title: submandibular gland and sublingual gland,two female C57BL/6N (6–8 weeks old) mice,scRNAseq replicate-Sample 4

city: Chongqing

first: yanan

last: li

state: Chongqing

address: 426 Songshi North Road, Yubei Distrinct, Chongqing

department: Department of Endodontics

institute: Stomatological Hospital of Chongqing Medical University

description:
submandibular gland and sublingual gland,two female C57BL/6N (6–8 weeks old) mice,scRNAseq
10x Genomics

data_processing:
A total of 15,707 cells were sequenced at a depth of 295 million reads, with a mean of 18,816 reads per cell and 689 median genes per cell. The output from the 10X Genomics Cell Ranger v6.0.1 pipeline was used as input into the R analysis package Seurat v4.1.1.Data were normalized using Seurat’s LogNormalize with a scale factor of 10,000.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Single-cell suspensions from freshly isolated SMGs and SLGs from two female C57BL/6N (6–8 weeks old) mice were generated for scRNA-seq analysis. The working solution was prepared with Collagenase type I, II and IV, hyaluronidase, dispase and pancreatin. The cut tissue was placed into this working solution and incubated at 37 °C for 30 min.
Library was performed according to the manufacter’s instructions (10x single-cell 3-terminal transcriptome). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: primary cell

value: Multiple cell types

value: WT

value: physiological status


title: TU0056_TBneg_Class_Mo

status: Public on Jan 03 2023

type: SRA

city: La Jolla

first: Julie

last: Burel

state: CA

address: 9420 Athena Circle

country: USA

institute: La Jolla Institute of Immunology

description: Microscaled (SmartSeq2) cDNA amplification - RNA seq

library_source: transcriptomic

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The reads were then aligned to UCSC hg19 reference genome using TopHat (v 1.4.1) (Trapnell et al., 2009). DUST scores were calculated with PRINSEQ Lite (v 0.20.3) (Schmieder et al., 2011) and low-complexity reads (DUST > 4) were removed from the BAM files.  The alignment results were parsed via the SAMtools (Li et al., 2009) to generate SAM files. Read counts to each genomic feature were obtained with the htseq-count program (v 0.6.0) (Anders et al., 2014) using the “union” option.
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were against the GRCh38 reference genome and Gencode v27 annotations using STAR v2.6.1 (default options)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: GRCh38.gencode.v27B
Supplementary_files_format_and_content: read count matrix with rows as genes and columns as cells

molecule: polyA RNA

organism: Homo sapiens

source_name: Cryopreserved PBMC

growth_protocol: Cells were directly isolated post thawing of cryopreserved PBMC samples and lysed, no culture were involved.

extract_protocol:
Cryopreserved PBMC were thawed, stained with antibodies, and 100,000 memory CD4 T cells sorted using BD Aria 3 cell sorter direclty in Trizol. Memory cells were defined as the combination of CCR7-CD45RA-, CCR7-CD45RA+ and CCR7+CD45RA- populations. Total RNA was purified using a miRNAeasy micro kit (Qiagen, USA) and quantified by qPCR as described previously (Seumois et al., 2012).
Purified total RNA (1 to 5 ng) was amplified following the smart-seq2 protocol (16 cycles of cDNA amplification) (Picelli et al., 2014). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina).

treatment_protocol: No specific treatment involved

tag: disease group

value: TBneg

tag: geographic location

value: USA:San Diego

tag: cell subset

value: Classical CD14+CD16- monocytes


title: submandibular gland and sublingual gland,two female C57BL/6N (6–8 weeks old) mice,scRNAseq replicate-Sample 3

country: China

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: Bald-3 substrate hyphae rep1

city: Beijing

first: Zhenpeng

last: Zhang

address: 38 Life Science Park Road

institute: Beijing Proteome Research Center

description:
972M3_1
Achaeostreptomyces halophilum YIM 93972

data_processing:
cDNA libraries were sequenced by paired-end 100 bp sequencing on an Illumina HiSeq2000 system.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Achaeostreptomyces halophilum YIM 93972 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Transcript count, TPM and FPKM were calculated using a protocol.
Genome_build: Genome of Achaeostreptomyces halophilum YIM 93972 (Genome_Achaeostreptomyces_halophilum_93972.fasta, Annotation_Achaeostreptomyces_halophilum_93972.xlsx).
Supplementary_files_format_and_content: transcript counts: transcript counts.
Supplementary_files_format_and_content: transcript tpm: transcript tpm.
Supplementary_files_format_and_content: transcript fpkm: transcript fpkm.

organism: Halocatena halophila

source_name: Hyphae

growth_protocol: The wild and mutated strains of Achaeostreptomyces halophilum YIM 93972 were spread on a layer of 0.20 μm BioTrace NT Nitrocellulose Transfer Membrane (Pall China, Beijing, China) covered on an ISP 4 medium containing 25% NaCl and 2% agar in 85 mm diameter Petri dish.

extract_protocol:
The total RNA was extracted and analyzed as described previously. Briefly, total RNA was extracted with Trizol method. The TruSeqTM Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) was used to prepare the cDNA libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To obtain the poorly differentiated and undifferentiated strains, a NTG-based mutagenesis experiment was applied.

value: Bald type

value: Hyphae


title: Muscle 10 days post NTX [EC_WT: 10d-2]

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

country: Canada

institute: University of British Columbia

data_processing:
Illumina base call files were de-multiplexed by bcl2fastq2 on Basespace. Adaptor sequences were trimmed and low-quality reads (< 35 base pairs) were discarded. Additionally, Bowtie was used to remove read pairs that aligned against abundant sequences. Demultiplexed read sequences were then aligned to the mm10 genome reference using STAR aligner. The number of aligned reads to each annotated gene was tallied with RnaReadCounter to generate read-count matrices for all samples, which were used as inputs for downstream analyses. Bowtie, STAR, and RnaReadCounter are tools built under RNA-Seq Alignment (v 1.1).
Assembly: mm10
Supplementary files format and content: Matrix table with raw counts for every gene and sample

source_name: Skeletal muscle (Tibialis Anterior)

extract_protocol:
Muscle were digested, single cell suspension stained and the different cell populations were sorted as following: FAP as CD45-/CD31-/EGFP+, inflammatory cells as CD45+/CD31-, myogenic progenitors as CD45-/CD31-/a7+/VCAM+, and endothelial cells as CD45-/CD31+ using PDGFRa EGFP wild type B6 background and CCR2KO mouse. Pericytes were sorted as CD45-/CD31-/Sca1-/NG2+ using the NG2 DsRed wild type B6 background mouse. Total tissue was digested from wild type B6 background mouse. RNA extraction was performed with RNAzol based protocol.
Sample quality control was performed using the Agilent 2100 Bioanalyzer. Qualifying samples were then prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs). Sequencing was performed on the Illumina NextSeq 500 with Paired End 43bp × 43bp reads.

treatment_protocol: Skeletal muscle (Tibialis Anterior) was injected with myotoxin (notexin).

value: Muscle 10 days post NTX

value: Endothelial cells

tag: sorted as


title: TU0025_LTBI_Class_Mo

value: LTBI


title: submandibular gland and sublingual gland,two female C57BL/6N (6–8 weeks old) mice,scRNAseq replicate-Sample 2


title: submandibular gland and sublingual gland,two female C57BL/6N (6–8 weeks old) mice,scRNAseq replicate-Sample 1


title: Bald-2 substrate hyphae rep2

description:
972M2_2
Achaeostreptomyces halophilum YIM 93972


title: Bald-2 substrate hyphae rep3

description:
972M2_3
Achaeostreptomyces halophilum YIM 93972


title: TU0024_LTBI_Class_Mo


title: TU0023_LTBI_Class_Mo


title: Muscle 1 day post NTX [Pericyte_WT: 1d]

value: Muscle 1 day post NTX

value: Pericytes


title: Muscle 10 days post NTX [EC_WT: 10d-1]


title: H3K27Ac_PPO2_2

city: CINCINNATI

first: Richard

middle: Q.

last: Lu

state: OH

address: 3333 Burnet Avenue

department: CBDI

institute: Cincinnati Childrens Hosp Med Ctrl

library_source: genomic

data_processing:
Cut&Run-seq reads in FASTQ format were first subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments. The programs used in these steps were FastQC v0.11.7, Trim Galore! v0.4.2 and cutadapt v1.9.1. The trimmed reads were aligned to the reference rat genome version Rn5 with the program BOWTIE v2.3.4.1. Aligned reads were stripped of duplicate reads withthe program sambamba v0.6.8. Peaks were called using the program MACS v2.1.2 using the narrow and broad peaks mode for Cut&Run-Seq,
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

molecule: genomic DNA

growth_protocol: DMEM/F12, serum free media, supplemented with FGF, EGF, ITS, Heparin, progesterone. Cells were cultured at 37C at 5% CO2.

