title: P10_5 [Z10_B1_5_S21]

data_processing:
Base calling was performed by bcl2fastq v 2.20
Quality trimming was performed using fastp v0.23.2
Alignment was performed using STAR v2.7.10a
Gene counts were performed with RSEM v1.3.3
Normalization was performed with DESeq2 v1.31.15
Assembly: Biospyder Zebrafish S1500+ Surrogate Gene Set
Supplementary files format and content: count_table.csv is a genes by samples count matrix of raw counts from the STAR alignments

tag: developmental stage

value: 120-hours post fertilization

value: DMSO

tag: duration of_chemical_exposure

value: 5 days

value: Dimethyl sulfoxide

tag: chemical exposure_dates

tag: i7 index_id

value: GGGTTGTTA

value: TempO-Seq


title: 3W Minoxidil (MXD) - 3W Control (Cy3) x 3W NXD (Cy5)

status: Public on Apr 17 2024

type: RNA

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

country: Japan

institute: University of Tsukuba

description:
3W Minoxidil (MXD)
0031_1_3
Dye-swap (Cy3/Cy5) of Cont vs N-CE 3W mouse back skin

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scanner G2600D SG17204584

data_processing: Software: Feature Extraction ver 12.0.3.1

molecule: total RNA

organism: Mus musculus

source_name: 3W Vehicle-treated back skin Cy3

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: Experimental protocols were reviewed and approved by the Animal Care Committee of Hoshi University School of Pharmacy and Pharmaceutical Sciences. Male C57BL/6 mice (8 weeks-old) purchased from Tokyo Laboratory Animals Science Co., Ltd. (Tokyo, Japan). The animals were housed at the Animal Institution in Hoshi University. They were maintained in cages in a ventilated animal room with controlled temperature and relative humidity with a 12 h light : 12 h dark cycle with free access to water and rodent chow.

extract_protocol: QIAGEN, Rneasy Micro kit

treatment_protocol: Preliminary experiments were conducted with WO at 5, 10, and 20% concentrations. C57BL/6 mice were divided into 3 groups (6 mice per group): WO 20%, MXD 3%, and VC (propylene glycol: ethanol: water (5:3:2) was used as the vehicle control group). Briefly, starting the day after shaving, 200 μL of the adjusted sample was applied daily to the backs of the mice for observation and photography, and sampling.

tag: strain

tag: tissue

value: back skin

source_name: 3W 3% Minoxidil-treated back skin Cy5


title: 3W Whale Oil (WO) - 3W Control (Cy5) x 3W WO (Cy3)

description:
3W Whale Oil (WO)
0031_1_2
Dye-swap (Cy3/Cy5) of Cont vs MXD 3W mouse back skin

source_name: 3W 20% Whale Oil-treated back skin Cy3

source_name: 3W Vehicle-treated back skin Cy5


title: RNA Individual 6 skin fibroblast cells, Dexamethasone, Time0

type: SRA

city: Los Angeles

first: Marcelo

last: Francia

state: CA

address: 1771 Beloit Avenue, Unit 204

department: Neuroscience

country: USA

institute: University of California, Los Angeles

library_source: transcriptomic

data_processing:
Fastqc software was used to assess the quality of the raw files. Low quality reads were trimmed using TrimGalore and Cutadapt.
Alignment of reads was performed with the STAR software and to human gene ensembl version GrCh38. STAR was indexed to the genome using the –runMode genomeGenerate function. For aligning, STAR was run with the parameters –outFilterType BySJout –outFilterMultimapNmax 20 –alignSJoverhangMin 8 –alignSJDBoverhangMin 1 –outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 -alignIntronMax 1000000 -alignMatesGapMax 1000000.
Samtools was used to index the aligned files from STAR
Read counts were associated with genes using featureCounts software with the NCBI GRCh38 gene annotation file
Assembly: GrCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Homo sapiens

source_name: Skin

growth_protocol: Fibroblast cell lines were thawed out and grown to confluence in T75 culture flasks in standard culture media (DMEM containing 10% fetal bovine serum (FBS) and 1x Penicillin-Streptomycin)

extract_protocol:
RNA from cell lysates was extracted using the Qiagen RNeasy mini kit (Qiagen 74106). Cell lysates were extracted in a randomized order to prevent batch effects in downstream analysis. In order to collect total RNA including small RNAs, the standard extraction protocol (Purification of Total RNA from Animal Cells using Spin Technology) was adjusted by making the following changes: (i) adding 1.5 volumes of 100% ethanol, instead of 70%, after the lysis step (step 4 in handbook protocol) and (ii) adding 700 mL of buffer RWT (Qiagen 1067933) instead of the provided RW1 (step 6 in handbook protocol).
RNA library preps were made using the Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit

treatment_protocol: 5 days after being plated the cells were treated  with 100 nM Dexamethasone for 30 min. Cells were then washed with PBS and switched to collection media (DMEM containing 5% FBS and 1x Penicillin-Streptomycin). Collection started 12 hours after Dexamethasone treatment, and continued every 4 hours for a 48 hour period

value: Skin

tag: cell type

value: Fibroblast cells

tag: treatment

value: Dexamethasone

tag: time

value: Time 0


title: RNA Individual 5 skin fibroblast cells, Dexamethasone, Time48

value: Time 48


title: P10_4 [Z10_B1_4_S20]

city: Ottawa

first: John

last: Stead

state: ON

address: 1125 Colonel By Drive

department: Department of Neuroscience

country: Canada

institute: Carleton University

organism: Danio rerio

growth_protocol: Zebrafish embryos were cultured in water from the ZebTEC housing system (Techniplast, Montreal, Canada) maintaining a temperature of 28 Celsius degrees, pH of 7.4, and conductivity of 2-400μS.

extract_protocol:
Total RNAs were extracted using a Qiagen Mini kit (Qiagen, Toronto, Canada), followed by the manufacter's protocol
RNA libraries were prepared in a 96-sample TempO-Seq S1500+ Zebrafish Surrogate Assay panel (BioSpyder Technologies, California, USA). Each sample was diluted with an equal volume of 2X Enhanced Lysis Buffer. All samples were annealed with detector oligo probes and sequentially processed in digestion, ligation, and amplification steps according to the manufacturer’s protocol. Equal amounts of each sample’s libraries were pooled in a 1.5 ml microtube and purified using NucleoSpin® Gel and PCR Cleanup Kits (Macherey-Nagel, Düren, Germany). Purified pooled libraries were sequenced on an Illumina NextSeq 2000 using a P2 Reagent kit and a 100 cycle flow cell (Illumina, USA).
TempO-Seq S1500+ Zebrafish Surrogate Assay - Index E set was used

treatment_protocol: Zebrafish embryos were exposed from 3-4 hours post fertilization (hpf) to 120 hpf in 16 ml Petri-dish of 0.1 % dimethylsulfoxide (DMSO) and chemical renewal of 8 ml was daily in every Petri-dish.

tag: chemical

tag: chemical long_name

tag: dose

tag: rna extraction_batch

tag: rna extraction_date

tag: i5 index_id

tag: library well

tag: protocol


title: A549 cells, Ctrl, 10 ng/mL IFN, rep3

city: Raleigh

first: Xinxia

last: Peng

address: 1060 William Moore Drive

institute: NC State

data_processing:
Illumina RNA-seq reads were mapped against the human genome assembly version 38 (Hg38) using STAR version 2.7.9a. Custom STAR parameters were set as follows: limitOutSAMoneReadBytes: 1000000, outSAMprimaryFlag: AllBestScore, outFilterType: BySJout, alignSJoverhangMin: 8, alignSJDBoverhangMin: 3, outFilterMismatchNmax: 999, alignIntronMin: 20, alignIntronMax: 1000000, alignMatesGapMax: 1000000, outFilterMultimapNmax: 20; otherwise, default STAR parameters were used.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample as generated by STAR

growth_protocol: A549 cell lines were maintained in F-12K media with 10% fetal bovine serum (FBS) at 37°C in a 5% CO2 incubator.

extract_protocol:
Total RNA was isolated from cells following the TRIzol isolation method (Invitrogen). All samples were quantified and assayed to confirm minimum RNA integrity number of at least 9.4 using an Agilent Bioanalyzer (RNA 6000 Pico Kit, catalog no. 5067-1513).
500 ng of total RNA per sample underwent mRNA capture and was then fragmented at 94°C for 6 min. Sequencing libraries were prepared according to the manufacturer’s protocol using eleven cycles of final amplification (KAPA mRNA HyperPrep Kit, catalog no. KK8580 and KAPA UDI Adapter Kit, catalog no. KK8727). Libraries underwent QC prior to sequencing using an Agilent Bioanalyzer (High Sensitivity DNA Kit, catalog no. 5067-4626).

treatment_protocol: A549 cells were seeded overnight at 150,000 cells per well in 12-well plates in 1.5 mL media to reach ~80% confluency the next day. The media was then removed, and the cell monolayer was washed with 1X DPBS prior to interferon treatment. Cells were treated with fresh A549 media with or without human IFN-β recombinant protein (R&D Systems™ 8499IF010) at 1 ng/mL or 10 ng/mL for 6 hours.

tag: cell line

value: epithelial cell

tag: genotype

value: GFP knockdown

value: 10 ng/mL IFN-B


title: GDO_hFOB 1.19, transfected with custom CRISPRi sgRNA pool 7

city: Philadelphia

first: Mitchell

middle: L

last: Conery

state: PA

address: 3615 Civic Center Blvd

department: Center for Spatial and Functional Genomics

institute: Children's Hospital of Philadelphia

description: 10x Genomics

data_processing:
Single-cell FASTQs were initially processed using the CellRanger pipeline (10x Genomics Cell Ranger 3.0.0) with default settings.
We then used CellBender to denoise and filter the raw CellRanger outputs separately for each of the eight pools.
The number of droplets and expected number of cells were visually estimated from each pool’s unique molecular identifier (UMI) curve, and we ran Cellbender with a learning rate of 0.00005, 150 training epochs, and a false-positive rate of 1%.
After CellBender we used UMAP projections and violin plots implemented in Scanpy to visualize the remaining droplets for each pool and quickly recognized that all pools but the second contained two clusters of droplets, one with a high number of UMIs and genes per droplet and the other with a low level of cellular complexity. The second pool had an overall low level of complexity indicative of mostly empty droplets and was discarded.
For the remaining pools we used the Leiden algorithm to cluster the cells and retained only the high complexity cluster.
The remaining droplets were then combined across pools and visualized using UMAP and violin plots. We discarded droplets with >10% mitochondrial reads and >90,000 UMI to remove suspected dying cells and doublets respectively.
Assembly: hg19
Supplementary files format and content: Standardized h5seurat single-cell output file of QCed cells and tab-delimited file of sgRNAs per cell.
Library strategy: scCRISPR screen

source_name: hFOB 1.19, transfected with custom CRISPRi sgRNA pool, differentiated 5 days

growth_protocol: Stock hFOB-CRISPRi-KRAB-Pooled-sgRNA cells were grown in 100mm plates under Blasticidin/Puromycin selection for 2 days at 33.5°C, then differentiated for 5 days at 39.5°C.

extract_protocol:
Cells were removed from plates with TrypLE, counted, and diluted to 1000cells/ul in DPBS+1% FBS. RNA was extracted from cells and sgRNAs were barcode captured following manufacturer's instructions as part of 10X Genomics sequencing.
Library was constructed according to the manufacturer's instructions (10X Genomics scRNA-seq, GEX libraries) and Feature Barcoded CRIPSR Capture (CRISPR Capture libraries) at the CHOP Center for Applied Genomics.

treatment_protocol: To generate the hFOBs containing our custom sgRNAs, the same helper hFOB-dCas9-CRISPRi-KRAB cells were used for transduction. Cells were transduced at low MOI (0.2) plus polybrene (8ug/ml) with a Sigma-Aldrich custom sgRNA lentiviral pool (titer = 5.3 x 108 TU/ml).

