_GEX

city: Pittsburgh

first: Anthony

middle: Richard

last: Cillo

state: PA

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

country: USA

institute: University of Pittsburgh

description: gene expression feature barcode matrix

data_processing:
Demultiplexing raw reads with bcl2fastq2 (Illumina, v2.20.0)
Cellranger count (10X Genomics, v3.1.0) to generate feature barcode matrices
CITEseqCount (v1.4.3) to identify TotalSeq-C associated UMI counts for sample demultiplexing
Creation of unified feature barcode expression matrix with Seurat (v3.1.2) in R (v.3.6.0)
Genome_build: GRCh38 + SARS-COV-2 (NC_045512.2)
Supplementary_files_format_and_content: Feature barcode expression matrices create with bcl2fastq and CellRanger Count
Supplementary_files_format_and_content: CITEseq feature barcode matrix
Supplementary_files_format_and_content: gene expression feature barcode matrix

source_name: Peripheral blood mononuclear cells

extract_protocol:
Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse.
Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols.

tag: time point

value: day 1, day 10

tag: disease

value: Peripheral blood mononuclear cells


title: non-stimulated PBMCs of AD, biological rep3

description: gene expression in non-stimulated PBMCs of AD patient 3

source_name: non-stimulated PBMCs of AD patient 3

value: 12years old


title: U2OS_rep2_single_nuclei

description: single nuclei CUT&Tag


title: Young HSC

source_name: 10 week hematopoietic stem cells


title: aged MPP4 3h

description: aged MPP4 after cytokine stimulation(3h)

data_processing:
alignment:TopHat2 (version 2.0.13; with default parameters) and Bowtie2 (version 2.1.0) were used for alignment to the reference mouse genome (mm10 from the University of California, Santa Cruz Genome Browser;) with annotation data from iGenomes (Illumina)
Row count for each gene symbol are generated by StringTie
Data normalization:DESeq2
DESeq2 were used to perform statistical analysis for differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: TPM_gene.txt, gene_norm_count_ntd.txt

source_name: 20 month multipotent progenitor 4s after cytokine stimulation (3h)

extract_protocol:
Total RNA was extracted using RNeasy Plus Micro Kit (Qiagen)
Total RNA were subjected to reverse transcription and amplification with a SMARTer Ultra Low Input RNA Kit for Sequencing (Clontech). After sonication with an ultrasonicator (Covaris), the libraries for RNA-seq were generated from fragmented DNA with 8 cycles of amplification using a NEB Next Ultra DNA Library Prep Kit (New England BioLabs). After the libraries were quantified using the Bioanalyzer (Agilent), samples were subjected to sequencing with Hiseq1500 (Illumina) and 61 cycles of the sequencing reactions were performed.

treatment_protocol: Young and aged cells were stimulated with a mixture of cytokines (SCF, TPO, GM-CSF, IL-1, IL-6, and IL-11) (BioLegend) in S-Clone SF-O3 (Sanko Junyaku) supplemented with 10% FBS, 50 μM 2-ME, and 1% GPS

value: Murine bone marrow derived MPP4s

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150- CD48+ Flt3+

value: cytokine stimulation(3h)


title: U2OS_MCF7_mix_single_nuclei

description: single nuclei CUT&Tag

value: BG4 single-chain antibody


title: COVID_12_day_5_day_10_PBMC_GEX

description: gene expression feature barcode matrix

value: day 5, day 10


title: T6_T2

value: Trametinib


title: T6_T3


title: COVID_11_day_1_day_5_PBMC_GEX

description: gene expression feature barcode matrix

value: day 1, day 5


title: T6_T1

value: LLC1 cells


title: aged MPP3 3h

description: aged MPP3 after cytokine stimulation(3h)

source_name: 20 month multipotent progenitor 3s after cytokine stimulation (3h)

value: Murine bone marrow derived MPP3s

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150- CD48+ Flt3-


title: U2OS_rep1_single_nuclei

description: single nuclei CUT&Tag

value: 10X single nuclei


title: aged MPP3 0h

description: aged MPP3 before stimulation

source_name: 20 month multipotent progenitor 3s

value: before stimulation


title: T6_CP3

value: Cisplatin-Pemetrexed

value: 6 hours


title: non-stimulated PBMCs of AD, biological rep2

description: gene expression in non-stimulated PBMCs of AD patient 2

source_name: non-stimulated PBMCs of AD patient 2

value: PBMCs

value: Male

value: 10 years old


title: U2OS_MCF7_10k_bg4_10X_6th_ref_rep1_tec1

description: CUT&Tag

extract_protocol: Bulk G4 CUT&Tag (single nuclei reference): Harvested cells were fixed in 0.1% formaldehyde in PBS for 2min at room temperature and quenched with glycine at a final concentration of 0.075M. Nuclei were extracted by incubating the fixed cells in 1mL NE1 buffer (20mM HEPES pH7.5, 10mM KCl, 0.5mM spermidine, 0.1% Triton X-100 and 20% glycerol in nuclease-free water with a Roche Complete Protease Inhibitor EDTA-Free tablet) for 10min on ice, washed once with 1mL PBS and resuspended in 500µL 1% BSA antibody buffer (2mM EDTA, 1% BSA, 0.05% digitonin, 20mM HEPES pH7.5, 150mM KCl, 0.5mM spermidine in nuclease-free water with a Roche Complete Protease Inhibitor EDTA-free tablet). Following wash steps were performed through centrifugations at 4°C for 3min at 600×g in a swinging bucket rotor for the initial steps, and then at 4°C for 3min at 300×g after third antibody incubation step when the nuclei were in Dig-300 buffer. 500,000 fixed nuclei were transferred to 0.2mL Lo-retention tubes and washed twice with 200µL 1% BSA antibody buffer, resuspended in 50µL 1% BSA antibody buffer and incubated at 25°C for 1h at 600rpm. 2µL of 5.4µM BG4 scFv was added to each sample and incubated in cold room overnight at 600rpm. After that, cells were washed twice with 100µL dig-wash buffer and then incubated in 50µL dig-wash buffer with 2µL of anti-flag antibody (Cell Signaling Technology Cat# 2368, RRID:AB_2217020) at 25°C for 1h at 600rpm. Next, cells were washed twice with 100µL dig-wash buffer and then incubated in 50µL dig-wash buffer with 0.5µL of anti-rabbit antibody (Antibodies-Online Cat# ABIN101961, RRID:AB_10775589) at 25°C for 1h at 600rpm. Cells were washed three times with 100µL Dig-300 buffer (20mM HEPES pH7.5, 300mM KCl, 0.5mM spermidine, 0.01% digitonin in nuclease-free water with a Roche Complete Protease Inhibitor EDTA-free tablet) and then incubated in 1:250 dilution of pA-Tn5 in 50µL Dig-300 buffer at 25°C for 1h at 600rpm. To activate tagmentation, cells were washed three times with 100µL Dig-300 buffer and incubated in 100µL tagmentation buffer (10mM MgCl2 in Dig-300 buffer) at 37°C for 1h in thermocycler and mixed every 10min. After tagmentation, BSA was added to the samples to a final concentration of 1% and centrifuged at 4°C for 3min at 600×g. The nuclei were washed twice with 1X diluted nuclei buffer with 1% BSA by centrifugation at 4°C for 3min at 600×g and resuspended in 25µL 1X diluted nuclei buffer on ice. Then, the nuclei were checked and counted by staining with trypan blue and observed under microscope using hemocytometer. 100µL of extraction buffer (0.5mg/mL proteinase K, 0.5% SDS in 10mM Tris-HCl pH8.0) was added to 10,000 tagmented nuclei, mixed by vortexing, and incubated at 55°C for 1h at 800rpm. Tagmented DNA was purified using phenol/chloroform extraction and ethanol precipitation. The pellet was dissolved in 25µL elution buffer 1 (10mM Tris-HCl pH8, 1mM EDTA, 1/400 RNAseA in nuclease-free water) by vortexing and incubated at 37°C for 10min at 800rpm. In each 0.2mL PCR tube, 25µL NEBNext HiFi 2x PCR master mix (NEB, M0541), 2µL of 10µM Ad1, 2µL of 10µM Ad2 [Buenrostro, J.D. et al. Nature (2015)] and 21µL DNA were added. The PCR profile was as follow: 72°C for 5 min, 98°C for 30s, followed by 10 cycles of 98°C for 10s and 63°C for 10s, and one cycle of 72°C for 1 minute. Libraries were purified using 1.3X Ampure XP beads and eluted 25µL 10mM Tris-HCl for 5min at room temperature. Pooled libraries were size selected and concentrated using Ampure XP beads and eluted in 10mM Tris-HCl. The libraries were sequenced on a Illumina NextSeq 500 sequencer with a paired-end format of 36 bp x 2 using the High Output kit.