extract_protocol:
CUT&RUN was performed following the published protocol (Skene and Henikoff, 2017). 200,000 cells were harvested by centrifugation (600 g, 3 min) and. Cells were washed by in 1 ml Wash Buffer (20 mM HEPES-KOH pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1x Roche cOmpleteTM) for twice followed by addition of 10 µl pre-activated concanavalin A coated magnetic beads (Bangs Laboratories-BP531). Tubes were held on mixing platform at RT for 10 mins, then placed on a magnet stand and pull off the liquid. Add 100 µL cold Antibody Buffer to each sample, and 1 µL antibody (1:100 dilution) to each sample and incubate on nutator overnight at 4ºC. Beads with cells were washed in 1 ml Digitonin Buffer (20 mM HEPES-KOH pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1x Roche cOmpleteTM,0.05% digitonin.) for twice, and resuspended in 50 µL Digitonin Buffer. Add 2.5 µL CUTANA pAG-MNase (20x stock) to each sample, and gently vortex. Incubate samples for 10 min at RT. Beads with cells were washed in 1 ml Digitonin Buffer for twice. Remove liquid and add 50 µL cold Digitonin Buffer to each sample, keep sample in 0 ºC block. Add 1 µL 100 mM CaCl2 to samples, incubate for 30 min in 0 ºC block. Add 50 µL Stop Buffer to each sample, and gently vortex to mix. Incubate tube for 30 min at 37ºC for release cleaved fragments. Cleaved fragments were purified by Qiagen MinElute PCR Purification Kit.  DNA fragments were extracted from the supernatant and used for the construction of sequencing libraries.
Libraries were prepared for Illumina sequencing with Library Prep for CUT&RUN with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645).  Libraries were sequenced by NovaSeq PE150

value: Mouse Brain Glioma

tag: chip antibody

value: H3K27ac antibody (pAb) Active Motif 39133


title: Muscle 7 days post NTX [EC_WT: 7d-3]

value: Muscle 7 days post NTX


title: Bald-3 substrate hyphae rep2

description:
972M3_2
Achaeostreptomyces halophilum YIM 93972


title: Bald-2 substrate hyphae rep1

description:
972M2_1
Achaeostreptomyces halophilum YIM 93972


title: Muscle 7 days post NTX [EC_WT: 7d-2]


title: Muscle 7 days post NTX [EC_WT: 7d-1]


title: TU0022_LTBI_Class_Mo


title: TU0011_LTBI_Class_Mo


title: Bald-1 substrate hyphae rep3

description:
972M1_3
Achaeostreptomyces halophilum YIM 93972


title: Muscle 14 days post NTX [EC_WT: 14d]

value: Muscle 14 days post NTX


title: Muscle 6 days post NTX [EC_WT: 6d-3]

value: Muscle 6 days post NTX


title: H3K27Ac_PPO1_1


title: Bald-1 substrate hyphae rep1

description:
972M1_1
Achaeostreptomyces halophilum YIM 93972


title: Muscle 6 days post NTX [EC_WT: 6d-2]

value: WT


title: Transitional-2 substrate hyphae rep3

description:
972T2_3
Achaeostreptomyces halophilum YIM 93972

value: Transitional type


title: Chicken_T7

city: Bareilly

first: SARAVANAN

last: RAMAKRISHNAN

state: Uttar Pradesh

address: Izatnagar

country: India

institute: ICAR-Indian Veterinary Research Institute

data_processing:
Quality Check (fastqc 0.11)
Quality trim (trimmomatic 0.36)
Mapping (tophat 2.1.0)
DEG Analysis (DESeq_1.28.0, DESeq2_1.16.1 and baySeq_2.10.0)
Functional annotation ( g:Profiler)
Genome_build: GRCg6a (GCA_000002315.5)
Supplementary_files_format_and_content: Three excel files representing gene counts (gene_counts), rpkm values (rpkm_val) and  gene expression (DEG_stats)  and  one text file (gprofiler_results)  representing  functional annotation

organism: Gallus gallus

source_name: Spleen

extract_protocol:
At 24 hour post administration (p.i.), all chicken were euthanized humanely, spleen was harvested aseptically. Total RNA was extracted from spleen samples (1 each for treatment and control) usingTRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Resiquimod (R-848) was adminstered to a chicken (treatment ) and untreated bird was kept as control

value: Spleen

value: R-848 administered


title: TU0005_LTBI_Class_Mo

value: USA:San Diego

value: Classical CD14+CD16- monocytes


title: Chicken_control

value: control


title: Transitional-2 substrate hyphae rep2

description:
972T2_2
Achaeostreptomyces halophilum YIM 93972

value: Hyphae


title: TT0121_ATB_V1_Class_Mo

description: The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns

value: South Africa


title: Transitional-2 substrate hyphae rep1

description:
972T2_1
Achaeostreptomyces halophilum YIM 93972


title: TT0121_ATB_V2_Class_Mo


title: Muscle 5 days post NTX [EC_WT: 5d-2]

value: Muscle 5 days post NTX

value: Endothelial cells


title: Muscle 5 days post NTX [EC_WT: 5d-1]


title: TU0013_LTBI_Class_Mo

value: LTBI


title: H3K27Ac_PPO2_1

value: Mouse Brain Glioma


title: Bald-1 substrate hyphae rep2

description:
972M1_2
Achaeostreptomyces halophilum YIM 93972

value: Bald type


title: Transitional-1 substrate hyphae rep3

description:
972T1_3
Achaeostreptomyces halophilum YIM 93972


title: H3K27Ac_PPO1_2

value: H3K27ac antibody (pAb) Active Motif 39133


title: TT0120_ATB_V2_Class_Mo


title: Muscle 4 days post NTX [EC_WT: 4d-2]

value: Muscle 4 days post NTX


title: Muscle 4 days post NTX [EC_WT: 4d-1]


title: TT0120_ATB_V1_Class_Mo


title: Transitional-1 substrate hyphae rep2

description:
972T1_2
Achaeostreptomyces halophilum YIM 93972


title: TU0010_LTBI_Class_Mo


title: Transitional-1 substrate hyphae rep1

description:
972T1_1
Achaeostreptomyces halophilum YIM 93972


title: TT0119_ATB_V2_Class_Mo


title: Muscle 3 days post NTX [EC_WT: 3d-5]

value: Muscle 3 days post NTX


title: U2OS MYC-ER Replicate 1 MYC-ON CT72

city: Rochester

first: Brian

middle: James

last: Altman

state: NY

address: 601 Elmwood Avenue Box 633

department: Biomedical Genetics

institute: University of Rochester

data_processing:
Raw reads were demultiplexed using bcl2fastq2-v2.17.1.14.
Processed reads were mapped to transcripts using Salmon 1.3.0 in mapping-based mode for paired-end samples, using a decoy-aware transcriptome built from Gencode v35 GRCh38 primary assembly genome and v35 transcriptome.  Salmon further filtered out ambiguous reads or reads that corresponded to decoy fragments.
Transcripts were collapsed to gene-level using Tximport 1.12.3 using Gencode v35 transcriptome.  Genes were annotated with symbols using the Ensembl GRCh38.101 transcriptome annotations.
Tximport normalized raw counts to Transcripts-Per-Million (TPM).
Assembly: hg38
Supplementary files format and content: Tab-delimited text with GENEID (Column A), SYMBOL (Column B) and TPM data of samples (Columns C-CG)

source_name: osteosarcoma cancer

growth_protocol: Cells were cultured in DMEM high glucose with 10% fetal bovine serum in a 5% CO2 incubator.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plus kit according to manufacturer's instructions.
For replicate 1, Illumina TruSeq Stranded Kit with ribosomal depletion. For replicate 2, Illumina TruSeq Stranded PolyA Kit.  Libraries were sequenced on an Illumina HiSeq 4000 as 100SR (single-end),  yielding an average of 74.3 million reads per sample for Replicate 1, and 40.9 million reads per sample for Replicate 2. .  Note that each sample was run on 5-7 lanes.

value: osteosarcoma cancer

value: osteosarcoma cancer cells

value: MYC-ER

value: 4OHT (MYC-ON), dexamethasone

tag: time


title: Muscle 6 days post NTX [EC_WT: 6d-1]

value: Muscle 6 days post NTX

value: WT


title: Wild substrate hyphae rep3

description:
972W2_3
Achaeostreptomyces halophilum YIM 93972

value: Wild type


title: TT0117_ATB_V2_Class_Mo

value: Classical CD14+CD16- monocytes


title: skin, psoriasis 12

type: RNA

city: Tartu

first: Ana

last: Rebane

address: Ravila 14B

department: Institute of Biomedicine and Translational Medicine

country: Estonia

institute: University of Tartu

description:
SK PS12
MicroRNA expression data from skin samples

hyb_protocol: Hybridization step was done for 17 hr at 48ºC on microRNA 4.1 microarray plates. Microarray plates were hybridized, stained and washed in the Affymetrix GeneTitan Multi-Channel (MC) Instrument using the Hyb-Wash-Scan workflow.

scan_protocol: Microarray plates were scanned using the the Affymetrix GeneTitan Multi-Channel (MC) Instrument.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) software using Affymetrix default analysis settings and normalized using default control probes and RMA-DABG method.

label: biotin

source_name: skin sample of psoriasis adult patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA.

extract_protocol: Total RNA (including microRNAs) was isolated from a skin tissue punch (3-4 mm in diameter) using Qiazol (Qiagen, Hilden, Germany) reagent and Total RNA Zol-out kit (A&A Biotechnology, Gdynia, Poland) according to the manufacturer’s instructions

treatment_protocol: All skin samples were collected at exacerbation stage prior to hospitalization of the patients. One punch biopsy skin sample (3-4 mm in diameter) was taken from the marginal zone of lesional skin from the patients with AD or PV, and from a non-sun-exposed site from the control subjects. . All skin samples were kept frozen at -80ºC until assay.

tag: subject status

value: psoriasis adult patient

value: skin


title: skin, psoriasis 11

description:
SK PS11
MicroRNA expression data from skin samples


title: skin, psoriasis 10

description:
SK PS10
MicroRNA expression data from skin samples


title: Muscle 3 days post NTX [EC_WT: 3d-4]

value: Endothelial cells


title: skin, psoriasis 9

description:
SK PS09
MicroRNA expression data from skin samples


title: Muscle 3 days post NTX [EC_WT: 3d-3]


title: skin, psoriasis 7

description:
SK PS07
MicroRNA expression data from skin samples


title: TT0116_ATB_V2_Class_Mo

value: South Africa


title: TT0117_ATB_V1_Class_Mo


title: Wild substrate hyphae rep2

description:
972W2_2
Achaeostreptomyces halophilum YIM 93972

value: Hyphae


title: Wild substrate hyphae rep1

description:
972W2_1
Achaeostreptomyces halophilum YIM 93972


title: Wild aerial  hyphae rep3

description:
972W1_3
Achaeostreptomyces halophilum YIM 93972


title: TT0116_ATB_V1_Class_Mo


title: Muscle 3 days post NTX [EC_WT: 3d-2]


title: Muscle 3 days post NTX [EC_WT: 3d-1]


title: TT0114_ATB_V2_Class_Mo


title: TT0114_ATB_V1_Class_Mo


title: Wild aerial  hyphae rep2

description:
972W1_2
Achaeostreptomyces halophilum YIM 93972


title: skin, psoriasis 5

description:
SK PS05
MicroRNA expression data from skin samples


title: skin, psoriasis 6

description:
SK PS06
MicroRNA expression data from skin samples


title: Wild aerial  hyphae rep1

description:
972W1_1
Achaeostreptomyces halophilum YIM 93972


title: Muscle 2 days post NTX [EC_WT: 2d-5]

value: Muscle 2 days post NTX


title: skin, psoriasis 4

description:
SK PS04
MicroRNA expression data from skin samples


title: skin, psoriasis 3

description:
SK PS03
MicroRNA expression data from skin samples


title: MM-hsfa1a-line2-HS-1h Rep3

city: Paris

first: Jing

last: An

address: 630 Rue Noetzlin

country: France

institute: Universite Paris Saclay

description: Bio rep 3

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads were mapped using bowtie2 v 2.3.5 with the following setting "bowtie2 --very-sensitive" against the genome of SollycM82_v1.0.
Quality filtering: mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30 " to remove reads of quality under 30
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the commands "samtools fixmate -m"  and "samtools markdup -r "
Raw read counts were extracted using featureCounts based on the gene annotations in SollycM82_v1.0.gtf
Differentially expressed genes were identified using R 3.5.1(www.R-project.org) and the package DESeq2 (adj. p value < 0.05)
Assembly: SollycM82_v1.0
Supplementary files format and content: Count matrix of all samples obtained with featureCounts

organism: Solanum lycopersicum

source_name: Leaf

growth_protocol: Plants were grown in pots in growth chambers at 24 °C under long-day (16 h of light) conditions.