value: hFOB1.19 cells

value: human fetal osteoblasts

value: transfected with custom 296-sgRNA pool

value: differentiated 5 days

tag: pool

tag: library type

value: GDO


title: GDO_hFOB 1.19, transfected with custom CRISPRi sgRNA pool 6

description: 10x Genomics


title: P10_3 [Z10_B1_3_S19]

tag: developmental stage

value: 120-hours post fertilization

value: DMSO

tag: duration of_chemical_exposure

value: 5 days

value: Dimethyl sulfoxide

tag: chemical exposure_dates

tag: i7 index_id


title: GDO_hFOB 1.19, transfected with custom CRISPRi sgRNA pool 5

description: 10x Genomics

tag: cell type

tag: treatment

tag: time


title: RNA Individual 5 skin fibroblast cells, Dexamethasone, Time44

tag: tissue

value: Skin

value: Time 44


title: A549 cells, Ctrl, 1 ng/mL IFN, rep3

value: 1 ng/mL IFN-B


title: A549 cells, Ctrl, mock, rep3

value: mock


title: P10_2 [Z10_B1_2_S18]

tag: chemical

tag: chemical long_name

tag: dose

tag: rna extraction_batch

value: GGGTTGTTA

value: TempO-Seq


title: GDO_hFOB 1.19, transfected with custom CRISPRi sgRNA pool 4

description: 10x Genomics


title: P10_1 [Z10_B1_1_S17]

tag: rna extraction_date

tag: i5 index_id

tag: library well

tag: protocol


title: RNA Individual 5 skin fibroblast cells, Dexamethasone, Time40

value: Fibroblast cells

value: Dexamethasone

value: Time 40


title: A549 cells, Ctrl, mock, rep2

tag: cell line

value: epithelial cell

tag: genotype

value: GFP knockdown


title: GDO_hFOB 1.19, transfected with custom CRISPRi sgRNA pool 3

description: 10x Genomics

value: hFOB1.19 cells

value: human fetal osteoblasts

value: transfected with custom 296-sgRNA pool

value: differentiated 5 days

tag: pool

tag: library type


title: A549 cells, VILMIRg2, 10 ng/mL IFN, rep3

value: VILMIR knockdown

value: 10 ng/mL IFN-B


title: RNA Individual 5 skin fibroblast cells, Dexamethasone, Time36

value: Skin

value: Time 36


title: RNA Individual 5 skin fibroblast cells, Dexamethasone, Time32

value: Time 32


title: A549 cells, VILMIRg2, 10 ng/mL IFN, rep2


title: GDO_hFOB 1.19, transfected with custom CRISPRi sgRNA pool 2

description: 10x Genomics

value: GDO


title: GDO_hFOB 1.19, transfected with custom CRISPRi sgRNA pool 1

description: 10x Genomics


title: A549 cells, VILMIRg2, 10 ng/mL IFN, rep1


title: RNA Individual 5 skin fibroblast cells, Dexamethasone, Time28

value: Time 28


title: RNA Individual 5 skin fibroblast cells, Dexamethasone, Time24

value: Time 24


title: A549 cells, VILMIRg2, 1 ng/mL IFN, rep3

value: 1 ng/mL IFN-B


title: A549 cells, VILMIRg2, 1 ng/mL IFN, rep2


title: RNA-seq_hFOB 1.19, differentiated 5 days at 39.5⁰C, rep2

data_processing:
RNA-seq data were aligned to the hg19 genome with STAR v. 2.6.0c and gene counts were obtained using HTseq, with flags -f bam -r name -s reverse -t exon -m intersection-strict, to count genes from GENCODE Release 19 (GRCh37.p13) annotation plus annotation for lincRNAs and sno/miRNAs from the UCSC Table Browser (downloaded 7/7/2016).
Normalized counts for the uniquely mapped read pairs were generated through the transcript per million read method with effective gene length and the resulting values were used in the computation of gene expression percentiles.
Assembly: hg19
Supplementary files format and content: Processed tpm data is stored in a single file for all replicates. The third column denotes the replicate for each line.

source_name: hFOB1.19 cells

growth_protocol: Cells were differentiated 5 days at 39.5⁰C

extract_protocol:
We isolated total RNA from hFOBs using TRIzol reagent (Invitrogen) following manufacturer instructions and depleted it of rRNA utilizing the Ribo-Zero rRNA Removal Kit (Illumina).
We prepared RNA-seq libraries with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) following standard protocols. We sequenced libraries on one S2 flow cell on an Illumina NovaSeq 6000, generating ~200 million paired-end 50 bp reads per sample.

value: Differentiated 5 days at 39.5 degrees C


title: RNA Individual 5 skin fibroblast cells, Dexamethasone, Time20

value: Fibroblast cells

value: Dexamethasone

value: Time 20


title: RNA Individual 5 skin fibroblast cells, Dexamethasone, Time16

value: Time 16


title: A549 cells, VILMIRg2, 1 ng/mL IFN, rep1

value: epithelial cell


title: RNA Individual 5 skin fibroblast cells, Dexamethasone, Time12

value: Time 12


title: RNA-seq_hFOB 1.19, differentiated 5 days at 39.5⁰C, rep1

description: Processed tpm data is stored in a single file for all replicates. The third column denotes the replicate for each line.

value: hFOB1.19 cells

value: human fetal osteoblasts


title: hFOB 1.19, differentiated 5 days at 39.5⁰C, rep3

description:
Processed ibed files contain 1 and 4-fragment interactions compiled across all samples. Columns 1-3 cover the position of the promoter regions and columns 4-6 the positions of the fragments interacting with them.
chicagoRes_1frag.ibed
chicagoRes_4frag.ibed

library_source: genomic

data_processing:
We pre-processed paired-end reads from the three hFOB replicates using the HICUP pipeline (v0.5.9) aligning reads to the hg19 reference genome with bowtie.
We called significant promoter interactions with genes from the GENCODE Release 19 gene set (GRCh37.p13) at 1-DpnII fragment resolution using CHiCAGO (v1.1.8) with default parameters except for binsize set to 2500.
We also called significant interactions at 4-DpnII fragment resolution by artificially grouping four consecutive DpnII fragments and inputting them into CHiCAGO using default parameters except for removeAdjacent which was set to False.
We considered interactions with a CHiCAGO score > 5 at either 1-fragment or 4-fragment resolution to be significant interactions and converted significant interactions to ibed format for use in variant to gene mapping.
Assembly: hg19
Supplementary files format and content: Processed tab-delimited ibed files have been created in standard format by combining data across replicates as described above. Only significant interactions are displayed.
Library strategy: Capture-C

molecule: genomic DNA

growth_protocol: Cells were differentiated by increasing culture temperature to 39.5°C and were harvested for ATAC-seq and Capture-C five days post-differentiation.

extract_protocol:
For this protocol, 107 fixed hFOB cells were resuspended in dH2O supplemented with protease inhibitor cocktail and incubated on ice for 10 minutes twice. After setting aside 50μl of cell suspension for pre-digestion QC, the remaining sample was divided into 6 tubes. All incubation reactions were carried out in a Thermomixer (BenchMark) shaking at 1,000 rpm. Samples were pre-digested for 1 hour at 37°C after adding 0.3% SDS, 1x NEB DpnII restriction enzyme buffer and dH2O. We then added a 1.7% solution of Triton X-100 to each tube and continued the incubation an additional hour. In the sample tubes only, we added 10µL of DpnII (NEB, 50 U/μl) and continued the incubation until the end of the day when another 10μl DpnII was added to each sample to digest overnight. The next morning, we added another 10μl DpnII and incubated for a final 2−3 hours. We removed 100µL of each digestion reaction, pooled them into two 1.5ml tube, and set them aside for digestion efficiency QC. We heat inactivated the remaining samples at 65°C for 20 minutes, before cooling on ice for 20 minutes. We ligated digested samples overnight at 16°C with T4 DNA ligase (HC ThermoFisher, 30U/μl) and 1X ligase buffer. The next day, we spiked an additional T4 DNA ligase into each sample and incubated another few hours. We then de-crosslinked the samples overnight at 65°C with Proteinase K (20mg/ml, Denville Scientific) along with pre-digestion and digestion controls. The following morning, we incubated the controls and ligated samples for 30 minutes. at 37°C with RNase A (Millipore) prior to phenol/chloroform extraction, ethanol precipitation at −20°C, and centrifugation at 4°C and 3000 rpm for 45 minutes to pellet the samples, while controls were pelleted at 14,000 rpm. Pellets were washed in 70% ethanol and centrifuged again as described above. We resuspended the 3C library and control pellets in dH2O and stored both at −20°C. We measured sample concentrations by Qubit and assessed digestion and ligation efficiencies by gel electrophoresis on a 0.9% agarose gel and by quantitative PCR (SYBR green, Thermo Fisher).
DNA from each 3C library (10ug) was sheared to an average fragment size of 350bp using a QSonica Q800R (60% amplitude, 30 seconds on / 30 seconds off, 2-minute intervals for 5 total intervals) at 4°C. After shearing, DNA was purified using AMPureXP beads (Agencourt), DNA size was confirmed on a Bioanalyzer 2100 (Agilent) and DNA concentration measured via Qubit. Libraries were prepared for selection using the SureSelect XT Library Kit (Agilent) following the manufacturer protocol and once again bead purified, then checked for size and concentration as described above. One microgram of adaptor-ligated library was hybridized using the SureSelect XT capture kit (Agilent) and our custom-designed 41K promoter Capture-C probe set. After amplification and purification, we assessed the quantity and quality of the captured libraries one final time. We paired-end sequenced all promoter-focused capture-C libraries on the Illumina NovaSeq 6000 platform with 51bp read length.


title: CUT&RUN against H3K27ac in 16 hpf zebrafish posterior trunk replicate 2

city: Geneva

first: Aurelie

last: Hintermann

address: 30 quai Ernest-Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

data_processing:
*library strategy: CUT&RUN
All scripts necessary to reproduce the analyses are available at https://github.com/AurelieHintermann/HintermannBoltEtAl2024.
Raw CUT&RUN paired-end reads were processed with CutAdapt version 4.1 (-a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 30 -m 15) to remove TruSeq adapters and bad quality bases.
Filtered reads were mapped on danRer11 where alternative contigs were removed with bowtie2 version 2.4.5 with the following parameters: --very-sensitive --no-unal --no-mixed --no-discordant --dovetail -X 1000.
Only alignments with mapping quality above 30 were kept (Samtools v1.16.1). PCR duplicates were removed by Picard version 3.0.0 (http://broadinstitute.github.io/picard/index.html).
BAM files were converted to BED with bedtools version 2.30.0. Peaks were called and coverage was generated by MACS2 version 2.2.7.1 with --nomodel --keep-dup all --shift -100 --extsize 200 --call-summits -B. Coverages were normalized to million mapped reads.
Assembly: danRer11
Supplementary files format and content: *narrowPeak.gz: peaks from MACS2
Supplementary files format and content: *bw: coverage from MACS2 normalized to million mapped reads

source_name: posterior trunk

extract_protocol:
Zebrafish samples were processed according to (10.1038/nprot.2018.015), using a final concentration of 0.02% digitonin (Apollo APOBID3301).
Library was constructed as described in (10.1038/nprot.2018.015)

value: posterior trunk

tag: Stage

tag: antibody

value: H3K27ac (Abcam, ab4729)

value: wild type


title: A549 cells, VILMIRg2, mock, rep3

tag: cell type

value: VILMIR knockdown

tag: treatment

value: mock


title: RNA Individual 5 skin fibroblast cells, Dexamethasone, Time8

tag: tissue

value: Skin

tag: time

value: Time 8


title: hFOB 1.19, differentiated 5 days at 39.5⁰C, rep2


title: A549 cells, VILMIRg2, mock, rep2


title: CUT&RUN against H3K27ac in 16 hpf zebrafish posterior trunk replicate 1


title: RNA Individual 5 skin fibroblast cells, Dexamethasone, Time4

value: Time 4


title: hFOB 1.19, differentiated 5 days at 39.5⁰C, rep1

value: Differentiated 5 days at 39.5 degrees C


title: A549 cells, VILMIRg2, mock, rep1


title: CUT&RUN against H3K27me3 in 16 hpf zebrafish posterior trunk replicate 1

value: H3K27me3 (Merck Millipore, 07–449)


title: RNA-seq_hFOB 1.19, differentiated 5 days at 39.5⁰C, rep3


title: pediatric hMSCs, undifferentiated, 17 year-old, male, donor 6

description:
IDR optimal narrow peaks called using the ENCODE pipeline and aligned to GRCh38 are stored in standard narrow peak format.
Control_Pediatric.idr.optimal_peak.narrowPeak.gz

data_processing:
ATAC-seq peaks were called for hFOBs, pediatric osteoblasts, osteoclasts, and chondrocytes using the ENCODE ATAC-seq pipeline and default settings.
Briefly, this pipeline input pair-end reads from the biological replicates for each cell type and aligned them to GRCh38 using bowtie, removing any duplicate reads from the alignment.
The pipeline then called narrow peaks independently for each replicate using macs2 and removed peaks in ENCODE blacklist regions (ENCFF001TDO).
Quality-control metrics were checked against the ENCODE recommended standards, and any data sets found not to meet standards, namely the 0, 8, and 12-day differentiated osteoclasts, were discarded from further analysis.
For the S-LDSC analysis, we used the irreproducible discovery rate (IDR) optimal peak sets. Where we reused the hFOB ATAC-seq results for target selection in our CRISPRi screen, we re-ran the ENCODE pipeline, aligning this time to hg19, and used the less stringent pooled peak sets.
Assembly: GRCh38
Supplementary files format and content: Standard narrow peak files in gzipped format were created using the irreproducible discover rate procedure in the ENCODE pipeline.

