title: SK7334

description: Library name: IA1101


title: Ctrl6

status: Public on Aug 20 2025

type: SRA

city: Chongqing

first: Guo

middle: Jing

last: Ma

address: Yuzhong Road

country: China

institute: Chongqing medical university

description: Library name: HC-6

library_source: transcriptomic single cell

data_processing:
SnRNA-seq data analysis was performed by NovelBio Co.,Ltd. with NovelBrain Cloud Analysis Platform (www.novelbrain.com). We applied fastp  with default parameter filtering the adaptor sequence and removed the low quality reads to achieve the clean data. Cells contained over 200 expressed genes and mitochondria UMI rate below 10% passed the cell quality filtering and mitochondria genes were removed in the expression table.
The 'Ctrl vs Dep DEGs.tsv' files included all DEGs; We identified DEGs between the groups and used functional FindMarkers under the following criteria: 1. log2 |FC| > 0.25; 2. FDR < 0.05 (Bonferroni correction); 3. min.pct > 0.1.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism: Mus musculus

source_name: prefrontal cortex

extract_protocol:
Briefly, the frozen tissue was homogenized in NLB buffer which contain 250 mM Sucrose, 10 mM Tris-HCl, 3 mM MgAc2, 0.1% Triton X-100 (SigmaAldrich, USA), 0.1 mM EDTA, 0.2U/μL RNase Inhibitor (Takara, Japan). Various concentration of sucrose was used to purify the nucleus. The concentration of nucleus was adjusted to about 1000 nuclei / μL for snRNA-Seq.
The snRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3' V3 Reagent Kits (10X Genomics, Pleasanton, USA). Briefly, cells nuclei were concentrated to 1000 nuclei/μL than loaded into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs). After the RT step, GEMs were broken and barcoded-cDNA was purified and amplified. The amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors and index PCR amplified. The final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific, USA) and the size distribution of the libraries were determined using a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent, USA). All libraries were sequenced by Novaseq6000 (Illumina, USA) on a 150 bp paired-end run.

tag: tissue

value: prefrontal cortex

tag: group

value: healthy control


title: E58 human metacarpal, digit 4, rep 2

city: Cambridge

first: Terence

last: Capellini

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

country: USA

institute: Harvard University

description: Library name: HM4_early_rep2

library_source: genomic

data_processing:
concatenate reads
adapter trimming with NGmerge v0.3
Alignment to hg38 with Bowtie2 v2.3.4.1
duplicate removal with picard v2.9.0
mitochondrial read filtering with removeChrom.py
peak calling with MACS2 v2.1.1.2 -f bampe --nolambda –bdg --verbose
IDR https://github.com/nboley/idr
idr --samples rep1file rep2file --peak-list pooled_peaks --input-file-type narrowPeak --output-file IDR_output --rank p.value --soft-idr-threshold 0.05 –plot
Assembly: hg38
Supplementary files format and content: bed format; contains the coordinates of the peaks called

molecule: genomic DNA

organism: Homo sapiens

source_name: Metacarpal, digit IV

growth_protocol: in vivo collected human autopod chondrocytes from E53-E74

extract_protocol:
Embryonic tissue was microdissected under a light microscope in 5% fetal bovine serum in Dulbecco’s Modified Eagle Medium (DMEM) on ice. The pooled phalanges (proximal and distal for digit I; proximal, intermediate, and distal for digits II-V) and metapodials were collected separately for all digits in both the fore- and hind limbs. The right and left sides of each element were pooled together. ATAC-seq protocol was performed as described in Young et al., 2022. After ATAC-seq, samples were then sent out for 1-2 rounds of sequencing on an Illumina NovaSeq 6000 at the Harvard Bauer Core in order to obtain at least 40 million reads per sample.
ATAC-seq protocol was performed as described in Young et al., 2022.

treatment_protocol: Human products of conception were collected from late first-trimester terminations through the Laboratory of Developmental Biology in full compliance with the ethical guidelines of the National Institutes of Health and with the approval of the University of Washington Institutional Review Boards for the collection and distribution of human tissues for research, and Harvard University for the receipt and use of such materials. The Laboratory of Developmental Biology obtained written consent from all tissue donors.

value: Metacarpal, digit IV

tag: cell type

value: chondrocytes

tag: Sex

value: Male


title: Ctrl3

description: Library name: HC-3


title: Ctrl4

description: Library name: HC-4


title: Ctrl2

description: Library name: HC-2


title: E58 human metacarpal, digit 3, rep 2

description: Library name: HM3_early_rep2

source_name: Metacarpal, digit III

value: Metacarpal, digit III


title: iSCBEM, Day5

city: Dallas

first: Leijie

last: Li

state: Texas

address: 5323 Harry Hines Blvd.

department: Molecular Biology

institute: UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER

description:
Library name: Sample 3
caltured for 5 days

data_processing:
Cellranger v8.0.1 and the human reference genome (GRCh38) - 2024-A were used to calculate gene counts for each cell.
Seurat v5.0.1 and DoubletFinder v2.0.3 were then employed for quality control across all samples. Cells were filtered with expressed genes ranging between 500 and 9,000, mitochondrial gene expression percentages below 10%, and total counts between 200 and 90,000.
Zhao's human embryo model (PMID: 39543283) was used for unbiased  cell type annotation and comparison with published human embryo data.
Seurat was subsequently used for cell clustering and generating UMAP figures.
Assembly: Human reference (GRCh38) - 2024-A
Supplementary files format and content: Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx) for each sample

molecule: total RNA

source_name: H9_GFP-NLS & H9_iYAP-5SA & H9_iGATA6

growth_protocol: 5iLA_iYAP-5SA and 5iLA_iGATA6 cells were subjected to generation of integrated models, following 3 days doxycycline induction. iYAP-5SA, iGATA6, and  unmodified cells were dissociated with TryPLE for 5 min and incubated 20 min on gelatin-coated dishes at 37oC under 5% CO2 5% O2 condition in N2B27 basal medium supplemmted with 1 μg/mL Doxycyclin and CEPT cocktail to deplete MEF feeder cells. While mTeSR culture did not contain MEF cells, unmodified PSCs were also incubated on gelatin-coated dishes to coordinate timing with other cell types. Aggrewell 800 plate was prepared by pre-coating with anti-adherence solution and centrifuging at 1,000g for 5 min. After depleting MEF cells, the cell suspension was filtered through a 40 μm mesh to a 15-mL conical tubes containing 10 mL medium and centrifuged at 50g for 5min. The cell pellets were resuspended with N2B27 basal medium supplemmted with 1 μg/mL Doxycyclin and CETP cocktail at a concentration of 2.88×104: 0.96 ×104: 0.48–1.92 ×104 (iYAP-5SA: iGATA6 : unmodified) cells per 1 mL. The number of unmodified cells need to be optimized for each line. After washing the pre-coated aggrewell plate with PBS once, 1 mL of the cell suspension was seeded dropwise and centrifuged at 200g for 2min, resulting 96: 32: 16–64 (iYAP-5SA: iGATA6: unmodified) cells per microwell. The plate was placed at 37oC under 5% CO2 5% O2 condition. The day of aggregation was designated as day 0. On the following day (day 1), the medium was carefully removed and washed with 0.2 mL N2B27 medium twice, followed by 1 mL N2B27 basal medium addition to each well. On day 2, 1 mL N2B27 basal medium was carefully added, resulting in 2 mL in each well. On day 3, whole aggregates were washed out from each well with 1 mL of EBC and transferred to one well of suspension culture 6-well plate with 1 mL of EBC medium, resulting in 2 mL medium per well (∼300 aggregates per well). In the process of protocol optimization, IVC1 and conditioned IVC1/EBC medium with immortalized primary endometrial stromal cells were also used. The 6-well plate was placed at 37oC under 5% CO2 and shaked at 80 rpm. The 2 mL culture medium was refreshed everyday from day 4 onward. For several experiments (Fig. 3B, 3C, and etc.), 30 aggregates with visible cavity-like structures (top 10%) were picked-up as a quality control on day 6.

extract_protocol:
To dissociate iSCBEMs (Days 3, 5, and 7) into single cells, the iSCBEMs were centrifuged after adding 10 times the volume of PBS to the medium. The pelleted iSCBEMs were then resuspended in 2 mL of TrypLE supplemented with 1 mU/μL DNase I in 35 cm Petri dishes and incubated at 37°C while shaking on an orbital shaker at 80 rpm, with pipetting performed every 5 minutes. Day 3 and Day 5 iSCBEMs were incubated for 15 minutes, whereas Day 7 iSCBEMs were incubated for 20 minutes. To stop trypsinization, 2 mL of EBC medium (containing 20% FBS) was added. The starting cells (Day 0) were processed similarly to the iSCBEM generation protocol. After trypsinization, the cells were depleted of MEFs by incubating them for 20 minutes on gelatin-coated dishes at 37°C under 5% CO₂ and 5% O₂ conditions in N2B27 basal medium supplemented with 1 μg/mL doxycycline and the CEPT cocktail. The resulting cell populations were mixed at a 1:1:1 ratio for subsequent use. After washing the cells twice with PBS supplemented with 0.5% BSA and isolating dissociated cells using a 30 μm filter, cell number and viability were assessed using standard trypan blue staining procedures. All samples demonstrated a viability rate of over 85%. The dissociated cells were then resuspended in PBS supplemented with 0.05% BSA, and 20,000 cells were processed using the 10x Genomics Chromium platform with the Chromium GEM-X Single Cell 5' Kit v3 and Chromium GEM-X Single Cell 5' Chip Kit v3.
Chromium GEM-X Single Cell 5' Kit v3

tag: cell line

value: H9_GFP-NLS & H9_iYAP-5SA & H9_iGATA6

value: pluripotent stem cells

tag: genotype

tag: treatment

value: 5 days culture after aggregation


title: iSCBEM, Day3

description:
Library name: Sample 2
caltured for 3 days

value: 3 days culture after aggregation


title: iSCBEM, Day7

description:
Library name: Sample 4
caltured for 7 days

value: 7 days culture after aggregation


title: E58 human metacarpal, digit 2, rep 2

description: Library name: HM2_early_rep2

source_name: Metacarpal, digit II

value: Metacarpal, digit II


title: iSCBEM, Day0

description:
Library name: Sample 1
caltured for 0 days

value: iYAP-5SA and iGATA6 cells were treated with Dox for 3 days, after which the cells were mixed at a 1:1:1 ratio.


title: E58 human metacarpal, digit 1, rep 2

description: Library name: HM1_early_rep2

source_name: Metacarpal, digit I

value: Metacarpal, digit I


title: E58 human foot phalanges, digit 1, rep 2

description: Library name: FP1_early_rep2

source_name: Foot phalanges, digit I

value: Foot phalanges, digit I


title: Wild-Type,Muscle,Time60 r3

city: Kansas City

first: Bowen

last: Yang

state: Missouri

department: Computational Biology

institute: Stowers Institute for Medical Research

description: Library name: L64933

library_source: transcriptomic

data_processing:
Raw sequencing data was basecalled and demultiplexed with bclconvert v3.10.5
Reads were aligned to reference using the STAR (v2.7.19b) aligner
RSEM v1.3.1 was used to extract TPM/FPKM data.
Read counts were extracted from STAR's output and normalized with EdgeR (v3.36.0)
Assembly: P. mesoamericanus (UCSC GCF_021234165.1)
Supplementary files format and content: TSV file with raw gene counts for each samples

molecule: polyA RNA

organism: Pteronotus mesoamericanus

source_name: Muscle

growth_protocol: Adult male Pteronotus parnellii bats were wild-caught from the Lamanai Archaeological Reserve in Belize under approved collection permits. Animals were housed temporarily in dark, breathable cloth bags in a quiet environment for up to 2 hours before sampling. Animals were maintained at ambient field temperature prior to tissue collection.

extract_protocol:
Skeletal muscle tissue was dissected in the field immediately post-euthanasia and flash frozen in LN2. Samples were stored at –80°C until processing. Total RNA was extracted from 10mg of tissue following the manufacturer’s protocol for the Maxwell® RSC simplyRNA Tissue Kit (Promega, Cat# AS1340). RNA integrity was confirmed using an Agilent Bioanalyzer prior to library preparation.
RNA libraries for RNA-Seq were prepared using NEBNext Ultra II kit following manufacturer's instructions.