value: bulk fixed nuclei


title: MCF7_10k_bg4_10X_6th_ref_rep2_tec1

description: CUT&Tag


title: U2OS_10k_bg4_10X_6th_ref_rep2_tec1

description: CUT&Tag


title: aged MPP4 0h

description: aged MPP4 before stimulation

source_name: 20 month multipotent progenitor 4s

value: Murine bone marrow derived MPP4s

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150- CD48+ Flt3+


title: ARDS_4_day_1_day_5_PBMC_GEX

description: gene expression feature barcode matrix

value: Acute respiratory distress syndrome

value: Peripheral blood mononuclear cells


title: aged MPP2 0h

description: aged MPP2 before stimulation

source_name: 20 month multipotent progenitor 2s

value: Murine bone marrow derived MPP2s

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150+ CD48+ Flt3-


title: COVID_10_day_5_day_10_PBMC_GEX

description: gene expression feature barcode matrix

value: day 5, day 10


title: MCF7_10k_none_MCF7_2nd_rep2_tec1

description: CUT&Tag

extract_protocol: Bulk G4 CUT&Tag: Harvested cells were fixed in 0.1% formaldehyde in PBS for 2min at room temperature and quenched with glycine at a final concentration of 0.075M. Fixed cells were then resuspended in wash buffer (20mM HEPES pH7.5, 150mM KCl, 0.5mM spermidine in nuclease-free water with a Roche Complete Protease Inhibitor EDTA-free tablet) and cell concentration was measured again for cellNO samples at this stage. 100µL of the cell suspension was mixed with 10µL pre-washed concanavalin A beads (in 20mM HEPES pH7.5, 10mM KCl, 1mM CaCl2, 1mM MnCl2 in nuclease-free water) at 25°C for 10min at 600rpm. Following wash steps were performed using magnetic rack. Bead-bound fixed cells were washed twice with wash buffer and then incubated in 50µL antibody buffer (2mM EDTA, 0.1% BSA, 0.05% digitonin in wash buffer) with 4µL of 5.4µM BG4 scFv (no primary antibody was added for IgG control samples) at 25°C for 2h at 600rpm. Next, cells were washed twice with 100µL dig-wash buffer (0.05% digitonin in wash buffer) and then incubated in 50µL dig-wash buffer with 2µL of anti-flag antibody (Cell Signaling Technology Cat# 2368, RRID:AB_2217020) at 25°C for 1h at 600rpm. After that, cells were washed three times with 500µL dig-wash buffer and then incubated in 50µL dig-wash buffer with 0.5µL of anti-rabbit antibody (Antibodies-Online Cat# ABIN101961, RRID:AB_10775589) at 25°C for 1h at 600rpm. Cells were washed three times with 500µL dig-wash buffer and then incubated in 1:250 dilution of pA-Tn5 in 50µL Dig-300 buffer (20mM HEPES pH7.5, 300mM KCl, 0.5mM spermidine, 0.01% digitonin in nuclease-free water with a Roche Complete Protease Inhibitor EDTA-free tablet) at 25°C for 1h at 600rpm. To activate tagmentation, cells were washed three times with 500µL Dig-300 buffer and then incubated in 300µL tagmentation buffer (10mM MgCl2 in Dig-300 buffer) at 37°C for 1h at 600rpm. After tagmentation, the cells were washed twice with 500µL TAPS wash buffer (10mM TAPS, 0.2mM EDTA in nuclease-free water). 100µL of extraction buffer (0.5mg/mL proteinase K, 0.5% SDS in 10mM Tris-HCl pH8.0) was added to each sample, mixed by vortexing, and incubated at 55°C for 1h at 800rpm. Tagmented DNA was purified through phenol/chloroform extraction and ethanol precipitation. The pellet was dissolved in 25µL elution buffer 1 (10mM Tris-HCl pH8, 1mM EDTA, 1/400 RNAseA in nuclease-free water) by vortexing and incubated at 37°C for 10min at 800rpm. In each 0.2mL PCR tube, 25µL NEBNext HiFi 2x PCR master mix, 2µL of 10µM Ad1, 2µL of 10µM Ad2 [Buenrostro, J.D. et al. Nature (2015)] and 21µL tagmented DNA were added. The PCR profile was as follow: 72°C for 5 min, 98°C for 30s, followed by 10 cycles of 98°C for 10s and 63°C for 10s, and one cycle of 72°C for 1 minute. Libraries were purified using 1.3X Ampure XP beads and eluted 25µL 10mM Tris-HCl for 5min at room temperature. Pooled libraries were size selected and concentrated using Ampure XP beads and eluted in 10mM Tris-HCl. The libraries were sequenced on a Illumina NextSeq 500 sequencer with a paired-end format of 36 bp x 2 using the High Output kit.

value: control-noPrimary antibody

value: bulk fixed cells


title: aged MPP1 3h

description: aged MPP1 after cytokine stimulation(3h)

source_name: 20 month multipotent progenitor 1s after cytokine stimulation (3h)

value: Murine bone marrow derived MPP1s

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150+ CD48- Flt3-

value: cytokine stimulation(3h)


title: ARDS_2_day_5_day_10_PBMC_GEX

description: gene expression feature barcode matrix


title: T6_NT3

value: LLC1 cells

value: No treatment

value: 6 hours


title: aged MPP1 0h

description: aged MPP1 before stimulation

source_name: 20 month multipotent progenitor 1s

value: before stimulation


title: COVID_1_day_1_day_5_PBMC_GEX

description: gene expression feature barcode matrix

value: day 1, day 5


title: T6_NT1


title: young MPP4 0h

description: young MPP4 before stimulation

source_name: 10 week multipotent progenitor 4s

value: Murine bone marrow derived MPP4s


title: aged MPP2 3h

description: aged MPP2 after cytokine stimulation(3h)

source_name: 20 month multipotent progenitor 2s after cytokine stimulation (3h)


title: MCF7_50k_bg4_MCF7_2nd_rep2_tec2

description: CUT&Tag

value: BG4 single-chain antibody


title: young MPP3 3h

description: young MPP3 after cytokine stimulation(3h)

source_name: 10 week multipotent progenitor 3s after cytokine stimulation (3h)

value: Murine bone marrow derived MPP3s

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150- CD48+ Flt3-


title: MCF7_10k_none_MCF7_1st_rep1_tec1

description: CUT&Tag


title: Healthy_5_Healthy_6_PBMC_CITEseq

description: CITEseq feature barcode matrix

data_processing:
Library strategy: CITE-Seq
Demultiplexing raw reads with bcl2fastq2 (Illumina, v2.20.0)
Cellranger count (10X Genomics, v3.1.0) to generate feature barcode matrices
CITEseqCount (v1.4.3) to identify TotalSeq-C associated UMI counts for sample demultiplexing
Creation of unified feature barcode expression matrix with Seurat (v3.1.2) in R (v.3.6.0)
Genome_build: GRCh38 + SARS-COV-2 (NC_045512.2)
Supplementary_files_format_and_content: Feature barcode expression matrices create with bcl2fastq and CellRanger Count
Supplementary_files_format_and_content: CITEseq feature barcode matrix
Supplementary_files_format_and_content: gene expression feature barcode matrix

value: Healthy donor

value: Peripheral blood mononuclear cells


title: young MPP3 0h

description: young MPP3 before stimulation

source_name: 10 week multipotent progenitor 3s


title: TASc-4

city: Shanghai

first: Youqiong

last: Ye

address: 280 Chongqing south road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat and paired-end clean reads were aligned to the reference genome using Hisat2.
HTSeq was used to count the reads numbers mapped to each gene.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file included read count for each gene

source_name: mouse TASc isolated from PDAC of KPC mice

growth_protocol: 6-week-old tamoxifen-inducible KPC mice were administered a solution with- or without-tamoxifen (Sigma-Aldrich; cat#T5648) induction (20 mg/kg, i.p. injection, 5 consecutive days) (Madisen et al., 2010). At the age of 4 months, pancreases from KPC mice without tamoxifen induction or PDAC tumors from KPC mice with tamoxifen induction were suspended into single cell suspensions, described as follows: pancreases were digested as a single cell suspension using an enzyme mixture (250 U/mL Hyaluronidase Type I-S (Sigma; #H3506), 160 U/mL Collagenase Type I (Sigma; #C1639) in DMEM-F12). The tumor isolated from the KPC mice with Tamoxifen induction was digested as a single cell suspension using a mouse Tumor Dissociation kit (Miltenui Biotec Inc.; #130-096-730). After the lysis of red blood cells (RBC Lysis Buffer, BioLegend; #420302), single-cell suspensions were subjected to removal of the dead cells using a dead cell removal kit (Miltenyi Biotec; #130-090-101) and then blocked with anti-CD16/32 (BioLegend; #156604) for 20 min on ice. The cell suspensions were then stained with anti-nerve growth factor receptor Alexa Fluor488 conjugated antibody (Sigma; #MAB5592X) for 1 hrs at RT, and then subjected to cell sorting using the BD FACSMelody™ Cell Sorter. Total RNA from each sample was extracted using Trizol Reagent following standard protocols and mRNA sequencing was performed.

extract_protocol:
Total RNA from each sample was extracted using Trizol Reagent (ThermoFisher Scientific) following standard protocols. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PDAC-derived TASc

tag: facs antibody

value: anti-NGFRA-Alexa Fluor488 conjugated Antibody (Sigma; cat#MAB5592X)


title: T6_CP1

source_name: LLC1 cells

value: Cisplatin-Pemetrexed


title: MCF7_50k_none_MCF7_1st_rep1_tec1

description: CUT&Tag

value: control-noPrimary antibody

value: bulk fixed cells


title: Healthy_3_Healthy_4_PBMC_CITEseq

description: CITEseq feature barcode matrix

source_name: Peripheral blood mononuclear cells


title: Healthy_7_ARDS_3_day_1_PBMC_CITEseq

description: CITEseq feature barcode matrix

value: NA, day 1

value: Healthy donor, Acute respiratory distress syndrome


title: young MPP2 3h

description: young MPP2 after cytokine stimulation(3h)

source_name: 10 week multipotent progenitor 2s after cytokine stimulation (3h)

value: Murine bone marrow derived MPP2s

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150+ CD48+ Flt3-

value: cytokine stimulation(3h)


title: young MPP4 3h

description: young MPP4 after cytokine stimulation(3h)

source_name: 10 week multipotent progenitor 4s after cytokine stimulation (3h)

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150- CD48+ Flt3+


title: MCF7_10k_bg4_MCF7_2nd_rep2_tec1

description: CUT&Tag


title: ARDS_1_day_1_day_5_PBMC_GEX

description: gene expression feature barcode matrix

value: day 1, day 5

value: Acute respiratory distress syndrome


title: Healthy_10_ARDS_5_day_1_PBMC_CITEseq

description: CITEseq feature barcode matrix


title: MCF7_10k_bg4_MCF7_1st_rep1_tec1

description: CUT&Tag

value: BG4 single-chain antibody


title: TASc-2

treatment_protocol: pancreases were digested as a single cell suspension using an enzyme mixture (250 U/mL Hyaluronidase Type I-S (Sigma; #H3506), 160 U/mL Collagenase Type I (Sigma; #C1639) in DMEM-F12). The tumor isolated from the KPC mice with Tamoxifen induction was digested as a single cell suspension using a mouse Tumor Dissociation kit (Miltenui Biotec Inc.; #130-096-730). After the lysis of red blood cells (RBC Lysis Buffer, BioLegend; #420302), single-cell suspensions were subjected to removal of the dead cells using a dead cell removal kit (Miltenyi Biotec; #130-090-101) and then blocked with anti-CD16/32 (BioLegend; #156604) for 20 min on ice. The cell suspensions were then stained with anti-nerve growth factor receptor Alexa Fluor488 conjugated antibody (Sigma; #MAB5592X) for 1 hrs at RT, and then subjected to cell sorting using the BD FACSMelody™ Cell Sorter.


title: Healthy_8_Healthy_9_PBMC_CITEseq

description: CITEseq feature barcode matrix


title: MCF7_50k_bg4_MCF7_2nd_rep2_tec1

description: CUT&Tag


title: MCF7_50k_bg4_MCF7_1st_rep1_tec2

description: CUT&Tag


title: ARDS_3_day_5_day_10_PBMC_GEX

description: gene expression feature barcode matrix

value: day 5, day 10


title: TASc-5


title: young MPP2 0h

description: young MPP2 before stimulation

source_name: 10 week multipotent progenitor 2s

value: before stimulation


title: T6_CP2

value: LLC1 cells

value: 6 hours


title: MCF7_50k_none_MCF7_2nd_rep2_tec1

description: CUT&Tag


title: TASc-1

value: PDAC-derived TASc

value: anti-NGFRA-Alexa Fluor488 conjugated Antibody (Sigma; cat#MAB5592X)


title: young MPP1 3h

description: young MPP1 after cytokine stimulation(3h)

source_name: 10 week multipotent progenitor 1s after cytokine stimulation (3h)

value: Murine bone marrow derived MPP1s

value: IL-7- Lin- Sca-1+ c-kit+  CD34+ CD150+ CD48- Flt3-


title: Schwann-5

source_name: mouse Schwann cells isolated from pancreas of KPC mice

value: Pancreas-derived Schwann cells


title: young MPP1 0h

description: young MPP1 before stimulation

source_name: 10 week multipotent progenitor 1s


title: Schwann-4


title: Aged HSC H3K27ac after stimulation

description: H3K27ac of Aged HSC after cytokine stimulation (3hour)

data_processing:
Library strategy: CUT&Tag
Sequences were aligned to mouse genome sequences (mm10) with Bowtie2(default setting) .
Mapped reads are subsampled with samtools to make numbers of reads same in all samples.
Macs2(ver2.2.6) was used to call peaks with nomodel, narrow peak option. With a q-value cutoff of 0.001
For visualization to make bigwig files,we used bamCoverage of deeptools with option  " --binSize 20 --normalizeUsing CPM --smoothLength 60"
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: 20 month hematopoietic stem cells after stimulation