source_name: pediatric hMSCs

extract_protocol:
Fresh hFOBs, pediatric osteoblasts, and osteoclasts were harvested via Trypsin or TrypLE, followed by a series of DPBS washes steps. 50,000 cells from each sample were pelleted at 550 × g for 5 minutes at 4 °C. The cell pellet was then resuspended in 50 μl cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and centrifuged immediately at 550 × g for 10 minminutes at 4 °C. The nuclei were resuspended in transposition reaction mix (2x TD Buffer (Illumina Cat #FC-121–1030, Nextera), 2.5 µl Tn5 Transposase (Illumina, 20034197 Cat #FC-121–1030, Nextera) and Nuclease Free H2O) on ice and then incubated for 45 minminutes at 37°C. The transposed DNA was then purified using the MinElute Kit (Qiagen), eluted with 10.5 μl elution buffer (EB), frozen and sent to the Center for Spatial and Functional Genomics at CHOP. Chondrocytes were processed using a similar procedure which involved taking from each human donor (N=3), suspensions of 75,000 cells. These were centrifuged at 550 X g for 5 min at 4°C, resuspended in 50 µl of ice-cold PBS, and centrifuged once more at 550 X g for 5 minutes at 4 °C. The final cell pellets were resuspended in 50 µl of ice-cold lysis buffer (10 mM Tris-HCL, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 550 X g for 10 minutes at 4 °C. The supernatant was discarded, cells were placed on wet ice, and the TDE1 Tagment DNA Enzyme and Buffer Kit (Illumina, #20034197) was utilized according to the manufacturer's instructions. Briefly, chondrocytes were incubated in the TDE1 reaction buffer for 45 minutes at 37°C, followed by addition of 10 µl of 3 M sodium acetate to stop the reaction. Nucleic acid purification was performed using the Qiagen MinElute Kit (#28204) following the manufacturer's instructions.
The transposed DNA was PCR amplified and indexed using the Illumina Nextera Kit (Illumina) and NEBNext High-Fidelity 2x PCR Master Mix (NEB) for 12 cycles to generate each library. The PCR reaction was subsequently purified using AMPureXP beads (Agencourt).

value: pediatric hMSCs

value: Undifferentiated


title: RNA Individual 5 skin fibroblast cells, Dexamethasone, Time0

value: Fibroblast cells

value: Dexamethasone

value: Time 0


title: A549 cells, VILMIRg1, 10 ng/mL IFN, rep3

value: epithelial cell

value: 10 ng/mL IFN-B


title: ATAC-seq in fish 16 hpf posterior trunk replicate 3

data_processing:
All scripts necessary to reproduce the analyses are available at https://github.com/AurelieHintermann/HintermannBoltEtAl2024.
Raw ATAC-seq paired-end reads were processed with CutAdapt version 4.1 (-a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q 30 -m 15) to remove Nextera adapters and bad quality bases.
Filtered reads were mapped on mm39 for mouse samples and danRer11 where alternative contigs were removed for fish samples with bowtie2 version 2.4.5 with the following parameters: --very-sensitive --no-unal --no-mixed --no-discordant --dovetail -X 1000. Only pairs mapping concordantly outside of mitochondria were kept (Samtools v1.16.1)
PCR duplicates were removed by Picard version 3.0.0 (http://broadinstitute.github.io/picard/index.html). BAM files were converted to BED with bedtools version 2.30.0. Peaks were called and coverage was generated by MACS2 version 2.2.7.1 with --nomodel --keep-dup all --shift -100 --extsize 200 --call-summits -B. Coverages were normalized to million mapped reads.
Assembly: mm39
Assembly: danRer11
Supplementary files format and content: *narrowPeak.gz: peaks from MACS2
Supplementary files format and content: *bw: coverage from MACS2 normalized to million mapped reads

extract_protocol:
Mouse and fish tissues were isolated and placed into 1x PBS containing 10% FCS on ice. Collagenase (Sigma-Aldrich C9697) was added to 50ug/ml and incubated at 37º for 20 minutes with shaking at 900rpm.
Cells were washed 3x in 1x PBS. The number of cells was counted and viability confirmed to be greater than 90%. An input of 50000 cells was then processed according to previous description.

value: posterior trunk

tag: Sex

value: 16 hpf

tag: strain

value: AB, Tu, TL


title: RNA Individual 4 skin fibroblast cells, Dexamethasone, Time48

value: Time 48


title: pediatric hMSC-osteoblasts, differentiated 6 days, 17 year-old, male, donor 6

description:
IDR optimal narrow peaks called using the ENCODE pipeline and aligned to GRCh38 are stored in standard narrow peak format.
6Day_Pediatric.idr.optimal_peak.narrowPeak.gz

source_name: pediatric hMSCs differentiated to osteoblasts

value: Differentiated 6 days with BMP2 stimulation


title: ATAC-seq in fish 16 hpf posterior trunk replicate 2

value: wild type


title: A549 cells, VILMIRg1, 10 ng/mL IFN, rep2

value: VILMIR knockdown


title: pediatric hMSC-osteoblasts, differentiated 3 days, 17 year-old, male, donor 6

description:
IDR optimal narrow peaks called using the ENCODE pipeline and aligned to GRCh38 are stored in standard narrow peak format.
3Day_Pediatric.idr.optimal_peak.narrowPeak.gz

value: pediatric hMSCs differentiated to osteoblasts

value: Differentiated 3 days with BMP2 stimulation


title: A549 cells, VILMIRg1, 10 ng/mL IFN, rep1


title: pediatric hMSCs, undifferentiated, 16 year-old, male, donor 5


title: A549 cells, VILMIRg1, 1 ng/mL IFN, rep3

value: 1 ng/mL IFN-B


title: RNA Individual 4 skin fibroblast cells, Dexamethasone, Time40

value: Skin

value: Time 40


title: iWAT, TAN4_12AM

city: New York

first: Prashant

last: Rajbhandari

state: New York

address: 1468 Madison Ave, Annenberg 18-10

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Reads were aligned to the mouse genome (NCBI37/mm9) with TopHat v1.3.3 and allowed one alignment with up to two mismatches per read. mRNA RPKM values were calculated using Seqmonk’s mRNA quantitation pipeline. A gene was included in the analysis if it met all the following criteria: the maximum RPKM reached four at any time point, the gene length was >200 bp
Differential expression analysis. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Enrichment analysis of differentially expressed genes. The Reactome database brings together the various reactions and biological pathways of human model species. Reactome pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. We used clusterProfiler software to test the statistical enrichment of differentially expressed genes in the Reactome pathway.
Circadian analysis and clustering. The differential gene expression analyses were conducted with R packages Limma and EdgeR. Count data from the RNA sequencing pipeline were used. Gene expressed less than 10 counts were excluded. This resulted in a total of 5,733 genes from differential analyses. Differential analyses were based on limma linear regression by contrasting treatment (TAN) and control (ad-lib) groups at the same time point, i.e., TAN 8 AM vs AL 8 AM, and for each comparison, differentially expressed genes as defined by adjusted test P-values. For circadian analyses, dryR package (https://github.com/naef-lab/dryR) was used. Pathway enrichment and gene expression analysis were performed using Express Analyst (https://github.com/xia-lab/ExpressAnalystR.git) and shinyGO (https://github.com/gexijin/shinygo.git) R packages.  Protein-protein functional enrichment and networks are generated using Network enrichment (https://github.com/xia-lab/NetworkAnalystR.git) package using STRING database; Confidence cutoff > 900. Gene count, correlation matrix, and enrichment table source data are documented as supplementary tables 1-4.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Gene count and FPKM

source_name: iWAT

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen). The aqueous phase containing the RNA was loaded onto a gDNA Eliminator Spin Column (Qiagen, USA) for elimination of genomic DNA, and RNA was isolated using the RNeasy Plus kit (Qiagen) according to manufacturer’s instructions. Total RNA (500 to 1000 ug) was reverse transcribed into cDNA using the M-MLV reverse transcriptase (Invitrogen),
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: iWAT

tag: age

value: 8 months  old

value: TAN


title: pediatric hMSC-osteoblasts, differentiated 6 days, 16 year-old, male, donor 5


title: RNA Individual 4 skin fibroblast cells, Dexamethasone, Time36

value: Fibroblast cells

value: Dexamethasone

value: Time 36


title: iWAT, TAN4_12PM


title: A549 cells, STAT1g1, 10 ng/mL IFN, rep2

value: epithelial cell

value: STAT1 knockdown

value: 10 ng/mL IFN-B


title: pediatric hMSC-osteoblasts, differentiated 3 days, 16 year-old, male, donor 5


title: RNA Individual 4 skin fibroblast cells, Dexamethasone, Time32

value: Time 32


title: RNA Individual 4 skin fibroblast cells, Dexamethasone, Time28

value: Time 28


title: iWAT, TAN4_8AM


title: RNA Individual 4 skin fibroblast cells, Dexamethasone, Time44

value: Time 44


title: A549 cells, STAT1g1, 1 ng/mL IFN, rep2


title: Mutant Cerebellum E16.5_205659810062_R06C01

type: genomic

city: Hamburg

first: Ulrich

last: Schüller

address: Martinistraße 52

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Bisulfite conversion was performed with the EZ DNA Methylation kit (Zymo Research, CA, USA) before amplification, fragmentation, and hybridization to the Illumina Infinium Mouse Methylation BeadChip using standard Illumina protocol.

scan_protocol: Illumina iScan microarray scanner

data_processing: SeSAMe

label: Cy3, Cy5

source_name: cerebellum, FFPE punch

label_protocol: Standard Illumina Protocol

extract_protocol: DNA isolation from FFPE tissue was performed using the Maxwell RSC DNA FFPE kit (Promega Corporation, WI, USA).

value: brain


title: Mutant Cerebellum E16.5_205659810062_R01C02


title: Control Cerebellum E16.5_205659810062_R05C01

value: cre-negative


title: iWAT, TAN4_8PM


title: Mutant Cerebellum E16.5_205659810062_R02C01


title: A549 cells, STAT1g1, mock, rep2

value: mock


title: RNA Individual 4 skin fibroblast cells, Dexamethasone, Time24

value: Skin

value: Time 24


title: pediatric hMSCs, undifferentiated, 16 year-old, female, donor 4

value: pediatric hMSCs

value: Undifferentiated


title: Control Cerebellum E16.5_205659810062_R01C01


title: Control Cerebellum E16.5_205659810062_R03C01


title: pediatric hMSC-osteoblasts, differentiated 6 days, 16 year-old, female, donor 4

value: pediatric hMSCs differentiated to osteoblasts

value: Differentiated 6 days with BMP2 stimulation


title: A549 cells, VILMIRg1, 1 ng/mL IFN, rep1

value: VILMIR knockdown

value: 1 ng/mL IFN-B


title: iWAT, TAN4_4PM

value: iWAT

value: 8 months  old

value: TAN


title: iWAT, TAN4_4AM


title: pediatric hMSCs, undifferentiated, 18 year-old, female, donor 3


title: pediatric hMSC-osteoblasts, differentiated 3 days, 16 year-old, female, donor 4

value: Differentiated 3 days with BMP2 stimulation


title: iWAT, TAN3_12AM


title: RNA Individual 4 skin fibroblast cells, Dexamethasone, Time20

value: Fibroblast cells

value: Dexamethasone

value: Time 20


title: A549 cells, VILMIRg1, mock, rep1

value: epithelial cell


title: RNA Individual 4 skin fibroblast cells, Dexamethasone, Time16

value: Time 16


title: A549 cells, STAT1g1, 10 ng/mL IFN, rep1

value: STAT1 knockdown

value: 10 ng/mL IFN-B


title: RNA Individual 4 skin fibroblast cells, Dexamethasone, Time12

value: Skin

value: Time 12


title: A549 cells, STAT1g1, 1 ng/mL IFN, rep1


title: iWAT, TAN3_8PM


title: pediatric hMSC-osteoblasts, differentiated 3 days, 18 year-old, female, donor 3