extract_protocol:
Total RNA were extracted from 1g of 4-week-old tomato fourth leaves with Nucleospin RNA kit (Macherey-Nagel), according to the manufacturer’s instructions.
RNA-seq libraries were prepared from 2μg of total RNA using NEBNext Ultra II Directional RNA library Preparation Kit (NEB) according to the manufacturer’s instructions. RNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent) and subjected to 1 × 75 bp high-throughput sequencing by NextSeq 500 (Illumina).

treatment_protocol: 4 weeks old plants were treated at 45°C for 0h and 1h in a climatic chamber (Aralab).

tag: cultivar

value: cv. Moneymaker background

value: RNAi knock-down line

value: Leaf

value: Heat stress 1h


title: Muscle 2 days post NTX [EC_WT: 2d-4]


title: MM-hsfa1a-line2-HS-1h Rep2

description: Bio rep 2


title: TT0112_ATB_V2_Class_Mo

description: The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns


title: TT0112_ATB_V1_Class_Mo


title: Muscle 2 days post NTX [EC_WT: 2d-3]


title: MM-hsfa1a-line2-HS-1h Rep1

description: Bio rep 1


title: Muscle 2 days post NTX [EC_WT: 2d-2]


title: TT0111_ATB_V2_Class_Mo


title: MM-hsfa1a-line1-HS-1h Rep3

description: Bio rep 3


title: TT0109_ATB_V2_Class_Mo


title: skin, psoriasis 2

description:
SK PS02
MicroRNA expression data from skin samples


title: Muscle 2 days post NTX [EC_WT: 2d-6]


title: skin, control 10

description:
SK CT10
MicroRNA expression data from skin samples

source_name: skin sample of healthy control adult

value: healthy control adult


title: MM-hsfa1a-line1-HS-1h Rep2

description: Bio rep 2


title: skin, control 8

description:
SK CT08
MicroRNA expression data from skin samples


title: skin, psoriasis 1

description:
SK PS01
MicroRNA expression data from skin samples


title: skin, control 9

description:
SK CT09
MicroRNA expression data from skin samples


title: skin, control 7

description:
SK CT07
MicroRNA expression data from skin samples


title: Muscle 1 day post NTX [EC_WT: 1d-3]

value: Muscle 1 day post NTX


title: Muscle 2 days post NTX [EC_WT: 2d-1]


title: MM-hsfa1a-line1-HS-1h Rep1

description: Bio rep 1


title: TT0108_ATB_V2_Class_Mo


title: MM-WT-HS-1h Rep3

description: Bio rep 3


title: Muscle 1 day post NTX [EC_WT: 1d-2]


title: TT0108_ATB_V1_Class_Mo


title: MM-WT-HS-1h Rep2

description: Bio rep 2


title: Muscle undamaged [EC_WT: 0d-4]

value: Muscle undamaged


title: MM-WT-HS-1h Rep1

description: Bio rep 1


title: skin, control 6

description:
SK CT06
MicroRNA expression data from skin samples


title: TT0107_ATB_V2_Class_Mo


title: TT0107_ATB_V1_Class_Mo


title: Muscle undamaged [EC_WT: 0d-3]


title: TT0109_ATB_V1_Class_Mo


title: skin, control 2

description:
SK CT02
MicroRNA expression data from skin samples


title: TT0106_ATB_V2_Class_Mo


title: skin, control 5

description:
SK CT05
MicroRNA expression data from skin samples


title: MM-hsfa1a-line2-HS-0h Rep3

description: Bio rep 3

value: Heat stress 0h


title: skin, control 4

description:
SK CT04
MicroRNA expression data from skin samples


title: TT0106_ATB_V1_Class_Mo


title: MM-hsfa1a-line2-HS-0h Rep2

description: Bio rep 2


title: Muscle undamaged [EC_WT: 0d-2]

value: WT


title: Muscle undamaged [EC_WT: 0d-1]


title: Muscle 10 days post NTX [MP_WT: 10d-2]

value: Muscle 10 days post NTX

value: Myogenic Progenitors


title: MM-hsfa1a-line2-HS-0h Rep1

description: Bio rep 1


title: TT0105_ATB_V2_Class_Mo

value: Classical CD14+CD16- monocytes


title: skin, control 1

description:
SK CT01
MicroRNA expression data from skin samples

value: skin


title: MM-hsfa1a-line1-HS-0h Rep3

description: Bio rep 3


title: MM-hsfa1a-line1-HS-0h Rep2

description: Bio rep 2


title: Muscle 10 days post NTX [MP_WT: 10d-1]


title: Muscle 1 day post NTX [EC_WT: 1d-1]

value: Endothelial cells


title: skin, atopic dermatitis 11

description:
SK AD11
MicroRNA expression data from skin samples

source_name: skin sample of atopic dermatitis adult patient

value: atopic dermatitis adult patient


title: skin, atopic dermatitis 12

description:
SK AD12
MicroRNA expression data from skin samples


title: Muscle 7 days post NTX [MP_WT: 7d]

value: Muscle 7 days post NTX


title: TT0105_ATB_V1_Class_Mo

value: South Africa


title: TT0075_TBneg_Class_Mo

value: TBneg


title: skin, atopic dermatitis 10

description:
SK AD10
MicroRNA expression data from skin samples


title: MM-hsfa1a-line1-HS-0h Rep1

description: Bio rep 1

value: cv. Moneymaker background

value: RNAi knock-down line


title: skin, atopic dermatitis 9

description:
SK AD09
MicroRNA expression data from skin samples


title: TT0070_ATB_V2_Class_Mo


title: Muscle 6 days post NTX [MP_WT: 6d-2]

value: Muscle 6 days post NTX


title: TT0070_ATB_V1_Class_Mo


title: TT0069_ATB_V2_Class_Mo


title: MM-WT-HS-0h Rep2

description: Bio rep 2

value: Leaf


title: MM-WT-HS-0h Rep3

description: Bio rep 3


title: skin, atopic dermatitis 8

description:
SK AD08
MicroRNA expression data from skin samples


title: Muscle 5 days post NTX [MP_WT: 5d]

value: Muscle 5 days post NTX


title: skin, atopic dermatitis 7

description:
SK AD07
MicroRNA expression data from skin samples


title: MM-WT-HS-0h Rep1

description: Bio rep 1


title: Muscle 4 days post NTX [MP_WT: 4d]

value: Muscle 4 days post NTX


title: TT0069_ATB_V1_Class_Mo

description: The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns


title: Muscle 3 days post NTX [MP_WT: 3d-2]

value: Muscle 3 days post NTX


title: RNA_M82_HS_6h_rep1

description: Bio rep 1

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar PE $input1 $input2 $output1Paired $output1Unpaired $output2Paired $output2Unpaired ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads were mapped using bowtie2 v 2.3.5 with the following setting "bowtie2 --very-sensitive" against the genome of SollycM82_v1.0.
Quality filtering: mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30 " to remove reads of quality under 30
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the commands "samtools fixmate -m"  and "samtools markdup -r "
Raw read counts were extracted using featureCounts based on the gene annotations in SollycM82_v1.0.gtf
Differentially expressed genes were identified using R 3.5.1(www.R-project.org) and the package DESeq2 (adj. p value < 0.05)
Assembly: SollycM82_v1.0
Supplementary files format and content: Count matrix of all samples obtained with featureCounts

treatment_protocol: 4 weeks old plants were treated at 45°C for 0h, 1h and 6h in a climatic chamber (Aralab).

value: cv. M82 (Tomato cultivar M82)

value: WT

value: Heat stress 6h


title: TT0059_ATB_V1_Class_Mo

value: Classical CD14+CD16- monocytes


title: Muscle 3 days post NTX [MP_WT: 3d-1]

value: Myogenic Progenitors


title: skin, atopic dermatitis 6

description:
SK AD06
MicroRNA expression data from skin samples

value: skin


title: TT0058_TBneg_Class_Mo


title: RNA_M82_HS_1h_rep1

description: Bio rep 1

value: Heat stress 1h


title: skin, atopic dermatitis 5

description:
SK AD05
MicroRNA expression data from skin samples

value: atopic dermatitis adult patient


title: skin, atopic dermatitis 3

description:
SK AD03
MicroRNA expression data from skin samples


title: Muscle 2 days post NTX [MP_WT: 2d-1]

value: Muscle 2 days post NTX


title: Muscle 6 days post NTX [MP_WT: 6d-1]


title: RNA_M82_HS_0h_rep2

description: Bio rep 2

value: Heat stress 0h


title: RNA_M82_HS_6h_rep2

description: Bio rep 2


title: skin, atopic dermatitis 2

description:
SK AD02
MicroRNA expression data from skin samples


title: TT0051_TBneg_Class_Mo

value: TBneg

value: South Africa


title: RNA_M82_HS_0h_rep1

description: Bio rep 1


title: TT0059_ATB_V2_Class_Mo


title: serum, psoriasis 27

description:
MicroRNA expression data from serum samples
SER PS27.rma-dabg.chp Signal

source_name: serum sample of psoriasis adult patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA.