extract_protocol:
After FACSsorting, we used CUT&Tag-IT™ Assay Kit (Active motif). Anti-H3K27ac (Cat.8173, Cell signaling),Anti-H3K4me1(Cat.39498,Active motif) were used.
We used CUT&Tag-IT™ Assay Kit (Active motif) to library construction

treatment_protocol: Aged HSCs were stimulated with a mixture of cytokines (SCF, TPO, GM-CSF, IL-1, IL-6, and IL-11) (BioLegend) in S-Clone SF-O3 (Sanko Junyaku) supplemented with 10% FBS, 50 μM 2-ME, and 1% GPS

value: Murine bone marrow derived HSCs

value: IL-7- Lin- Sca-1+ c-kit+  CD34- CD150+ CD48- Flt3-

value: cytokine stimulation (3hour)


title: Schwann-3


title: COVID_7_day_10_PBMC_ETA_CITEseq

description: CITEseq feature barcode matrix

source_name: Peripheral blood mononuclear cells, endotracheal aspirate

value: day 10


title: COVID_7_day_1_day_5_PBMC_CITEseq

description: CITEseq feature barcode matrix

value: Peripheral blood mononuclear cells


title: Healthy_1_Healthy_2_PBMC_CITEseq

description: CITEseq feature barcode matrix

value: Healthy donor


title: U2OS_10k_bg4_10X_5th_ref_rep1_tec1

description: CUT&Tag

value: bulk fixed nuclei


title: Aged HSC H3K4me1

source_name: 20 month hematopoietic stem cells


title: COVID_6_day_10_COVID_18_day_1_CITEseq

description: CITEseq feature barcode matrix

value: day 1, day 10


title: MCF7_50k_bg4_MCF7_1st_rep1_tec1

description: CUT&Tag

value: BG4 single-chain antibody

value: bulk fixed cells


title: MCF7_10k_bg4_10X_5th_ref_rep1_tec1

description: CUT&Tag


title: Schwann-2


title: Aged HSC H3K27ac


title: MC38_WT_28d_10

city: Boston

first: Eric

last: Muise

state: MA

address: 33 Ave. Louis Pasteur

department: GPGX

institute: Merck

data_processing:
Cleaned reads were aligned to the Mouse.B38 genome reference using the Omicsoft Aligner with a maximum of 2 allowed mismatches.
Gene level raw counts, and FPKM, were determined by the OSA algorithm as implemented in Omicsoft Array Studio and using Ensembl.R86 gene models.
Genome_build: Mouse.B38
Supplementary_files_format_and_content: Tab-delimited text file include FPKM values for each Sample. Each column corresponds to one sample (barcode).

source_name: Tumor

growth_protocol: WT mice were subcutaneously injected on the right flank with MC-38 cells (1x106) and received PD-1 Ab injection day 7, 11 and day 15 post-tumor implant. PD-1cKO and littermate control mice were subcutaneously injected on the right flank with MC-38 cells (1x106) and day 6-7 post-tumor cell injection the mice received injections of tamoxifen on 5 consecutive days.

extract_protocol:
For tumor tissue RNA isolation, organs were homogenized into RNA STAT-60 (Tel-Test Inc., Friendswood, TX) using a polytron homogenizer, then total RNA extracted according to the manufacturer's instructions. After isopropanol precipitation, total RNA was re-extracted with phenol:chloroform:isoamyl alcohol (25:24:1) (Sigma-Aldrich, St. Louis, MO).
Sequencing was performed using the Truseq stranded total RNA RiboZero library preparation kit (Catalog #: RS-122-2201) according to the manufacturer’s instructions (Illumina, San Diego, CA). The resulting cDNA libraries were sequenced on an Illumina (HiSeqTM 4000) using a 50-base paired-end run.

treatment_protocol: WT mice were randomized day 7 post-tumor implant and for PD-1 antibody (Ab) experiments, mice were dosed intraperitoneally every 4 days on 4 separate occasions with 5 mg/kg anti-mouse PD-1 Ab muDX400. PD-1cKO mice were randomized day 7 post-tumor implant and tamoxifen (Sigma-Aldrich) dissolved in 1:9 ratio of ethanol:sunflower oil at a stock concentration of 10 mg/mL was injected intraperitoneally at a dose of 40 mg/kg on 5 consecutive days. Tamoxifen injections were administered to both PD-1cKO and littermate controls.

tag: replicate group

value: tamoxifen

value: 28 day

tag: genotype

value: WT


title: COVID_5_day_1_day_5_PBMC_CITEseq

description: CITEseq feature barcode matrix

value: day 1, day 5


title: COVID_6_day_1_day_5_PBMC_CITEseq

description: CITEseq feature barcode matrix


title: Young HSC H3K27ac

source_name: 10 week hematopoietic stem cells

tag: antibody


title: Schwann-1

value: anti-NGFRA-Alexa Fluor488 conjugated Antibody (Sigma; cat#MAB5592X)


title: TASc-3

value: PDAC-derived TASc


title: K562_100k_None_cellNO_rep2_tecx

description: CUT&Tag

tag: cell number

value: control-noPrimary antibody

tag: input type


title: K562_10k_bg4_cellNO_rep2_tec2

description: CUT&Tag


title: MC38_WT_28d_9


title: COVID_8_day_1_COVID_9_day_1_PBMC_CITEseq

description: CITEseq feature barcode matrix

value: day 1


title: K562_10k_None_cellNO_rep2_tecx

description: CUT&Tag


title: COVID_4_day_5_COVID_10_day_1_PBMC_CITEseq

description: CITEseq feature barcode matrix

value: day 5, day 10


title: Young HSC LPS sample2

description: Young HSCs after LPS treatment and 4week interval

data_processing:
Sequences were aligned to mouse genome sequences (mm10) with Bowtie2(default setting) .
Mapped reads are subsampled with samtools to make numbers of reads same in all samples.
Macs2(ver2.2.6) was used to call peaks with nomodel, narrow peak option. With a q-value cutoff of 0.001
For visualization to make bigwig files,we used bamCoverage of deeptools with option  " --binSize 20 --normalizeUsing CPM --smoothLength 60"
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: hematopoietic stem cells treated with LPS

extract_protocol:
Transposase reaction was performed using nuclei prepared from freshly sorted 20,000 cells of each fraction
Libraries were then generated using a NEBNext Ultra DNA Library Prep Kit (New England BioLabs, Beverly, MA, USA). Library DNA was size-selected (240 - 360 bps) with BluePippin (Sage Science, Beverly, MA, USA). Sequencing was performed using HiSeq1500 (Illumina) with a single-read sequencing length of 60 bp.

treatment_protocol: cytokines stimulation:(SCF, TPO, GM-CSF, IL-1, IL-6, and IL-11)  LPS and polyIpolyC treatment : 10 μg LPS (InvivoGen) and　125 μg pIpC (InvivoGen) or PBS

tag: cell type

value: Murine bone marrow derived HSCs

tag: surface markers

value: IL-7- Lin- Sca-1+ c-kit+  CD34- CD150+ CD48- Flt3-

value: LPS treatment


title: K562_50k_None_cellNO_rep2_tecx

description: CUT&Tag


title: COVID_3_day_1_COVID_4_day_1_PBMC_CITEseq

description: CITEseq feature barcode matrix

value: Peripheral blood mononuclear cells


title: COVID_24_day_1_PBMC_ETA_CITEseq

description: CITEseq feature barcode matrix

value: Peripheral blood mononuclear cells, endotracheal aspirate


title: MC38_WT_28d_7


title: MC38_WT_28d_8


title: K562_50k_bg4_cellNO_rep2_tec2

description: CUT&Tag


title: Young HSC PBS sample2

description: Young HSCs after PBS treatment and 4week interval

source_name: hematopoietic stem cells treated with PBS

tag: age

tag: strain

value: PBS treatment


title: T6_NT2

tag: cell line

value: LLC1 cells

tag: treatment

value: No treatment

value: 6 hours


title: MC38_WT_28d_6

value: tamoxifen

value: 28 day


title: K562_100k_bg4_cellNO_rep2_tec2

description: CUT&Tag

value: BG4 single-chain antibody

value: bulk fixed cells


title: MC38_WT_28d_5

value: WT


title: K562_50k_bg4_cellNO_rep2_tec1

description: CUT&Tag


title: Young HSC H3K4me1


title: COVID_21_day_1_PBMC_ETA_CITEseq

description: CITEseq feature barcode matrix

tag: tissue


title: COVID_20_day_1_COVID_23_day_1_PBMC_CITEseq

description: CITEseq feature barcode matrix


title: COVID_2_day_10_ARDS_2_day_1_PBMC_CITEseq

description: CITEseq feature barcode matrix

value: day 1, day 10

value: Acute respiratory distress syndrome, COVID-19


title: Aged HSC 3hour after stimulation

description: Aged HSC after cytokine stimulation (3h)

value: cytokine stimulation (3h)


title: K562_100k_bg4_cellNO_rep2_tec1

description: CUT&Tag


title: Aged HSC 0hour

description: Aged HSC before cytokine stimulation

value: Murine bone marrow derived HSCs

value: before cytokine stimulation


title: K562_10k_None_cellNO_rep1_tecx

description: CUT&Tag

value: control-noPrimary antibody


title: K562_10k_bg4_cellNO_rep2_tec1

description: CUT&Tag


title: MC38_WT_28d_3


title: MC38_WT_28d_4


title: Young HSC LPS sample1

value: IL-7- Lin- Sca-1+ c-kit+  CD34- CD150+ CD48- Flt3-

value: LPS treatment


title: K562_50k_None_cellNO_rep1_tecx

description: CUT&Tag


title: COVID_20_day_5_COVID_19_day_5_PBMC_CITEseq

description: CITEseq feature barcode matrix

value: day 5

value: Peripheral blood mononuclear cells


title: MC38_WT_28d_2


title: Young HSC 3hour after stimulation

description: Young HSC after cytokine stimulation (3h)


title: COVID_2_day_1_day_5_PBMC_CITEseq

description: CITEseq feature barcode matrix

value: day 1, day 5


title: Young HSC PBS sample1

value: PBS treatment


title: Young HSC 0hour

description: Young HSC before cytokine stimulation


title: COVID_18_day_5_PBMC_ETA_CITEseq

description: CITEseq feature barcode matrix

value: Peripheral blood mononuclear cells, endotracheal aspirate


title: K562_100k_None_cellNO_rep1_tecx

description: CUT&Tag


title: MC38_WT_28d_1

value: tamoxifen

value: 28 day


title: 182DouncePos

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

data_processing:
Following sequencing, reads were trimmed, aligned, differential expression statistics and correlation analyses were performed in Strand NGS software package (v4.0) (Strand Life Sciences).
Alignment and filtering criteria included: adapter trimming, fixed 2bp trim from 5’ and 2bp from 3’ ends, a maximum number of one novel splice allowed per read, a minimum of 90% identity with the reference sequence, a maximum of 5% gap, trimming of 3’ end with Q<30.
Alignment was performed directionally with Read 1 aligned in reverse and Read 2 in forward orientation. Normalization was performed with the DESeq2 algorithm.
Transcripts with an average read count value >5 in at least 100% of the samples in at least one group were considered expressed at a level sufficient for quantitation per tissue and those transcripts below this level were considered not detected/not expressed and excluded, as these low levels of reads are close to background and are highly variable.
For statistical analysis of differential expression, a one-way ANOVA or two-way ANOVA with the factors of TRAP fraction and treatment and a Benjamini-Hochberg Multiple Testing Correction followed by Student-Newman Keuls post hoc test were used (FDR<0.1). For those transcripts meeting this statistical criterion, a fold change >|2| cutoff was used to eliminate those genes which were statistically significant but unlikely to be biologically significant and orthogonally confirmable due to their very small magnitude of change.
Genome_build: Mm10 build of the mouse genome (2014.11.26)
Supplementary_files_format_and_content: Data matrix with raw and normalized counts of all expressed genes.