treatment_protocol: Each bat was orally administered a glucose solution at a dose of 4.5 g/kg body weight. Skeletal muscle tissue (pectoralis major) was collected at one of three timepoints: 0 min (baseline), 30 min, or 60 min after glucose administration. Animals were deeply anesthetized with isoflurane prior to sampling and euthanized by cardiac puncture followed by exsanguination before tissue dissection

value: Muscle

value: Wild Type

value: Fed with Sugar

tag: time


title: Wild-Type,Muscle,Time60 r4

description: Library name: L64953


title: Wild-Type,Muscle,Time60 r5

description: Library name: L64955


title: Dep6

description: Library name: Dep-6

value: prefrontal cortex

value: chronic social defeat stress (CSDS) model


title: Dep5

description: Library name: Dep-5


title: E58 human hand phalanges, digit 5, rep 2

description: Library name: HP5_early_rep2

source_name: Hand phalanges, digit V

value: Hand phalanges, digit V

value: chondrocytes


title: Wild-Type,Muscle,Time60 r2

description: Library name: L64911


title: Wild-Type,Muscle,Time60 r1

description: Library name: L64887


title: Wild-Type,Muscle,Time30 r3

description: Library name: L64934


title: E58 human hand phalanges, digit 4, rep 2

description: Library name: HP4_early_rep2

source_name: Hand phalanges, digit IV

value: Hand phalanges, digit IV

value: Male


title: E58 human hand phalanges, digit 3, rep 2

description: Library name: HP3_early_rep2

source_name: Hand phalanges, digit III

value: Hand phalanges, digit III


title: Wild-Type,Muscle,Time30 r1

description: Library name: L64882


title: Wild-Type,Muscle,Time30 r2

description: Library name: L64914


title: Dep4

description: Library name: Dep-4


title: Wild-Type,Muscle,Time0 r4

description: Library name: L64932


title: Dep3

description: Library name: Dep-3


title: E58 human hand phalanges, digit 2, rep 2

description: Library name: HP2_early_rep2

source_name: Hand phalanges, digit II

value: Hand phalanges, digit II


title: Wild-Type,Muscle,Time0 r3

description: Library name: L64912


title: Dep1

description: Library name: Dep-1


title: Wild-Type,Muscle,Time10 r2

description: Library name: L64954


title: Ctrl1

description: Library name: HC-1

value: healthy control


title: E53 human metatarsal, digit 5, rep 1

description: Library name: FM5_early_rep1

source_name: Metatarsal, digit V

value: Metatarsal, digit V


title: Wild-Type,Muscle,Time0 r1

description: Library name: L64899


title: cPhp1_4

city: Louisville

first: Richard

middle: J

last: Lamont

state: KY

address: 570 S Preston St.

department: Oral Immunology and Infectious Diseases

institute: University of Louisville School of Dentistry

description:
Library name: Sample 29
cPhp1_4

data_processing:
Reads aligned to transcriptome using STAR tool, generating .bam file.
Quantification of .bam file using Salmon, generating tab-separated processed data file (.txt)
Assembly: P. gingivalis ATCC 33277 genome (accession AP009380.1)
Supplementary files format and content: tab separated text file with two columns: gene names (Name) and number of reads (NumReads); https://bacteria.ensembl.org/Porphyromonas_gingivalis_atcc_33277_gca_000010505/Info/Index/
Supplementary files format and content: Each row corresponds to a single gene with its corresponding counts.

organism: Porphyromonas gingivalis

source_name: In vitro culture

growth_protocol: Bacteria were cultured anaerobically (85% Nitrogen, 10% carbon dioxide, 5% hydrogen), at 37 degrees Celsius in trypticase soy broth (TSB) supplemented with 1 mg/ml yeast extract, 5 ug/ml hemin, and 1 ug/ml menadione. When necessary, erythromycin (10 ug/mL) or gentamicin (50 ug/ml) was added to the medium for isogenic mutants.

extract_protocol:
Collected abscess material was briefly spun at  150 x g for 3 min at 4 degress Celsius to pellet any mouse cells present. The supernatant was transferred to a new tube and spun at 5000 x g for 5 min at 4 degrees Celsius to pellet bacteria cells. The supernatant was removed and cell pellet resuspened into TRIzol™ Reagent (Invitrogen cat #15596026) and total RNA extraction was caried out using the Qiagen RNeasy Plus Mini Kit (Qiagen cat #74136) following manufacturer protocol including an optional DNAse treatment step and eluting into nuclease-free water. Each sample of total RNA suspended in nuclease-free water was then shipped on dry ice to a commercial vendor for RNA sequencing.
Library construction was performed by Novogene. In brief, a strand-specific library was constructed with rRNA removal for 150-bp paired-end sequencing on an Illumina NovaSeq 6000.

treatment_protocol: 6-8 week old Balb/cJ mice were inoculated subcutaneously in the ventral surface of the right thigh with 1.5x10^9 bacterial cells grown to mid-logarithmic growth phase from on eo fthe following Pg strains: paraental wildtype ATCC 33277 (WT), Δltp1, or Δphp1. The abscess was allowed to develop for 24-48 hours, after which abscess material was collected via sterile swab into chilled sterile, pre-reduced PBS solution.

value: In vitro culture

value: php1 mutant


title: light_damage_WT

city: Hamburg

first: Andreas

last: Neueder

address: Falkenried 94

department: Center for Molecular Neurobiology (ZMNH)

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description:
Library name: SCC0013_4
10x Genomics

data_processing:
Sequencing data were demultiplexing with the 10x Genomics Cell Ranger software pipeline (v.7.0.1). Reads were mapped and quantified using the Alevin-Fry framework (alevin-fry v0.8.1, salmon v1.10.1, pyroe v0.9.2, python v3.9.16). To this end, we created a splici index using the 10x genomics mouse mm10 reference data (refdata-gex-mm10-2020-A) with a read length of 90. Reads were mapped with the salmon alevin command using ISR as the library type and chromiumV3 as the library type. We used sketch mode to generate a rad file by pseudoalignment with structural constraints. Next, we generated a barcode permit list using the 10x Genomics barcodes whitelist (3M-february-2018.txt). Additionally, we filtered reads that mapped to the reverse complement strand of transcripts by specifying -d fw. Lastly, UMIs per-gene and per-cell were quantified using the 'cr like' strategy.
Assembly: mouse mm10 (refdata-gex-mm10-2020-A)
Supplementary files format and content: alevin-fry output files: barcodes.txt, features.txt, quants.mat.gz

source_name: retina

extract_protocol:
Mice were euthanized by CO2 exposure followed by cardiac perfusion with 10 ml ice-cold PBS. Eyes were immediately dissected to isolate the retinae. Retinae were dissected in 500µl 0.25mM DMEM/HEPES containing 120 U/ml papain (Carl Roth, #9001-73-4), 225 U/ml collagenase IV (Worthington, #LS004188) and 20 U/ml DNase I (Worthington, #LS006344). Prior to digestion at 8°C for 45 minutes, each sample was mechanically triturated by pipetting. After digestion, cell suspensions were filtered through a 50µm cell strainer. Retinae from 3 to 5 mice were pooled to obtain sufficient cell numbers. To  remove dead cells and debris, cell suspension was incubated with magnetic beads (DeadCell Removal Kit, Milteny, # 130-090-101). Cells were sorted through MS Columns (Milteny, # 130-042-201) installed in an OctoMacs magnet (Milteny, # 130-042-109) according to manufactures protocol. Intact and viable single cells were collected and resuspended in ultra-pure BSA (1:1000, Thermo Fisher, #AM2616). Prior to processing for sc RNAseq, the single-cell suspensions were again filtered through a 40 µm strainer. Cell concentrations were assessed using an automated cell counter. The concentration for each sample was adjusted to approximately 1,000 cells/µL resulting in approx. 10,000 cells per reaction.
We used the 3' 10x Genomics Chromium Single Cell Gene Expression protocol (v3.1) to capture and barcode mRNA transcripts from the single cell suspensions.  Briefly, the cell suspensions, together with barcoded gel beads, master mix, and partitioning oil, was loaded on a 10x Genomics Chromium Next GEM chip. Using a Chromium Controller, the cells were partitioned into "gel bead in emulsions" (GEMs). Within each GEM, reverse transcription was followed by barcoding of transcripts with a unique 10x barcode and unique molecular identifiers (UMIs). The cDNA was purified using Silane dynabeads followed by PCR amplification. The amplified cDNA was fragmented, end repaired and A-tailed to create compatible ends for adapter ligation. Sequencing adapters (P5 and P7) were ligated to the cDNA fragments, and a sample index was added during a final round of PCR amplification, enabling multiplexing of samples in a single sequencing run. The constructed libraries were purified using AMPure XP beads before cDNA concentration and fragment size distribution were assessed using a Qubit Fluorometer and an Agilent Bioanalyzer. Libraries were pooled in equimolar ratios for sequencing. Libraries were sequenced on an Illumina NovaSeq 6000 platform using the 100 cycle S2 reagent kit in paired-end mode. Sequencing parameters were set to 28 bp for Read 1 (cell barcode and UMI), 8 bp for the i7 index (sample index), and 91 bp for Read 2 (cDNA insert). We aimed for a sequencing depth of approximately 50,000 reads per cell.

treatment_protocol: Experimental 6–9 week-old mice were dark-adapted in cyclic dim light (< 50 lux) followed by a period of complete darkness for 18 h prior to light damage. Mice were then placed in reflective cages and exposed to diffuse cool, white fluorescent light coming from the top of the cage with an intensity of 5000 lx for 30 min. After light exposure, mice were allowed to recover for 6 h in dim light, and then sacrificed. Light damage experiments were always performed in the early morning. Mice which were dark adapted but did not receive light damage served as control mice.

value: retina

value: WT


title: E53 human metatarsal, digit 4, rep 1

description: Library name: FM4_early_rep1

source_name: Metatarsal, digit IV

value: Metatarsal, digit IV


title: control_WT

description:
Library name: SCC0013_2
10x Genomics

value: control


title: cPhp1_2

description:
Library name: Sample 27
cPhp1_2


title: cLtp1_5

description:
Library name: Sample 25
cLtp1_5

value: ltp1 mutant


title: cPhp1_1

description:
Library name: Sample 26
cPhp1_1


title: Mouse Ccne1 4C PDS

city: Hong Kong

first: Feng

address: Room 503, 5/F, Li Ka Shing Medical Sciences Building, Prince of Wales Hospital

department: Chemical Pathology

institute: The Chinese University of Hong Kong

description:
Library name: Ccne1_PDS_4C
C2C12 cell Ccne1 4C-seq in PDS treatment

data_processing:
150 bp paired-end reads were merged and aligned to mouse genome (mm10) and analyzed with pipe4C. Bigwig file was generated by pipe4C, peak calling was performed with PeakC.
Assembly: mm10
Supplementary files format and content: rds and bed file
Library strategy: 4C-Seq

source_name: muscle

growth_protocol: The C2C12 cell line was cultured in the DMEM medium containing 10% FBS and 1% P/S.

extract_protocol:
Approximately 3 million C2C12 cells were cross-linked with 2% (v/v) formaldehyde for 10 min at room temperature and quenched by 0.125 M glycine. The samples were lysed in ice-cold lysis buffer [50 mM tris-HCl (pH=7.5), 150 mM NaCl, 5 mM EDTA, 0.5% NP40, 1% Triton X-100 with complete proteinase inhibitors] on ice for 20 min. Samples were then centrifuged at 700g for 5 min. Pelleted nuclei were washed once with 400 μl 1.2x Dpn II buffer [dilute 10x Dpn II buffer by H2O]. The supernatant was discarded, the nuclei were resuspended in 500 μl Dpn II buffer, and 15 μl 10% SDS was added followed by incubation at 37°C for 1 hour with 900 rpm shaking. After incubation. 75 μl of 20% Triton X-100 was added to quench the SDS and then incubated at 37°C for 1 hour with 900 rpm shaking. 200 units of Dpn II restriction enzyme (NEB, R0543) was added, and chromatins were digested at 37°C for overnight. Samples were incubated at 65°C for 20 min to inactivate Dpn II and then cooled to room temperature. 5.7 mL H2O, 700 μl 10x NEB T4 DNA ligase buffer and 3350 units of NEB T4 ligase (NEB, M0202) were added to samples and mixed by swirling at room temperature for overnight. 300 μg of proteinase kinase (Invitrogen, AM2548) was added to samples and incubate at 65°C water bath for overnight. 300 μg of RNase A (Thermo Scientific, EN0531) was then added to samples and the samples were incubated at 37°C for 45 min. The samples were subjected to phenol/chloroform/isoamyl extraction and ethanol precipitation and finally resuspended in 150 μl of 10 mM tris-HCl (pH=7.5). The purified DNA samples was then mixed with 50 μl rCutSmart (NEB, B6004), 295 μl H2O and 50 units of Nla III (NEB, R0125). The mixture was incubated at 37°C with shaking at 500 rpm shaking on the ThermoMixer overnight. The Nla III restriction enzyme was inactivated by incubating at 65°C for 25 min. A ligation mix containing 12.1 mL H2O, 1.4 mL NEB T4 DNA ligase buffer and 100 units of T4 ligase was added to samples, and samples were incubated at room temperature overnight. The samples were purified using phenol/chloroform/isoamyl, precipitated with ethanol, and dissolved in 250 μl tris-HCl (pH=7.5). Finally, the DNA was then purified with QIAquick PCR Purification Kit (QIAGEN, 28104). A total of 800 ng of purified DNA were used as template for 20 cycles of PCR with Phanta Master Mix (Vazyme, P51101), and the PCR products were purified with NucleoSpin Gel and PCR Clean-up kit (MACHEREY-NAGEL, 740609).
For DNA library construction, a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, E7645S) was used according to the manufacturer’s instructions.