value: pediatric hMSCs differentiated to osteoblasts


title: RNA Individual 4 skin fibroblast cells, Dexamethasone, Time8

value: Time 8


title: pediatric hMSC-osteoblasts, differentiated 6 days, 18 year-old, female, donor 3

value: Differentiated 6 days with BMP2 stimulation


title: pediatric hMSCs, undifferentiated, 18 year-old, male, donor 2

value: pediatric hMSCs

value: Undifferentiated


title: A549 cells, STAT1g1, mock, rep1

value: mock


title: iWAT, TAN3_8AM

value: iWAT

value: 8 months  old

value: TAN


title: A549 cells, Ctrl, 10 ng/mL IFN, rep2

value: GFP knockdown


title: iWAT, TAN3_4PM


title: pediatric hMSC-osteoblasts, differentiated 6 days, 18 year-old, male, donor 2


title: iWAT, TAN3_12PM


title: A549 cells, Ctrl, 1 ng/mL IFN, rep2

value: 1 ng/mL IFN-B


title: RNA Individual 3 skin fibroblast cells, Dexamethasone, Time48

value: Fibroblast cells

value: Dexamethasone

value: Time 48


title: iWAT, TAN3_4AM


title: pediatric hMSC-osteoblasts, differentiated 3 days, 18 year-old, male, donor 2

value: Differentiated 3 days with BMP2 stimulation


title: A549 cells, Ctrl, 10 ng/mL IFN, rep1

value: epithelial cell

value: 10 ng/mL IFN-B


title: RNA Individual 3 skin fibroblast cells, Dexamethasone, Time44

value: Skin

value: Time 44


title: iWAT, TAN2_12PM


title: pediatric hMSCs, undifferentiated, 15 year-old, female, donor 1


title: iWAT, TAN2_12AM


title: pediatric hMSC-osteoblasts, differentiated 6 days, 15 year-old, female, donor 1

value: pediatric hMSCs differentiated to osteoblasts

value: Differentiated 6 days with BMP2 stimulation


title: RNA Individual 3 skin fibroblast cells, Dexamethasone, Time40

value: Time 40


title: RNA Individual 3 skin fibroblast cells, Dexamethasone, Time36

value: Time 36


title: A549 cells, Ctrl, 1 ng/mL IFN, rep1


title: A549 cells, VILMIRg1, mock, rep2

value: VILMIR knockdown

value: mock


title: pediatric hMSC-osteoblasts, differentiated 3 days, 15 year-old, female, donor 1


title: iWAT, TAN2_8PM

value: iWAT

value: 8 months  old

value: TAN


title: RNA Individual 4 skin fibroblast cells, Dexamethasone, Time4

value: Fibroblast cells

value: Time 4


title: iWAT, TAN2_8AM


title: iWAT, TAN2_4PM


title: RNA Individual 3 skin fibroblast cells, Dexamethasone, Time32

value: Dexamethasone

value: Time 32


title: hFOB 1.19, undifferentiated, rep 3

description:
IDR optimal narrow peaks called using the ENCODE pipeline and aligned to GRCh38 are stored in standard narrow peak format.
hFOB_Perm.idr.optimal_peak.narrowPeak.gz

source_name: human fetal osteoblast 1.19 cells (hFOBs)

value: Undifferentiated by growing at 33.5C


title: RNA Individual 4 skin fibroblast cells, Dexamethasone, Time0

value: Time 0


title: U2OS DIvA exp12 Dam-RAD51 ChIC BRCA1 (KIN4665.index44)

city: Utrecht

first: Kim

last: de Luca

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Libraries were demultiplexed based on the sample-specific barcode present in R1, using custom pipelines (available at: https://github.com/KindLab/scDamAndTools).
Demultiplexed reads were aligned using hisat2 (v2.1.0). For samples containing DamID readout: each read was prefixed with a "GA" dimer to improve alignment rates (since DamID molecules originate from GA/TC cleavage). For samples containing ChIC readout: from non-aligned reads, the GA prefix was removed, and reads were realigned and considered as ChIC molecules.
Genomic reads were then counted per genomic position (considering UMIs), and counts were aggregated at the desired resolution (1-kb or 100-kb bins).
Regions of significant enrichment and depletion were identified at 1-kb resolution, using an adapted version of multi-scale representation of genomic signals (MSR), as described in (PMID: 24727652).
Assembly: hg19
Supplementary files format and content: Single-cell counts: count tables per library and genomic readout (DamID or ChIC), containing UMI-unique counts per 100-kb interval, for all single-cell samples.
Supplementary files format and content: MSR: per genomic readout (DamID or ChIC), all segments across all single cells, called at 1-kb resolution.

growth_protocol: Cell lines were grown in DMEM containing high glucose, GlutaMAX supplement, and sodium pyruvate (Gibco) supplemented with 10% fetal bovine serum (FBS; Sigma-Aldrich) and 1X Penicillin Streptomycin (Gibco), at 37 °C with 5% CO2. For maintenance, cells were split 1/10 every 3 days and routinely tested for Mycoplasma.

extract_protocol:
For ChIC experiments, cells were treated as described for DamID, after which nuclei were isolated and permeabilized, incubated with primary antibody, then incubated with pA-MNase (Protein A IgG-binding domain fused to micrococcal nuclease, for antibody-specific binding) and Hoechst (for DNA content staining). If the primary antibody was raised in mouse, nuclei were incubated with secondary antibody (rabbit anti-mouse) before incubation with pA-MNase. Nuclei were filtered through a 20-µm mesh before FACS.
DamID on single cells was performed as previously described in detail (PMID: 32350457). Briefly, after FACS, cells were lysed and treated with proteinase K, after which methylated GATCs resulting from Dam enzyme activity were specifically digested with DpnI. Double-stranded adapters containing cell-specific barcodes and a T7 promoter were ligated to the blunt (DpnI-cleaved) DNA ends. Cells with non-overlapping barcodes were pooled together to undergo in vitro transcription (IVT), amplifying the genomic DamID-specific product in a linear manner. Library preparation was then performed on the amplified RNA, to generate molecules compatible with Illumina sequencing. ChIC was performed as previously described in detail (PMID: 36539617). After FACS, proximity-based cleaving by pA-MNase was activated (for exactly 30 min on ice), followed by inactivation and proteinase K treatment. MNase-cleaved ends were then blunted and phosphorylated, and double-stranded adapters were ligated. For one experiment, A-tailing was performed after end repair of MNase-cleaved ends, followed by ligation of T-tailed adapters. DNA molecules were then further processed for sequencing as in scDamID2. Combinatorial profiling of DamID and ChIC was performed with the same procedures of nuclei isolation, antibody treatment, FACS, and molecular preparation as for scChIC. After end repair of MNase-cleaved ends, the scDamID procedure was followed, namely DpnI digestion to enrich for Dam-methylated GATCs, adapter ligation, and subsequent library preparation steps.

treatment_protocol: For experimental procedures, cells were plated the day prior, to achieve 60-70% confluency during induction treatment. Dam-POIs were stabilized by addition of 500 nM Shield1 ligand (AOBIOUS, dissolved in DMSO to 500 mM) for 4 h for Dam-53BP1, and 8 h for Dam-RAD51. Nuclear translocation of AsiSI-ER was simultaneously induced by addition of 300 nM 4-hydroxytamoxifen (4OHT; Sigma, dissolved in ethanol to 13 mM). Cells were harvested by washing twice with PBS0 followed by trypsinization with 1X TrypLE (Gibco), inactivation with DMEM, pipetting to yield a single-cell suspension, and centrifugation at 300 g. For DamID FACS, cell pellets were resuspended in growth medium containing 10 µg/mL Hoechst 34580 per 1x106 cells and incubated for 45-60 minutes at 37 °C, for live DNA content staining. Prior to sorting, cell suspension was passed through a 20-µm mesh.

value: Human bone osteosarcoma epithelium

value: scDam&ChIC


title: RNA Individual 3 skin fibroblast cells, Dexamethasone, Time28

value: Skin

value: Time 28


title: hFOB 1.19, undifferentiated, rep 2

value: human fetal osteoblast 1.19 cells (hFOBs)


title: RNA Individual 3 skin fibroblast cells, Dexamethasone, Time24

value: Time 24


title: RNA Individual 3 skin fibroblast cells, Dexamethasone, Time20

value: Time 20


title: iWAT, TAN1_12PM


title: iWAT, TAN2_4AM


title: U2OS DIvA exp09 Dam-RAD51 ChIC MDC1 (KIN4665.index42)


title: hFOB 1.19, differentiated 5 days at 39.5⁰C, rep 4

description:
IDR optimal narrow peaks called using the ENCODE pipeline and aligned to GRCh38 are stored in standard narrow peak format. Pooled peaks called using the ENCODE pipeline and aligned to hg19 are also available in standard narrow peak format.
hFOB_Diff.idr.optimal_peak.narrowPeak.gz
hFOB_Diff.pooled_peak.hg19.narrowPeak.gz

value: Differentiated 5 days at 39.5⁰C


title: iWAT, TAN1_12AM

value: iWAT


title: A549 cells, Ctrl, mock, rep1

value: epithelial cell

value: GFP knockdown

value: mock


title: RNA Individual 3 skin fibroblast cells, Dexamethasone, Time16

value: Fibroblast cells

value: Time 16


title: U2OS DIvA exp11 Dam-53BP1 / Dam-RAD51 ChIC yH2AX (KIN4665.index40)


title: U2OS DIvA exp11 Dam-53BP1 / Dam-RAD51 ChIC XRCC4 (KIN4665.index39)


title: hFOB 1.19, differentiated 5 days at 39.5⁰C, rep 2


title: hFOB 1.19, undifferentiated, rep 1


title: iWAT, TAN1_8AM

value: 8 months  old

value: TAN


title: iWAT, TAN1_8PM


title: hFOB 1.19, differentiated 5 days at 39.5⁰C, rep 1


title: U2OS DIvA exp09 Dam-RAD51 ChIC MDC1 (KIN4665.index45)


title: iWAT, TAN1_4PM


title: U2OS DIvA exp08 Dam-53BP1 ChIC 53BP1 (KIN4665.index04)


title: RNA Individual 3 skin fibroblast cells, Dexamethasone, Time4

value: Dexamethasone

value: Time 4


title: U2OS DIvA exp12 Dam-53BP1 ChIC BRCA1 (KIN4665.index43)

value: Human bone osteosarcoma epithelium

value: scDam&ChIC


title: U2OS DIvA expT1 Dam-RAD51 (KIN4612.index07)

value: scDam&T


title: RNA Individual 3 skin fibroblast cells, Dexamethasone, Time0

value: Skin

value: Time 0


title: In-vitro differentiated osteoclasts, differentiated for 4 days with RANKL, donor 2

description:
IDR optimal narrow peaks called using the ENCODE pipeline and aligned to GRCh38 are stored in standard narrow peak format.
Osteoclasts.idr.optimal_peak.narrowPeak.gz

source_name: In-vitro differentiated osteoclasts

value: In-vitro differentiated osteoclasts

value: Differentiated for 4 days with media containing 33ng/ml M-CSF, 66ng/ml human RANKL and 1ng/ml TGF-beta1


title: RNA Individual 2 skin fibroblast cells, Dexamethasone, Time48

value: Time 48


title: hFOB 1.19, differentiated 5 days at 39.5⁰C, rep 3

value: human fetal osteoblast 1.19 cells (hFOBs)

value: Differentiated 5 days at 39.5⁰C


title: chondrocytes, extracted from knee articular cartilage, donor 3

description:
IDR optimal narrow peaks called using the ENCODE pipeline and aligned to GRCh38 are stored in standard narrow peak format.
Chondrocytes.idr.optimal_peak.narrowPeak.gz

source_name: Primary chondrocytes extracted from knee articular cartilage


title: RNA Individual 2 skin fibroblast cells, Dexamethasone, Time44

value: Time 44


title: U2OS DIvA exp09 Dam-53BP1 ChIC MDC1 (KIN4337.index18)


title: RNA Individual 3 skin fibroblast cells, Dexamethasone, Time12

value: Fibroblast cells

value: Time 12


title: RNA Individual 3 skin fibroblast cells, Dexamethasone, Time8

value: Time 8


title: iWAT, AL4_8PM

value: iWAT

value: 8 months  old

value: Ad-Lib


title: RNA Individual 2 skin fibroblast cells, Dexamethasone, Time40

value: Dexamethasone

value: Time 40


title: In-vitro differentiated osteoclasts, differentiated for 4 days with RANKL, donor 3