source_name: brain

extract_protocol:
Purification of ribosomal-bound, microglial-specific RNA was performed as previously described (Chucair-Elliott et al., 2020; Kang et al., 2018; Roh et al., 2018) with slight modifications. For TRAP from whole tissue, a hemisected half-brain was minced into small pieces and homogenized in 1.5 ml ice-cold complete homogenization buffer (50 mM Tris, pH 7.4; 12 mM MgCl2; 100 mM KCl; 1% NP-40; 1 mg/ml sodium heparin; 1 mM DTT; 100 µg/mL cycloheximide (#C4859-1ML, Millipore Sigma); 200 units/ml RNaseOUT Recombinant Ribonuclease Inhibitor (#10777019; Thermofisher); 0.5 mM Spermidine (#S2626, Sigma), 1X complete EDTA-free Protease Inhibitor Cocktail (#11836170001; Millipore Sigma)) with a glass dounce tissue grinder set (#D8938; 15 times with pestle A). For TRAP from cells, microglial cells were sorted by a variety of methods (FACSAria, AutoMACS, Tyto, AutoMACS to Tyto). After pelleting cells at 1000 x g for 10 min at 4°C, cells were resuspended in 400 ul of complete ice-cold homogenization buffer, transferred to a glass dounce tissue grinder set, and homogenized 15 times with pestle A. Volume was brought up to 1.5 mL with complete homogenization buffer. Homogenates (from tissue or cells) were transferred to 2 mL round-bottom tubes and centrifuged at 12,000 x g for 10 minutes at 4°C. After centrifugation, 100 µL of the supernatant was saved as “RNA” input. The remaining supernatant was transferred to a 2 mL round-bottom tube and incubated with 5 µg/µl of anti-GFP antibody (ab290; Abcam) at 4°C with end-over-end rotation for one hour. Dynabeads Protein G for Immunoprecipitation (#10003D; Thermofisher) were washed three times in 1 ml ice-cold low-salt wash buffer (50mM Tris, pH 7.5; 12mM MgCl2; 100mM KCl; 1% NP-40; 100μg/ml cycloheximide; 1mM DTT). After removal of the last wash, the homogenate/antibody mixture was transferred to the 2 ml round-bottom tube containing the washed Protein-G Dynabeads and incubated at 4°C with end-over-end rotation overnight. Magnetic beads were collected using a DynaMag-2 magnet and the unbound- ribosomes and associated RNA discarded. Beads and GFP-bound polysomes were then washed three times with 0.5 ml of high-salt wash buffer (50mM Tris, pH 7.5; 12mM MgCl2; 300mM KCl; 1% NP-40; 100μg/ml cycloheximide; 2mM DTT). Following the last wash, 350 µL of Buffer RLT (Qiagen) supplemented with 3.5 µl 2-β mercaptoethanol (#444203, Sigma) was added directly to the beads and incubated with mixing on a ThermoMixer (Eppendorf) for 10 minutes at room temperature. The beads were magnetically separated and the supernatant containing the target bead-bound polysomes and associated RNA was transferred to a new tube. 350 µl of 100% ethanol was added to the tube (“TRAP” fraction: enriched in transcriptome associated to EGFP-tagged ribosomes) and then loaded onto a RNeasy MinElute column. RNA was isolated using RNeasy Mini Kit (#74104, Qiagen), according to manufacturer’s instructions. RNA was quantified with a Nanodrop 2000c spectrophotometer (Thermofisher Scientific) and its quality assessed by HSRNA screentape with a 2200 Tapestation analyzer (Agilent Technologies).
Directional RNA-Seq libraries were made from 5-100 ng RNA, as previously described (Chucair-Elliott et al., 2020; Chucair-Elliott et al., 2019). Briefly, poly-adenylated RNA was captured using NEBNext Poly(A) mRNA Magnetic Isolation Module (#NEBE7490L; New England Biolabs, Ipswich, MA) and then processed using NEBNext Ultra II Directional Library Prep Kit for Illumina (#NEBE7760L; New England Biolabs) for the creation of cDNA libraries, according to the manufacturer’s instruction. Library sizing was performed with HS RNA ScreenTape (#5067-5579; Agilent Technologies) and libraries were quantified by Qubit HSDNA (#Q32851, Thermo). The libraries for each sample were pooled at 4 nM concentration and sequenced using an Illumina NovaSeq 6000 system (SP PE50bp) at the Oklahoma Medical Research Foundation Clinical Genomics Center.

treatment_protocol: At ~3 months of age, Cx3cr1-NuTRAP mice received a daily intraperitoneal (ip) injection of tamoxifen (Tam) solubilized in 100% sunflower seed oil by sonication (100 mg/kg body weight) to induce cre recombination in microglia (Cx3cr1+).

tag: sort method

value: Cell suspension (no sort)

tag: trap fraction

value: TRAP Pos Fraction

tag: experiment

value: Inhibitor Comparison

tag: inhibitors

value: Dounce 4dC Dissociation

value: brain


title: COVID_18_day_10_PBMC_ETA_CITEseq

description: CITEseq feature barcode matrix

tag: time point

value: day 10

tag: disease


title: MC38_PD1cKO_28d_10

tag: replicate group

tag: genotype


title: MC38_PD1cKO_28d_9


title: COVID_16_day_5_day_10_PBMC_CITEseq

description: CITEseq feature barcode matrix

value: day 5, day 10


title: 182DounceInput

value: TRAP Input


title: K562_50k_bg4_cellNO_rep1_tec2

description: CUT&Tag

tag: cell number

tag: antibody

value: BG4 single-chain antibody

value: bulk fixed cells


title: K562_10k_bg4_cellNO_rep1_tec2

description: CUT&Tag

tag: input type


title: K562_10k_bg4_cellNO_rep1_tec1

description: CUT&Tag


title: 181DounceInput


title: K562_50k_bg4_cellNO_rep1_tec1

description: CUT&Tag


title: MC38_PD1cKO_28d_7


title: COVID_15_day_10_COVID_16_day_1_PBMC_CITEseq

description: CITEseq feature barcode matrix

value: day 1, day 10


title: 180DouncePos


title: K562_100k_bg4_cellNO_rep1_tec2

description: CUT&Tag


title: K562_100k_bg4_cellNO_rep1_tec1

description: CUT&Tag


title: 180DounceInput


title: 181DouncePos


title: MC38_PD1cKO_28d_6


title: MC38_PD1cKO_28d_5


title: MC38_PD1cKO_28d_4


title: 179DouncePos


title: 179DounceInput


title: U2OS_100k_bg4_bulk_rep3_tec2

description: CUT&Tag


title: COVID_17_day_1_day_5_PBMC_CITEseq

description: CITEseq feature barcode matrix

value: Peripheral blood mononuclear cells


title: COVID_15_day_1_day_5_PBMC_CITEseq

description: CITEseq feature barcode matrix

value: day 1, day 5


title: U2OS_100k_None_bulk_rep3_tecx

description: CUT&Tag

value: control-noPrimary antibody


title: MC38_PD1cKO_28d_3


title: U2OS_100k_bg4_bulk_rep3_tec1

description: CUT&Tag


title: G-SmoAMPK4

city: Atanta

first: Tim

last: Gershon

state: GA

address: Emory University School of Medicine

department: Pediatrics

institute: Emory University

data_processing:
Raw sequence data were processed in a Linux environment using Drop-seq Tools V1.13. (https://github.com/broadinstitute/Drop-seq/releases) to generate a digital expression (DGE) matrix
alignment: Star aligner was used version 2.5.4a
DGE creation: We first convert Fastq to BAM/SAM format and merge samples that were sequenced across multiple lanes.
full downstream pipeline code: https://github.com/malawsky/Gershon_single-cell
Genome_build: Genome_build: mm10 genome
Supplementary_files_format_and_content: Supplementary_files_format_and_content: digital expression matrix

source_name: mouse medulloblastoma

extract_protocol:
Brains were cut in half sagittally and drop-fixed in 4% paraformaldehyde for IHC, and half cerebellum or tumor collected for Drop-Seq.Cells were dissociated using the Papain Dissociation System (Worthington Biochemical) according to the manufacturer’s protocol, as in our prior studies. https://www.nature.com/articles/s41467-019-13657-6#Sec18.
Drop-Seq 3' biased cell-indexed cDNA libraries were prepared according to the Drop-seq protocol V3.1 (ref. 32), with full details available online (http://mccarrolllab.com/dropseq/). Cell and bead concentrations were both set to between 95 and 110/μL.  to high-throughput sequencing facility that does their own QC before running samples.  cDNA libraries were prepared for sequencing using standard Illumina protocols (Multiplexed samples using nextera indexes so that libraries could be pooled)

value: untreated

tag: age at harvest


title: COVID_13_day_1_day_5_PBMC_CITEseq

description: CITEseq feature barcode matrix


title: G-SmoAMPK3


title: MC38_PD1cKO_28d_2

value: tamoxifen


title: MC38_PD1cKO_28d_1

value: 28 day


title: COVID_13_day_10_COVID_14_day_1_PBMC_CITEseq

description: CITEseq feature barcode matrix


title: K562_100k_None_bulk_rep3_tecx

description: CUT&Tag


title: G-SmoAMPK2


title: COVID_11_day_10_COVID_12_day_1_PBMC_CITEseq

description: CITEseq feature barcode matrix


title: K562_100k_bg4_bulk_rep3_tec2

description: CUT&Tag


title: MC38_PD1_2dose_8d_5

value: 8 day

value: WT


title: COVID_11_day_1_day_5_PBMC_CITEseq

description: CITEseq feature barcode matrix


title: COVID_10_day_5_day_10_PBMC_CITEseq

description: CITEseq feature barcode matrix


title: COVID_14_day_5_day_10_PBMC_CITEseq

description: CITEseq feature barcode matrix


title: K562_100k_bg4_bulk_rep3_tec1

description: CUT&Tag


title: COVID_1_day_1_day_5_PBMC_CITEseq

description: CITEseq feature barcode matrix


title: MC38_PD1_2dose_8d_4


title: U2OS_100k_None_bulk_rep2_tecx

description: CUT&Tag


title: U2OS_100k_bg4_bulk_rep2_tec2

description: CUT&Tag


title: ARDS_4_day_1_day_5_PBMC_CITEseq

description: CITEseq feature barcode matrix

value: Acute respiratory distress syndrome


title: MC38_PD1_2dose_8d_3


title: G-SmoAMPK1


title: MC38_PD1_2dose_8d_2


title: HHcy

city: Beijing

first: Xiaolong

last: Ma

address: Xueyuan Road 38, Haidian Distrinct, Beijing, China

department: Department of Physiology and Pathophysiology

institute: Peking University Health Science Center

data_processing:
Raw sequencing data were processed using Cell Ranger (version 2.2.0) to demultiplex raw data and generate FASTQ files, aligned, and counted with Cell Ranger pipelines.
Genome_build: mm10-2020-A
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: aortic CD45+ cells