value: muscle

value: myoblast

value: PDS

tag: batch


title: cLtp1_4

description:
Library name: Sample 24
cLtp1_4


title: E53 human metatarsal, digit 2, rep 1

description: Library name: FM2_early_rep1

source_name: Metatarsal, digit II

value: Metatarsal, digit II

value: chondrocytes


title: cLtp1_3

description:
Library name: Sample 23
cLtp1_3


title: cWT_5

description:
Library name: Sample 20
cWT_5

value: Wildtype (WT)


title: Mouse Ccne1 4C DMSO

description:
Library name: Ccne1_DMSO_4C
C2C12 cell Ccne1 4C-seq in DMSO treatment

value: DMSO


title: E53 human foot phalanges, digit 5, rep 1

description: Library name: FP5_early_rep1

source_name: Foot phalanges, digit V

value: Foot phalanges, digit V

value: Male


title: E53 human metatarsal, digit 1, rep 1

description: Library name: FM1_early_rep1

source_name: Metatarsal, digit I

value: Metatarsal, digit I


title: cPhp1_5

description:
Library name: Sample 30
cPhp1_5

value: In vitro culture


title: Dep2

description: Library name: Dep-2

source_name: prefrontal cortex

value: prefrontal cortex

value: chronic social defeat stress (CSDS) model


title: Mouse MuSC ASC PDS MAX bio rep1

description:
Library name: MAX-PDS_rep1
Mouse MuSC ASC48 PDS MAX bio rep1

data_processing:
The raw data was first pre-processed by initial quality assessment, adapters trimming, and low-quality filtering and then mapped to the mouse reference genome (mm10) using Bowtie2, and only the non-redundant reads were kept.
The peaks (sites) were identified using MACS2. During the peak calling, the cutoff was set to p value euqals to 0.001 or q value equals to 0.05, for G4, H3K4me3, and MAX CUT&RUN-Seq experiment.
Assembly: mm10 or hg38
Supplementary files format and content: Bigwig,narrowPeak

source_name: skeletal muscle

growth_protocol: Freshly isolated muscle stem cells were cultured in growth medium (F10 medium containing 20% FBS, 5 ng/mL basic fibroblast growth factor (bFGF) and 1% P/S). To induce differentiation, after cultured for 72h the cell medium was altered to differentiation medium (F10 with 2% HS and 1% P/S) under the same culture environment.

extract_protocol:
Skeletal muscle tissue from mouse hindlimb and forelimb muscles were dissected, gently minced with blades and digested with Collagenase II (1000U/ml) in Ham’s F10 for 90 minutes in a shaking water bath at 37°C. Digested tissue was then washed twice with rinsing media (10% HS, in Ham’s F-10) and centrifuged at 700 xg at 4°C for 5 minutes. Second digestion was performed by adding Collagenase II (1000U/ml) and Dispase (11U/ml) in rinsing media and incubated in shaking water bath at 37°C for 30 minutes. Digested tissue was passed through a 20-gauge needle for 12 times and filtered through a 40 μm filter followed by spinning at 700 xg for 5 min at 4°C. For mouse muscles, MuSCs were then sorted out by FACS Aria Fusion (BD) and collected as GFP+ groups. For human muscles, cells were stained with antibodies and FITC-(CD45-, CD31-, CD34-) APC+(CD29+) PE-CY7+ (CD56+) cells were sorted out as human MuSCs. Isolated satellite cells were immediately collected or were cultured in Ham’s F10 supplemented with 20% FBS and bFGF (0.025 μg/ml) (growth medium) for other assays. CUT&RUN protocol is referred to CUT&RUN assay kit (Cell Signaling Technology, 86652,).
For DNA library construction, a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, E7645S) was used according to the manufacturer’s instructions.

value: skeletal muscle

value: mouse primary muscle stem cell

value: 48h-treated activated muscle stem cell


title: E53 human foot phalanges, digit 4, rep 1

description: Library name: FP4_early_rep1

source_name: Footphalanges, digit IV

value: Footphalanges, digit IV


title: Wild-Type,Muscle,Time0 r2

description: Library name: L64904

value: Muscle

value: Wild Type

value: Fed with Sugar


title: cWT_1

description:
Library name: Sample 16
cWT_1


title: cWT_2

description:
Library name: Sample 17
cWT_2


title: E58 human hand phalanges, digit 1, rep 2

description: Library name: HP1_early_rep2

source_name: Hand phalanges, digit I

value: Hand phalanges, digit I


title: Mouse MuSC ASC DMSO MAX bio rep1

description:
Library name: MAX-DMSO_rep1
Mouse MuSC ASC48 DMSO MAX bio rep1


title: cWT_4

description:
Library name: Sample 19
cWT_4


title: Mouse MuSC ASC PDS H3K4me3 bio rep2

description:
Library name: H3K4ME3-PDS_rep2
Mouse MuSC ASC48 PDS H3K4me3 bio rep2

value: PDS


title: cWT_3

description:
Library name: Sample 18
cWT_3

value: Wildtype (WT)


title: aLtp1_4

description:
Library name: Sample 14
aLtp1_4

source_name: Mouse Abscess Material

value: Mouse Abscess Material

value: ltp1 mutant


title: E53 human metatarsal, digit 3, rep 1

description: Library name: FM3_early_rep1

source_name: Metatarsal, digit III

value: Metatarsal, digit III

value: chondrocytes

value: Male


title: aLtp1_2

description:
Library name: Sample 12
aLtp1_2


title: cLtp1_1

description:
Library name: Sample 21
cLtp1_1

value: In vitro culture


title: E53 human foot phalanges, digit 3, rep 1

description: Library name: FP3_early_rep1

source_name: Foot phalanges, digit III

value: Foot phalanges, digit III


title: cPhp1_3

description:
Library name: Sample 28
cPhp1_3

value: php1 mutant


title: E53 human foot phalanges, digit 2, rep 1

description: Library name: FP2_early_rep1

source_name: Foot phalanges, digit II

value: Foot phalanges, digit II


title: aLtp1_5

description:
Library name: Sample 15
aLtp1_5


title: aLtp1_1

description:
Library name: Sample 11
aLtp1_1


title: Mouse MuSC ASC PDS H3K4me3 bio rep1

description:
Library name: H3K4ME3-PDS_rep1
Mouse MuSC ASC48 PDS H3K4me3 bio rep1

value: skeletal muscle

value: mouse primary muscle stem cell

value: 48h-treated activated muscle stem cell


title: aLtp1_3

description:
Library name: Sample 13
aLtp1_3


title: cLtp1_2

description:
Library name: Sample 22
cLtp1_2


title: E53 human foot phalanges, digit 1, rep 1

description: Library name: FP1_early_rep1

source_name: Foot phalanges, digit I

value: Foot phalanges, digit I


title: Mouse MuSC ASC DMSO H3K4me3 bio rep2

description:
Library name: H3K4ME3-DMSO_rep2
Mouse MuSC ASC48 DMSO H3K4me3 bio rep2

value: DMSO


title: Mouse MuSC ASC DMSO H3K4me3 bio rep1

description:
Library name: H3K4ME3-DMSO_rep1
Mouse MuSC ASC48 DMSO H3K4me3 bio rep1


title: aPhp1_2

description:
Library name: Sample 7
aPhp1_2


title: E53 human metacarpal, digit 4, rep 1

description: Library name: HM4_early_rep1

source_name: Metacarpal, digit IV

value: Metacarpal, digit IV


title: Mouse MuSC ASC MAX bio rep1

description:
Library name: ASC_MAX_rep1
Mouse MuSC ASC48 MAX bio rep1

value: 48h-cultured activated muscle stem cell


title: aPhp1_4

description:
Library name: Sample 9
aPhp1_4


title: E53 human metacarpal, digit 5, rep 1

description: Library name: HM5_early_rep1

source_name: Metacarpal, digit V

value: Metacarpal, digit V


title: aPhp1_3

description:
Library name: Sample 8
aPhp1_3

value: Mouse Abscess Material


title: aPhp1_5

description:
Library name: Sample 10
aPhp1_5


title: Mouse MuSC DSC G4 bio rep2

description:
Library name: DSC_G4_rep2
Mouse MuSC DSC G4 bio rep2

value: 96h-cultured differentiated muscle stem cell


title: aWT_5

description:
Library name: Sample 5
aWT_5

value: Wildtype (WT)


title: Mouse MuSC DSC G4 bio rep3

description:
Library name: DSC_G4_rep3
Mouse MuSC DSC G4 bio rep3


title: aWT_4

description:
Library name: Sample 4
aWT_4


title: aWT_3

description:
Library name: Sample 3
aWT_3


title: E53 human metacarpal, digit 3, rep 1

description: Library name: HM3_early_rep1

source_name: Metacarpal, digit III

value: Metacarpal, digit III

value: chondrocytes


title: Mouse MuSC DSC G4 bio rep1

description:
Library name: DSC_G4_rep1
Mouse MuSC DSC G4 bio rep1


title: aWT_1

description:
Library name: Sample 1
aWT_1


title: E53 human metacarpal, digit 1, rep 1

description: Library name: HM1_early_rep1

source_name: Metacarpal, digit I

value: Metacarpal, digit I

value: Male


title: aWT_2

description:
Library name: Sample 2
aWT_2


title: E53 human hand phalanges, digit 5, rep 1

description: Library name: HP5_early_rep1

source_name: Hand phalanges, digit V

value: Hand phalanges, digit V


title: FUR mutant Haemophilus influenzae RdkW20 in anaerobiosis replica 3

city: Mutilva Baja

first: Junkal

last: Garmendia

address: Pamplona, 123

country: Spain

institute: Instituto de Agrobiotecnologia, Consejop Superior de Investigaciones Científicas

description:
Library name: FUR_mutant_anaerobiosis_rep3
Anaerobiosis

data_processing:
The adapters were removed from the sequenced libraries by TrimGalore v0.6.10 (www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters for paired-end Illumina reads and reads <20 bps and/or error rate (TrimGalore option “-e”) higher than 0.1 were discarded.
Previously to the mapping step, the genome was indexed with STAR v2.7.10 with the parameters –runMode genomeduplicated reads were marked with Picard tools v3.2 (https://broadinstitute.github.io/picard/)Generate –genomeSAindexNbases 9.4. The remaining reads were mapped to the H. influenzae RdKW20 (GCA_000027305.1) genome using STAR using default parameters with the following exceptions: “–outputMultimapperOrder random” and “–twopassMode basic.”
Duplicated reads were marked with Picard tools v3.2 (https://broadinstitute.github.io/picard/)
Quantification was done by HTSeq-count included into HTSeq v.2.0.5, using the NCBI annotation in GTF format with the option “–stranded no.”
Statistical analysis and FPKM calculation were done using DESeq2 v1.44.0 (R package). Expression tracks were generated with the function bamCoverage included into the software deepTools v3.5.2. with the parameter –normalizeUsing RPKM.
Assembly: GCA_000027305.1
Supplementary files format and content: Genome broser tracks are provided with BigWig format
Supplementary files format and content: Tabular-text files with gene counts are provided.

organism: Haemophilus influenzae

source_name: Bacteria

growth_protocol: l  H. influenzae clinical strains were recovered from COPD respiratory samples (BioProject accession number PRJNA282520). H. influenzae strains were grown at 37ºC on PolyViteX (PVX) agar (bioMérieux, 43101), on brain-heart infusion (BHI, Condalab, 1400.10) agar supplemented with 10 μg/mL hemin (Merck, H9039) and 10 μg/mL nicotinamide adenine dinucleotide (NAD, Merck, N0632), referred to as sBHI agar, or on supplemented Haemophilus Test Medium agar (HTM, Oxoid, CM0898), referred to as sHTM agar. H. influenzae liquid cultures were grown at 37ºC in sBHI. Solid and liquid cultures were grown aerobically in 5% CO2, or under static anaerobic conditions in an anaerobic workstation (Don Withlety A25). To monitor growth, H. influenzae strains were grown on PVX agar for 12 h in aerobiosis or anaerobiosis in all cases. Erythromycin 11 μg/mL (Erm11) or Spectinomycin 50 μg/mL (Spec50) were used when required.