extract_protocol: Total RNA (including microRNAs) was isolated from 150 μl of serum samples using Qiazol (Qiagen, Hilden, Germany) reagent and Total RNA Zol-out kit (A&A Biotechnology, Gdynia, Poland) according to the manufacturer’s instructions

treatment_protocol: All serum samples were collected at exacerbation stage prior to hospitalization of the patients. Separation of serum was performed by centrifugation at 1500g for 15 minutes at 4ºC after 60 minutes clotting process at room temperature. All serum samples were kept frozen at -80ºC until assay.

value: psoriasis adult patient

value: serum


title: TT0050_TBneg_Class_Mo


title: serum, psoriasis 26

description:
MicroRNA expression data from serum samples
SER PS26.rma-dabg.chp Signal


title: Muscle 1 day post NTX [MP_WT: 1d-1]

value: Muscle 1 day post NTX


title: serum, psoriasis 25

description:
MicroRNA expression data from serum samples
SER PS25.rma-dabg.chp Signal


title: HiChIP_Pol2_1h_rep1

description: Bio rep 1

data_processing:
library strategy: HiChIP
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar PE $input1 $input2 $output1Paired $output1Unpaired $output2Paired $output2Unpaired ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads were mapped using HiC-Pro v 2.11.4 with the following setting "BOWTIE2_GLOBAL_OPTIONS = --very-sensitive -L 30 --score-min L,-0.6,-0.6 --end-to-end --reorder BOWTIE2_LOCAL_OPTIONS =  --very-sensitive -L 20 --score-min L,-0.6,-0.6 --end-to-end --reorder GENOME_FRAGMENT = SollycM82_v1.0_dpnii.bed" against the genome of SollycM82_v1.0.
Assembly: SollycM82_v1.0
Supplementary files format and content: allValidPairs.txt files for generating contact matrices

extract_protocol:
The nuclei were isolated from 4-week-old tomato fourth leaves with the same procedure as for the in situ Hi-C experiments. The Hi-ChIP protocol from Mumbach et al. 2016 was then applied using the DpnII restriction enzyme (NEB) and an anti-RNA polymerase II antibody (Abcam, ab26721).
DNA libraries were prepared using NEBNext Ultra II DNA library preparation kit (NEB) according to the manufacturer’s instructions (10 cycles for the PCR amplification step). DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent) and the libraries were subjected to 2 × 75 bp high-throughput sequencing by NextSeq 500 (Illumina).

value: Leaf


title: skin, atopic dermatitis 4

description:
SK AD04
MicroRNA expression data from skin samples


title: HiChIP_Pol2_0h_rep1

description: Bio rep 1


title: RNA_M82_HS_1h_rep2

description: Bio rep 2


title: Muscle 2 days post NTX [MP_WT: 2d-2]


title: TT0049_LTBI_Class_Mo

value: LTBI


title: Muscle undamaged [MP_WT: 0d-3]

value: Muscle undamaged


title: TT0048_LTBI_Class_Mo


title: Muscle undamaged [MP_WT: 0d-2]

value: WT


title: TT0057_TBneg_Class_Mo


title: TT0047_TBneg_Class_Mo


title: HiC_M82_HS_6h_rep2

description: Bio rep 2

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar PE $input1 $input2 $output1Paired $output1Unpaired $output2Paired $output2Unpaired ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads were mapped using HiC-Pro v 2.11.4 with the following setting "BOWTIE2_GLOBAL_OPTIONS = --very-sensitive -L 30 --score-min L,-0.6,-0.6 --end-to-end --reorder BOWTIE2_LOCAL_OPTIONS =  --very-sensitive -L 20 --score-min L,-0.6,-0.6 --end-to-end --reorder GENOME_FRAGMENT = SollycM82_v1.0_dpnii.bed" against the genome of SollycM82_v1.0.
Assembly: SollycM82_v1.0
Supplementary files format and content: allValidPairs.txt files for generating contact matrices

extract_protocol:
In situ Hi-C experiments were performed according to Concia et al (2020) using DpnII enzyme (New England Biolabs).
DNA libraries were prepared using NEBNext Ultra II DNA library preparation kit (NEB) according to the manufacturer’s instructions (10 cycles for the PCR amplification step). DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent) and the libraries were subjected to 2 × 75 bp high-throughput sequencing by NextSeq 500 (Illumina).

value: cv. M82 (Tomato cultivar M82)

value: Heat stress 6h


title: Muscle undamaged [MP_WT: 0d-1]

value: Myogenic Progenitors


title: serum, psoriasis 21

description:
MicroRNA expression data from serum samples
SER PS21.rma-dabg.chp Signal


title: Muscle 1 day post NTX [MP_WT: 1d-2]


title: HiC_M82_HS_6h_rep1

description: Bio rep 1


title: serum, psoriasis 24

description:
MicroRNA expression data from serum samples
SER PS24.rma-dabg.chp Signal


title: Muscle 14 days post NTX [Inflammatory_WT: 14d]

value: Muscle 14 days post NTX

value: Inflammatory cells


title: serum, psoriasis 20

description:
MicroRNA expression data from serum samples
SER PS20.rma-dabg.chp Signal


title: TT0044_TBneg_Class_Mo

value: Classical CD14+CD16- monocytes


title: HiC_M82_HS_1h_rep2

description: Bio rep 2

value: Heat stress 1h


title: TT0046_LTBI_Class_Mo


title: Muscle 10 days post NTX [Inflammatory_WT: 10d]

value: Muscle 10 days post NTX


title: serum, psoriasis 18

description:
MicroRNA expression data from serum samples
SER PS18.rma-dabg.chp Signal


title: TT0041_TBneg_Class_Mo

value: TBneg


title: HiC_M82_HS_1h_rep1

description: Bio rep 1


title: Muscle 7 days post NTX [Inflammatory_WT: 7d-3]

value: Muscle 7 days post NTX


title: HiC_M82_HS_0h_rep2

description: Bio rep 2

value: Heat stress 0h


title: TT0040_TBneg_Class_Mo

value: South Africa


title: Muscle 7 days post NTX [Inflammatory_WT: 7d-2]


title: Muscle 7 days post NTX [Inflammatory_WT: 7d-1]


title: DAP_Halo-tag Rep1

description: Bio rep 1

data_processing:
library strategy: AmpDAP-seq
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads data were mapped using bowtie2 v 2.3.5 with the following setting "bowtie2 --very-sensitive" against the genome of SollycM82_v1.0.
Quality filtering: mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30 " to remove reads of quality under 30
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the commands "samtools fixmate -m"  and "samtools markdup -r "
Peak calling: peaks of read density were called with macs2 2.2.7.1 with the command "macs2 callpeak  -t sample.bam -c Input.bam -g 829069930 -q 0.05 --extsize 150 --bw 500 -B -n --outdir "
Bigwig generation: read density was scored with s3norm with the default parameters
Assembly: SollycM82_v1.0
Supplementary files format and content: s3norm normalized bigwigs

extract_protocol:
AmpDAP-seq assays were performed according to Anna Bartlett et al. (2017) with modifications. Briefly, gDNA was extracted from 4-week-old tomato fourth leaves, fragmented, and a library was generated using NEBNext Ultra II DNA library preparation kit (NEB, #E7645S/L, #E7103S/L). Separately, SolycHsfA1a open reading frames (ORFs) were transferred to the Gateway-compatible pIX-HALO expression vector and expressed using Promega TNT™ Coupled Wheat Germ Extract Systems (Promega, cat. no. L4130). The expressed proteins were immobilized on Magne HALO-Tag beads (Promega, G728A), washed and incubated with the DNA library.
After bead washing, DNA was eluted and amplified with indexed NEBNext primers (20 PCR cycles were used). DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent) and subjected to 1 × 75 bp high-throughput sequencing by NextSeq 500 (Illumina). Two independent biological replicates were generated.

value: Halo-tag


title: serum, psoriasis 15

description:
MicroRNA expression data from serum samples
SER PS15.rma-dabg.chp Signal

value: psoriasis adult patient

value: serum


title: serum, psoriasis 14

description:
MicroRNA expression data from serum samples
SER PS14.rma-dabg.chp Signal


title: TT0036_ATB_V2_Class_Mo


title: Muscle 6 days post NTX [Inflammatory_WT: 6d-2]

value: Muscle 6 days post NTX


title: TT0036_ATB_V1_Class_Mo


title: HiC_M82_HS_0h_rep1

description: Bio rep 1

value: WT

value: Leaf


title: Muscle 6 days post NTX [Inflammatory_WT: 6d-1]


title: DAP_HSFA1a-Halo-tag Rep1

description: Bio rep 1

value: cv. M82 (Tomato cultivar M82)


title: TT0033_ATB_V1_Class_Mo


title: serum, psoriasis 11

description:
MicroRNA expression data from serum samples
SER PS11.rma-dabg.chp Signal


title: serum, psoriasis 13

description:
MicroRNA expression data from serum samples
SER PS13.rma-dabg.chp Signal


title: TT0033_ATB_V2_Class_Mo

description: The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns


title: Muscle 5 days post NTX [Inflammatory_WT: 5d-2]

value: Muscle 5 days post NTX


title: M82-HS-0h ChIP-seq_Input Rep1

description: Bio rep 1

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads data were mapped using bowtie2 v 2.3.5 with the following setting "bowtie2 --very-sensitive" against the genome of SollycM82_v1.0.
Filtering step: Mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30  "mapping_quality >= 30"
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the command "samtools fixmate -m  and samtools markdup -r "
Peak calling: peaks of read density were called with macs2 2.2.7.1 with the command "macs2 callpeak  -t sample.bam   -c Input.bam -g 829069930 -p 0.05 --extsize 150 --bw 500 -B -n --outdir
Bigwig generation: read density was scored with s3norm with the default paramaters
Assembly: SollycM82_v1.0
Supplementary files format and content: s3norm normalized bigwig for plots generated with ComputeMatrix plotprofile of Deeptools

extract_protocol:
ChIP-seq assays were performed on 4-week-old tomato fourth branch of leaves according to Bio-protocol of Ramirez-Prado, J.S. et al (2021) by using anti-H3K27me1 (Millipore, 07-448), anti-H3K9ac (Millipore, 07-352), anti-H3K14ac (Millipore, 07-353), anti-H3K18ac (Millipore, 07-354), anti-H3K27ac (Abcam, ab4729), anti-H3K4me3 (Millipore, 07-473) and anti-polymerase II (Abcam, ab26721) antibodies.
ChIP-seq libraries were prepared from 10ng of DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s instructions. Two independently biological replicates were generated for each time point of heat stress. DNA libraries were checked for quality and quantified using an Agilent 2100 Bioanalyzer (Agilent) and subjected to 1 × 75 bp high-throughput sequencing by NextSeq 500 (Illumina).