extract_protocol:
Aortas were isolated and digested as previously described (Cai, et al., 2020; Winkels, et al., 2018). Briefly, after sacrificed mice, we firstly perfuse the aortas by PBS, and then harvested whole aortas by pulling of all of the adipose tissue and collecting all aortic layer including the adventitia into RPMI 1640 medium containing 10% (v/v) fetal bovine serum (FBS) on ice, we cut the aortas into fine pieces and digested in HBSS containing 450U/mL Collagenase I (Sigma Aldrich), 250 U/mL Collagenase XI (Sigma Aldrich), 120 U/mL Hyaluronidase (Sigma Aldrich) and 120 U/mL DNase I (Warthington) at 37℃ with reciprocal shaking (60 rpm/min) for 1 hour. Detached cells were then filtered through a 40 μm cell strainer (BD Biosciences), and red cells were excluded by Red Cell Lysis Buffer. Subsequently the remaining cells were washed with 37℃ pre-warmed 1640 containing 10% FBS (500g, 5min) and suspended with PBS. Cells were then stained with FITC anti-mouse CD45 antibody (Biolegend, 103108) (1:100), Hoechst 33342 (Invitrogen, H3570) (1:1000) for 10 min at room temperature, then stained with LIVE/DEADTM Fixable Near-IR Dead Cell Stain Kit (Invitrogen, L34975) for 5 min at room temperature. After PBS washing, cells were suspended in PBS. Single CD45+ live cells (Hoechst+/Dead Cell Stain-/CD45+) were sorted into PBS with 0.04% BSA using a BD FACS SymphonyS6 (BD Biosciences) before single cell RNA-sequencing.
A Chromium Single Cell 3’ Reagent Kits v3 was used and Standard 10X Chromium Single Cell 3’ v3 (10X Genomics GemCode Technology) protocols were followed for scRNA-seq.

tag: cell type

value: immune cells in aortas

value: Supplemented with drinking water with Hcy (1.8 g/L) for 4 weeks


title: WD

tag: strain

value: Supplemented with western diet for 4 weeks


title: U2OS_100k_bg4_bulk_rep2_tec1

description: CUT&Tag

tag: cell line


title: ARDS_3_day_5_day_10_PBMC_CITEseq

description: CITEseq feature barcode matrix

source_name: Peripheral blood mononuclear cells

value: day 5, day 10


title: Ctrl

tag: treatment

value: Control


title: 6M POW6 [LD3]

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

data_processing:
Sequenced reads were mapped to mm10 mouse genome assembly using STAR 2.7.3a with default parameters.
Aligned reads were quantified for gene counts, filtered to exclude genes  with high noise or a maximum count of less than or equal to 50.
The filtered counts were median ratio normalized and tested for statistical significance using DESeq2.
All steps were performed using the Partek® Flow® Software.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: plantaris

extract_protocol:
Plantaris muscles were flash frozen in liquid nitrogen and RNA was isolated using TRIzol and the Zymo MicroPrep Kit and prepared for RNA-sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Adult male (>4 months) mice were subjected to progressive weighted wheel running (PoWeR) for 8 weeks then detrained for 12 weeks. Age-matched mice served as controls.

tag: tissue

value: Skeletal Muscle

value: Sedentary

tag: age

tag: Sex

value: male


title: 6M POW5 [LD2]


title: MC38_PD1_1dose_4d_5

value: 4 day


title: ARDS_2_day_5_day_10_PBMC_CITEseq

description: CITEseq feature barcode matrix

value: Peripheral blood mononuclear cells


title: K562_100k_None_bulk_rep2_tecx

description: CUT&Tag

value: control-noPrimary antibody

value: bulk fixed cells


title: K562_100k_bg4_bulk_rep2_tec2

description: CUT&Tag

value: BG4 single-chain antibody


title: ARDS_1_day_1_day_5_PBMC_CITEseq

description: CITEseq feature barcode matrix

value: day 1, day 5


title: 6M POW4 [LD1]


title: K562_100k_bg4_bulk_rep2_tec1

description: CUT&Tag


title: 9M PoW+DT3 [DT8]


title: 9M PoW+DT2 [DT7]


title: Human H3K4me3 and RbBP5 [BC4605_S5]

city: Bethesda

first: Keji

last: Zhao

state: MD

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

institute: national Institute of Health

data_processing:
library strategy: ACT2-seq
Basecalls performed
In each library, two Tn5 Adapter Sequences were used (adapter-1 and adapter-2). Pairs of reads will be selected into three groups. The first group of reads refer to either read1 or read2 contain adapter-1 sequence. The second group of reads refer to either read1 or read2 contain adapter-2 sequence. The third group of reads refer to both read1 and read2 contain different adapter sequences. Different groups of reads were mapped to the human reference genome hg19 using Bowtie2, and Duplicated reads were removed based on mapping position. The software SICER will be used to identify the enriched regions.
Genome_build: hg19
Supplementary_files_format_and_content:
Adaptor_seq.txt: First column) The name of adapter. Second column) Adapter Sequence.
BC4603_A2R1-1_or_A2R2-1.uniq-W200-G200-E100.scoreisland.txt: read count data for H3K4me3 binding.  First column) Chromosome, Second column) Start, Third column) End, Fourth column) Peak score. Each row refer to an enriched region.
BC4603_A2R1-4_or_A2R2-4.uniq-W200-G200-E100.scoreisland.txt: read count data for H3K27ac binding.  First column) Chromosome, Second column) Start, Third column) End, Fourth column) Peak score. Each row refer to an enriched region.
BC4603_AcoArich_hg19_60_0_mapq10_noDup-W200-G200-E100.scoreisland.txt: read count data for co-binding of H3K4me3 and H3K27ac.  First column) Chromosome, Second column) Start, Third column) End, Fourth column) Peak score. Each row refer to an enriched region.
BC4605_A2R1-2_or_A2R2-2.uniq-W200-G200-E100.scoreisland.txt: read count data for H3K4me3 binding.  First column) Chromosome, Second column) Start, Third column) End, Fourth column) Peak score. Each row refer to an enriched region.
BC4605_A2R1-4_or_A2R2-4.uniq-W200-G200-E100.scoreisland.txt: read count data for RbBP5 binding.  First column) Chromosome, Second column) Start, Third column) End, Fourth column) Peak score. Each row refer to an enriched region.
BC4605_AcoArich_hg19_60_0_mapq10_noDup-W200-G200-E100.scoreisland.txt: read count data for for co-binding of H3K4me3 and RbBP5.  First column) Chromosome, Second column) Start, Third column) End, Fourth column) Peak score. Each row refer to an enriched region.

extract_protocol:
Cells were crosslinked by incubating for 10 min in 10 ml of culture medium supplemented with 0.25% formaldehyde. The cells were pelleted and washed twice in 10 ml of PBS. 1 million cells were transferred to a 1.5 ml tube and suspended in 1 ml of freshly prepared RIPA Buffer (150 mM NaCl, 0.2% SDS, 0.1% sodium deoxycholate, and 1% Triton X-100 in TE buffer pH 7.5) for 10 minutes. The permeabilized cells were pelleted at 850*g for 2 min and the supernatant was carefully removed to ~ 50 ml. The cells were suspended in 1 ml of Wash Buffer (50 mM Tris pH 8.0, 150 mM NaCl, 0.05% Triton X-100, 2 mM EDTA). The cells were pelleted as above, and the supernatant was removed to ~ 50 ml. The cell suspension was diluted to 1 ml using Wash Buffer to generate an approximate concentration of one thousand cells per microliter. The cell suspension was gently mixed, and 50 ml of this suspension was added to each of the sample tubes containing the first set of antibody-PA-Tn5 complexes. The samples were mixed gently and incubated for 30 min at room temperature to allow the complexes to bind to chromatin. After incubation, 1 ml of Wash Buffer was added to each sample, and the tubes were sealed and mechanically rotated for 5 min at room temperature. The cells were pelleted at 850*g, and the supernatant was removed to ~ 50 ml. At this point, 3 ml of an annealed 50 mM “blocking adapter” were added to each sample. The blocking adapter is any annealed Tn5 complex adapter that features a barcode sequence that is not used in any of the samples. The samples were gently mixed and incubated at room temperature for 10 min to allow the blocking adapter to bind to any residual PA-Tn5 complexes that did not take up their original adapters. After incubation with the blocking adapter, the second set of prepared antibody-PA-Tn5 complex solutions were added to the matching samples. The samples were mixed gently and incubated at room temperature for 30 min. 500 ul of Wash Buffer was added to each sample, and the tubes were sealed and mechanically rotated for 5 min at room temperature. The cells were pelleted at 850*g, and the supernatant was removed to ~ 50 ml. The 500 ml wash and pelleting steps were repeated once. Each sample was diluted to ~ 100 ul using Wash Buffer and received 1.5 ml of 1 M MgCl2. The samples were mixed by pipetting and incubated at 37 °C for one hour to allow targeted tagmentation to occur.
The tagmentation reactions were halted by adding 8 ml of 0.5 M EDTA to each sample. The samples were mixed by vortexing and incubated at 80 °C for 5 min to deactivate the transposase. Each sample received 2 ml of 10% SDS and 1 ml of 20 mg/ml proteinase K enzyme. The samples were incubated at 55 °C for 60 min. After the incubation, the samples were purified using a MinElute PCR Purification Kit and an elution volume of 20 ml. After purification, samples may be stored at -20 °C until library preparation is performed.


title: MC38_PD1_1dose_4d_3


title: Human H3K4me3 and H3K27ac [BC4603_S3]


title: MC38_PD1_1dose_4d_2


title: U2OS_100k_bg4_bulk_rep1_tec2

description: CUT&Tag


title: MC38_PD1_1dose_4d_1


title: U2OS_100k_None_bulk_rep1_tecx

description: CUT&Tag


title: U2OS_100k_bg4_bulk_rep1_tec1

description: CUT&Tag


title: 9M PoW+DT1 [DT6]


title: PDL_tension_5

city: Hong Kong

first: Yifan

last: Lin

address: No.34 Hospital Road

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Paired-end sequencing of the library was performed using the NovaSeq 6000 system (Illumina).
Raw data in FASTQ format were processed to remove adapter sequences and low-quality reads.
The sequencing reads were then aligned to the human genome GRCh38 using HISAT2.
FeatureCount was used to retrieve the reads mapped to each gene and generate the expression count matrix.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: PDL

growth_protocol: PDL cells were isolated from PDL tissue using tissue explanation outgrowth method. PDL tissue was scraped gently from the middle third of the root surface using a scalpel to avoid contamination with gingiva or dental pulp. Then PDL tissues were minced to small fragments approximately 1mm3, placed into cell and tissue culture flask, and incubated for 1 hour at 37°C. Then the explants were  cultured in α-Modified Eagle’s Medium supplemented with 10% (v/v) foetal bovine serum, 100 U/mL penicillin and 0.1 mg/mL streptomycin and incubated at 37°C in an atmosphere with 5% carbon dioxide. After the cells growing out from the explants had reached confluence around the explants, cells were passaged, and cultured in a new flask.