extract_protocol:
l  RNA for sequencing was isolated from bacteria grown in sBHI to OD600=0.3. H. influenzae was grown for 12 h on PVX agar. Two to five colonies were inoculated into 10 mL sBHI, grown for 12 h at 90 r.p.m., diluted into 20 mL fresh sBHI to OD600=0.05, and grown to OD600=0.3 at 180 r.p.m. Next, 7 mL bacterial cultures were recovered, pelleted (4,000 r.p.m, 4 min), flash frozen, and stored at -80ºC. Bacterial RNA was isolated using NucleoSpin RNA kit (Macherey-Nagel). Alternatively, bacterial suspensions collected from PVX agar anaerobic growth were normalized to OD600=0.4 in sBHI, 5 mL aliquots were transferred to 50 mL-Falcon tubes with 20 mL sBHI and grown to OD600=0.3 also in static anaerobiosis. Next, 25 mL bacterial cultures were recovered, pelleted (4,000 r.p.m, 4 min), flash frozen, and stored at -80ºC.
Total RNA was isolated using TRIzol reagent (Invitrogen). In both cases, to prevent any DNA interference, a second DNase digestion was performed using RNase-free DNase and cleaning on a RNeasy Mini column (Qiagen). Purified RNA was quantified on a Nanodrop OneC (Thermofisher Scientific), libraries were checked for quality control with RNA 6000 Nano LabChips (Agilent 2,100 Bioanalyzer), and sequenced by Admera Health on an Illumina HiSeq platform with 2×150 bp reads, estimated 20M PE reads per sample, 10M in each direction. Three replicates per sample type were sequenced.

tag: strain

value: Bacteria

value: RdKW20 derivative strain where the FUR gene has been inactivated


title: FUR mutant Haemophilus influenzae RdkW20 in anaerobiosis replica 2

description:
Library name: FUR_mutant_anaerobiosis_rep2
Anaerobiosis


title: Mouse MuSC AS-48h G4 bio rep2

description:
Library name: ASC-48h_G4_rep2
Mouse MuSC ASC48 G4 bio rep2

value: skeletal muscle

value: mouse primary muscle stem cell


title: E53 human hand phalanges, digit 4, rep 1

description: Library name: HP4_early_rep1

source_name: Hand phalanges, digit IV

value: Hand phalanges, digit IV


title: FUR mutant Haemophilus influenzae RdkW20 in anaerobiosis replica 1

description:
Library name: FUR_mutant_anaerobiosis_rep1
Anaerobiosis


title: Wild type Haemophilus influenzae RdkW20 in anaerobiosis replica 3

description:
Library name: WT_anaerobiosis_rep3
Anaerobiosis

value: Haemophilus influenzae, non typeable, RdKW20 strain


title: Mouse MuSC AS-48h G4 bio rep1

description:
Library name: ASC-48h_G4_rep1
Mouse MuSC ASC48 G4 bio rep1


title: E53 human hand phalanges, digit 3, rep 1

description: Library name: HP3_early_rep1

source_name: Hand phalanges, digit III

value: Hand phalanges, digit III


title: Wild type Haemophilus influenzae RdkW20 in anaerobiosis replica 1

description:
Library name: WT_anaerobiosis_rep1
Anaerobiosis


title: aPhp1_1

description:
Library name: Sample 6
aPhp1_1

value: php1 mutant


title: E53 human hand phalanges, digit 1, rep 1

description: Library name: HP1_early_rep1

value: Hand phalanges, digit I


title: Wild type Haemophilus influenzae RdkW20 in anaerobiosis replica 2

description:
Library name: WT_anaerobiosis_rep2
Anaerobiosis


title: Mouse MuSC ASC-24h G4 bio rep3

description:
Library name: ASC-24h_G4_rep3
Mouse MuSC ASC24 G4 bio rep3

value: 24h-cultured activated muscle stem cell


title: Mouse MuSC ASC-24h G4 bio rep2

description:
Library name: ASC-24h_G4_rep2
Mouse MuSC ASC24 G4 bio rep2


title: E74 human metacarpal, digit 3, rep 3

description: Library name: HM3_late_rep4

value: Female


title: Mouse MuSC ASC-24h G4 bio rep1

description:
Library name: ASC-24h_G4_rep1
Mouse MuSC ASC24 G4 bio rep1


title: Mouse MuSC FISC G4 bio rep3

description:
Library name: FISC_G4_rep3
Mouse MuSC FISC G4 bio rep3

value: freshly isolated muscle stem cell


title: E53 human metacarpal, digit 2, rep 1

description: Library name: HM2_early_rep1

source_name: Metacarpal, digit II

value: Metacarpal, digit II


title: E74 human hand phalanges, digit 3, rep 3

description: Library name: HP3_late_rep4

value: chondrocytes


title: Mouse MuSC AS-48h G4 bio rep3

description:
Library name: ASC-48h_G4_rep3
Mouse MuSC ASC48 G4 bio rep3

source_name: skeletal muscle

value: 48h-cultured activated muscle stem cell


title: E67 human metatarsal, digit 5, rep 3

description: Library name: FM5_late_rep3

source_name: Metatarsal, digit V

value: Metatarsal, digit V

value: Male


title: E67 human metatarsal, digit 3, rep 3

description: Library name: FM3_late_rep3

value: Metatarsal, digit III


title: Mouse MuSC FISC G4 bio rep2

description:
Library name: FISC_G4_rep2
Mouse MuSC FISC G4 bio rep2


title: E67 human metatarsal, digit 4, rep 3

description: Library name: FM4_late_rep3

source_name: Metatarsal, digit IV

value: Metatarsal, digit IV


title: E67 human metatarsal, digit 2, rep 3

description: Library name: FM2_late_rep3

source_name: Metatarsal, digit II

value: Metatarsal, digit II


title: Mouse MuSC FISC G4 bio rep1

description:
Library name: FISC_G4_rep1
Mouse MuSC FISC G4 bio rep1

value: skeletal muscle

value: mouse primary muscle stem cell


title: Mouse MuSC ASC NC MicroC tech2

description: Library name: siNC_Micro-C_tech2

data_processing:
The Micro-C raw data was mapped to the mouse reference genome (mm10) using bwa. Next, we used the parse module of the pairtools pipeline to find ligation junctions in Micro-C libraries. Then the parsed pairs were then sorted using pairtools sort, and PCR duplication pairs were removed by pairtools dedup. Finally, pairtools split was used to generate .pairs files and .bam files. Loops were identified by HiCCUPS using parameters (-k KR -t 20) and scaled to 5 kb resolution. Cool files were generated by cooler to further compare the interaction difference. Interaction comparisons were calculated by HiCcompare, ‘A’ value cutoff was set to 15 to filter out interactions with low average expression. Adjusted p value cutoff was set to 0.1 to identify the significant interaction change.
Assembly: mm10
Supplementary files format and content: .hic

growth_protocol: Freshly isolated muscle stem cells were cultured in F10 medium containing 20% FBS,5 ng/mL basic fibroblast growth factor (bFGF) and 1% P/S.

extract_protocol:
Micro-C for muscle stem cells was performed following published protocol for mammalian Micro-C. Briefly, cells were first crosslinked at 1 ml per million cells of 3mM DSG crosslinker (MedChemExpress, HY-114697) for 35 min at room temperature and then 1% formaldehyde was added and incubated for 10 more minutes. The crosslink was quenched with 0.375 M Tris(pH 7.0) for 5 min. Cells were pelleted at 1000g  at 4 °C for 5 min and resuspended with ice-cold PBS. 1 Million cells were split into each tube and pelleted by centrifugation. After snap frozen in liquid nitrogen, cells were kept at -80°C. For cell lysis, cells were thawed on ice for 5 min, and lysed with 0.5 ml MB 1 buffer (10 mM Tris–HCl, pH 7.5, 50 mM NaCl, 5 mM, MgCl2, 3 mM CaCl2, 0.2% NP-40, 1×PIC) on ice for 20 min, washed once with MB 1 buffer, then resuspended in 100 ul MB1 buffer. Mnase concentration for muscle stem cells was predetermined using MNase titration experiments. Chromatin was digested by adding 0.1 ul Mnase (NEB, M0247S) and incubating for 20 min at 37 °C, 1000rpm. Digestion was stopped by adding 8 μl of 500 mM EGTA and incubating at 65 °C for 10 min. Cells were then washed twice with ice-cold MB2 buffer (10 mM Tris–HCl, pH 7.5, 50 mM NaCl, 10 mM, MgCl2). The Mnase digested DNA ends were polished with T4 PNK (NEB M0201), followed by DNA polymerase Klenow fragment (NEB M0210), and then repaired and labeled by adding biotinylated dATP and dCTP (Jena Bioscience, NU-835-BIO14-S and NU-809-BIOX-S, respectively), and TTP/GTP. After washing with buffer MB3 (50 mM Tris–HCl, 10 mM, MgCl2 ). Ligation was performed for 4 h at room temperature using T4 DNA ligase (NEB M0202). Dangling ends were removed by a 15-minute incubation with Exonuclease III (NEB 0206) at 37 °C. DNAs were de-crosslinked overnight at 65°C. After DNA extraction by ethanol precipitation, size selection was performed using DNA purification beads to enrich ligated fragments at about 230bp. Then biotin selection was done using 10 μl Dynabeads MyOne Streptavidin C1 beads (Invitrogen 65001).
For DNA library construction, a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, E7645S) was used according to the manufacturer’s instructions.

value: 48h-treated activated muscle stem cell

value: siNC


title: E67 human metatarsal, digit 1, rep 3

description: Library name: FM1_late_rep3

source_name: Metatarsal, digit I

value: Metatarsal, digit I


title: E67 human foot phalanges, digit 5, rep 3

description: Library name: FP5_late_rep3

source_name: Foot phalanges, digit V

value: Foot phalanges, digit V


title: Mouse MuSC ASC siMAX MicroC tech1

description: Library name: siMAX_Micro-C_tech1

value: siMAX


title: E67 human foot phalanges, digit 4, rep 3

description: Library name: FP4_late_rep3

source_name: Footphalanges, digit IV

value: Footphalanges, digit IV


title: Mouse MuSC ASC NC MicroC tech1

description: Library name: siNC_Micro-C_tech1


title: E67 human foot phalanges, digit 3, rep 3

description: Library name: FP3_late_rep3

source_name: Foot phalanges, digit III

value: Foot phalanges, digit III


title: Mouse MuSC ASC DMSO MicroC

description: Library name: DMSO_Micro-C

value: DMSO


title: E67 human foot phalanges, digit 1, rep 3

description: Library name: FP1_late_rep3

source_name: Foot phalanges, digit I

value: Foot phalanges, digit I

value: chondrocytes


title: Mouse MuSC ASC siMAX bio rep2

description:
Library name: ASC_siMAX_RNA_rep2
Mouse MuSC ASC siMAX bio rep2

data_processing:
The adapter and low-quality sequences were trimmed from 3' to 5' ends for each read, and the reads shorter than 50 bp were discarded. The clean reads were aligned to the mouse (mm10) or human (hg38) reference genome with Hista2. Next, we used Cufflinks to quantify the gene expression. Genes were identified as DEGs if the absolute log2foldchange of expression level is greater than 0.5 and the adjusted p-value is <0.05 between two stages/conditions by DESeq2.
Assembly: mm10 or hg38
Supplementary files format and content: Bigwig

growth_protocol: Freshly isolated muscle stem cells were cultured in F10 medium containing 20% FBS, 5 ng/mL basic fibroblast growth factor (bFGF) and 1% P/S.

extract_protocol:
RNAs were extracted by Trizol reagent referred to it's protocal (Ambion, 15596)
Total RNAs were subject to polyA selection (Ambion, 61006) followed by library preparation using NEBNext Ultra II RNA Library Preparation Kit (NEB, E7770S).