treatment_protocol: 4 weeks old plants were treated at 45°C 0h, 1h and 6h in the climatic chamber (aralab).


title: Muscle 5 days post NTX [Inflammatory_WT: 5d-1]


title: serum, psoriasis 10

description:
MicroRNA expression data from serum samples
SER PS10.rma-dabg.chp Signal


title: serum, psoriasis 6

description:
MicroRNA expression data from serum samples
SER PS06.rma-dabg.chp Signal


title: serum, psoriasis 7

description:
MicroRNA expression data from serum samples
SER PS07.rma-dabg.chp Signal


title: TT0039_LTBI_Class_Mo

value: LTBI


title: M82-HS-0h ChIP-seq_H3K27me1 Rep1

description: Bio rep 1


title: TT0032_LTBI_Class_Mo


title: Muscle 4 days post NTX [Inflammatory_WT: 4d-2]

value: Muscle 4 days post NTX

value: Inflammatory cells


title: serum, psoriasis 4

description:
MicroRNA expression data from serum samples
SER PS04.rma-dabg.chp Signal


title: serum, psoriasis 1

description:
MicroRNA expression data from serum samples
SER PS01.rma-dabg.chp Signal


title: M82-HS-6h ChIP-seq_RNAPII Rep2

description: Bio rep 2

value: Heat stress 6h


title: TT0030_LTBI_Class_Mo

value: Classical CD14+CD16- monocytes


title: TT0029_LTBI_Class_Mo


title: Muscle 4 days post NTX [Inflammatory_WT: 4d-1]


title: M82-HS-6h ChIP-seq_RNAPII Rep1

description: Bio rep 1


title: Muscle 3 days post NTX [Inflammatory_WT: 3d-4]

value: Muscle 3 days post NTX


title: TT0028_LTBI_Class_Mo


title: serum, control 16

description:
MicroRNA expression data from serum samples
SER CT16.rma-dabg.chp Signal

source_name: serum sample of healthy control adult

value: healthy control adult


title: Muscle 3 days post NTX [Inflammatory_WT: 3d-3]


title: TT0027_ATB_V2_Class_Mo


title: M82-HS-1h ChIP-seq_RNAPII Rep1

description: Bio rep 1

value: Heat stress 1h


title: Muscle 3 days post NTX [Inflammatory_WT: 3d-2]


title: serum, control 15

description:
MicroRNA expression data from serum samples
SER CT15.rma-dabg.chp Signal


title: TT0027_ATB_V1_Class_Mo

value: South Africa


title: M82-HS-0h ChIP-seq_RNAPII Rep2

description: Bio rep 2

value: Heat stress 0h


title: M82-HS-0h ChIP-seq_RNAPII Rep1

description: Bio rep 1


title: Muscle 2 days post NTX [Inflammatory_WT: 2d-6]

value: Muscle 2 days post NTX


title: TT0026_LTBI_Class_Mo


title: M82-HS-6h ChIP-seq_H3K27ac Rep1

description: Bio rep 1


title: Muscle 3 days post NTX [Inflammatory_WT: 3d-1]


title: TT0022_ATB_V2_Class_Mo


title: serum, control 14

description:
MicroRNA expression data from serum samples
SER CT14.rma-dabg.chp Signal

value: serum


title: serum, control 17

description:
MicroRNA expression data from serum samples
SER CT17.rma-dabg.chp Signal


title: M82-HS-1h ChIP-seq_H3K27ac Rep1

description: Bio rep 1


title: TT0022_ATB_V1_Class_Mo


title: Muscle 2 days post NTX [Inflammatory_WT: 2d-4]


title: M82-HS-1h ChIP-seq_RNAPII Rep2

description: Bio rep 2


title: TT0020_LTBI_Class_Mo


title: Muscle 2 days post NTX [Inflammatory_WT: 2d-3]


title: serum, control 13

description:
MicroRNA expression data from serum samples
SER CT13.rma-dabg.chp Signal


title: M82-HS-0h ChIP-seq_H3K27ac Rep1

description: Bio rep 1


title: M82-HS-6h ChIP-seq_H3K18ac Rep1

description: Bio rep 1


title: TT0019_LTBI_Class_Mo


title: Muscle 2 days post NTX [Inflammatory_WT: 2d-2]


title: DAP_HSFA1a-Halo-tag Rep2

description: Bio rep 2


title: M82-HS-1h ChIP-seq_H3K18ac Rep1

description: Bio rep 1


title: serum, control 12

description:
MicroRNA expression data from serum samples
SER CT12.rma-dabg.chp Signal


title: serum, control 9

description:
MicroRNA expression data from serum samples
SER CT09.rma-dabg.chp Signal


title: serum, control 11

description:
MicroRNA expression data from serum samples
SER CT11.rma-dabg.chp Signal


title: TT0017_LTBI_Class_Mo


title: M82-HS-0h ChIP-seq_H3K18ac Rep1

description: Bio rep 1


title: TT0016_LTBI_Class_Mo


title: Muscle 2 days post NTX [Inflammatory_WT: 2d-5]


title: Muscle 1 day post NTX [Inflammatory_WT: 1d-4]

value: Muscle 1 day post NTX


title: serum, control 8

description:
MicroRNA expression data from serum samples
SER CT08.rma-dabg.chp Signal


title: serum, control 7

description:
MicroRNA expression data from serum samples
SER CT07.rma-dabg.chp Signal


title: TT0013_LTBI_Class_Mo


title: Muscle 1 day post NTX [Inflammatory_WT: 1d-3]

value: WT


title: M82-HS-6h ChIP-seq_H3K9ac Rep1

description: Bio rep 1

value: Leaf


title: M82-HS-1h ChIP-seq_H3K9ac Rep1

description: Bio rep 1

value: cv. M82 (Tomato cultivar M82)


title: Muscle 1 day post NTX [Inflammatory_WT: 1d-2]


title: serum, control 6

description:
MicroRNA expression data from serum samples
SER CT06.rma-dabg.chp Signal


title: TT0011_LTBI_Class_Mo

description: The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns


title: serum, control 5

description:
MicroRNA expression data from serum samples
SER CT05.rma-dabg.chp Signal


title: serum, control 4

description:
MicroRNA expression data from serum samples
SER CT04.rma-dabg.chp Signal


title: Muscle 1 day post NTX [Inflammatory_WT: 1d-1]


title: M82-HS-0h ChIP-seq_H3K9ac Rep1

description: Bio rep 1


title: serum, control 10

description:
MicroRNA expression data from serum samples
SER CT10.rma-dabg.chp Signal


title: M82-HS-6h ChIP-seq_H3K4me3 Rep2

description: Bio rep 2


title: serum, control 3

description:
MicroRNA expression data from serum samples
SER CT03.rma-dabg.chp Signal


title: Muscle 2 days post NTX [Inflammatory_WT: 2d-1]


title: TT0008_TBneg_Class_Mo

value: TBneg


title: Muscle undamaged [Inflammatory_WT: 0d-2]

value: Muscle undamaged


title: serum, control 2

description:
MicroRNA expression data from serum samples
SER CT02.rma-dabg.chp Signal


title: M82-HS-6h ChIP-seq_H3K4me3 Rep1

description: Bio rep 1


title: TT0007_LTBI_Class_Mo

value: LTBI


title: Muscle undamaged [Inflammatory_WT: 0d-1]

value: Inflammatory cells


title: serum, control 1

description:
MicroRNA expression data from serum samples
SER CT01.rma-dabg.chp Signal


title: TT0005_LTBI_Class_Mo


title: M82-HS-1h ChIP-seq_H3K4me3 Rep2

description: Bio rep 2


title: AH_C7

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

data_processing:
Base calling with NextSeq Control/RTA v2 and FASTQ file generation with bcl2fastq v2.20.0.422
Adapter clipping and trimming with cutadapt 2.5.
Mapping to RefSeq GRCm38.p6 Mouse genome with STAR version 2.7.2b and raw read counting with featureCounts v 1.6.4 using the RefSeq annotation.
Differential Expression analysis with DESeq2_1.24.0
Genome_build: Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6)
Supplementary_files_format_and_content: CSV: Raw read table

source_name: Adult heart control

extract_protocol:
Left cardiac ventricles were collected from neonatal hearts left untreated or transferred with adult T cells 36h after myocardial infarction and kept in RNAlater solution for 24h at 4°C. RNA was purified using the RNAeasy Plus Micro Kit (ID: 74034)
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA kit (Illumina) with total RNA as input for mRNA capture with oligo-dT beads

tag: strain

value: Experimental myocardial infarction


title: serum, atopic dermatitis 46

description:
MicroRNA expression data from serum samples
SER AD46.rma-dabg.chp Signal

source_name: serum sample of atopic dermatitis adult patient

value: atopic dermatitis adult patient


title: M82-HS-0h ChIP-seq_H3K4me3 Rep2

description: Bio rep 2


title: TT0003_ATB_V2_Class_Mo

value: Classical CD14+CD16- monocytes


title: AH_C6


title: TT0010_LTBI_Class_Mo


title: AH_C5


title: AH_T4

source_name: Adult heart + adult T cells


title: serum, atopic dermatitis 38

description:
MicroRNA expression data from serum samples
SER AD38.rma-dabg.chp Signal


title: TT0003_ATB_V1_Class_Mo


title: C-HiC-M82-6h-rep2

description: Bio rep 2

data_processing:
library strategy: Capture Hi-C
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar PE $input1 $input2 $output1Paired $output1Unpaired $output2Paired $output2Unpaired ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads data were mapped using HiC-Pro v 2.11.4 with the following setting "BOWTIE2_GLOBAL_OPTIONS = --very-sensitive -L 30 --score-min L,-0.6,-0.6 --end-to-end --reorder BOWTIE2_LOCAL_OPTIONS =  --very-sensitive -L 20 --score-min L,-0.6,-0.6 --end-to-end --reorder GENOME_FRAGMENT = SollycM82_v1.0_dpnii.bed" against the genome of SollycM82_v1.0.
Assembly: SollycM82_v1.0
Supplementary files format and content: allValidPairs.txt files for generating contact matrices

extract_protocol:
For capture Hi-C, the in situ Hi-C libraries were used for the capture step. Capture was performed by using SureSelect XT Target Enrichment System for Illumina Paired-End Multiplexed Sequencing Library (Agilent) according to manufacturer’s recommendations. 1.5Kb length of all of Solanum lycopersicum cv. M82 (Tomato cultivar M82) promoters were selected and 212,735 probes (length of each probe = 120 bp) were designed to catch all promoters. Capture step was performed by using 1µg of in situ Hi-C libraries following manufacturer’s recommendation.
DNA libraries were prepared using NEBNext Ultra II DNA library preparation kit (NEB) according to the manufacturer’s instructions (10 cycles for the PCR amplification step). The quality of the libraries was assessed using a 2100 Bioanalyzer (Agilent), and the libraries were subjected to 2 × 75 bp paired-end high-throughput sequencing by NextSeq 500 (Illumina).