extract_protocol:
Total RNA was extracted from cultured cells using the RNeasy Cell Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 12% tensile strain for 12 hours

value: PDL cell

value: tensile strain


title: K562_100k_None_bulk_rep1_tecx

description: CUT&Tag

data_processing:
Library strategy: CUT&TAG
After checking sequencing quality with FastQC, bases with quality score below 20 were trimmed from both reads using cutadapt (V, cutadapt -q 20). Resulting reads were aligned to hg38 with bwa mem and aligned reads that were not overlapping the ENCODE black list were saved into bam (samtools view -Sb -F780 -q 10). Duplicate reads were identified and removed using Picard (Picard MarkDuplicates) and de-duplicated bam were sorted and indexed. In order to find enrichment loci with SEACR, deduplicated bam files were transformed into bedpe files (bedtools bamtobed -bedpe) and then only fragments with size below 1000bp (awk '{if ($1==$4 && $6-$2 < 1000)) print $0}') were kept. Next, coverage of the <1000bp fragments across human genome was computed using bedtools genomecov and reported in bedgraph format.
SEACR was used to identify regions of local enrichments. Bedgraphs obtained from selecting only  fragments of maximym 1kb  were used as input files for SEACR   (SEACR_1.3 $bdg_1000 0.05 non stringent). Peaks with a minimum coverage of 8 reads have been kept for further analysis. Peaks from individual libraries were combined together if replicates were available. Regions observed in 2 technical replicates (n=2) were selected as representative of the biological sample (multi2.bed, supp. files). When multiple biological replicates (i.e. different passages) were available, multi2 regions observed in a minimum two of them were used to generate consensus regions (bio.bed, supp. files)
multi2.bed files represent consensus for the same biological replicate across 2 technical replicates; bio.bed is the list of consensus loci across the available biological replicates.
Genome_build: hg38
Supplementary_files_format_and_content: .bw: bigwig genomic track file obtained normalising signal in 10bp window by total library size (RPM)
Supplementary_files_format_and_content: .bed: peaks


title: PDL_tension_4


title: PDL_tension_3


title: MC38_PD1_2dose_8d_1

value: 8 day

value: WT


title: MC38_Isotype_2dose_8d_5

value: isotype


title: MC38_PD1_1dose_4d_4


title: MC38_Isotype_2dose_8d_4


title: PDL_tension_2


title: 9M UT2 [DT3]

value: Detrained


title: MC38_Isotype_2dose_8d_3


title: K562_100k_bg4_bulk_rep1_tec2

description: CUT&Tag


title: PDL_tension_1


title: K562_100k_bg4_bulk_rep1_tec1

description: CUT&Tag


title: MC38_PD1cKO_28d_8

value: tamoxifen

value: 28 day


title: MC38_Isotype_2dose_8d_2


title: 9M UT3 [DT4]

value: Skeletal Muscle


title: 6M PoW3 [PoW16]

value: Exercise


title: PDL_control_5

value: untreated


title: PDL_control_4


title: MC38_Isotype_2dose_8d_1


title: PMN - donor_38 timepoint_1

city: Brno

first: Marco

last: De Zuani

address: Pekarska, 53

department: CTM

country: Czech Republic

institute: FNUSA - ICRC

data_processing:
Raw reads were quality checked, preprocessed and mapped to the reference genome (Ensembl GRCh38) with gene annotation (Ensembl v94).
Mapped reads were counted and summarized to genes.
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: TSV files containing read summaries expoerted from featureCounts, including the raw read counts for each gene

source_name: Polymorphonuclear cells from peripheral blood

extract_protocol:
Polymorphonuclear cells were isolated from peripheral blood after gradient centrifugation using Lymphoprep (1.077 g/ml, Alere Technologies), carefully harvesting the top part of the bottom layer. Remaining red blood cells were lysed with RBC lysis buffer (BD Bioscience) and clean PMNs were washed twice with PBS. PMNs were directly lysed in TRI-reagent (Sigma-Aldrich). Total RNA was isolated using the RNeasy mini kit (QIAGEN).
An Illumina sequencing library was prepared using the NEBNext Ultra II Directional RNA Library Prep Kit fo Illumina. 250ng of total RNA were used for library preparation.

tag: individual

tag: condition

value: septic shock

value: peripheral blood

value: Polymorphonuclear cells

tag: timepoint

value: TP1 - ICU admission

tag: 5 days outcome

value: survived

value: Female


title: PMN - donor_37 timepoint_1

value: deceased

value: Male


title: PMN - donor_38 timepoint_2

value: TP2 - 3 days post-ICU admission


title: MC38_Isotype_1dose_4d_5

tag: replicate group

tag: time point

value: 4 day

value: WT


title: MC38_Isotype_1dose_4d_4

value: isotype

tag: genotype


title: 9M UT1 [DT2]

value: Detrained

value: male


title: PDL_control_3

value: PDL cell


title: PMN - donor_34 timepoint_2


title: 6M UT3 [PoW17]

value: Skeletal Muscle

value: Sedentary


title: PDL_control_1

value: untreated


title: PMN - donor_34 timepoint_1

value: septic shock

value: peripheral blood


title: MC38_Isotype_1dose_4d_3


title: 6M UT1 [PoW3]


title: 6M UT2 [PoW12]


title: MC38_Isotype_1dose_4d_2


title: PDT3

city: Nanjing

first: Wen

last: Sun

address: 140 Hanzhong Road

institute: Nanjing Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 40%;    Cell Gene Number < 10000;   Cell Gene Number > 200.  PCA and tSNE/UMAP analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: TSV file contain counts for each sample

source_name: Periodontal tissues_PDT

extract_protocol:
Periodontal tissues  were dissociated to single cell.
RNA libraries were generated by BD Rhapsody singel cell RNA-seq and prepared for sequencing using standard Illumina protocols

tag: group

value: Severe Chronic Periodontitis after Treatment (PDT)

tag: gender

value: Periodontal tissues


title: PMN - donor_28 timepoint_1

value: Polymorphonuclear cells

value: TP1 - ICU admission


title: MC38_Isotype_1dose_4d_1


title: 6M PoW2 [PoW15]

value: Exercise


title: PMN - donor_27 timepoint_2

value: TP2 - 3 days post-ICU admission

value: survived

value: Male


title: 6M PoW1 [PoW13]


title: PDT2

value: Female


title: AMDT_intnuc_3

data_processing:
Base calling with Illumina Software
Raw FASTQ files were adapter, filled-in nucleotides, and quality trimmed using TrimGalore
The effect of trimming and overall quality distribution was determined using FastQC
Alignment was performed using Bismark
Read totals were called using Bismark Methylation Extractor
Genome_build: A custom genome assembly to interrogate both nuclear and rDNA methylation was generated by adding the consensus rDNA repeat sequences, BK000964.3, as a separate chromosome to the GRCm39 (GCA_000001635.9) mouse reference genome assembly.
Supplementary_files_format_and_content: Bismark coverage data (.cov files) are generated from Bismark Methylation Extractor and contains the methylated count and total count at each position within the genome

source_name: AMDT_intnuc, HSA-GFP

extract_protocol:
DNA was isolated from the plantaris myonuclei or interstitial nuclei using the Quick-DNA™ Miniprep Plus kit (Zymo Research, D4068) as specified in the protocol.
"Classic" RRBS library preparation was performed by digesting genomic DNA with 30 units of MspI enzyme (New England BioLabs, R0106), and fragments were ligated to pre-annealed adapters containing 5’-methyl-cyotosine. Adapter-ligated fragments ≥50 base pairs were recovered using the DNA Clean & Concentrator Kit (Zymo Research, D4003) and bisulfite-converted using the EZ DNA Methylation-Lightning KitTM (Zymo Research, D5030) following the standard protocol. Preparative-scale PCR was performed, and the products were purified again using the Clean and Concentrator kit.

treatment_protocol: Plantaris myonuclei and interstitial nuclei were isolated by FACS and DNA were extracted and reduced representation bisulfite sequencing (RRBS) for whole-genome and ribosomal DNA-specific analysis.

tag: nucleus type

value: interstitial nuclei


title: AMDT_intnuc_2


title: MC38_Baseline_3

value: WT


title: PMN - donor_27 timepoint_1

tag: cell type


title: MC38_Baseline_1


title: PDT1


title: PMN - donor_26 timepoint_2


title: MC38_Baseline_2


title: PD5

source_name: Periodontal tissues_PD

value: Severe Chronic Periodontitis (PD)


title: PDL_control_2

value: PDL cell


title: AMDT_intnuc_1

value: Skeletal Muscle

value: Sedentary


title: PMN - donor_26 timepoint_1

value: septic shock


title: PD4


title: MC38_CellLine_3

source_name: Cell Line


title: AMDT_myonuc_2

source_name: AMDT_myonuc, HSA-GFP

value: plantaris myonuclei


title: AMDT_myonuc_3


title: MC38_CellLine_2


title: PD3


title: AMDT_myonuc_1


title: MC38_CellLine_1


title: PD2


title: PMN - donor_24 timepoint_1

value: peripheral blood


title: DT_intnuc_3

source_name: DT_intnuc, HSA-GFP

value: Detrained


title: DT_intnuc_2


title: PD1

value: Periodontal tissues


title: PMN - donor_22 timepoint_1

value: Polymorphonuclear cells

value: TP1 - ICU admission

value: deceased


title: WT Naive rep 4

city: Heidelberg

first: Martina

last: Seiffert

address: Im Neuenheimer Feld 280

department: Department of Molecular Genetics

country: Germany

institute: German Cancer Research Center

data_processing:
Base calls performed with Illumina RTA 2.7.7.
Trimming of sequencing reads was done using Trimmomatic version 0.36 (Bolger et al, 2014). Trimmed reads were mapped to the mouse genome (mm9) with boIsotypeie2 (Langmead et al, 2009) using the options “--very- sensitive -X 2000”.
After removing reads, which overlapped regions contained in the ENCODE blacklist, all duplicated reads were discarded with rmdup of SAMtools version 1.3 (Li et al, 2009). Reads mapping to the mitochondrial genome were removed.
For downstream analysis and calculation of the coverage tracks all sequencing reads were shifted to be positioned at the cutting site of the Tn5 transposase comprising 29 bp to correspond to the region occupied by the Tn5 transposase (Adey et al, 2010).
DiffBind (R package) was used to identify differentially accessible peaks with DESeq2. Picard (CollectInsertSizeMetrics) was used to estimate insert size distribution.
Genome_build: mm9
Supplementary_files_format_and_content: peak files

source_name: Naive CD8+ T cells

extract_protocol:
CD8+ T cells from mouse spleen were sorted by flow cytometry for naive (Lineage (CD19, CD11b, NK1.1)negative, TCRbeta+, CD8+ CD127+, CD44-), memory (Lineage (CD19, CD11b, NK1.1)negative, TCRbeta+, CD8+ CD127+, CD44+), effector PD-1int (Lineage (CD19, CD11b, NK1.1)negative, TCRbeta+, CD8+ CD127-, CD44+, PD1int)  and effector PD-1hi (Lineage (CD19, CD11b, NK1.1)negative, TCRbeta+, CD8+ CD127-, CD44+, PD1hi) CD8+ T cells in PBS + 5%FCS.
Sorted cells were incubated with Tn5 transposase (Nextera DNA Library Preparation Kit; Illumina) at 37°C for 30 min in the presence of 0.125 % Igepal CA-630 (Sigma-Aldrich). Tn5 transposase was stopped with EDTA (final conc. 9 mM; Invitrogen). The ATAC-seq libraries were purified with Ampure XP beads (Beckman Coulter), after the barcodes were added by 13-14 PCR cycles.