title: Mouse MuSC ASC siMAX bio rep1

description:
Library name: ASC_siMAX_RNA_rep1
Mouse MuSC ASC siMAX bio rep1


title: E67 human metacarpal, digit 5, rep 3

description: Library name: HM5_late_rep3

source_name: Metacarpal, digit V

value: Metacarpal, digit V


title: E67 human metacarpal, digit 4, rep 3

description: Library name: HM4_late_rep3

source_name: Metacarpal, digit IV

value: Metacarpal, digit IV

value: Male


title: E67 human metacarpal, digit 3, rep 3

description: Library name: HM3_late_rep3

source_name: Metacarpal, digit III

value: Metacarpal, digit III


title: Mouse MuSC ASC siMAX MicroC tech2

description: Library name: siMAX_Micro-C_tech2


title: E67 human metacarpal, digit 2, rep 3

description: Library name: HM2_late_rep3

value: Metacarpal, digit II


title: Mouse MuSC ASC PDS bio rep2

description:
Library name: ASC_PDS_RNA_rep2
Mouse MuSC ASC PDS bio rep2

value: skeletal muscle

value: PDS


title: E67 human hand phalanges, digit 5, rep 3

description: Library name: HP5_late_rep3

source_name: Hand phalanges, digit V

value: Hand phalanges, digit V


title: E67 human foot phalanges, digit 2, rep 3

description: Library name: FP2_late_rep3

source_name: Foot phalanges, digit II

value: Foot phalanges, digit II


title: E67 human hand phalanges, digit 3, rep 3

description: Library name: HP3_late_rep3

value: Hand phalanges, digit III


title: Mouse MuSC ASC bio rep2

description:
Library name: ASC_RNA_rep2
Mouse MuSC ASC bio rep2

value: mouse primary muscle stem cell

value: 48h-cultured activated muscle stem cell


title: E67 human metacarpal, digit 1, rep 3

description: Library name: HM1_late_rep3

source_name: Metacarpal, digit I

value: Metacarpal, digit I


title: Mouse MuSC ASC PDS bio rep1

description:
Library name: ASC_PDS_RNA_rep1
Mouse MuSC ASC PDS bio rep1

value: 48h-treated activated muscle stem cell


title: Mouse MuSC ASC DMSO bio rep2

description:
Library name: ASC_DMSO_RNA_rep2
Mouse MuSC ASC DMSO bio rep2

value: DMSO


title: E67 human hand phalanges, digit 4, rep 3

description: Library name: HP4_late_rep3

source_name: Hand phalanges, digit IV

value: Hand phalanges, digit IV


title: Mouse MuSC ASC PDS MicroC

description: Library name: PDS_Micro-C


title: Mouse MuSC ASC siNC bio rep1

description:
Library name: ASC_siNC_RNA_rep1
Mouse MuSC ASC siNC bio rep1

value: siNC


title: E67 human hand phalanges, digit 2, rep 3

description: Library name: HP2_late_rep3

source_name: Hand phalanges, digit II

value: Hand phalanges, digit II

value: chondrocytes


title: Mouse MuSC FISC bio rep1

description:
Library name: FISC_RNA_rep1
Mouse MuSC FISC bio rep1

source_name: skeletal muscle

value: freshly isolated muscle stem cell


title: Mouse MuSC ASC bio rep1

description:
Library name: ASC_RNA_rep1
Mouse MuSC ASC bio rep1


title: E67 human hand phalanges, digit 1, rep 3

description: Library name: HP1_late_rep3

source_name: Hand phalanges, digit I

value: Hand phalanges, digit I

value: Male


title: Mouse MuSC ASC siNC bio rep2

description:
Library name: ASC_siNC_RNA_rep2
Mouse MuSC ASC siNC bio rep2

value: skeletal muscle


title: B0092, HNC rep 4

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

description: Library name: S8

data_processing:
Fastq files were processed using the nf-core/rnaseq pipeline (version 3.12.0, https://nf-co.re/rnaseq/3.12).
Sequencing adapters were removed using Cutadapt (version 3.4) as part of the trimgalore package (version 0.6.7).
Reads were aligned using STAR (version 2.7.9a) to the mouse transcriptome (GRCm39, gene annotation from Ensembl release 104).
Gene quantification was performed using Salmon (version 1.10.1).
Tables with transcript and gene counts were generated by the tximport R package (version 1.26.0) under R version 4.2.2.
Assembly: GRCm39
Supplementary files format and content: Txt file containg gene counts

source_name: skeletal muscle (quadriceps)

growth_protocol: B0092 cells were grown in DMEM F-12 media supplemented with 10% FBS and 1x penicillin/streptomycin, and maintained at 37 C in a humidified atmosphere supplemented with 5% C02. Cells were maintained at low passages in T182cm^2 flasks until they reached ~90% confluence, where they were then passaged.

extract_protocol:
Total RNA from skeletal muscle (quadriceps) was isolated using the RNeasy Mini Kit (Qiagen)
Universal Plus mRNA-Seq library preparation kit with NuQuant (Nugen/Tecan)

treatment_protocol: Mice were injected with 5x10^5 B0092 cells (in 200uL sterile PBS) subcutaneously in the nape region of the neck and then sacrificed after 36 days of tumor growth.

value: skeletal muscle (quadriceps)

value: Head and neck squamous cell carcinoma

value: wild type

value: B0092 (tumor)


title: E72 human metatarsal, digit 4, rep 2

description: Library name: FM4_late_rep2

source_name: Metatarsal, digit IV

value: Metatarsal, digit IV


title: E72 human metatarsal, digit 5, rep 2

description: Library name: FM5_late_rep2

source_name: Metatarsal, digit V

value: Metatarsal, digit V


title: Mouse MuSC FISC bio rep2

description:
Library name: FISC_RNA_rep2
Mouse MuSC FISC bio rep2

value: mouse primary muscle stem cell


title: Mouse MuSC ASC DMSO bio rep1

description:
Library name: ASC_DMSO_RNA_rep1
Mouse MuSC ASC DMSO bio rep1

value: 48h-treated activated muscle stem cell


title: B0092, HNC rep 3

description: Library name: S7


title: B0092, Control rep 4

description: Library name: S4

value: PBS (vehicle)


title: E72 human metatarsal, digit 3, rep 2

description: Library name: FM3_late_rep2

source_name: Metatarsal, digit III

value: Metatarsal, digit III


title: E72 human metatarsal, digit 2, rep 2

description: Library name: FM2_late_rep2

source_name: Metatarsal, digit II

value: Metatarsal, digit II


title: B0092, HNC rep 2

description: Library name: S6


title: B0092, HNC rep 1

description: Library name: S5


title: E72 human foot phalanges, digit 5, rep 2

description: Library name: FP5_late_rep2

source_name: Foot phalanges, digit V

value: Foot phalanges, digit V


title: E72 human foot phalanges, digit 4, rep 2

description: Library name: FP4_late_rep2

source_name: Footphalanges, digit IV

value: Footphalanges, digit IV

value: chondrocytes


title: E72 human foot phalanges, digit 3, rep 2

description: Library name: FP3_late_rep2

source_name: Foot phalanges, digit III

value: Foot phalanges, digit III


title: B0092, Control rep 1

description: Library name: S1


title: E72 human foot phalanges, digit 2, rep 2

description: Library name: FP2_late_rep2

value: Foot phalanges, digit II

value: Male


title: RNAseq_S598_CD8_MHV_D7_Spleen_Old_4

first: Chen

last: Yao

address: 5901 FOREST PARK RD, NS6 218

institute: UT Southwestern Medical Center

description: Library name: RNAseq_S598_CD8_MHV_D7_Spleen_Old_4

data_processing:
RNA-seq library were aligned to mouse genome (mm10) using STAR (2.5.4a). Transcript abundance of pseudo-aligned RNA-seq reads to ENSEMBL transcripts were quanlified with kallisto (v0.44.0).
Assembly: mm10
Supplementary files format and content: txt files of TPM.

extract_protocol:
Lung fragments or sorted S598 tetramer + CD8 T cells were used for RNA extraction using the qiagen rna extraction kit.
RNAseq libraries were generated using NEBNext Ultra II RNA Library Prep Kit for Illumina.

value: Spleen

value: ex vivo

value: S598 Tetramer+ CD8


title: E72 human metacarpal, digit 5, rep 2

description: Library name: HM5_late_rep2

source_name: Metacarpal, digit V

value: Metacarpal, digit V


title: E72 human foot phalanges, digit 1, rep 2

description: Library name: FP1_late_rep2

source_name: Foot phalanges, digit I

value: Foot phalanges, digit I


title: RNAseq_S598_CD8_MHV_D7_Spleen_Old_3

description: Library name: RNAseq_S598_CD8_MHV_D7_Spleen_Old_3


title: B0092, Control rep 2

description: Library name: S2

value: skeletal muscle (quadriceps)

value: Head and neck squamous cell carcinoma

value: wild type


title: RNAseq_S598_CD8_MHV_D7_Spleen_Old_2

description: Library name: RNAseq_S598_CD8_MHV_D7_Spleen_Old_2


title: E72 human metacarpal, digit 4, rep 2

description: Library name: HM4_late_rep2

source_name: Metacarpal, digit IV

value: Metacarpal, digit IV


title: RNAseq_S598_CD8_MHV_D7_Spleen_Young_4

description: Library name: RNAseq_S598_CD8_MHV_D7_Spleen_Young_4


title: E72 human metacarpal, digit 1, rep 2

description: Library name: HM1_late_rep2

value: Metacarpal, digit I


title: E72 human metatarsal, digit 1, rep 2

description: Library name: FM1_late_rep2

source_name: Metatarsal, digit I

value: Metatarsal, digit I


title: E72 human metacarpal, digit 2, rep 2

description: Library name: HM2_late_rep2

source_name: Metacarpal, digit II

value: Metacarpal, digit II


title: RNAseq_S598_CD8_MHV_D7_Spleen_Young_3

description: Library name: RNAseq_S598_CD8_MHV_D7_Spleen_Young_3


title: Intergenic control BCMA CAR T cells (C6M3)

first: Kevin

last: Bi

address: 300 Binney Street

institute: Broad Institute

description: Library name: C6M3_intergenic

data_processing:
Reads were adapter- and quality-trimmed using Trimmomatic (v.0.36). Trimmed reads were quantified by pseudoalignment to GRCh38 using Kallisto (v.0.44.0). Abundance estimates were then transformed into gene counts using Tximport (v.1.8.0).
Assembly: GRCh38
Supplementary files format and content: csv file includes aggregated gen count values for each Sample

source_name: T cell

extract_protocol:
CAR+ T cells were sorted on a Sony SH800 Cell Sorter. Following sorting, RNA was isolated using the Qiagen RNeasy Micro Kit (Cat-no. 74004).
Bulk RNA sequencing libraries were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Cat-no. E7765) and sequenced on an Illumina NextSeq 500 instrument.

value: T cell

value: Intergenic control KO


title: E72 human hand phalanges, digit 5, rep 2

description: Library name: HP5_late_rep2

source_name: Hand phalanges, digit V

value: Hand phalanges, digit V

value: chondrocytes


title: Intergenic control BCMA CAR T cells (C6M2)

description: Library name: C6M2_intergenic


title: RNAseq_S598_CD8_MHV_D7_Spleen_Young_2

description: Library name: RNAseq_S598_CD8_MHV_D7_Spleen_Young_2


title: Intergenic control BCMA CAR T cells (C6M1)

description: Library name: C6M1_intergenic


title: B0092, Control rep 3

description: Library name: S3

value: PBS (vehicle)


title: RNAseq_S598_CD8_MHV_D7_Spleen_Young_1

description: Library name: RNAseq_S598_CD8_MHV_D7_Spleen_Young_1

value: Spleen


title: E72 human hand phalanges, digit 4, rep 2

description: Library name: HP4_late_rep2

source_name: Hand phalanges, digit IV

value: Hand phalanges, digit IV

value: Male


title: CDKN1B KO BCMA CAR T cells (C10M4)

description: Library name: C10M4_CDKN1B_g2

value: CDKN1B KO


title: RNAseq_Whole_tissue_MHV_D7_Lung_Old_4

description: Library name: RNAseq_Whole_tissue_MHV_D7_Lung_Old_4

source_name: Whole tissue

value: Lung

value: ex vivo

value: Whole tissue


title: CDKN1B KO BCMA CAR T cells (C10M3)

description: Library name: C10M3_CDKN1B_g2


title: CDKN1B KO BCMA CAR T cells (C10M2)

description: Library name: C10M2_CDKN1B_g2


title: RNAseq_Whole_tissue_MHV_D7_Lung_Old_3

description: Library name: RNAseq_Whole_tissue_MHV_D7_Lung_Old_3


title: RNAseq_S598_CD8_MHV_D7_Spleen_Old_1

description: Library name: RNAseq_S598_CD8_MHV_D7_Spleen_Old_1

value: S598 Tetramer+ CD8


title: E72 human hand phalanges, digit 2, rep 2

description: Library name: HP2_late_rep2

source_name: Hand phalanges, digit II

value: Hand phalanges, digit II


title: CDKN1B KO BCMA CAR T cells (C9M1)

description: Library name: C9M1_CDKN1B_g1


title: CUT&TAG H3K27ac 48hr post lenti infection with  empty vector CMK cells

city: Oxford

first: David

last: Cruz

address: John Radcliffe Hospital/Headley Way

department: Radcliffe Department of Medicine

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine, Oxford University

description: Library name: H3K27ac-48hr-CMK-EV

data_processing:
Lane specific FASTQ files for each sample were merged before processing. We utilized CUT-RUNTools 2.0  to process bulk CUT&Tag FASTQ files using the standard ‘CUT&Tag’ pipelines with ‘75  bp fastq sequence length’
Assembly: GRCh38
Supplementary files format and content: Big WIG
Library strategy: CUT&Tag

source_name: Hematopoietic

growth_protocol: CMK cells were cultured in IMDM basal media supplemented with 20% FBS (Cat no: 21875034, Gibco) and 1% Pen/Strep (Cat no: 15140122, Gibco). SET2 cells were cultured in RPMI basal media supplemented with 20% FBS and 1% Pen/Strep. JURKAT, THP1, K562, HEL and TF1 cells were cultured in RPMI basal media supplemented with 10% FBS and 1% Pen/Strep. TF1 cells were additionally supplemented with 20 ng/mL of recombinant human GM-CSF (Cat No: 300-03, Prepotech).