value: Heat stress 6h


title: serum, atopic dermatitis 40

description:
MicroRNA expression data from serum samples
SER AD40.rma-dabg.chp Signal


title: TT0001_ATB_V2_Class_Mo


title: serum, atopic dermatitis 35

description:
MicroRNA expression data from serum samples
SER AD35.rma-dabg.chp Signal


title: AH_T3


title: C-HiC-M82-6h-rep1

description: Bio rep 1


title: TT0001_ATB_V1_Class_Mo


title: serum, atopic dermatitis 34

description:
MicroRNA expression data from serum samples
SER AD34.rma-dabg.chp Signal


title: AH_T2


title: TT0006_LTBI_Class_Mo


title: C-HiC-M82-1h-rep2

description: Bio rep 2

value: Heat stress 1h


title: M82-HS-1h ChIP-seq_H3K4me3 Rep1

description: Bio rep 1


title: serum, atopic dermatitis 24

description:
MicroRNA expression data from serum samples
SER AD24.rma-dabg.chp Signal


title: NH_C9

source_name: Neonatal heart control


title: M82-HS-0h ChIP-seq_H3K4me3 Rep1

description: Bio rep 1


title: NH_C8


title: NH_C7


title: C-HiC-M82-1h-rep1

description: Bio rep 1


title: C-HiC-M82-0h-rep2

description: Bio rep 2


title: serum, atopic dermatitis 22

description:
MicroRNA expression data from serum samples
SER AD22.rma-dabg.chp Signal


title: C-HiC-M82-0h-rep1

description: Bio rep 1


title: serum, atopic dermatitis 18

description:
MicroRNA expression data from serum samples
SER AD18.rma-dabg.chp Signal


title: NH_T4

source_name: Neonatal heart + adult T cells


title: ATAC_M82_6h_rep1

description: Bio rep 1

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar PE $input1 $input2 $output1Paired $output1Unpaired $output2Paired $output2Unpaired ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads were mapped using bowtie2 v 2.3.5 with the following setting "bowtie2 --very-sensitive" against the genome of SollycM82_v1.0.
Quality filtering: mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30 " to remove reads of quality under 30
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the commands "samtools fixmate -m"  and "samtools markdup -r "
Bigwig generation: read density was scored with s3norm with the default parameters
Assembly: SollycM82_v1.0
Supplementary files format and content: s3norm normalized bigwigs

extract_protocol:
Approximately 100 mg of 4-weeks-old tomato fourth leaves were ground, passed through a 100 µm filter and the nuclei were isolated using nuclei isolation buffer (0.25M sucrose, 10mM Tris-HCl pH8, 10mM MgCl2, 1% Triton X-100, 5mM 2-mercapto-ethanol, 0.1 mM  protease inhibitors). The nuclei were re-suspended in 2× TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, Dimethyl Formamide 20%) and 2.5 µl of Tn5 transposase (Illumina FC-121-1030) were added. Transposition reaction was performed at 37 °C for 30 min, and DNA was purified using a Qiagen MinElute Kit (QIAGEN, Cat.No.28004).
DNA libraries were amplified for a total of 10 cycles as described by Buenrostro et al. (Nat Methods.2013) and Jegu et al. (Genome Biol. 2017). DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent) and subjected to 2 × 75 bp high-throughput sequencing by NextSeq 500 (Illumina).


title: ATAC_M82_1h_rep1

description: Bio rep 1


title: AH_T1


title: serum, atopic dermatitis 13

description:
MicroRNA expression data from serum samples
SER AD13.rma-dabg.chp Signal


title: NH_C6


title: ATAC_M82_6h_rep2

description: Bio rep 2


title: serum, atopic dermatitis 9

description:
MicroRNA expression data from serum samples
SER AD09.rma-dabg.chp Signal


title: NH_T5


title: serum, atopic dermatitis 15

description:
MicroRNA expression data from serum samples
SER AD15.rma-dabg.chp Signal


title: serum, atopic dermatitis 1

description:
MicroRNA expression data from serum samples
SER AD01.rma-dabg.chp Signal


title: ATAC_M82_1h_rep2

description: Bio rep 2


title: NH_T2


title: ATAC_M82_0h_rep2

description: Bio rep 2


title: serum, atopic dermatitis 20

description:
MicroRNA expression data from serum samples
SER AD20.rma-dabg.chp Signal


title: serum, atopic dermatitis 8

description:
MicroRNA expression data from serum samples
SER AD08.rma-dabg.chp Signal


title: NH_T1


title: serum, atopic dermatitis 3

description:
MicroRNA expression data from serum samples
SER AD03.rma-dabg.chp Signal


title: serum, atopic dermatitis 5

description:
MicroRNA expression data from serum samples
SER AD05.rma-dabg.chp Signal


title: ATAC_M82_0h_rep1

description: Bio rep 1


title: SAMPLE 17_F3

status: Public on Jan 02 2023

city: Singapore

first: Chit Fang

last: Cheok

address: 61 Biopolis Drive

department: IMCB

country: Singapore

institute: A*STAR

hyb_protocol: Hybridized into 2 Human HT-12 v4.0 BeadChips

scan_protocol: Scanned on the iScan (Illumina).

data_processing: The data files were quantified in GenomeStudio Version 2011.1 (Illumina) and normalised in Limma via quantile normalization

label: biotin, cy3_hyb

source_name: HCT116, Wildtype

label_protocol: Labelled using Illumina TotalPrep RNA Amplification kit Lot # 1105025 (Ambion)

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit

treatment_protocol: Isogenic P53KO obtained from Bunz et al, 1999 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC408422/)

value: wild ytpe

tag: source

value: Colon Adenocarcinoma

tag: batch

tag: replicate

value: Biolgical Replicate 3, Techinical Replicate 2


title: SAMPLE 11_B3

value: Biolgical Replicate 1, Techinical Replicate 2


title: SAMPLE 10_B1

value: Biolgical Replicate 1, Techinical Replicate 1


title: SAMPLE 12_B5

value: Biolgical Replicate 1, Techinical Replicate 3


title: SAMPLE 16_F1

value: Biolgical Replicate 3, Techinical Replicate 1


title: SAMPLE 18_F5

value: Biolgical Replicate 3, Techinical Replicate 3


title: SAMPLE 4_D1

source_name: HCT116, p53isogenic knockout

value: p53isogenic knockout

value: Biolgical Replicate 2, Techinical Replicate 1


title: SAMPLE 9_D11


title: SAMPLE 6_D5

value: Biolgical Replicate 2, Techinical Replicate 3


title: SAMPLE 3_A5


title: SAMPLE 7_D7


title: Sca1[+]/CD140a[-] cells Injury

city: Ankara

first: Cetin

last: Kocaefe

state: Sihhiye

address: Hacettepe University School of Medicine

department: Dept. of Medical Biology

country: Turkey

institute: Hacettepe University School of Medicine

description: Sca1[+]/CD140a[-] immunophenotype

data_processing:
Generated uBAM files were initially de-multiplexed and trimmed using FastX toolkit
Reads were aligned to Ensembl mouse genome (GRCm38/mm10 release 90) using STAR
Read counts were further normalized using DESeq2 for R
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Processed data file is the normalized samples/gene counts matrix table generated via DeSeq2 software

source_name: Tibialis anterior muscle

growth_protocol: Mice were fed with standard rodent chow and ad libitum tap water.

extract_protocol:
Total RNA was isolated from freshly sorted stromal cell populations using Trizol Reagent (Invitrogen 15596-026) according to manufacturer’s recommendations. RNA quantitation was performed using Qubit™ RNA HS Assay Kit (Invitrogen Q32852).
20-100 ng of total RNA was employed to prepare mRNA library using QuantSeq 3’mRNA-Seq Library Prep Kit (Lexogen) according to manufacturer’s standard protocol. Libraries were quantitated using Qubit dsDNA high sensitive quantitation kit (Invitrogen Q32854).  100 pM of library dilutions were prepared, barcoded and pooled using emulsion PCR using PI Hi-Q OT2 200 (Thermo Fisher Scientific) and Ion One Touch 2 (Thermo Fisher Scientific). After clonal DNA amplification, libraries were purified from magnetic beads using Ion One Touch ES device. Sequencing was accomplished using Ion PI Hi-Q Sequencing 200 reagents (Thermo Fisher Scientific A26434) on an Ion PI Chip v3 (Thermo Fisher A26771) and Ion Proton system (Thermo Fisher 4476610).