title: iWAT, AL4_8AM


title: chondrocytes, extracted from knee articular cartilage, donor 2

value: Primary chondrocytes extracted from knee articular cartilage


title: U2OS DIvA exp08 Dam-53BP1 ChIC 53BP1 (KIN4337.index16)

value: Human bone osteosarcoma epithelium

value: scDam&ChIC


title: chondrocytes, extracted from knee articular cartilage, donor 1


title: RNA Individual 2 skin fibroblast cells, Dexamethasone, Time36

value: Skin

value: Time 36


title: RNA Individual 2 skin fibroblast cells, Dexamethasone, Time32

value: Time 32


title: U2OS DIvA exp09 Dam-RAD51 ChIC MDC1 (KIN4337.index15)


title: iWAT, TAN1_4AM

value: TAN


title: iWAT, AL4_4PM


title: iWAT, AL4_4AM


title: RNA Individual 2 skin fibroblast cells, Dexamethasone, Time28

value: Time 28


title: iWAT, AL4_12AM


title: P18,tumor,replicate3,scRNA-seq

city: Beijing

first: Ying

last: Xu

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

country: China

institute: Peking University

library_source: transcriptomic single cell

data_processing:
The raw sequencing data was processed by DNBelab_C_Series_HT_scRNA-analysis-software to obtain gene expression profiles used for downstream analysis.
We filtered out cells expressing less than 500 genes, and cells with more than 30% transcripts mapped to mitochondrial genes.
Doublets were predicted with the package Scrublet, and then removed from the data.
Assembly: hg38
Supplementary files format and content: tab-separated values files and matrix files

source_name: colorectal cancer

extract_protocol:
To isolate single cells, patient-derived organoids or CRC tissues were incubated with TrypLE Express at 37°C for 20-30 min. The cells were then filtered through a 20 μm cell strainer, after which live cells were counted using a hemocytometer.
According to the manufacture ’ s introduction, Single-cell RNA-seq libraries wereconstructed using Single Cell 3 ’ Library andGel Bead Kit V3.1

value: colorectal cancer

tag: group

value: tumor


title: P18,tumor,replicate4,scRNA-seq


title: iWAT, AL3_12PM


title: P18,tumor,replicate2,scRNA-seq


title: RNA Individual 2 skin fibroblast cells, Dexamethasone, Time24

value: Fibroblast cells

value: Time 24


title: U2OS DIvA expT1 Dam-RAD51 (KIN4223.index25)

value: scDam&T


title: iWAT, AL3_12AM

value: iWAT

value: 8 months  old


title: RNA Individual 2 skin fibroblast cells, Dexamethasone, Time20

value: Dexamethasone

value: Time 20


title: U2OS DIvA exp07 Dam-RAD51 ChIC BRCA1 (KIN4213.index28)


title: U2OS DIvA expT1 Dam-53BP1 (KIN4223.index22)


title: U2OS DIvA exp11 Dam-53BP1 (KIN4665.index37)

value: scDamID


title: iWAT, AL3_8PM

value: Ad-Lib


title: RNA Individual 2 skin fibroblast cells, Dexamethasone, Time16

value: Time 16


title: P18,tumor,replicate1,scRNA-seq


title: P18,current PDO,replicate4,scRNA-seq

source_name: colorectal cancer PDO

value: colorectal cancer PDO

value: current PDO


title: U2OS DIvA exp08 Dam-53BP1 ChIC 53BP1 (KIN4213.index20)

value: Human bone osteosarcoma epithelium

value: scDam&ChIC


title: iWAT, AL3_8AM


title: P18,current PDO,replicate3,scRNA-seq


title: RNA Individual 2 skin fibroblast cells, Dexamethasone, Time12

value: Skin

value: Time 12


title: iWAT, AL4_12PM


title: U2OS DIvA expT1 Dam-53BP1 (KIN4612.index06)


title: U2OS DIvA exp08 Dam-RAD51 ChIC 53BP1 (KIN4337.index29)


title: RNA Individual 2 skin fibroblast cells, Dexamethasone, Time8

value: Time 8


title: iWAT, AL3_4PM


title: U2OS DIvA exp04 Dam-RAD51 ChIC H3K36me3 (KIN4149.index03)


title: P18,current PDO,replicate2,scRNA-seq


title: In-vitro differentiated osteoclasts, differentiated for 4 days with RANKL, donor 1

value: In-vitro differentiated osteoclasts

value: Differentiated for 4 days with media containing 33ng/ml M-CSF, 66ng/ml human RANKL and 1ng/ml TGF-beta1


title: U2OS DIvA exp07 Dam-53BP1 ChIC BRCA1 (KIN4117.index12)


title: iWAT, AL3_4AM


title: RNA Individual 2 skin fibroblast cells, Dexamethasone, Time4

value: Fibroblast cells

value: Time 4


title: P18,current PDO,replicate1,scRNA-seq


title: U2OS DIvA exp08 Dam-RAD51 ChIC 53BP1 (KIN4213.index27)


title: iWAT, AL2_12PM

value: iWAT

value: 8 months  old


title: RNA Individual 2 skin fibroblast cells, Dexamethasone, Time0

value: Dexamethasone

value: Time 0


title: U2OS DIvA exp07 Dam-RAD51 ChIC BRCA1 (KIN4117.index11)


title: P12,CiPDO,replicate1,RNA-seq

data_processing:
Trimmed sequencing reads were mapped to hg38 using STAR.
Read counts were extracted with htseq-count.
Assembly: hg38
Supplementary files format and content: tab-separated text files including raw counts for each sample
Supplementary files format and content: csv file including raw counts for each sample

source_name: epithelial cells

value: epithelial cells

value: CiPDO


title: U2OS DIvA expT1 Dam-RAD51 (KIN3801.index04)

value: scDam&T


title: iWAT, AL2_12AM

value: Ad-Lib


title: RNA Individual 1 skin fibroblast cells, Dexamethasone, Time48

value: Time 48


title: P13,CiPDO,replicate1,RNA-seq


title: U2OS DIvA expT1 Dam-RAD51 (KIN3801.index03)

value: Human bone osteosarcoma epithelium


title: RNA Individual 1 skin fibroblast cells, Dexamethasone, Time44

value: Skin

value: Time 44


title: iWAT, AL2_8PM


title: iWAT, AL2_8AM


title: U2OS DIvA expT1 Dam-53BP1 (KIN3801.index02)


title: RNA Individual 1 skin fibroblast cells, Dexamethasone, Time40

value: Time 40


title: P3,CiPDO,replicate3,RNA-seq


title: U2OS DIvA expT1 Dam-53BP1 (KIN3801.index01)


title: RNA Individual 1 skin fibroblast cells, Dexamethasone, Time36

value: Time 36


title: iWAT, AL2_4AM


title: P7,CiPDO,replicate3,RNA-seq


title: RNA Individual 1 skin fibroblast cells, Dexamethasone, Time32

value: Time 32


title: RNA Individual 1 skin fibroblast cells, Dexamethasone, Time28

value: Fibroblast cells

value: Time 28


title: P1,CiPDO,replicate3,RNA-seq


title: U2OS DIvA exp10 Dam-53BP1 (KIN3633.index43)

value: scDamID


title: U2OS DIvA exp10 Dam-53BP1 / Dam-RAD51 (KIN3633.index44)


title: P15,CiPDO,replicate3,RNA-seq


title: U2OS DIvA exp10 Dam-RAD51 (KIN3633.index42)


title: RNA Individual 1 skin fibroblast cells, Dexamethasone, Time24

value: Time 24


title: P14,CiPDO,replicate3,RNA-seq


title: iWAT, AL1_8PM

value: iWAT

value: 8 months  old


title: U2OS DIvA exp04 Dam-RAD51 ChIC H3K9me3 / H3K36me3 (KIN3633.index34)

value: scDam&ChIC

value: H3K9me3, H3K36me3


title: P3,CiPDO,replicate2,RNA-seq

value: epithelial cells

value: CiPDO


title: U2OS DIvA exp04 ChIC H3K9me3 / H3K36me3 (KIN3633.index33)

value: scChIC


title: RNA Individual 1 skin fibroblast cells, Dexamethasone, Time20

value: Dexamethasone

value: Time 20


title: RNA Individual 1 skin fibroblast cells, Dexamethasone, Time16

value: Skin

value: Time 16


title: P10,CiPDO,replicate1,RNA-seq


title: iWAT, AL1_8AM

value: Ad-Lib


title: iWAT, AL2_4PM


title: iWAT, AL1_4AM


title: U2OS DIvA exp03 Dam-RAD51 ChIC 53BP1 (KIN3633.index32)

value: Human bone osteosarcoma epithelium


title: P1,CiPDO,replicate2,RNA-seq


title: iWAT, AL1_12PM


title: U2OS DIvA exp03 ChIC 53BP1 (KIN3633.index31)


title: P15,CiPDO,replicate2,RNA-seq


title: RNA Individual 1 skin fibroblast cells, Dexamethasone, Time4

value: Fibroblast cells

value: Time 4


title: 14IMMHCII rep 5

city: London

first: Derek

middle: W

last: Gilroy

address: 5 University Street

country: United Kingdom

institute: UCL

data_processing:
Quality control of the FASTQ.files was performed on FASTQC Version 0.11.9
alignment program HISAT2 version 2.1.0
SAMTOOL version 1.9 was then used to convert BAM files to sorted SAM files
Through subread version 2.01, featureCounts was used to map the read locations to the genomic regions using the GRCm38 construct
Assembly: GRCm38
Supplementary files format and content: .txt file containing counts

source_name: interstitial macrophages

extract_protocol:
Phenol-chloroform extraction
NEBNext Low Input mRNA kit

value: interstitial macrophages

value: 14 post S. pneumonia


title: U2OS DIvA exp08 Dam-RAD51 (KIN3445.index46)

value: scDamID


title: RNA Individual 1 skin fibroblast cells, Dexamethasone, Time8

value: Time 8


title: P14,CiPDO,replicate2,RNA-seq


title: U2OS DIvA exp08 Dam-RAD51 (KIN3445.index45)


title: P3,CiPDO,replicate1,RNA-seq


title: U2OS DIvA exp01 ChIC 53BP1 (KIN3383.index04)


title: RNA Individual 1 skin fibroblast cells, Dexamethasone, Time0

value: Time 0


title: 14IMDN rep 5


title: iWAT, AL1_12AM

value: iWAT

value: 8 months  old


title: 14AM rep 5


title: P7,CiPDO,replicate1,RNA-seq

value: epithelial cells

value: CiPDO


title: P1,CiPDO,replicate1,RNA-seq


title: P7,CiPDO,replicate2,RNA-seq


title: U2OS DIvA exp01 ChIC 53BP1 (KIN3383.index03)

value: scChIC


title: NIMDN rep 5

value: Naïve


title: RNA Individual 1 skin fibroblast cells, Dexamethasone, Time12

value: Skin

value: Dexamethasone

value: Time 12


title: ATAC Individual 6 skin fibroblast cells, Dexamethasone, Time44

data_processing:
Fastqc software was used to assess the quality of the raw files. Low quality reads were trimmed using TrimGalore and Cutadapt.
Alignment of the raw reads data to human gene Ensembl version GRCh38 was performed using bowtie2 with a 2kb insert size and allowing up to 4 alignments. Reads within black-listed regions alongside PCR duplicates were removed with samtools.
MACS2 software was used to identify open chromatin regions, with parameters -g hs -q 0.01 –nomodel –shift -100 –extsize 200 –keep-dup all -B. PCR.
To compare the ATAC-seq signal across timepoints and subjects, we created a consensus bed file using the bedtools function merge function, combining all the overlapping peak regions across timepoints and subjects into a single bed file.
Featurecounts software was then used to assign read counts to those regions
Assembly: GrCh38
Supplementary files format and content: narrowPeak file

extract_protocol:
For the collection of cells for the ATAC protocol, cells were dissociated using 500uL of prewarmed TrypLE (ThermoFisher 12604013) and left for 5 min at 37°C. TrypLE was inactivated using 500uL of DMEM. Cells were then counted using the Logos Biosystems LUNA-FL automated cell counter, and 50x10^4 cells were used as input for tagmentation.
ATAC seq libraries were generated following the previously described protocol (Buenrostro et al. 2015) and sequenced with 75-base double end reads, and sequenced at a targeted depth of 61M reads per sample.