extract_protocol:
After tagmentation, DNA was isolated with the use of the Monarch PCR & DNA clean up kit (Cat no: T1030L, NEB) by resuspending 50 uL of each reaction with 700 uL of DNA Binding Buffer and following the manufacturer’s recommendation thereafter. DNA was eluted in 22 uL of elution buffer
21 ul of DNA were mixed with 25 uL of 2X NEBNext HiFi PCR Master mix (NEB), 2 uL of 10 uM P5 primer, 2 uL of 10 uM indexed P7 primer. 50 uL of amplified DNA were cleaned up with 1.2X AMPure XP beads as per manufacturer’s recommendation. DNA was quantified with Qubit fluorometer. Indexed libraries were pool proportionally and sequence with 150-bp paired end in a NexSeq 500 to achieve at least 5 million reads per sample.

treatment_protocol: 1E5 cells were used for H3K27ac marks or 3E5 cells for GATA1 or GATA2 binding. To remove cell debris and cell culture media, cells were washed twice in 500 uL of Wash Buffer (20 mM HEPES pH7.6,150 mM NaCl, 0.5 mM spermidine, 2% BSA, 1% protease inhibitor) and permeabilized with 200 uL of Antibody Buffer (Wash Buffer supplemented with 2mM EDTA, 0.005 % Digitonin in DMSO, 0.01% NP40) for 5 minutes in ice. Permeabilized cells were spun down for 5 minutes at 500g and resuspended in 50 uL Antibody Buffer. 2 uL SNAP-CUTANATM K-MetStat Panel were added to each H3K27ac reaction (Cat: 19-1002, EpiCypher). Nuclei were captured with 10 uL activated ConA magnetic beads (Cat: 93569S, Cell Signaling) and incubated for 20 min at room temperature. Afterwards, samples were incubated with 5 uL of anit-GATA1-C’ (Cell Signaling, clone : D24E4), 3 uL of anti-GATA1-N’ (Cell Signaling, clone : D52H6), or 5 uL anti-GATA2 (Cell Signaling, clone: E9T6F), 0.4 uL of anti-H3K27ac (Diagenode, clone: C15410196) or 5 uL rabbit IgG XP® Isotype Control (Cell Signaling, clone: DA1E, cat no: 66362) for 3 hrs, on a nutator at 4 °C. Antibody buffer was removed and permeabilized cells were resuspended in 50 uL of Dig Wash Buffer (Wash Buffer supplemented with 0.005% Digitonin and 0.01% NP40) with 1 uL of secondary antibody (clone: NBP1-72763, Novus Biologicals). Samples were incubated for 1 hr at room temperature on a nutator. Then, samples were washed twice with 200 uL Dig Wash Buffer and resuspended in 50 uL of dig 300 Wash Buffer (Dig Wash buffer supplemented with 150 mM NaCL). 2.5 uL of CUTANA™ pAG-Tn5 (Cat no: 15-101, EpiCypher) were added to each sample. Samples were incubated for were incubated for 1 hr at room temperature on a nutator. Then, samples were washed twice with 200 uL of dig 300 Wash Buffer and resuspended in 50 uL of Tagmentation Buffer (dig 300 Wash Buffer supplemented with 10mM MgCl2). Samples were incubated for 1 hr at 37 °C in a thermocycler.

value: Hematopoietic

value: CMK

value: Transformed leukemic cell

value: empty vector

value: 48hr post lenti


title: E72 human hand phalanges, digit 3, rep 2

description: Library name: HP3_late_rep2

source_name: Hand phalanges, digit III

value: Hand phalanges, digit III


title: RNAseq_Whole_tissue_MHV_D7_Lung_Old_2

description: Library name: RNAseq_Whole_tissue_MHV_D7_Lung_Old_2


title: E72 human metacarpal, digit 3, rep 2

description: Library name: HM3_late_rep2

source_name: Metacarpal, digit III

value: Metacarpal, digit III

value: chondrocytes


title: RNAseq_Whole_tissue_MHV_D7_Lung_Old_1

description: Library name: RNAseq_Whole_tissue_MHV_D7_Lung_Old_1


title: CDKN1B KO BCMA CAR T cells (C10M1)

description: Library name: C10M1_CDKN1B_g2

value: T cell


title: CUT&TAG H3K27ac 48hr post lenti infection with  empty vector HEL cells

description: Library name: H3K27ac-48hr-HEL-EV

value: HEL


title: CUT&TAG H3K27ac 48hr post lenti infection with GATA2 coding sequence in HEL cells

description: Library name: H3K27ac-48hr-HEL-GATA2

value: GATA2 cds


title: E72 human hand phalanges, digit 1, rep 2

description: Library name: HP1_late_rep2

source_name: Hand phalanges, digit I

value: Hand phalanges, digit I

value: Male


title: CUT&TAG H3K27ac 48hr post lenti infection with GATA2 coding sequence in CMK cells

description: Library name: H3K27ac-48hr-CMK-GATA2


title: RNAseq_Whole_tissue_MHV_D7_Lung_Young_4

description: Library name: RNAseq_Whole_tissue_MHV_D7_Lung_Young_4

value: Lung

value: ex vivo


title: CUT&TAG H3K27ac 48hr post lenti infection with GATA2 coding sequence in JURKAT cells

description: Library name: H3K27ac-48hr-JURKAT-GATA2

value: JURKAT


title: CUT&TAG H3K27ac 48hr post lenti infection with  empty vector JURKAT cells

description: Library name: H3K27ac-48hr-JURKAT-EV


title: CUT&TAG H3K27ac 48hr post lenti infection with empty vector in K562 cells

description: Library name: H3K27ac-48hr-K562-EV


title: E72 human metatarsal, digit 5, rep 1

description: Library name: FM5_late_rep1

source_name: Metatarsal, digit V

value: Metatarsal, digit V


title: CUT&TAG H3K27ac 48hr post lenti infection with GATA2 coding sequence in K562  cells

description: Library name: H3K27ac-48hr-K562-GATA2

value: Hematopoietic


title: CUT&TAG H3K27ac 48hr post lenti infection with  empty vector in SET2 cells

description: Library name: H3K27ac-48hr-SET2-EV


title: RNAseq_Whole_tissue_MHV_D7_Lung_Young_3

description: Library name: RNAseq_Whole_tissue_MHV_D7_Lung_Young_3

value: Whole tissue


title: E72 human metatarsal, digit 4, rep 1

description: Library name: FM4_late_rep1

source_name: Metatarsal, digit IV

value: Metatarsal, digit IV


title: E72 human metatarsal, digit 3, rep 1

description: Library name: FM3_late_rep1

source_name: Metatarsal, digit III

value: Metatarsal, digit III


title: CUT&TAG H3K27ac 48hr post lenti infection with GATA2 coding sequence in SET2 cells

description: Library name: H3K27ac-48hr-SET2-GATA2

value: Transformed leukemic cell

value: 48hr post lenti


title: E72 human metatarsal, digit 2, rep 1

description: Library name: FM2_late_rep1

source_name: Metatarsal, digit II

value: Metatarsal, digit II


title: CUT&TAG H3K27ac 48hr post lenti infection with  empty vector in TF1 cells

description: Library name: H3K27ac-48hr-TF1-EV

value: empty vector


title: CUT&TAG H3K27ac 48hr post lenti infection with GATA2 coding sequence in TF1 cells

description: Library name: H3K27ac-48hr-TF1-GATA2


title: E72 human metatarsal, digit 1, rep 1

description: Library name: FM1_late_rep1

value: Metatarsal, digit I

value: chondrocytes


title: CUT&TAG H3K27ac 48hr post lenti infection with empty vector in THP1 cells

description: Library name: H3K27ac-48hr-THP1-EV


title: SM_8

city: Clayton

first: Stephanie

middle: Irene

last: Studniberg

state: VIC

address: 19 Innovation Walk

department: Microbiology

country: Australia

institute: Infection Discovery Program, Monash Biomedicine Discovery Institute

data_processing:
Raw sequence reads in FASTQ file format were aligned to the human reference genome GRCh38/hg38 using the align() function in Bioconductor package Rsubread (v 2.10.5) with default parameters.
Fragments of aligned sequences overlapping Gencode human genes (GRCh38.p13) were quantified with featureCounts, with Gencode v38 primary assembly annotation used in the quantification.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files were written from the R prompt: columns represent gene symbols, total gene length (total base count of all exons) and the number of fragments mapping to the gene.

source_name: PBMCs

extract_protocol:
Total RNA was isolated from 2x10^5 PBMCs using the RNeasy Plus Mini Kit (QIAGEN) following manufacturers' instructions.
Libraries were prepared with either 25ng or 50ng total RNA using Illumina TruSeq RNA Library Prep Kit (<100ng) following manufacturers' instructions.

treatment_protocol: PBMCs were frozen at collection.

value: PBMCs

tag: disease state

value: symptomatic (SM) P. vivax malaria


title: scRNAseq_S598_CD8_MHV_D7_Lung_Old_HTO

description:
Library name: scRNAseq_S598_CD8_MHV_D7_Lung_Old_HTO
10x GenomicsHTO

library_source: other

data_processing:
ScRNAseq: Fastq files of gene expression and Hashtag libraries were aligned to mm10 using cellranger count (Cell Ranger v6.0.0), which perform filtering, barcode counting, and UMI counting at the same time.
Assembly: mm10
Supplementary files format and content: ScRNA-Seq: matrix H5 files
Library strategy: CITE-seq

molecule: other

extract_protocol:
CD45+ leukocytes were sorted from the lung. S598 tetramer + CD8 T cells were sorted from the spleen or the lung.
We used Chromium Next GEM Single Cell 5' Kit (10x Genomics) to generate scRNA-Seq libraries according to the manufacturer’s protocol.

value: S598 Tetramer+ CD8


title: CUT&TAG H3K27ac 48hr post lenti infection with GATA2 coding sequence in THP1 cells

description: Library name: H3K27ac-48hr-THP1-GATA2

value: GATA2 cds


title: RNAseq_Whole_tissue_MHV_D7_Lung_Young_1

description: Library name: RNAseq_Whole_tissue_MHV_D7_Lung_Young_1

value: Lung

value: ex vivo


title: SM_9


title: SM_7


title: SM_5


title: SM_6


title: scRNAseq_S598_CD8_MHV_D7_Lung_Young_HTO

description:
Library name: scRNAseq_S598_CD8_MHV_D7_Lung_Young_HTO
10x Genomics HTO


title: E72 human foot phalanges, digit 5, rep 1

description: Library name: FP5_late_rep1

source_name: Foot phalanges, digit V

value: Foot phalanges, digit V

value: Male


title: E72 human foot phalanges, digit 3, rep 1

description: Library name: FP3_late_rep1

source_name: Foot phalanges, digit III

value: Foot phalanges, digit III


title: scRNAseq_S598_CD8_MHV_D7_Lung_Old_GEX

description:
Library name: scRNAseq_S598_CD8_MHV_D7_Lung_Old_GEX
10x Genomics GEX

data_processing:
ScRNAseq: Fastq files of gene expression and Hashtag libraries were aligned to mm10 using cellranger count (Cell Ranger v6.0.0), which perform filtering, barcode counting, and UMI counting at the same time.
Assembly: mm10
Supplementary files format and content: ScRNA-Seq: matrix H5 files


title: SM_4


title: SM_2


title: E72 human foot phalanges, digit 2, rep 1

description: Library name: FP2_late_rep1

data_processing:
concatenate reads
adapter trimming with NGmerge v0.3
Alignment to hg38 with Bowtie2 v2.3.4.1
duplicate removal with picard v2.9.0
mitochondrial read filtering with removeChrom.py
peak calling with MACS2 v2.1.1.2 -f bampe --nolambda –bdg --verbose
IDR https://github.com/nboley/idr
idr --samples rep1file rep2file --peak-list pooled_peaks --input-file-type narrowPeak --output-file IDR_output --rank p.value --soft-idr-threshold 0.05 –plot
Assembly: hg38
Supplementary files format and content: bed format; contains the coordinates of the peaks called