treatment_protocol: Acute muscle injury was generated with cardiotoxin injection (20uM in steril PBS, Sigma C5759) into tibialis anterior muscles

value: Swiss white

value: skeletal muscle

tag: cell tytpe

value: stromal cells

value: 3rd day Cardiotoxin injection


title: SAMPLE 14_E3

value: Biolgical Replicate 2, Techinical Replicate 2


title: Sca1[+]/CD140a[+] cells Injury

description: Sca1[+]/CD140a[+] immunophenotype


title: Sca1[+]/CD140a[-] cells Control

description: Sca1[+]/CD140a[-] immunophenotype

value: Control


title: SAMPLE 8_D9


title: Sca1[-]/CD140a[+] cells Control

description: Sca1[-]/CD140a[+] immunophenotype


title: HEI193-12.5-3

type: genomic

city: SAN FRANCISCO

first: John

last: Liu

state: California

address: 35 Medical Center Way

institute: UCSF

hyb_protocol: Samples are then hybridized overnight to an 8-sample BeadArray, in which the WGA-DNA molecules anneal to locus-specific DNA oligomers linked to individual bead types. The oligomer probe designs follow the Infinium I and II chemistries, in which base extension follows hybridization to a locus-specific oligomer. With respect to the Infinium I probes, there are two different bead types for each locus, one with an oligomer that anneals specifically to the methylated version of the locus, while the other oligomer anneals to the unmethylated version of the locus. The probes terminate complementary to the interrogated CpG site for methylated loci, or complementary to the TpG for unmethylated alleles. A matched oligomer-template DNA molecule hybrid will allow for the incorporation of a labeled nucleotide immediately upstream (5’) to the interrogated CpG (or TpG) site. However, if the probe and template are mismatched, then primer extension will not occur. Adenine and thymine nucleotides are labeled with cy5 (red), while cytosine nucleotides are labeled with cy3 (green). No insertion of guanine nucleotides occurs in Infinium I assays. Of note, the identity of the dye is representative of the nucleotide adjacent to the CpG dinucleotide. The methylation discrimination is derived from separate measurements from the two different types of beads present for each locus. For some loci, both measurements will be cy3, and for others both will be cy5. The Infinium type II chemistry is a true two-color system. A matched oligomer-template DNA molecule hybrid will allow for the incorporation of a labeled nucleotide at the interrogated C or T of the CpG site. Adenine nucleotides labeled with cy5 (red) are incorporated across from unmethylated (TpG) sites, while guanine nucleotides labeled with cy3 (green) are incorporated across from methylated (CpG) sites.

scan_protocol: After the chemistry steps, BeadArrays are scanned and the raw signal intensities are extracted from the *.IDAT files using the ‘noob’ function in the minfi R package.

data_processing: To classify prospective vestibular schwannomas into molecular groups, a methylation-based classifier using differentially methylated probes from our discovery cohort of 66 tumors was used to construct a support vector machine (SVM) using caret version 6.0 in R version 3.6.0. A linear kernel SVM was constructed using training data comprising 75% of randomly selected samples from the discovery cohort with 10-fold cross validation. The top 2000 differentially methylated probes were used as variables. The model was applied to a test set comprising 25% of randomly selected samples from the discovery cohort, and receiver operating characteristics were acquired for 1000x resampling of test data. Methylation profiles were then processed using this statistical model for molecular group classification.

label: Cy5 and Cy3

source_name: schwannoma

label_protocol: Genomic DNA (1000 ng) is bisulfite converted using the Zymo EZ DNA methylation kit (Zymo Research, Irvine, CA) according to the manufacturer’s recommendations. The amount of bisulfite-converted DNA as well as the completeness of bisuflite conversion for each sample are assessed using a panel of MethyLight-based real-time PCR quality control assays as described previously (PMID: 18987824). Bisulfite-converted DNA is then used as a substrate for the Illumina EPIC BeadArrays, as recommended by the manufacturer and first described in Moran, 2016 (PMID: 26673039).   Specifically, each sample is whole genome amplified (WGA) and then enzymatically fragmented.

growth_protocol: Patient resection specimen

extract_protocol: DNA were isolated from tumor samples using the All-Prep Universal Kit (QIAGEN, Valencia, CA)

tag: experimental design

value: classification


title: HEI193-12.5-1


title: VS10


title: HEI193-12.5-2


title: HEI193-0-1


title: SAMPLE 5_D3

value: Colon Adenocarcinoma


title: SAMPLE 13_E1

value: wild ytpe


title: HEI193-0-2


title: SAMPLE 2_A3

value: Biolgical Replicate 1, Techinical Replicate 2


title: HEI193-0-3


title: VS6


title: SAMPLE 1_A1

value: Biolgical Replicate 1, Techinical Replicate 1


title: VS9


title: VS8


title: VS3


title: VS4


title: VS2


title: Sca1[+]/CD140a[+] cells Control

description: Sca1[+]/CD140a[+] immunophenotype


title: VS5


title: VS1


title: SAMPLE 15_E5


title: Sca1[-]/CD140a[+] cells Injury

description: Sca1[-]/CD140a[+] immunophenotype


title: S12

data_processing: Data preprocessing and normalization was performed using minfi version 1.30 in R version 3.6.0. Methylation probes with detection significance p>0.05 were excluded from analysis. Normalization was performed using functional normalization. Probes were filtered according to the following criteria: (i) exclusion of probes mapping to sex chromosomes (n=11,551), (ii) exclusion of probes containing a common single nucleotide polymorphism (SNP) within the targeted CpG site or on an adjacent base pair (n=24,536), and (iii) exclusion of probes not mapping uniquely to the human reference genome hg19 (n=9,993). A total of 815,630 probes were retained for further analysis. Methylation β values were calculated as the ratio of methylated probe intensity to the sum of methylated and unmethylated probe intensities and visualized on heatmaps in an absolute scale.

tag: type

tag: Sex

value: F

tag: age

tag: size

tag: eor

value: inflammatory tumor microenvironment

tag: lf

tag: lffp


title: S3_1

value: schwannoma


title: S69


title: S38

value: M


title: S9_2


title: S68


title: S53


title: S50


title: S28


title: S49


title: S64


title: S51


title: S3_2


title: S14


title: S52


title: S6_2


title: S9_1


title: S67


title: S27


title: S11


title: S30


title: S10


title: S55


title: S31


title: S56


title: S54


title: S6_1


title: S48


title: S26


title: S24


title: S29


title: S57


title: S44


title: S1_1


title: S36


title: S21


title: S13


title: S46


title: S22


title: S23


title: S63


title: SJALCL045621_D1

city: Memphis

first: Timothy

middle: Isham

last: Shaw

state: TN

address: 262 Danny Thomas Pl

department: Computational Biology

institute: St Jude Children's Research Hospital

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing:
The methylation score of each CpG site in the array is represented as a beta (β) value and was computed using the methylation module of the Geno meStudio software (version 1.9.0; Illumina). Beta-values were converted to M-values (39) prior to differential methylation analysis and clustering.
Processed data: Average Beta

source_name: ALCL Diagnosis

label_protocol: Illumina protocol

growth_protocol: Primary Tissue

extract_protocol: Genomic DNA (1 µg) from 37 ALCL was bisulfite converted by using the EZ DNA Methylation kit (Zymo Research Corp, Irvine, CA, USA). Converted samples were processed and hybridized to the Infinium MethylationEPIC BeadChip (850K) system (Illumina, San Diego, CA, USA).

tag: gender

tag: age at diagnosis

tag: sample source

value: Mesenteric

tag: histologic subtype

value: common


title: SJALCL045615_D1

value: Left neck:Cervical, supraclavicular, occipital, and pre-auricular


title: SJALCL017863_D1

value: Lymph node, left cervical supraclavicular


title: SJALCL017864_D1

value: Lymph node


title: S61_3


title: S20


title: S60_1


title: S37


title: SJALCL017852_D1


title: SJALCL017855_D1


title: SJALCL045635_D1

value: Skin


title: SJALCL017856_D1

value: LH


title: S60_2


title: S1_2


title: S61_1


title: SJALCL017850_R1

source_name: ALCL Relapse


title: CK5_CH891_3

city: 南昌

first: Jianmin

last: Bian

state: 江西 (Jiāngxī)

address: 志敏大道1101

institute: 江西农业大学

data_processing:
Illumina Hiseq4000 software used for basecalling.
The quality of sequenced reads were checked, and masked for low-complexity or low-quality sequence, then Hisat is used to compare the preprocessed Valid Data with reference genomes, and statistics are made separately according to the gene position information specified by the genome annotation file gtf.
Genome_build: Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
Supplementary_files_format_and_content: 4_genes_fpkm_expression.txt: Matrix table with FPKM values for every gene and every sample.

organism: Oryza sativa Indica Group

source_name: seedlings

growth_protocol: Thirty germinative seeds were placed in each dish, and the treatment groups (Cd) were treated with 200mg/L CdCl2 while the control groups (CK) with distilled water. Seedlings were maintained in the incubator at 28℃/25℃ for 16/8 h light/dark condition.

extract_protocol:
RNA was isolated using Trizol reagent Kit.
RNA libraries were prepared for sequencing using Illumina Hiseq4000 protocols.

treatment_protocol: After three days of cultivation, the seedlings of two rice varieties treated with cadmium and control were sampled respectively.

tag: developmental stage

value: germination stage

tag: tissue

value: seedlings

tag: treatment

value: control


title: CK5_CH891_2


title: S47


title: Cd5_CH891_3

value: cadmium


title: CK5_CH891_1


title: Cd5_CH891_2


title: S45


title: Cd5_CH891_1


title: SJALCL017859_D1


title: RNAseq_KO3A_1

city: Panjin

first: Yubo

address: Dagong Lu

institute: Dalian University of Technology

data_processing:
SOAP nuke software (v2.1.0) was used to remove reads with unknown bases more than 10% and low-quality reads (the ratio of the bases with quality value Q ≤ 15 greater than 50%).
Bowtie2 and HISAT (v2.1.0) were used to align clean reads to the reference genome hg19.
RSEM (v1.2.4) was then used to quantify the gene-expression level through the fragments per kilobase of transcript per million mapped reads (FPKM) method.
The differentially expressed genes (DEGs) were determined by DESeq2 (v1.18.1, fold change ≥ 2 and p value ≤ 0.05).
Assembly: hg19
Supplementary files format and content: counts.txt

source_name: breast

extract_protocol:
HA-FOXA1-WT and HA-FOXA1-3A cells were maintained in RPMI-1640 medium with 10% fetal calf serum. Approximately 2 x 10e7 cells were used for ChIP-seq assay. For HA-FOXA1-WT and HA-FOXA1-3A ChIP-seq, crosslinked chromatin complexes were immunoprecipitated with anti-HA-magnetic beads. For MECP2 ChIP-seq, crosslinked chromatin complexes were immunoprecipitated with anti-MECP2 antibody. For RNA-seq, total RNA was extracted from the HA-FOXA1-WT and HA-FOXA1-3A expressing cells using Trizol reagent (Invitrogen). RNA quality was checked by Agilent 2100 Bioanalyzer (Agilent Technologies, USA). RNA libraries were prepared for sequencing using standard protocols.
DNA-end repair, 3'-dA overhang and ligation of methylated sequencing adaptor. PCR amplification and size selection (usually 100-300bp, including adaptor sequence. Qualified library for sequencing. RNA-seq libraries were constructed using SMARTer cDNA library construction kit.