treatment_protocol: 5 days after being plated the cells were treated  with 100 nM Dexamethasone for 30 min. Cells were then washed with PBS and switched to collection media (DMEM containing 5% FBS and 1x Penicillin-Streptomycin)

value: Time 44


title: U2OS DIvA exp02 ChIC 53BP1 (KIN3383.index02)

value: Human bone osteosarcoma epithelium


title: ATAC Individual 6 skin fibroblast cells, Dexamethasone, Time48

value: Fibroblast cells

value: Time 48


title: ATAC Individual 6 skin fibroblast cells, Dexamethasone, Time40

value: Time 40


title: U2OS DIvA exp02 ChIC 53BP1 (KIN3383.index01)


title: ATAC Individual 6 skin fibroblast cells, Dexamethasone, Time36

value: Time 36


title: 14IMMHCII rep 4

value: interstitial macrophages

value: 14 post S. pneumonia


title: P14,CiPDO,replicate1,RNA-seq


title: U2OS DIvA exp02 Dam-RAD51 (KIN1555.index08)

value: scDamID


title: NIMLYVE rep 4


title: U2OS DIvA exp02 Dam-RAD51 (KIN1555.index07)


title: ATAC Individual 6 skin fibroblast cells, Dexamethasone, Time32

value: Time 32


title: 14IMLYVE rep 5


title: U2OS DIvA exp02 Dam-RAD51 (KIN1555.index06)


title: NIMLYVE rep 5


title: ATAC Individual 6 skin fibroblast cells, Dexamethasone, Time24

value: Time 24


title: NIMDN rep 4


title: 14IMLYVE rep 4


title: ATAC Individual 6 skin fibroblast cells, Dexamethasone, Time20

value: Time 20


city: Stanford

first: Ravindra

last: Majeti

address: 875 Blake Wilbur Dr Clinic F

institute: Stanford University

description:
Sample SU484 diagnosis single cell ATAC library
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

library_source: genomic single cell

data_processing:
ATAC-sea data was processed based on workflows similar to Corces et al. Science 201826. First, read trimming and quality control was performed using trim_galore using default parameters. Reads were aligned to the GRCh38 reference genome using bowtie2 and the --very-sensitive option. Aligned reads were converted to bam format and sorted using SAMtools, and deduplicated using Picard MarkDuplicates. Reads were subsequently indexed and mitochondrial reads were removed using SAMTools. TagAlign bed files from technical replicate libraries were generated using bedtools, shifted to find ATAC-seq cut sites, and pooled. Peaks were called using MACS2 using p-value cut-off of 0.01 and peaks falling within black list regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were removed. A consensus peak set was generated using methods from Corces et al. Science 201828. Briefly, called peaks were merged by merging all peak bed files and using an iterative removal process to resolve overlapping peaks. This approach resulted in a consensus set of 115,551 500bp fixed-width peaks covering accessible regions represented in at least 2 or more samples. Count matrices were generated using the consensus peak set, and the number of Tn5 cut sites in each peak were calculated using the CountOverlaps function from the GenomicRanges package in R.
Assembly: Processed data files aligned to hg38 reference genome.
Supplementary files format and content: R data file containing peak counts or gene accessibility scores for each sample.

source_name: AML

extract_protocol:
Sorted AML blasts were prepared for ATAC-seq as previously described54. 5,000-50,000 cells were washed in cold FACS buffer and spun at 4°C for 5 minutes at 500 rcf in a fix-angled centrifuge. Cell pellets were then resuspended in 50 uL of ATAC-seq resuspension buffer (RSB: 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water) with 0.1% NP40, 0.01% digitonin, and 0.1% Tween-20 and incubated on ice for three minutes. After lysis, 1 mL of ATAC-seq RSB with 0.1% Tween-20 was added and tubes were inverted six times to mix. Isolated nuclei were then spun at 4°C for 10 minutes at 500 rcf in a fix-angled centrifuge. Supernatant was removed and nuclei were resuspended in 50 uL transposition mix (25uL 2xTD buffer, 2.5 uL Tn5 transposase (100 nM final), 16.5 uL PBS, 0.5 uL 1% digitonin, 0.5 uL 10% Tween-20, and 5 uL nuclease-free water).
Transposition reactions were incubated at 37°C for 30 minutes in a thermomixer with shaking at 1000 rpm. Reactions were cleaned up using Qiagen MinElute Reaction Cleanup kits and processed as previously described. All libraries were amplified with a target concentration of 20 μl at 4 nM, which is equivalent to 80 femtomoles of product.
All libraries were sequenced on an Illumina NextSeq with 75 bp paired end reads.

value: AML

tag: individual

value: Sample SU484

tag: timepoint

value: Diagnosis

value: Bulk


title: U2OS DIvA exp02 Dam-RAD51 (KIN1555.index04)


description:
Sample SU484C relapse single cell ATAC library
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Sample SU484C

value: Relapse


description:
Sample SU360B relapse single cell ATAC library
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Sample SU360B


title: ATAC Individual 6 skin fibroblast cells, Dexamethasone, Time16

value: Skin

value: Fibroblast cells

value: Dexamethasone

value: Time 16


title: U2OS DIvA exp02 Dam-RAD51 (KIN1555.index05)

value: Human bone osteosarcoma epithelium


title: U2OS DIvA exp02 Dam-RAD51 (KIN1555.index03)


title: P15,CiPDO,replicate1,RNA-seq

value: epithelial cells

value: CiPDO


title: NIMMHCII rep 4

value: interstitial macrophages

value: Naïve


title: NIMMHCII rep 5


title: ATAC Individual 6 skin fibroblast cells, Dexamethasone, Time12

value: Time 12


description:
Sample SU360 diagnosis single cell ATAC library
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Sample SU360


title: 14IMMHCII rep 3

value: 14 post S. pneumonia


title: ATAC Individual 6 skin fibroblast cells, Dexamethasone, Time8

value: Time 8


title: U2OS DIvA exp02 Dam-RAD51 (KIN1555.index02)

value: scDamID


description:
Sample SU892 diagnosis single cell ATAC library
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Sample SU892

value: Diagnosis

value: Bulk


description:
Sample SU142 diagnosis single cell ATAC library
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Sample SU142


title: U2OS DIvA exp02 Dam-RAD51 (KIN1555.index01)


title: ATAC Individual 6 skin fibroblast cells, Dexamethasone, Time28

value: Skin

value: Fibroblast cells

value: Dexamethasone

value: Time 28


description:
Sample SU892B relapse single cell ATAC library
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Sample SU892B

value: Relapse


title: 14IMMHCII rep 2

value: interstitial macrophages


title: ATAC Individual 6 skin fibroblast cells, Dexamethasone, Time4

value: Time 4


description:
Sample SU142B relapse single cell ATAC library
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Sample SU142B


title: U2OS DIvA exp01 Dam untethered (KIN1554.index08)

value: Human bone osteosarcoma epithelium


title: 14IMDN rep 4

value: 14 post S. pneumonia


title: ATAC Individual 6 skin fibroblast cells, Dexamethasone, Time0

value: Time 0


title: GM_IL21_Day6_3

city: Boston

first: Yifei

last: Liao

state: Massachusetts

address: 181 Longwood Ave, 8th Floor

institute: Brigham and Women's hospital

data_processing:
Adaptor-trimmed reads were mapped to Akata EBV genome (Accession#: KC207813.1) or human GRCh37.83 transcriptome assembly using salmon (v1.10.0).
Quality control was performed using fastqc. Differentially expressed genes were identified in R (v4.0.3) using DESeq2 under default settings with the apeglm shrinkage estimator (https://doi.org/10.1093/bioinformatics/bty895) and annotations derived from the hg19 build from Ensembl release 75 and accessed via biomaRt. Volcano plots were generated in GraphPad Prism 8, using Log2 (Fold Change) and −Log10 (p value) data. Differentially expressed genes from each condition were subjected to Enrichr analysis and top 10 KEGG pathways with adjusted p value < 0.05 cutoff were visualized.
Assembly: GRCh37.83 (hg19), Akata EBV (Accession#: KC207813.1)
Supplementary files format and content: Excel sheets of the log2FC data are provided.

source_name: GM12878 cell line

growth_protocol: Human GM12878 and Mutu I cells were cultured in RPMI (Life Technologies) with 10% FBS at 37 degrees C and 5% CO2.

extract_protocol:
Total RNA was isolated using a RNeasy Mini kit with in-column genomic DNA digestion.
To construct indexed libraries, 1 μg of total RNA was used for polyA mRNA purification, using the NEBNext Poly(A) mRNA Magnetic Isolation Module, followed by library preparation using the NEBNext Ultra RNA Library Prep with Sample Purification Beads (#E7760L, New England Biolabs).

treatment_protocol: Human GM12878 or Mutu I cells were treated with cytokines or mock treated.

value: GM12878 cell line

value: B cells


title: ATAC Individual 5 skin fibroblast cells, Dexamethasone, Time48

source_name: Skin

value: Time 48


title: U2OS DIvA exp01 Dam untethered (KIN1554.index07)

value: scDamID


title: GM_IL21_Day6_2


title: GM_IL21_Day6_1


title: U2OS DIvA exp01 Dam-53BP1 (KIN1554.index06)


title: U2OS DIvA exp01 Dam-53BP1 (KIN1554.index05)


title: ATAC Individual 5 skin fibroblast cells, Dexamethasone, Time44

value: Skin

value: Time 44


title: NIMDN rep 3

value: Naïve


title: NIMLYVE rep 3


title: iWAT, AL1_4PM

value: iWAT

value: 8 months  old

value: Ad-Lib


title: ATAC Individual 5 skin fibroblast cells, Dexamethasone, Time40

value: Fibroblast cells

value: Dexamethasone

value: Time 40


title: ATAC Individual 5 skin fibroblast cells, Dexamethasone, Time36

value: Time 36


title: 14AM rep 4

value: interstitial macrophages


title: NIMMHCII rep 3


title: GM_IL15_Day6_3


title: GM_IL15_Day6_2


title: U2OS DIvA exp01 Dam untethered (KIN1554.index04)

value: Human bone osteosarcoma epithelium


title: 14AM rep 3

value: 14 post S. pneumonia


title: U2OS DIvA exp01 Dam-53BP1 (KIN1554.index02)


title: 14IMLYVE rep 3


title: ATAC Individual 5 skin fibroblast cells, Dexamethasone, Time32

value: Time 32


title: GM_IL15_Day6_1

value: GM12878 cell line

value: B cells


title: U2OS DIvA exp01 Dam untethered (KIN1554.index03)

value: scDamID


title: GM_Ctrl_Day6_3

value: mock


title: NIMDN rep 2


title: ATAC Individual 5 skin fibroblast cells, Dexamethasone, Time28

value: Skin

value: Time 28


title: U2OS DIvA exp01 Dam-53BP1 (KIN1554.index01)


title: ATAC Individual 5 skin fibroblast cells, Dexamethasone, Time24

value: Time 24


title: GM_Ctrl_Day6_2


title: 14IMDN rep 3


title: MCF7 TDP2 knockout 10 nM E2 treatment for 2h scRNA S8

first: Minhyung

last: Kim

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

data_processing:
For the RNA-seq data, we utilized the Illumina standards quality control pipeline to assesses base call quality and truncates low-quality reads. The quality of sequencing data was assessed using MultiQC software (v1.14). Sequence alignment and quantification were performed using the STAR (v2.7.5c)-RSEM (v1.3.1) pipeline. Reads overlapping exons in the annotation of Genome Reference Consortium Human Build 38 (GRCh38) will be identified. Genes were filtered out and excluded from downstream analysis if they failed to achieve raw read counts of at least 2 across all the libraries. Batch effects were corrected by ComBat in sva R package (v3.35.2). The trimmed mean of M-values normalization method (TMM) (version 1.6.1) was used for calculating normalized count data.
Single-cell RNA-seq was performed using the 10X Genomics scRNA-seq approach at the Cedars-Sinai Genomics Core. The Cell Ranger Single-Cell Software Suite was used for demultiplexing, barcode assignment and unique molecular identifiers (UMIs) quantification. The reads were aligned to the hg38 reference genome using a pre-built annotation package obtained from the 10X Genomics website. All lanes per sample were processed using the ‘cellranger count’ function. The output from different lanes was then aggregated using ‘cellranger aggr’ with –normalise set to ‘none.’
Assembly: GRCh38
Supplementary files format and content: The excel file include raw count and TMM normalized and batch corrected data.