source_name: Foot phalanges, digit II

value: Foot phalanges, digit II


title: scRNAseq_S598_CD8_MHV_D7_Lung_Young_GEX

description:
Library name: scRNAseq_S598_CD8_MHV_D7_Lung_Young_GEX
10x Genomics GEX


title: E72 human foot phalanges, digit 4, rep 1

description: Library name: FP4_late_rep1

source_name: Footphalanges, digit IV

value: Footphalanges, digit IV


title: AM_11

value: asymptomatic (AM) P. vivax malaria


title: scRNAseq_S598_CD8_MHV_D7_Spleen_Old_HTO

description:
Library name: scRNAseq_S598_CD8_MHV_D7_Spleen_Old_HTO
10x GenomicsHTO

value: Spleen


title: SM_3


title: scRNAseq_S598_CD8_MHV_D7_Spleen_Old_GEX

description:
Library name: scRNAseq_S598_CD8_MHV_D7_Spleen_Old_GEX
10x Genomics GEX


title: SM_1


title: AM_10


title: RNAseq_Whole_tissue_MHV_D7_Lung_Young_2

description: Library name: RNAseq_Whole_tissue_MHV_D7_Lung_Young_2

value: Whole tissue


title: E72 human foot phalanges, digit 1, rep 1

description: Library name: FP1_late_rep1

source_name: Foot phalanges, digit I

value: Foot phalanges, digit I


title: AM_9


title: E72 human metacarpal, digit 5, rep 1

description: Library name: HM5_late_rep1

source_name: Metacarpal, digit V

value: Metacarpal, digit V


description:
Library name: scRNAseq_S598_CD8_MHV_D7_Spleen_Young_HTO
10x Genomics HTO


title: AM_8


title: AM_6


title: E72 human metacarpal, digit 2, rep 1

description: Library name: HM2_late_rep1

source_name: Metacarpal, digit II

value: Metacarpal, digit II

value: chondrocytes


title: AM_7

value: PBMCs


description:
Library name: scRNAseq_S598_CD8_MHV_D7_Spleen_Young_GEX
10x Genomics GEX

value: S598 Tetramer+ CD8


title: AM_5


title: AM_4


title: AM_3


title: E72 human metacarpal, digit 1, rep 1

description: Library name: HM1_late_rep1

source_name: Metacarpal, digit I

value: Metacarpal, digit I


title: AM_2


title: scRNAseq_Leukocyte_MHV_D7_Lung_Old_GEX

description:
Library name: scRNAseq_Leukocyte_MHV_D7_Lung_Old_GEX
10x Genomics GEX

value: Lung

value: CD45+ Leukocytes


title: E72 human hand phalanges, digit 5, rep 1

description: Library name: HP5_late_rep1

source_name: Hand phalanges, digit V

value: Hand phalanges, digit V


title: AM_1


title: HC_11

value: healthy control


description:
Library name: scRNAseq_Leukocyte_MHV_D7_Lung_Young_HTO
10x Genomics HTO

value: ex vivo


title: E72 human hand phalanges, digit 4, rep 1

description: Library name: HP4_late_rep1

source_name: Hand phalanges, digit IV

value: Hand phalanges, digit IV

value: Male


title: HC_10


title: HC_9


description:
Library name: scRNAseq_Leukocyte_MHV_D7_Lung_Young_GEX
10x Genomics GEX


title: HC_7


title: E72 human hand phalanges, digit 3, rep 1

description: Library name: HP3_late_rep1

source_name: Hand phalanges, digit III

value: Hand phalanges, digit III


title: HC_6


title: E72 human hand phalanges, digit 2, rep 1

description: Library name: HP2_late_rep1

source_name: Hand phalanges, digit II

value: Hand phalanges, digit II


title: E72 human hand phalanges, digit 1, rep 1

description: Library name: HP1_late_rep1

source_name: Hand phalanges, digit I

value: Hand phalanges, digit I


title: HC_4


title: E72 human metacarpal, digit 4, rep 1

description: Library name: HM4_late_rep1

source_name: Metacarpal, digit IV

value: Metacarpal, digit IV


title: HC_5


title: HC_3


title: scRNAseq_Leukocyte_MHV_D7_Lung_Old_HTO

description:
Library name: scRNAseq_Leukocyte_MHV_D7_Lung_Old_HTO
10x GenomicsHTO


title: HC_1


title: IGFBP7_1

city: Tsu city

first: Naoto

last: Fujiwara

state: Mie

address: 2-174 Edobashi

country: Japan

institute: Mie University

data_processing:
Raw sequencing reads were aligned to a human reference genome (GRCh39) using the STAR aligner, converted  into  transcript  abundance  data  by  the  Subread  package featureCounts, and normalized as the relative log expression by the DESeq2 package.
Assembly: GRCh39
Supplementary files format and content: gct format, normalized gene expression data.

growth_protocol: LX-2 (Merck Sigma-Aldrich, #SCC064) was cultured with DMEM and 2% fetal bovine serum.

extract_protocol:
The total RNA of the treated cells was extracted using TRI Reagent (Sigma-Aldrich).
Library preparation was performed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) and sequencing was performed with NovaSeq 6000, according to the manufacturer’s instructions.

treatment_protocol: After incubation without FBS for 18 hours, cells were treated with IGFBP-7 (100ng/mL, R&D, #1334-B7) or phosphate-buffered saline and were incubated for an additional 24 hours.

value: Hepatic stellate cell (HSC) line

value: wild type


title: IGFBP7_3


title: HC_2


title: IGFBP7_2


title: Control_3

value: PBS


title: Kaposi's sarcoma-derived cell line, size matched input 1

city: Haifa

first: Tamar

last: Lahav

address: Zor

department: Biology

country: Israel

institute: Technion

data_processing:
reads were trimmed and adapteres were removed using Cutadapt: Quality cutoff 14, Minimum length 18, NextSeq trimming 20
reads were mapped to repetative elements using RNA-STAR. Mapped reads were removed
reads were mapped to hg38 genome using RNA-STAR. --alignEndsType EndToEnd
PCR duplicates were removed using UMI
Peaks were called for each treatment differenly, on merged bam files for each replicate using PureCLIP v1.3.1
reads were counted to the peaks
Read counts were normalized, and differential enrichment between the eCLIP and their inputs was calculated using findgenomemotifs.pl from HOMER v4.10
Assembly: human (HG38) and KSHV (NC_009333.1)
Supplementary files format and content: Genome coverage bedgraphs were generated  using BEDtools v2.27.1

source_name: iSLK rKSHV

extract_protocol:
48 h hours post induction the cells were washed and crosslinking with 150 mJ/cm2 of UV light at 254 nm . Cell were lysed and sonicated with Diagenode Biorupter Sonication System with a low setting, at 4°C for 5 min 30 sec on/30 sec off. RNA was cleaved by RNase I for 3 minutes at 37°C.
3' RNA adapter were ligated to the RNA. RT performed by SuperScript III using a primer for the RNA adapter. Second adapter were ligated to the 3' end of the cDNA. Library amplify by PCR using Q5 polymerase. Library were size selected by 3% low melt agarose gel

treatment_protocol: 3x106 DOX inducable iSLK rKSHV

value: iSLK rKSHV

tag: fraction

value: input

value: KSHV


title: Control_2


title: HC_12

value: PBMCs


title: Kaposi's sarcoma-derived cell line, eCLIP2

value: eclip


title: HC_8


title: Control_1


title: SUB31, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1

city: Rockville

first: Johannes

last: Goll

state: MD

address: 401 N Washington St

department: Bioinformatics Service Group

institute: The Emmes Company

data_processing:
For RP, sequences of known human rRNAs, rRNA pseudogenes, tRNA pseudogenes, mitochondrial rRNAs (mtrRNAs), mitochondrial tRNAs (mt-tRNAs), mt-rRNA pseudogenes, and human tRNAs were obtained from the Ensembl database (Version 100, April 2020). In addition, known RNA sequences from GenBank (NR003285.3, NR003286.4, NR003287.4, NR023363.1) and two contaminant sequences provided by the laboratory (5’−ATGTACACGGAGTCGAGCTCAACCCGCAACGCGA−3’ and 5’ −ATGTACACGGAGTCGACCCAACGCGA−3’) were added to this sequence collection. These sequences were then used to build a Bowtie2 index of contaminant sequences. Next, 3’ and 5’ adapter sequences were trimmed from reads using Cutadapt (Version 2.10). Reads with Phred quality score of less than 20 for the majority of bases were removed using FASTQ quality filter from the FASTX Toolkit software package (Version 0.0.14). Reads that fell outside the typical length range of ribosomal footprints (25nt to 35nt) were removed. Reads were then aligned to the index of contaminant sequences using Bowtie2 (Version 2.4.1) with its local alignment option. Reads that mapped to contaminant sequences were removed, and those that did not were output to a FASTQ file for alignment to the reference genome. Reads were aligned to human reference GRCh38 using the gapped splice-aware aligner HISAT2 (Version 2.2.0). Additionally, the reads left unmapped by HISAT2 were attempted to be mapped to human reference GRCh38 in a second pass using Bowtie2 with its local alignment option. Gene expression quantification was carried out using the featureCounts function of the Subread package (Version 2.0.1). Reads that overlapped with multiple genes or mapped to multiple locations on the reference genome were excluded.
Supplementary files format and content: tab-delimited text includes raw counts of each ENSEMBL Gene ID for each Sample
Library strategy: Ribo-seq

source_name: peripheral blood mononuclear cells

extract_protocol:
PBMCs were removed from liquid nitrogen, placed on ice to thaw, and resuspended in 500 µl of ice-cold lysis buffer (polysome buffer (20 mM Tris pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/ml CHX) plus 25 U/ml DNase I (Ambion AM2222) and 1% Triton-X-100). Lysates were kept on ice for 10 min, triturated by passing them through a 26 G needle 10 times, and then clarified by centrifugation at 20,000 g for 10 min at 4 ᵒC.
RP libraries were prepared as originally described{Ingolia, 2012 #127} with minor modifications. The main modification was a previously described re-design of the primers and adapters used for library prep so that sequencing could be done on the Ion Proton platform{Vila-Sanjurjo, 2020 #129}. We also included two rounds of rRNA-depletion and the addition of an extra rRNA-depletion oligo to the depletion pools as previously documented{Vila-Sanjurjo, 2020 #129}.
Sequencing was done on the Ion Proton (Thermo-Fisher 4474779) with Ion PIv3 200pb kits (Thermo-Fisher 4488315). Despite being bar-coded, libraries were sequenced individually using one Ion PIv2 chip (Thermo-Fisher 4482321) per sample.

value: peripheral blood mononuclear cells

tag: day


title: PBS_d4

city: New York City

first: Florencia

last: Schlamp

state: New York

address: 435 East 30th Street

institute: NYU Langone Health

data_processing:
Data processing and quality control were performed using the RNAseq PE snakemake pipeline [https://github.com/mgildea87/RNAseq_PE].
Quality control of sequencing reads was assessed using FastQC (v.0.11.9) and MultiQC (v.1.10.1)
Reads were trimmed using fastp (v.0.20.1), and mapped to human reference genome hg38 using STAR (v.2.7.7a).
Genomic features were then assigned using Subread featureCounts (v.1.6.3)
Assembly: hg38
Supplementary files format and content: space-delimited text file includes raw counts per sample per gene

source_name: unvaccinated donor

growth_protocol: Cells were cultured in StemSpan SFEM II (STEMCELL Technologies) supplemented with stem cell factor (25 ng/ml; STEMCELL Technologies) and thrombopoietin (TPO; 25 ng/ml; R&D Systems) for 5 days. Then, cells were cultured only with TPO (25 ng/ml) until day 12.

extract_protocol:
Total RNA was isolated using Direct-zol RNA MicroPrep columns (Zymo Research).
Sequencing libraries were barcoded and prepared using the Clontech SMART-Seq HT with Nxt HT kit (Takara Bio USA), and libraries were sequenced single end (51bp) on an Illumina NovaSeq 6000 at the Genome Technology Center at NYU Langone.

treatment_protocol: On day 11, cells were exposed for 24 hours to either SARS-CoV-2 isolate WA1/2020, SARS-CoV-2 Delta variant (hCoV19/USA/PHC658/2021), SARS-CoV-2 Omicron BA.1 (hCoV19/USA/GA-EHC-2811C/2021) at multiplicity of infection (MOI) = 5 or vehicle (PBS).