tag: mouse strain

value: Naive CD8+ T cells

tag: injected tumor


title: PMN - donor_23 timepoint_1

value: Male


title: HC4

source_name: Periodontal tissues_HC

value: Healthy controls (HC)


title: DT_intnuc_1

value: interstitial nuclei


title: DT_myonuc_3

source_name: DT_myonuc, HSA-GFP


title: PMN - donor_24 timepoint_2

value: TP2 - 3 days post-ICU admission

value: survived

value: Female


title: HC2


title: PMN - donor_19 timepoint_1


title: HC3


title: PMN - donor_1 timepoint_1


title: WT Naive rep 3


title: WT Naive rep 2


title: Isotype Naive rep 1


title: Isotype Memory rep 3

source_name: Memory CD8+ T cells

value: Memory CD8+ T cells


title: DT_myonuc_2

value: Skeletal Muscle


title: CS1_AS_SH

city: New York

first: Chao

state: New York

address: 1130 Saint Nicholas Ave

department: Genetics & Development

institute: Columbia University Medical Center

description: A-S-CS

data_processing:
Basecalls performed using Illumina CASAVA version 1.7
For RNA-seq samples, reads count values for each gene were meatured by featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each gene in each sample.

source_name: Cell line

extract_protocol:
Total RNA was extracted from cell pellets using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to instructions from the manufacturer.
Library preparation was performed with ribosomal RNA depletion according to instructions from the manufacturer (NEB) to achieve greater coverage of mRNA and other long non-coding transcripts.

value: chondrosarcoma cell line

tag: cell line

tag: treatment

value: Treated by combination of 5-aza and SAHA


title: POW_intnuc_3

source_name: POW_intnuc, HSA-GFP

tag: tissue

value: Exercise

tag: age


title: in vivo OSCC+oral candidiasis xenograft - rep2 [OC_2]

city: Szeged

first: Attila

last: Szűcs

address: Somogyi utca 4

department: Faculty of Medical Research

country: Hungary

institute: University of Szeged

description:
OC_2
OCvsControl_DEG_all.tdf
fpkm_genename_invivo.tdf

data_processing:
Illumina Casava1.7 software used for basecalling.
Remove reads with adaptor contamination, uncertain nucleotides constitute more than 10 percent of either read or low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Mapping reads by hisat2 v2.0.5 with parameters --dta --phred33
Quantification by FeatureCounts v1.5.0-p3.
Differential expression Analysis by edgeR with parameters padj =< 0.05 and |log2(FoldChange)|>=1
Enrichment Analysis by ClusterProfiler v3.8.1 with parameter padj < 0.05.
GSEA Analysis by gseq c3.0.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: *.tdf: Tab-delimited text files include FPKM values, raw gene counts for each Sample and pvalue, padj value and log2 fold change values and gene descriptions (name, localisation, description, biotype and Transcription Factor family).

source_name: OSCC in mouse tongue

growth_protocol: HSC-2 (JCRB0622) cells were cultured in EMEM, while HO-1-N-1 (JCRB0831) cells in DMEM/F-12 medium, both containing 10% heat-inactivated (56°C, 30 min) fetal bovine serum (FBS) (EuroClone) supplemented with 4mM glutamine, 100U/mL penicillin and 100mg/mL streptomycin. Cells were maintained at 37°C in the presence of 5% CO2.

extract_protocol:
In vitro: mRNA was purified using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's protocol. RNA quality and quantity were analyzed by Bioanalyzer Instrument (Agilent). In vivo: Mice were sacrificed and tongues were removed. Mouse tongue tissues were removed from the tumor with the help of scalpel. 30mg tumor tissue was homogenized (Bioneer) in RLT buffer and RNA was extracted with RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions. RNA quality and quantity were analyzed by Bioanalyzer Instrument (Agilent).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol:
In vitro: 1x10^5 cancer cells were seeded into 24-well plates with three technical replicates. After 12h, the tumor cells were treated with zymosan (10µg/ml), heat-killed C. albicans (MOI 1:10), heat-killed C. parapsilosis (MOI 1:10), live C. albicans (MOI 1:25) or live C. parapsilosis (MOI 1:4) for 12h.
In vivo: Oral candidiasis was induced: calcium alginate swabs were placed in C. albicans suspension (1x10^9/ml) approximately 5 min prior to use, then saturated calcium alginate swabs were placed under the tongues of each mouse for 75 minutes.

tag: host

value: Mus musculus

tag: host strain

value: BALB/C

tag: injected cell line

value: oral candidiasis (C. albicans, SC5314)

value: OSCC in mouse tongue


title: Isotype PD1int rep 3

source_name: Effector PD1int CD8+ T cells

value: Effector PD1int CD8+ T cells


title: POW_intnuc_2

tag: condition


title: 1804 GFP

city: Palo Alto

first: Jeffrey

middle: Mao-Hwa

last: Liu

state: CA

address: 1642 College Avenue

institute: Stanford University

data_processing:
Cutadapt adaptor trimming: Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 2011 May 2;17(1):10.
HISAT2 alignment: Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015 Apr;12(4):357–60.
featureCounts quantify counts per gene: Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014 Apr 1;30(7):923–30.
Genome_build: human genome (GENCODE v32)
Supplementary_files_format_and_content: tab-delimited text files include raw counts  for each Sample ...

source_name: Lentiviral transduced human CD4

growth_protocol: thawed and incubated for 2h in complete X-VIVO15  at 106 cells/ml.

extract_protocol:
50,000 cells were lysed in Trizol-LS
KAPA mRNA HyperPrep Kit (KAPA Biosystems)
RNAqueous Micro Total RNA Isolation Kit (Thermo Fisher) including on-column DNAse digestion


title: in vivo OSCC+oral candidiasis xenograft - rep3 [OC_3]

description:
OC_3
OCvsControl_DEG_all.tdf
fpkm_genename_invivo.tdf


title: HC1

value: Periodontal tissues


title: CS1_ND

description: ND-CS

value: untreated


title: in vivo OSCC+oral candidiasis xenograft - rep4 [OC_4]

description:
OC_4
OCvsControl_DEG_all.tdf
fpkm_genename_invivo.tdf


title: Isotype Memory rep 2


title: 3364 IL10


title: POW_intnuc_1


title: Isotype PD1hi rep 3

source_name: Effector PD1hi CD8+ T cells

value: Effector PD1hi CD8+ T cells


title: 1804 IL10


title: in vivo OSCC+oral candidiasis xenograft - rep1 [OC_1]

description:
OC_1
OCvsControl_DEG_all.tdf
fpkm_genename_invivo.tdf


title: Isotype PD1int rep 2


title: POW_myonuc_3

source_name: POW_myonuc, HSA-GFP

value: plantaris myonuclei


title: 3364 GFP


title: POW_myonuc_2


title: 1437 IL10


title: DT_myonuc_1

value: Detrained


title: in vitro zymosan treatment - rep3 [HS_Z_3]

description:
HS_Z_3
HS_ZvsHS_C_DEG_all.tdf
fpkm_genename_invitro.tdf

source_name: oral squamous cell carcinoma

value: oral squamous cell carcinoma cell line

value: 10 mg/ml zymosan


title: in vitro zymosan treatment - rep2 [HS_Z_2]

description:
HS_Z_2
HS_ZvsHS_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: COVID_12_day_5_day_10_PBMC_CITEseq

description: CITEseq feature barcode matrix

data_processing:
Library strategy: CITE-Seq
Demultiplexing raw reads with bcl2fastq2 (Illumina, v2.20.0)
Cellranger count (10X Genomics, v3.1.0) to generate feature barcode matrices
CITEseqCount (v1.4.3) to identify TotalSeq-C associated UMI counts for sample demultiplexing
Creation of unified feature barcode expression matrix with Seurat (v3.1.2) in R (v.3.6.0)
Genome_build: GRCh38 + SARS-COV-2 (NC_045512.2)
Supplementary_files_format_and_content: Feature barcode expression matrices create with bcl2fastq and CellRanger Count
Supplementary_files_format_and_content: CITEseq feature barcode matrix
Supplementary_files_format_and_content: gene expression feature barcode matrix

source_name: Peripheral blood mononuclear cells

extract_protocol:
Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse.
Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols.

value: day 5, day 10

tag: disease

value: Peripheral blood mononuclear cells


title: Isotype Memory rep 1

value: Memory CD8+ T cells


title: Isotype PD1hi rep 2


title: POW_myonuc_1

value: Skeletal Muscle


title: 0938 IL10


title: Isotype PD1int rep 1


title: CON_intnuc_3

source_name: CON_intnuc, HSA-GFP

value: interstitial nuclei

value: Sedentary


title: in vitro zymosan treatment - rep1 [HS_Z_1]

description:
HS_Z_1
HS_ZvsHS_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: in vitro heat-killed C. parapsilosis treatment -rep3 [HS_hCp_3]

description:
HS_hCp_3
HS_hCpvsHS_C_DEG_all.tdf
fpkm_genename_invitro.tdf

value: heat-killed C. parapsilosis (CLIB214)


title: CON_intnuc_1


title: in vitro heat-killed C. parapsilosis treatment -rep2 [HS_hCp_2]

description:
HS_hCp_2
HS_hCpvsHS_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: CON_intnuc_2


title: Isotype PD1hi rep 1


title: α-IL-10R PD1hi rep 2


title: 0938 GFP


title: α-IL-10R PD1hi rep 3


title: in vitro heat-killed C. albicans treatment - rep3 [HS_hCa_3]

description:
HS_hCa_3
HS_hCavsHS_C_DEG_all.tdf
fpkm_genename_invitro.tdf

value: heat-killed C. albicans (SC5314)


title: in vitro heat-killed C. parapsilosis treatment -rep1 [HS_hCp_1]

description:
HS_hCp_1
HS_hCpvsHS_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: CON_myonuc_3

source_name: CON_myonuc, HSA-GFP


title: α-IL-10R PD1hi rep 1


title: 1437 GFP


title: CON_myonuc_2


title: in vitro heat-killed C. albicans treatment - rep2 [HS_hCa_2]

description:
HS_hCa_2
HS_hCavsHS_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: CON_myonuc_1


title: rancRNA_18-M2_polysome-associated mRNA_rep3

city: Bern

first: Norbert

last: Polacek

address: Freiestrasse 3

department: Chemistry and Biochemistry

country: Switzerland

institute: University of Bern

description:
mSeq of poly-A enriched RNA
mRNA

data_processing:
Quality control using fastqc tool.
Mapping performed using HISAT2; more than 95% mapping rate, -p 8.
Counting was performed using featureCounts.
Genome_build: Strain BY4742 (PRJNA260311, Oct-12-2014)
Supplementary_files_format_and_content: *.txt: Tab-delimited text file; counts table.

organism: Saccharomyces cerevisiae

source_name: yeast strain trm10∆

extract_protocol:
Yeast spheroplasts were electroporated with or without RNA, recovered and harvested by centrifugation. Pellets were opened using a FastPrep. Lysates were cleared by centrifugation and loaded on a density gradient for Ultracentrifugation. Fractions containing polysomes were pooled and RNA was extracted via hot acid phenol extraction.
Poly-A-Enrichment via oligo-dT-beads.
PolyA enriched mRNAs were transformed into a cDNA library using the Illumina TruSeq stranded mRNA Kit. Library size was determined using Qbit.