growth_protocol: Cells were cultured in phenol red-free medium supplemented with 5% FBS-charcoal stripped for 24 hours

extract_protocol: RNA was extracted using the RNeasy mini kit, and first strand cDNA synthesis was performed using Superscript III (Invitrogen)

treatment_protocol: 10 nM 17beta-estradiol was treated for 2 hours before extracting RNA.

value: epithelial cell

value: TDP2 knockout

value: 10 nM E2 treatment for 2h


title: ATAC Individual 5 skin fibroblast cells, Dexamethasone, Time20

value: Fibroblast cells

value: Dexamethasone

value: Time 20


title: MutuI_IL21_Day1_3

source_name: Mutu I cell line

value: Mutu I cell line


title: 14AM rep 2

value: interstitial macrophages


title: MCF7 WT 10 nM E2 treatment for 2h scRNA S6

value: WT


title: NIMLYVE rep 2

value: Naïve


title: GM_Ctrl_Day6_1

value: GM12878 cell line


title: ATAC Individual 5 skin fibroblast cells, Dexamethasone, Time12

value: Time 12


title: ATAC Individual 5 skin fibroblast cells, Dexamethasone, Time16

value: Time 16


title: MutuI_IL21_Day1_2

value: B cells


title: NIMDN rep 1


title: NAM rep 5


title: MCF7 WT Untreated scRNA S5

value: Untreated


title: ATAC Individual 5 skin fibroblast cells, Dexamethasone, Time8

value: Skin

value: Time 8


title: MutuI_IL21_Day1_1


title: ATAC Individual 5 skin fibroblast cells, Dexamethasone, Time4

value: Time 4


title: MutuI_IL4-CD40L_Day1_3


title: MutuI_IL4-CD40L_Day1_2


title: MCF7 WT 10 nM E2 treatment for 2h scRNA S2

value: epithelial cell


title: ATAC Individual 5 skin fibroblast cells, Dexamethasone, Time0

value: Time 0


title: MutuI_IL4-CD40L_Day1_1


title: 14IMLYVE rep 2

value: 14 post S. pneumonia


title: MCF7 TDP2 knockout Untreated scRNA S3

value: TDP2 knockout


title: ATAC Individual 4 skin fibroblast cells, Dexamethasone, Time48

value: Fibroblast cells

value: Dexamethasone

value: Time 48


title: MCF7 WT Untreated scRNA S1

value: WT


title: MCF7 TDP2 knockout Untreated scRNA S7


title: 14IMDN rep 2

value: interstitial macrophages


title: MCF7 TDP2KO E2-treated 2 hours bulk RNA-seq biological replicate 2

value: 10 nM E2 treatment for 2h


title: 14IMLYVE rep 1


title: MutuI_Ctrl_Day1_2

value: Mutu I cell line

value: mock


title: 14AM rep 1


title: MutuI_Ctrl_Day1_1

value: B cells


title: MCF7 TDP2KO Untreated bulk RNA-seq biological replicate 2

value: Untreated


title: MCF7 TDP2KO E2-treated 2 hours bulk RNA-seq biological replicate 1


title: ATAC Individual 4 skin fibroblast cells, Dexamethasone, Time40

value: Skin

value: Time 40


title: ATAC Individual 4 skin fibroblast cells, Dexamethasone, Time32

value: Time 32


title: NIMMHCII rep 2

value: Naïve


title: MCF7 TDP2KO Untreated bulk RNA-seq biological replicate 1

value: epithelial cell


title: NIMLYVE rep 1


title: female_RE8_24h

city: Stockholm

first: Paulo

middle: R.

last: Jannig

address: Solnavägen 9

department: Department of Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

description:
RE8_24h
CC_24h

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using STAR
Reads aligning to gene exons (Homo_sapiens.GRCh38.102.gtf) were counted using featureCounts program from Subread package, summarized at gene level.
Differentially expressed genes were identified with a false discovery rate (Benjamini- Hochberg method) adjusted p-value <0.05 using the DESeq2 R package. Genes with total raw counts less then 10 across all samples were excluded from analysis
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes normalized read counts for protein coding genes for all samples
Supplementary files format and content: tab-delimited text files includes differetial gene expression analysis output from DESeq2

molecule: polyA RNA

extract_protocol:
RNA was isolated using TRI Reagent (Sigma-Aldrich, St Louis, MO, USA). Tissue was homogenized using beads and the Fisher Bead Mill (Fisher, Hanover Park, IL, USA). RNA was further processed on columns using the Direct-zol Kit (Zymo Research, Irvine, CA, USA). Concentration and purity were determined using a BioTek Take3 micro-volume microplate with a BioTek PowerWave XS microplate reader (BioTek Instruments Inc., Winooski, VT).
Samples were purified by poly-A enrichment before library creation using Illumina TruSeq Stranded mRNA

tag: muscle

value: RE

tag: timepoint order

tag: sample id

tag: subject

value: CC

tag: subject number

tag: subject id

value: female

tag: age years

tag: height m

tag: weight kg

tag: bmi


title: ATAC Individual 4 skin fibroblast cells, Dexamethasone, Time28

tag: tissue

tag: cell type

value: Fibroblast cells

tag: treatment

value: Dexamethasone

tag: time

value: Time 28


title: female_RE8_8h

description:
RE8_8h
CC_8h

tag: Sex


title: MCF7 Parental E2-treated 2 hours bulk RNA-seq biological replicate 2

tag: cell line

tag: genotype

value: WT


title: female_RE8_3h

description:
RE8_3h
CC_3h

tag: muscle

tag: timepoint


title: ATAC Individual 4 skin fibroblast cells, Dexamethasone, Time16

value: Time 16


title: ATAC Individual 4 skin fibroblast cells, Dexamethasone, Time24

value: Time 24


title: 14IMDN rep 1

value: interstitial macrophages

value: 14 post S. pneumonia


title: MCF7 Parental E2-treated 2 hours bulk RNA-seq biological replicate 1

value: 10 nM E2 treatment for 2h


title: MutuI_Ctrl_Day1_3

value: Mutu I cell line

value: B cells

value: mock


title: NIMMHCII rep 1

value: Naïve


title: female_RE8_30m

description:
RE8_30m
CC_30m

tag: timepoint order

tag: sample id


title: MCF7 TDP2 knockout 10 nM E2 treatment for 2h scRNA S4

value: epithelial cell

value: TDP2 knockout


title: MCF7 Parental Untreated  bulk RNA-seq biological replicate 2

value: Untreated


title: NAM rep 4


title: ATAC Individual 4 skin fibroblast cells, Dexamethasone, Time12

value: Skin

value: Time 12


title: female_RE8_PRE

description:
RE8_PRE
CC_Pre

value: RE

value: PRE

tag: subject

value: CC

tag: subject number

value: female


title: NAM rep 3


title: MCF7 Parental Untreated bulk RNA-seq biological replicate 1

value: WT


title: 14IMMHCII rep 1

value: interstitial macrophages


title: male_RE7_24h

description:
RE7_24h
CA_24h

value: CA

tag: subject id

value: male

tag: age years


title: blood, 2000spins, 15minutes [N4-006]

city: changchun

first: weijie

last: zhai

address: jiefangdalu

department: neurology and nurosience center

institute: the first hospital of jilin university

data_processing:
FastQC: v0.11.7
Raw sequence data were generated as clean reads from Illumina NextSeq by real-time base calling and quality filtering. The clean reads were recorded in FASTQ format, containing the read information, sequences and quality encoding.
The identifier line, which begins with "＞", gives a name that are divided into three parts by underline. The first part of the character indicate sample name, the second part of the integer indicate rank the i-th out of all sequences, the third part is made up of character and integer. For example, the identifier line ">samplei_1_x123", the character "samplei" indicate sample name, the integer 1 indicate rank the first out of all sequences, the character "x" as an identifier and the subsequent integer 123 indicate the sequence have occur "123" time.
The trimmed reads (14nt _ length _ 40nt) are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2. The alignment result can be save to a file in TXT format for each sample. Bowtie outputs one alignment per line.
Supplementary files format and content: Expression_miRNA.xlsx: Excel file includes counts and CPM values for each Sample.

source_name: plasma

growth_protocol: The plasma was separated by 2000 spins for 15 minutes within 3 hours after blood collected from patients of VCID, NVCID, AD and NC. The extracted plasma was frozen in -80℃ until next use.

extract_protocol:
Agarose electrophoresis was used to check the integrity of total RNA samples, and then the samples were quantified on the NanoDrop ND-1000 instrument.
The completed libraries were quantified by Agilent 2100 Bioanalyzer. Libraries were mixed in equal amount according to the quantification results, and used for sequencing on the instrument.

tag: disease

value: HY

value: plasma


title: ATAC Individual 4 skin fibroblast cells, Dexamethasone, Time4

value: Fibroblast cells

value: Dexamethasone

value: Time 4


title: male_RE7_3h

description:
RE7_3h
CA_3h

tag: height m

tag: weight kg

tag: bmi


title: ATAC Individual 4 skin fibroblast cells, Dexamethasone, Time8

tag: tissue

tag: cell type

tag: treatment

value: Time 8


title: ATAC Individual 4 skin fibroblast cells, Dexamethasone, Time44

tag: time

value: Time 44


title: blood, 2000spins, 15minutes [N4-005]


title: NAM rep 1

value: Naïve


title: male_RE7_30m

description:
RE7_30m
CA_30m

tag: Sex


title: blood, 2000spins, 15minutes [N4-004]


title: ATAC Individual 4 skin fibroblast cells, Dexamethasone, Time36

value: Skin

value: Time 36


title: Chronic_11Day_2

city: Tallahassee

first: Elizabeth

last: Mazzio

state: Florida

address: College of Pharmacy and Pharmaceutical Sciences, 241 Fred Humphries Science Research Facility, 1515 MLK Blvd, Tallahassee , Florida 32307

institute: FAMU College of Pharmacy

description: Matrix, Control, LPS, T2, T3

data_processing:
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing polyA and polyG; 3) removing reads containing more than 5% of unknown nucleotides (N); 4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/,0. 11.9) including the Q20, Q30 and GC-content of the clean data. After that, a total of G bp of cleaned, paired-end reads were produced(20,21). Alignment with Reference Genome: We aligned reads of all samples to the mouse reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then mapping the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatches when mapping the reads to the reference. HISAT2 builds a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions
Assembly: The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using GffCompare Software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
Supplementary files format and content: After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value. Genes differential expression analysis was performed by DESeq2 software between two separate groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥2 were considered differentially expressed genes(23-25). Alternative Splicing (AS) Analysis: rMATS (version 4.1.1) (http://rnaseq-mats.sourceforge.net) was used to identify alternative splicing events and analyze differential alternative splicing events between samples. We identified AS events with a false discovery rate (FDR) p<0.05 in comparison as significant AS events. The classification of alternative splicing is as follows: SE: skipped exon MXE: mutually exclusive exon A5SS: alternative 5’ splice site A3SS: alternative 3’ splice site RI: retained intron (26,27)

growth_protocol: Mouse macrophage (RAW 264.7) cells were purchased from the American Type Culture Collection (Manassas, VA, USA). Cells were cultured in DMEM high glucose media [glucose 4500 mg/L] containing 5% FBS, 4 mM L-glutamine, and penicillin/streptomycin (100 U/0.1 mg/mL). Culture conditions were maintained at 37°C in 5% CO2/atmosphere, and cells were maintained every 2–3 d in preparation for sub-culture as required by experimentation.

extract_protocol:
Total RNA was extracted using the Trizol reagent (Thermo Fisher, CA, USA, cat. 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analyzed with Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, cat. 5067-1511); high-quality RNA samples with RIN number >7.0 were used to construct the sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature [Magnesium RNA Fragmentation Module (NEB, USA, cat. e6150) under 94℃, 5-7 min]. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, USA, cat. 1896649), which were next used to synthesize U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat. m0209), RNase H (NEB, cat. m0297) and dUTP Solution (Thermo Fisher, cat. R0133). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat labile UDG enzyme (NEB, cat. m0280) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec and then final extension at 72℃ for 5 min. The average insert size for the final cDNA libraries was 300±50 bp. In the end, we performed the 2×150 bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.
A cDNA library constructed by technology from the pooled RNA from murine species was sequenced and run with Illumina NovaseqTM 6000 sequence platform. Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of million 2 x 150 bp paired-end reads. The reading obtained from the sequencing machine include raw reads containing adapters or low-quality bases which will affect the following assembly and analysis.

treatment_protocol: Cells at all time points were fully viable, collected, and labeled : 1) Negative Control: Control Resting; 2) Positive Control: LPS treated acute 500 ng/mL (24 h); 3) Chronic 1; 7 d sustained LPS 500 ng/mL (chronic), and 4) Chronic 2 ; 11 d sustained LPS 500 ng/mL (chronic). At the end of the study, cell pellets and supernatants were collected and stored at -80°C.