value: CD34+ cells

value: Hematopoietic Stem and Progenitor Cells

tag: experiment no

value: M

tag: donor


title: Kaposi's sarcoma-derived cell line, eCLIP1


title: PBS_d3


title: SUB03, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day1


title: SUB30, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day8


title: PBS_d2


title: SUB38, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: Kaposi's sarcoma-derived cell line, size matched input 2

value: KHSV


title: PBS_d1


title: SUB25, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day2


title: Covid_Omicron_d4

value: SARS-CoV-2 Omicron BA.1


title: Covid_Omicron_d3


title: SUB22, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day8


title: SUB02, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day8


title: Covid_Omicron_d2


title: SUB29, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day2


title: Muscle_exercised 7

type: RNA

city: Kawasaki

first: Shihori

last: Tanabe

state: Kanagawa

address: 3-25-26, Tonomachi, Kawasaki-ku

department: Division of Risk Assessment

institute: National Institute of Health Sciences

description: Gene expression after execise

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Ver2.0 (G2519F#26652) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026652_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: human skeletal muscle, exercised

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the mirVana™ miRNA Isolation Kit (Life Technolgies Corporation, AM1561) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Biopsies from the quadricep muscles.

value: skeletal muscle

tag: gender

value: female

tag: protocol

value: exercised


title: Muscle_exercised 4

description: Gene expression after execise

tag: tissue


title: Muscle_exercised 5

description: Gene expression after execise


title: Muscle_exercised 3

description: Gene expression after execise


title: HeLaS3 Cells, OSM_SD36_2, ATAC

city: Cheongju-si

first: Junho

last: Noh

state: Chungcheongbuk-do

address: 1, Chungdae-ro, Seowon-gu

department: Biological science and biotechnology

country: South Korea

institute: Chungbuk National University

description: Library name: Sample 8

data_processing:
The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
To ensure data quality, the raw files were trimmed using Trim Galore (version 0.6.6, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with default parameters.
These trimmed reads were then aligned to the human genome (hg38 assembly) using Bowtie2 (version 2.3.5.1) with default parameters.
To identify peaks over background signals, the makeTagDirectory and findPeaks commands from HOMER (version 4.11.1) were utilized.
A FDR cutoff of 0.05 was employed. The total number of mapped reads for each sample was normalized to 10 million mapped reads. Differential peak analysis for the ATAC-seq data was performed using the getDifferentialPeaks command.
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: peaks.bed

source_name: Uterus; Cervix

growth_protocol: Human cervical cancer cell line HeLaS3 was cultured in RPMI 1640 (No. 11875-119; Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS; No. 16000-044; Gibco) and 1% penicillin– streptomycin (No. 15070-063; Gibco). The cell line was routinely cultured at 37°C in a humidified 5% CO2 incubator.

extract_protocol:
OSM, SD36-treated HeLaS3 (5 × 10^4 cells) was pretreated with 200 U/mL DNase (Worthington) for 30 min at 37 °C to remove free-floating DNA and digest DNA from dead cells. Then this medium was washed with DPBS. After cell harvesting through TrypLE Express, cell lysis was performed by adding a cold lysis buffer (48.5 μL RSB (resuspension buffer; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water), 0.5 μL 10% NP-40, 0.5 μL 10% Tween-20, 0.5 μL 1% Digitonin). This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 mL of RSB containing 0.1% Tween-20 (without NP-40 or digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 600 r.c.f. in a pre-chilled (4 °C) fixed-angle centrifuge. The supernatant was removed with two pipetting steps, as described before, and nuclei were resuspended in 50 μL of transposition mix (25 μL 2 × TD buffer, 2.5 μL Tn5 transposase, 16.5 μL PBS, 0.5 μL 1% digitonin, 0.5 μL 10% Tween-20, and 5 μL water) by pipetting up and down six times. Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1000 r.p.m. Reactions were cleaned up with MinElute Reaction Cleanup Kit.
Reactions were pre-amplified for 5 cycles using NEBNext High-Fidelity 2x PCR MasterMix (M0541L; NEB) with adapter primers. The amplification profiles were manually assessed to determine the number of additional cycles to amplify as previously described. The final amplified library samples were stored at -80 °C for ATAC-seq after library purification with AMPure XP (A63880; Beckman). Libraries were validated using the Agilent High Sensitivity D1000 kit (5067-5584, 5067-5585; Agilent) and were subjected to high-throughput sequencing using the Illumina HiSeq 2500 Sequencer.

treatment_protocol: HeLaS3 cells were treated with OSM (No. 30010T, PeproTech, Rocky Hill, NJ, USA) and SD-36 (No. HY129602, MedCheExpress, Monmouth Junction, NJ, USA) for 24 h.

value: Uterus; Cervix

value: Human cervical adenocarcinoma

value: WT


title: SUB03, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day8


title: HeLaS3 Cells, OSM_SD36_1, ATAC

description: Library name: Sample 7


title: Muscle_exercised 1

description: Gene expression after execise


title: Muscle_exercised 6

description: Gene expression after execise


title: Muscle_not exercised 3

description: Gene expression not exercised

source_name: human skeletal muscle, not exercised

value: not exercised


title: Muscle_exercised 2

description: Gene expression after execise


title: HeLaS3 Cells, SD36_2, ATAC

description: Library name: Sample 6


title: SUB31, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day2


title: Muscle_not exercised 2

description: Gene expression not exercised


title: Covid_Omicron_d1


title: Covid_Delta_d4

value: SARS-CoV-2 Delta variant


title: Muscle_not exercised 1

description: Gene expression not exercised


title: HeLaS3 Cells, SD36_1, ATAC

description: Library name: Sample 5


title: Covid_Delta_d3


title: HeLaS3 Cells, OSM_2, ATAC

description: Library name: Sample 4

value: OSM


title: Covid_Delta_d2


title: SUB10, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: HeLaS3 Cells, OSM_1, ATAC

description: Library name: Sample 3


title: SUB06, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day2


title: SUB19, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day8


title: Covid_Delta_d1


title: Covid_WA1_d4

value: SARS-CoV-2 isolate WA1/2020


title: Covid_WA1_d3


title: HeLaS3 Cells, Ctrl_2, ATAC

description: Library name: Sample 2

value: DMSO


title: SUB13, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day2

value: peripheral blood mononuclear cells


title: SUB20, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day2


title: HeLaS3 Cells, Ctrl_1, ATAC

description: Library name: Sample 1


title: Covid_WA1_d2

value: CD34+ cells


title: Covid_WA1_d1

value: Hematopoietic Stem and Progenitor Cells


title: 293T_dKO-N1P2_NSD1

city: WASHINGTON

first: Jia-Ray

last: Yu

state: DC

address: 7144 13th PL NW

institute: Virginia Tech

description: Library name: JY07_293T_dKO-N1P2_NSD1

data_processing:
Data was processed with the nf-core/chip-seq v2.1.0 pipeline, with default settings for 150bp reads.
Spike-in was performed by re-running the pipeline with dm6 genome, and dividing uniquely mapped paired hg38 reads by dm6 reads. The wild type sample’s ratio was set to 1, and mutant samples were calculated relative to the wild type. Coverage tracks were then generated using the bam_coverage function of deepTools, with the scaling factor manually set as calculated for each sample
Assembly: mm10, hg38
Supplementary files format and content: Supplementary_files_format_and_content:

source_name: Kidney

growth_protocol: 37 degree and 5% CO2 in humidified incubators.

extract_protocol:
crosslinked and sheared chromatin
NEBNext Ultra II

treatment_protocol: Spiked with equal amounts Drosophila chromatin for normalization

value: Kidney

value: fibroblast

value: rescued with NSD1-ΔPWWP2

tag: chip antibody


title: SUB38, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day8


title: SC-islet_control_treament

city: La Jolla

first: Maike

last: Sander

state: CA

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

description: Single cell RNA-seq with 10X Next GEM Single Cell 3’ v3.1 kit

data_processing:
Alignment to the genome and initial processing were performed using the 10x Genomics cellranger-7.2.0 pipeline
Assembly: hg38
Supplementary files format and content: Matrix file (mtx) including raw count matrix
Supplementary files format and content: Tab separate values (tsv) files containing barcode for each individual cell
Supplementary files format and content: Tab separate values (tsv) files containing official gene symbol of each mapped gene

source_name: Human embryonic stem cell-derived islet-organoid

growth_protocol: H1 cells were maintained and differentiated as previously described (Geusz RJ, et al., Nature Comm 2021).

extract_protocol:
From control and BMP4 treated SC-islet, nuclei were isolated from approximately 1,000 aggregates (~1,000 cells per aggregate) using a glass dounce in nuclei permeabilization buffer [0.1% Triton X-100 (Sigma-Aldrich, T8787), 1X Pierce Protease Inhibitor (Fischer, PIA32965), 1 mM DTT (Sigma-Aldrich, D9779), Recombinant RNase inhibitor (0.2 U/μl; Promega, 2% Fatty-acid-free BSA in PBS (Proliant, 7500804; Corning, 21-040-CV). Sample was incubated on a rotator for 5 min at 4°C and then centrifuged at 500g for 5 min (Eppendorf, 5920R; 4°C, ramp speed of 3/3). Supernatant was removed and pellet was resuspended in sort buffer [1mM EDTA (Invitrogen, 15575020), 0.2U/μL Recombinant RNAsin (Promega, PAN2515), 1% Fatty-acid-free BSA in PBS (Proliant, 7500804; Corning, 21-040-CV)] and stained with DRAQ7 (1:150; Cell Signaling Technology, 7406). 60,000 nuclei were sorted using an SH800 sorter (Sony) into 50 μl of collection buffer [1.0U/μL Recombinant RNAsin (Promega, PAN2515), 5% Fatty-acid-free BSA in PBS (Proliant, 7500804; Corning, 21-040-CV)]. Sorted nuclei were then centrifuged at 1000 g for 15 min (Eppendorf, 5920R; 4°C, ramp speed of 3/3), and supernatant was removed. Nuclei were resuspended in reaction buffer [RNase inhibitor (0.2U/μL Recombinant RNAsin (Promega, PAN2515), 1% Fatty-acid-free BSA in PBS (Proliant, 7500804; Corning, 21-040-CV)] and counted using a hemocytometer.
16,550 nuclei were loaded onto a Chromium controller (10x Genomics). Libraries were generated using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, PN-1000121) according to the manufacturer specifications. Complementary DNA was amplified for 12 PCR cycles. SPRISelect reagent (Beckman Coulter) was used for size selection and cleanup steps. Final library concentration was assessed by the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific), and fragment size was checked using TapeStation High Sensitivity D1000 (Agilent) to ensure that fragment sizes were distributed normally around 500 bp. Libraries were sequenced using a NextSeq 500 or NovaSeq 6000 (Illumina).

treatment_protocol: SC-islets were treated with 5 ng/ml BMP4 for 11 days

value: Pancreatic islet

tag: cell type

value: Pancreatic islet progenitors and endocrine cells

value: 11 days of control treatment


title: 293T_dKO-WTN1_H3K36me2

description: Library name: JY14_293T_dKO-WTN1_H3K36me2

value: rescued with WT NSD1


title: SC-islet_BMP_treatment

value: 11 days of BMP4 treatment


title: SUB07, diphtheria and tetanus toxoids and whole cell pertussis vaccine (DTwP), Day1


title: 293T_dKO-WTN1_NSD1

description: Library name: JY06_293T_dKO-WTN1_NSD1


title: Donor4_Con_resting

city: Cambridge

first: Fuguo

last: Liu

address: 500 Main Street

department: Koch Institute For Integrative Cancer Research at MIT

institute: Massachusetts Institute of Technology

data_processing:
RNA-seq reads were aligned to the human genome with Salmon (v0.14.1) using ensembl Homo sapiens GRCh38 (release 112) transcript annotations. The resulting counts were analyzed in R (v4.3.2) using tximport (v1.30.0) and DESeq2 (v 1.42.1) for differential expression analysis
Assembly: GRCh38
Supplementary files format and content: tab-delimited files include transcripts per million (TMP) counts and read counts

source_name: Whole blood

extract_protocol:
RNA was isolated using verrity chemagic™ RNA isolation Kit (CMG-1212)
cDNA libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770L) per the manufacturer’s instructions.

value: Whole blood

value: Natural killer cells


title: 37℃_OA (biol rep 3)

city: Shanghai

first: Yueqi

last: Zhang

address: 150 Jimo Road, Pudong New Area,Shanghai

institute: Shanghai East Hospital, School of Medicine, Tongji University

description: Library name: Sample_37_OA_3

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: Cartilage (OA)

extract_protocol:
Total RNA from human non-OA and OA chondrocytes cultured at the two temperatures was extracted with TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Cartilage (OA)

value: chondrocytes

value: 37℃ Culture


title: SUB15, diphtheria and tetanus toxoids and acellular pertussis vaccine (DTaP), Day2