tag: strain

tag: electroporation

tag: mrna fraction

value: polysome-associated


title: in vitro heat-killed C. albicans treatment - rep1 [HS_hCa_1]

description:
HS_hCa_1
HS_hCavsHS_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: rancRNA_18-M2_polysome-associated mRNA_rep2

description:
mSeq of poly-A enriched RNA
mRNA


title: 11/10 mef2:CD2- DNA

first: Stephen

last: Gisselbrecht

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

institute: Brigham and Women's Hospital

description: UMI-tagged amplicon containing degenerate sequence tag

data_processing:
Reads were processed to remove and retain UMI tags using a custom python script, available upon request.
Common 5' and 3' regions of the remaining sequence were removed using cutadapt 1.14.
The remaining sequence was mapped to a lookup table of degenerate sequence tags using bowtie.
The resulting file of tag-UMI pairs was processed to extract an UMI count using a custom python script, available upon request.
In R 3.5.1, DNA or RNA UMI counts per tag were normalized to total DNA or RNA UMI counts within each replicate and a normalized expression measure (RNA UMI count / DNA UMI count) calculated, then all replicates for one experiment were collected to give a table of individual normalized expression measurements.
In R 3.5.1, tables of all expression measurements within an experiment were filtered to remove individual measurements resulting from <65 DNA UMIs, then to remove enhancers measured in fewer than 4 replicates. Summary statistics (mean and s.e.m.) were calculated for enhancers passing these filters.
Genome_build: n/a
Supplementary_files_format_and_content: tagCounts files contain 4 columns: Enhancer, Tag, UMI count, and Read count
Supplementary_files_format_and_content: fullFiltered files contain 11 columns: Tag, Enhancer_RNA, UMI_count_RNA, Read_count_RNA, Enhancer_DNA, UMI_count_DNA, Read_count_DNA, normUMI_DNA, normUMI_RNA, normUMI, and replicate
Supplementary_files_format_and_content: fullSummaryFiltered files contain 6 columns: Enhancers, numTags, avgUMIcount, sdUMIcount, totalUMIcount, and standardError

organism: Drosophila melanogaster

source_name: sorted embryonic cells depleted of fusion-competent myoblasts

growth_protocol: Transformant male flies containing random picks from a pool of sequence-tagged reporter constructs were crossed to twi:CD2 or mef2[IE-D5]:CD2 virgin females in population cages. Embryos were collected for 2.25 hours from pre-layed cages and aged 11 hours at 18°.

extract_protocol:
RNA and DNA were simultaneously purified from sorted cells, using the back extraction method for DNA. RNA samples were treated with TURBO DNase and reverse-transcribed with a custom primer specific to the reporter gene amplicon.
A single round of primer extension with a custom primer specific to the reporter gene amplicon added an 8-base degenerate UMI sequence, along with the standard Illumina read 1 sequencing primer and Illumina P5 cluster generation primer. After SPRI purification, the target amplicon (including UMI) was amplified with an additional custom primer specific to the reporter gene and the Illumina P5 + read 1 sequencing primer.

treatment_protocol: Single-cell suspensions were prepared from dechorionated embryos and stained with Alexa647-anti-rat CD2 (Biorad MCA154A647), then CD2-positive and -negative populations were sorted.

value: reporter insertion pool crossed to mef2[IE-D5]:CD2


title: in vitro control - rep3 [HS_C_3]

description:
HS_C_3
HS_CavsHS_C_DEG_all.tdf
HS_CpvsHS_C_DEG_all.tdf
HS_hCavsHS_C_DEG_all.tdf
HS_hCpvsHS_C_DEG_all.tdf
HS_ZvsHS_C_DEG_all.tdf
fpkm_genename_invitro.tdf

value: no treatment


title: in vitro control - rep2 [HS_C_2]

description:
HS_C_2
HS_CavsHS_C_DEG_all.tdf
HS_CpvsHS_C_DEG_all.tdf
HS_hCavsHS_C_DEG_all.tdf
HS_hCpvsHS_C_DEG_all.tdf
HS_ZvsHS_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: 11/10 mef2:CD2- RNA


title: 11/9 mef2:CD2- DNA


title: in vitro Candida parapsilosis treatment -rep3 [HS_Cp_3]

description:
HS_Cp_3
HS_CpvsHS_C_DEG_all.tdf
fpkm_genename_invitro.tdf

value: live C. parapsilosis (CLIB214)


title: in vitro control - rep1 [HS_C_1]

description:
HS_C_1
HS_CavsHS_C_DEG_all.tdf
HS_CpvsHS_C_DEG_all.tdf
HS_hCavsHS_C_DEG_all.tdf
HS_hCpvsHS_C_DEG_all.tdf
HS_ZvsHS_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: 11/9 mef2:CD2- RNA


title: rancRNA_18-M2_total mRNA_rep3

description:
mSeq of poly-A enriched RNA
mRNA

extract_protocol:
Yeast spheroplasts were electroporated with or without RNA, recovered and harvested by centrifugation. Pellets were opened using a FastPrep. Lysates were cleared by centrifugation and total RNA was extracted by hot acid phenol extraction.
Poly-A-Enrichment via oligo-dT-beads.
PolyA enriched mRNAs were transformed into a cDNA library using the Illumina TruSeq stranded mRNA Kit. Library size was determined using Qbit.

value: total


title: rancRNA_18-M2_polysome-associated mRNA_rep1

description:
mSeq of poly-A enriched RNA
mRNA


title: in vitro Candida parapsilosis treatment -rep2 [HS_Cp_2]

description:
HS_Cp_2
HS_CpvsHS_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: in vitro Candida parapsilosis treatment -rep1 [HS_Cp_1]

description:
HS_Cp_1
HS_CpvsHS_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: 11/3 mef2:CD2- DNA


title: rancRNA_18-M2_total mRNA_rep2

description:
mSeq of poly-A enriched RNA
mRNA


title: 11/3 mef2:CD2- RNA


title: PD-1 hi IL10R8

description: aIL10R replicate 3

hyb_protocol: 20 μg of cRNA was then converted to sensestrand DNA (ss-cDNA). After fragmentation and terminal labeling, 5,5 ug of biotinylated ss-cDNA were hybridized for 17 hr at 45°C on Affymetrix Mouse Gene 2.0 ST Arrays

scan_protocol: Microarray scanning was done using an Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays.

data_processing: Samples were processed with Affymetrix Power Tools using 'Robust Microarray Analysis' approach for the normalization. Log2-transformed transcript-level gene expression was calculated for ‘meta’ probe sets. Quality control of the samples was carried out by examining average raw intensity signal (pm_mean) or mean absolute deviation of the residuals (all_probeset_mad_residual_mean). 'Detected above background' measure was used to filter ‘meta’ probe sets if less than 50% of probe sets were called as ‘detected’ (P value <0.05) within less than 50% of the samples in each experimental group.

source_name: Mouse spleen CD8 T-cells

label_protocol: Biotin-labeled ss-cDNA samples for hybridization on GeneChip™ Mouse Gene 2.0 ST Arrays (Affymetrix) were prepared according to Affymetrix's recommended sample labeling procedure as described in the Gene Chip WT Pico Reagent Kit guide

growth_protocol: C57BL/6 mice transplanted with murine CLL cells and after 5 weeks total RNA was isolated from PD-1hi effector CD8+ T-cell that were sorted by flow cytometry from spleen (Lin- TCRb+ CD8+ CD127low CD44int-hi PD-1hi)

extract_protocol: RNA was extracted from sorted cells using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol

treatment_protocol: After 3 weeks of transplantation, mice were treated with aIL-10R antibody or the corresponsing isotype controls every 3 weeks by intraperitoneal injection

tag: Sex

value: female

value: Mouse spleen CD8 T-cells


title: PD-1 hi IL10R9

description: aIL10R replicate 4


title: rancRNA_18-M2_total mRNA_rep1

description:
mSeq of poly-A enriched RNA
mRNA


title: PD-1 hi IL10R7

description: aIL10R replicate 2


title: 11/2 mef2:CD2- DNA


title: rancRNA_18_total mRNA_rep1

description:
mSeq of poly-A enriched RNA
mRNA


title: PD-1 hi IL10R6

description: aIL10R replicate 1


title: PD-1 hi Iso8

description: Isotype replicate 3


title: PD-1 hi Iso9

description: Isotype replicate 4


title: rancRNA_18_polysome-associated mRNA_rep2

description:
mSeq of poly-A enriched RNA
mRNA


title: 11/8 mef2:CD2- RNA


title: 11/8 mef2:CD2- DNA


title: no RNA_polysome-associated mRNA_rep3

description:
mSeq of poly-A enriched RNA
mRNA

value: no RNA


title: AT4 PD-1 hi CD8

description: PD-1hi replicate 4

source_name: Mouse spleen CD8 T-cells_PD-1hi

growth_protocol: C57BL/6 mice transplanted with murine CLL cells and after 6 weeks total RNA was isolated from splenic CD8+ T-cell (Lin- TCRb+ CD8+) subsets that were sorted by flow cytometry from leukemic mice (Naïve: CD127hi CD44low, Memory: CD127hi CD44hi, PD-1int effector: CD127low CD44int-hi PD-1int, and PD-1hi effector: CD127low CD44int-hi PD-1hi).

tag: gender

tag: transplanted with

value: murine CLL cells from Eµ-TCL1 mice

tag: timepoint

value: 6 weeks of transplantation

value: spleen CD8 T-cells

tag: cell subtype


title: 11/2 mef2:CD2- RNA


title: in vitro Candida albicans treatment - rep3 [HS_Ca_3]

description:
HS_Ca_3
HS_CavsHS_C_DEG_all.tdf
fpkm_genename_invitro.tdf

tag: cell line

tag: cell type

value: oral squamous cell carcinoma cell line

value: live C. albicans (SC5314)


title: rancRNA_18_polysome-associated mRNA_rep1

description:
mSeq of poly-A enriched RNA
mRNA


title: PD-1 hi Iso5

description: Isotype replicate 1

tag: tissue


title: in vitro Candida albicans treatment - rep1 [HS_Ca_1]

description:
HS_Ca_1
HS_CavsHS_C_DEG_all.tdf
fpkm_genename_invitro.tdf

tag: treatment


title: rancRNA_18_total mRNA_rep2

description:
mSeq of poly-A enriched RNA
mRNA


title: in vitro zymosan treatment - rep3 [HO_Z_3]

description:
HO_Z_3
HO_ZvsHO_C_DEG_all.tdf
fpkm_genename_invitro.tdf

value: 10 mg/ml zymosan


title: AT2 PD-1 hi CD8

description: PD-1hi replicate 2


title: in vitro Candida albicans treatment - rep2 [HS_Ca_2]

description:
HS_Ca_2
HS_CavsHS_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: no RNA_polysome-associated mRNA_rep2

description:
mSeq of poly-A enriched RNA
mRNA


title: in vitro zymosan treatment - rep2 [HO_Z_2]

description:
HO_Z_2
HO_ZvsHO_C_DEG_all.tdf
fpkm_genename_invitro.tdf


title: PD-1 hi Iso7

description: Isotype replicate 2


title: AT1 PD-1 hi CD8

description: PD-1hi replicate 1


title: AT3 PD-1 hi CD8

description: PD-1hi replicate 3


title: 11/1 mef2:CD2- RNA