tag: cell line

value: Macrophage

tag: genotype

value: monocyte/macrophage

value: Chronic 11 Day sustained LPS


title: male_RE7_PRE

description:
RE7_PRE
CA_Pre

tag: muscle

value: RE

tag: timepoint

value: PRE

tag: timepoint order


title: blood, 2000spins, 15minutes [N4-003]


title: Chronic_11Day_1

description: Matrix, Control, LPS, T2, T3


title: ATAC Individual 3 skin fibroblast cells, Dexamethasone, Time40

value: Time 40


title: female_RE6_3h

description:
RE6_3h
BV_3h

tag: sample id

tag: subject

value: BV

tag: subject number

value: female


title: Chronic_7Day_3

description: Matrix, Control, LPS, T2, T3

value: Chronic 7 Day sustained LPS


title: blood, 2000spins, 15minutes [N4-002]

tag: disease

value: HY

value: plasma


title: ATAC Individual 3 skin fibroblast cells, Dexamethasone, Time36

value: Fibroblast cells

value: Dexamethasone


title: female_RE6_30m

description:
RE6_30m
BV_30m

tag: subject id

tag: age years

tag: height m


title: Chronic_7Day_2

description: Matrix, Control, LPS, T2, T3


title: NAM rep 2

value: interstitial macrophages


title: ATAC Individual 3 skin fibroblast cells, Dexamethasone, Time32

tag: tissue

value: Time 32


title: blood, 2000spins, 15minutes [N3-006]

value: AD


title: female_RE6_PRE

description:
RE6_PRE
BV_Pre

tag: weight kg

tag: bmi


title: ATAC Individual 3 skin fibroblast cells, Dexamethasone, Time28

value: Skin

tag: cell type

tag: treatment

tag: time

value: Time 28


title: Chronic_7Day_1

description: Matrix, Control, LPS, T2, T3

tag: cell line

value: Macrophage

tag: genotype

value: monocyte/macrophage


title: female_RE5_24h

description:
RE5_24h
BP_24h

tag: muscle

value: RE

tag: timepoint

value: BP

tag: Sex


title: ATAC Individual 3 skin fibroblast cells, Dexamethasone, Time48

value: Time 48


title: blood, 2000spins, 15minutes [N3-005]


title: LPS_24H_Acute_3

description: Matrix, Control, LPS, T2, T3

value: Acute 24 hour LPS


title: ATAC Individual 3 skin fibroblast cells, Dexamethasone, Time24

value: Time 24


title: female_RE5_8h

description:
RE5_8h
BP_8h

tag: timepoint order

tag: sample id

tag: subject

value: female


title: blood, 2000spins, 15minutes [N3-004]

tag: disease


title: ATAC Individual 3 skin fibroblast cells, Dexamethasone, Time44

value: Time 44


title: LPS_24H_Acute_2

description: Matrix, Control, LPS, T2, T3


title: female_RE5_3h

description:
RE5_3h
BP_3h

tag: subject number

tag: subject id

tag: age years


title: ATAC Individual 3 skin fibroblast cells, Dexamethasone, Time20

tag: tissue

value: Time 20


title: blood, 2000spins, 15minutes [N3-003]

value: plasma


title: blood, 2000spins, 15minutes [N4-001]

value: HY


title: LPS_24H_Acute_1

description: Matrix, Control, LPS, T2, T3


title: blood, 2000spins, 15minutes [N3-001]


title: Control_3

description: Matrix, Control, LPS, T2, T3

value: Resting Control


title: ATAC Individual 3 skin fibroblast cells, Dexamethasone, Time12

value: Fibroblast cells

value: Dexamethasone

value: Time 12


title: Control_2

description: Matrix, Control, LPS, T2, T3


title: female_RE5_30m

description:
RE5_30m
BP_30m

tag: height m

tag: weight kg

tag: bmi


title: ATAC Individual 3 skin fibroblast cells, Dexamethasone, Time8

value: Skin

tag: cell type

tag: treatment

tag: time

value: Time 8


title: female_RE5_PRE

description:
RE5_PRE
BP_Pre

tag: muscle

value: PRE


title: blood, 2000spins, 15minutes [N2-006]

value: VCID


title: Control_1

description: Matrix, Control, LPS, T2, T3

tag: cell line

value: Macrophage

tag: genotype

value: monocyte/macrophage


title: ATAC Individual 3 skin fibroblast cells, Dexamethasone, Time0

value: Time 0


title: male_RE4_3h

description:
RE4_3h
BR_3h

value: RE

tag: timepoint

tag: timepoint order

value: BR

tag: Sex

value: male


title: blood, 2000spins, 15minutes [N2-004]

tag: disease


title: ATAC Individual 2 skin fibroblast cells, Dexamethasone, Time48

value: Time 48


title: male_RE4_30m

description:
RE4_30m
BR_30m

tag: sample id

tag: subject

tag: subject number


title: Kidney, ischemic

city: Durham

first: Jamie

last: Privratsky

state: NC

address: 303 Research Dr., Sands 101

department: Anesthesiology

institute: Duke University

description: 10X genomics

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were made using Cell Ranger software v7.0.0 (10X genomics)
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: kidney

extract_protocol:
Mice were perfused with ice-cold PBS via cardiac puncture after which the kidneys were harvested. Kidney digest was performed with liberase TM (0.3 mg/mL, Roche, Basel, Switzerland, #291963), hyaluronidase (10mg/mL, Sigma, H4272), DNaseI (20mg/mL) at 37 ̊C for 20 min. After centrifugation, cell pellets were incubated with ACK lysing buffer (ThermoFisher #A1049201) and again centrifuged. Pellets were incubated with 0.25%trypsin EDTA at 37 ̊C for 10 min with shaking at 100 rpm in bacterial shaker. Trypsin was inactivated using 10% fetal bovine serum in PBS. Cells were then washed and resuspended in DPBS supplemented with 0.04% bovine serum albumin. After filtration through a 30 m strainer, cells were loaded onto 10X Chromium System (10X Genomics) at 1000 cells/mcl
Library was performed according to manufacturer's instructions (single cell 3' v2 protocol, 10x Genomics)

tag: tissue

value: kidney

tag: strain

value: wildtype

tag: age

value: 19 weeks

value: 27 minutes ischemia, reperfusion for 24 hours


title: ATAC Individual 3 skin fibroblast cells, Dexamethasone, Time16

first: Marcelo

last: Francia

address: 1771 Beloit Avenue, Unit 204

institute: University of California, Los Angeles

value: Fibroblast cells

value: Dexamethasone

value: Time 16


title: ATAC Individual 2 skin fibroblast cells, Dexamethasone, Time44

value: Skin

value: Time 44


title: CD45+ CD11c+ cells, 20 Gy + fusion protein, replicate 3

city: CHICAGO

first: Jason

last: Bugno

state: IL

institute: University of Chicago

data_processing:
Raw data quality control was done using FastQC, trimming was performed using Trimmomatic. Sequenced reads were aligned to the mouse reference genome (mm10) using RNA STAR and quantified by featureCounts. Count data was further analyzed for differential expression using DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file of DESeq2 output

source_name: Tumor

growth_protocol: B16-OVA tumors were established in mice for 10 days

extract_protocol:
Tumors were collected on day 17. Single cells from tumors were harvested by digestion using 1 mg/mL collagenase IV and 200 μg/mL DNaseI for 45 minutes. Blocking was performed with anti-Fc receptor. Live CD45+ CD11c+ cells were flow sorted from tumors and mixed with Trizol for RNA extraction.
RNA library for sequencing was constructed using SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio)

treatment_protocol: At day 10 20 Gy was given. Mice receiving fusion protein received 20 mcg on day 10 and 10 mcg on day 14

value: Tumor

value: WT

value: 20 Gy + Fusion Protein


title: male_RE4_PRE

description:
RE4_PRE
BR_Pre

value: PRE

tag: subject id

tag: age years

tag: height m

tag: weight kg

tag: bmi


title: blood, 2000spins, 15minutes [N2-002]

value: VCID

value: plasma


title: blood, 2000spins, 15minutes [N3-002]

value: AD


title: CD45+ CD11c+ cells, 20 Gy + fusion protein, replicate 2

tag: cell type

tag: treatment


title: male_RE4_24h

description:
RE4_24h
BR_24h

tag: muscle

value: RE

tag: timepoint

value: BR

value: male


title: ATAC Individual 2 skin fibroblast cells, Dexamethasone, Time40

city: Los Angeles

tag: time

value: Time 40


title: ATAC Individual 2 skin fibroblast cells, Dexamethasone, Time36

value: Time 36


title: blood, 2000spins, 15minutes [N2-001]

tag: disease


title: male_RE3_24h

description:
RE3_24h
BO_24h

tag: timepoint order

tag: sample id

value: BO

tag: Sex


title: male_RE4_8h

description:
RE4_8h
BR_8h

tag: tissue

tag: subject

tag: subject number


title: male_RE3_8h

description:
RE3_8h
BO_8h

tag: subject id


title: CD45+ CD11c+ cells, 20 Gy, replicate 3

tag: genotype

value: 20 Gy


title: blood, 2000spins, 15minutes [N2-005]


title: ATAC Individual 2 skin fibroblast cells, Dexamethasone, Time32

value: Fibroblast cells

value: Dexamethasone

value: Time 32


title: blood, 2000spins, 15minutes [N1-005]

value: NVCID


title: male_RE3_3h

description:
RE3_3h
BO_3h

tag: age years

tag: height m


title: CD45+ CD11c+ cells, 20 Gy, replicate 2

value: Tumor

value: WT


title: Kidney, control

description: 10X genomics

value: kidney

tag: strain

value: wildtype

tag: age

value: 19 weeks

value: contralateral, uninjured kidney


title: ATAC Individual 2 skin fibroblast cells, Dexamethasone, Time28

value: Skin

tag: cell type

tag: treatment

value: Time 28


title: blood, 2000spins, 15minutes [N2-003]

value: VCID

value: plasma


title: male_RE3_30m

description:
RE3_30m
BO_30m

tag: muscle

value: RE

tag: timepoint

value: male

tag: weight kg

tag: bmi


title: CD45+ CD11c+ cells, 20 Gy, replicate 1

value: 20 Gy


title: ATAC Individual 2 skin fibroblast cells, Dexamethasone, Time24

value: Fibroblast cells

tag: time

value: Time 24


title: ATAC Individual 3 skin fibroblast cells, Dexamethasone, Time4

value: Dexamethasone

value: Time 4


title: CD45+ CD11c+ cells, Fusion protein, replicate 3

value: Tumor

value: Fusion Protein


title: male_RE3_PRE

description:
RE3_PRE
BO_Pre

value: PRE

tag: timepoint order

tag: sample id

value: BO

tag: Sex


title: ATAC Individual 2 skin fibroblast cells, Dexamethasone, Time20

tag: tissue

value: Time 20


title: blood, 2000spins, 15minutes [N1-003]

tag: disease

value: NVCID


title: male_RE2_24h

description:
RE2_24h
BN_24h

tag: subject

value: BN

tag: subject number

tag: subject id


title: blood, 2000spins, 15minutes [N1-004]


title: blood, 2000spins, 15minutes [N1-002]


title: ATAC Individual 2 skin fibroblast cells, Dexamethasone, Time16

value: Skin

value: Time 16


title: male_RE2_8h

description:
RE2_8h
BN_8h

tag: age years

tag: height m


title: CD45+ CD11c+ cells, 20 Gy + fusion protein, replicate 1

tag: cell type

tag: genotype

value: WT

value: 20 Gy + Fusion Protein


title: ATAC Individual 2 skin fibroblast cells, Dexamethasone, Time12

tag: treatment

value: Time 12


title: blood, 2000spins, 15minutes [N1-006]

value: plasma


title: blood, 2000spins, 15minutes [N1-001]


title: CD45+ CD11c+ cells, Fusion protein, replicate 1


title: male_RE2_3h

description:
RE2_3h
BN_3h

tag: muscle

value: RE

tag: timepoint

value: male


title: CD45+ CD11c+ cells, No Treatment, replicate 3

value: No Treatment


title: ATAC Individual 2 skin fibroblast cells, Dexamethasone, Time8

value: Fibroblast cells

value: Dexamethasone

value: Time 8


title: male_RE2_30m

description:
RE2_30m
BN_30m

tag: weight kg

tag: bmi