treatment_protocol: Generation of FOXA1 knockout MCF-7 cell using CRISPR-Cas9 genome editing (MCF-7 FOXA1 KO). The sequence coding human full-length (1-472aa) wild type (WT) human FOXA1 and O-GlcNAcylation site mutants (Thr432/Ser441/Ser443 → Ala, 3A) FOXA1 were subcloned into lentiviral luciferase expressing pLVX-IRES-Luc-Neo vector containing an N-terminal HA tag. Transfection of the MCF-7 FOXA1 KO cells were performed with Lentivirus according to the manufacturer’s instructions. The stably transfected cells were then selected by the addition of neomycin to the medium. MECP2 was transiently knockdown by MECP2 shRNA. ~2x10e7 cells were used as a unit of cells for each experiment.

value: breast

tag: cell line

tag: cell type

value: epithelial type of breast cancer cell

tag: genotype


title: RNAseq_KO3A_2

growth_protocol: RPMI-1640 medium with 10% fetal calf serum.


title: S43

tag: type


title: S41

tag: Sex


title: RNAseq_KOWT_1


title: S62

value: F

tag: age


title: RNAseq_KOWT_2


title: ChIPseq_KOWT_shMECP2_2

data_processing:
base-calling: in-house Illumina software
Bowtie2 (version: v2.2.5) was used to map clean reads to reference gene
peak-calling: MACS2 for ChIP-Seq; FPKM method was used in calculated RNA-seq expression level.
Deeptools was used for generating bigwig files. ChIPseeker for the annotation of peaks.
Assembly: hg19
Supplementary files format and content: bigwig

tag: antibody

value: anti-MECP2 antibody

value: KOWT


title: ChIPseq_KO3A_shMECP2_1


title: ChIPseq_KO3A_MECP2_2


title: ChIPseq_KOWT_shMECP2_1


title: S42

tag: size

tag: eor

value: inflammatory tumor microenvironment


title: ChIPseq_KO3A_shMECP2_2


title: ChIPseq_KOWT_MECP2_2


title: ChIPseq_KO3A_MECP2_1


title: ChIPseq_KOWT_MECP2_1


title: ChIPseq_KO3A_IP_HA_FOXA1_2

value: anti-HA-magnetic beads


title: S19

value: M

value: schwannoma

tag: lf

tag: lffp


title: S61_2


title: ChIPseq_KO3A_IP_HA_FOXA1_1


title: S66


title: ChIPseq_KOWT_IP_HA_FOXA1_1


title: S16


title: ChIPseq_KO3A_INPUT_HA_FOXA1_2


title: ChIPseq_KOWT_IP_HA_FOXA1_2


title: ChIPseq_KOWT_INPUT_HA_FOXA1_2


title: S40


title: ChIPseq_KO3A_INPUT_HA_FOXA1_1


title: Primary human neutrophils, LPS-treated, 6h biol rep 2

city: Montreal

first: Aiten

last: Ismailova

state: Quebec

address: 3655 Promenade Sir William Osler

institute: McGill University

data_processing:
Only RNA samples with OD 260/280 ratio greater than 1.7 and a RNA integrity number (RIN) > 7 were kept for downstream analysis.
These samples were submitted to McGill University and Genome Quebec Innovation Centre for paired-end sequencing at 50M reads by Illumina NovaSeq 6000S2 PE100.
Each RNAseq dataset had similar total number of RNAseq reads sequenced for each condition and total  GC  content. The  Phred  offset  quality  score  was  greater  than  30  for  all  RNAseq  datasets and  the minimum fragment size for alignment was set to 50. These settings yielded 70% to 85% of reads aligning to a gene using the RSubread and EdgeR packages in R. We filtered out genes with low read counts and included genes with counts of 10 or more for at least 1 treatment group (in all replicates) for downstream analysis.
Running the RNAseq quality control pipeline, it was determined that 3 and 2 replicates for control and LPS-treated conditions, respectively, were of high enough  quality  for  downstream  analysis.  We  obtained  read  counts  and  assessed  differential  gene expression using EdgeR and LIMMA R packages, respectively.
Quality control including read trimming and  filtering  out  low  quality  reads,  mapping  to GRCh38 genome  assembly,  summarization  by  gene, normalization and differential gene expression using the R packages EdgeR and DESeq2 was performed at McGill University and Genome Quebec Innovation Centre.
Assembly: GRCh38
Supplementary files format and content: excel file includes output of DESeq2 (differentially expressed genes and their associated log 2 fold changes, log CPM, p- and FDR values).

source_name: Primary human neutrophils

extract_protocol:
Total RNA was extracted using FavorPrep Blood/Cultured Cell Total RNA Mini Kit (FABRK 001, Favorgen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNAseq were prepared using NEBNext dual mRNASeq stranded library kit following manufacturer's protocol.

value: Primary human neutrophils

tag: time point

value: 1ug/ml LPS


title: ChIPseq_KOWT_INPUT_HA_FOXA1_1


title: AS_M_10

city: Cleveland

first: Ernest

middle: R

last: Chan

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
Illumina reads were mapped to reference genome using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Assembly: hg19
Supplementary files format and content: matrix.txt (tab delimited file containing FPKM values for each gene/sample)

source_name: Peripheral blood

extract_protocol:
total RNA was extracted as per Takara kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Stimulation of PBMCs with CytoSim for 4 hours then enrichment by interleukin (IL)-17-phycoerythrin (PE) cytokine secretion assay

tag: disease state

value: Ankylosing Spondylitis (AS)

value: Peripheral blood

value: PBMCs

value: Cytostim for 4 hours


title: S18


title: AS_M_8


title: AS_M_7


title: AS_M_6


title: Primary human neutrophils, LPS-treated, 6h biol rep 1


title: AS_M_5


title: AS_M_4


title: S15


title: AS_M_0


title: AS_M_3


title: AS_M_2


title: S58_2

value: reactive tumor microenvironment


title: AS_F_8


title: AS_F_7


title: AS_F_4


title: S59_2


title: AS_F_3


title: Primary human neutrophils, Control, 6h, biol rep 2

value: vehicle


title: AS_M_1


title: AS_F_1


title: S65


title: AS_M_9


title: AS_F_0


title: Ctrl_M_3

value: Control


title: S39


title: AS_F_5


title: Ctrl_M_2


title: Ctrl_M_1


title: Ctrl_M_0


title: S17


title: Ctrl_F_3


title: Ctrl_F_2


title: Ctrl_F_1


title: Ctrl_F_0


title: H3K27me3, Differentiating, normal glucose, donor 4

city: Stanford

first: Douglas

last: Porter

address: 269 Campus Drive

department: Dermatology

institute: Stanford

description: donor 4

data_processing:
Cutadapt (MARTIN, 2011) (v. 1.8.1) was used to remove NEBNext/TruSeq adapters (AGA TCG GAA GAG CAC ACG TCT GAA CTC CAG TCA and AGA TCG GAA GAG CGT CGT GTA GGG AAA GAG TGT).
Bowtie2 (Langmead and Salzberg, 2012) (v. 2.4.2) was used to map clipped reads to the hg38 genome, using the parameters –end-to-end –very-sensitive –no-mixed –no-discordant -I 10 -X 700.
Samtools was then used to add mate score tags (samtools fixmate -m), sort, mark duplicates (samtools markdup), and filter out unmapped reads and optical duplicates (samtools view -f 3 -F 1024).
MACS2 (Gaspar, 2018; Zhang et al., 2008) (v. 2.2.71) was run on the filtered bam files, controlling CUT&RUN samples to IgG samples, using the default parameters plus -f BAMPE --bdg. Peak regions across all samples were merged using bedtools (Quinlan and Hall, 2010) merge.
Assembly: hg38
Supplementary files format and content: Bigwig files countain reads.normalized to per-million reads.
Library strategy: CUT&RUN

source_name: Primary human keratinocytes

growth_protocol: Primary human keratinocytes were isolated from fresh surgically discarded newborn foreskin, and progenitor cells cultured in complete Keratinocyte-SFM (Life Technologies, #17005-142) and Medium 154 (Life Technologies #M-154-500).  For infection, the optimized viral titer was added to primary human keratinocytes together with polybrene (5 µg/mL). The next day, fresh media was added, and cells were selected using puromycin (1 µg/mL). Cells were infected with a HA-tagged DDX21 construct. Biological replicates were performed in keratinocytes using primary cells from at least 2 independent, unrelated donors.

extract_protocol:
CUT&RUN was performed on 0.5-1 million primary keratinocytes according to the EpiCypher protocol (“CUT&RUN Protocol v2.0”, revised 3/15/2022) and kit (EpiCypher, 14-1048), either using antibody to the endogenous DDX21 (ProteinTech, 10528-1-AP) or infected with virus expressing HA-tagged DDX21 (antibody: CST, #3724). Controls libraries were made for IgG and H3K27me (antibodies: IgG, CST, #2729; anti-H3K27me3, Active Motif, 39055). Nuclei were extracted by resuspending in 100 µL nuclei extraction buffer per 2.5 million cells (20 mM HEPES pH 7.5, 10 mM NaCl, 0.5 mM spermidine, 0.1% BSA, 0.1% NP-40, and 1 tablet Roche protease inhibitor per 10-20 mL) and incubating for 10 minutes on ice. 5-10 volumes of wash buffer were added, cells centrifuged, resuspended in wash buffer, and quantified using a Countess. Nuclei were bound to 10 µL activated Concanavalin A beads (EpiCypher, 21-1401) per sample, stained at 4°C  for 2 hrs to overnight with 1:50 antibody dilutions (anti-HA, CST, #3724; anti-DDX21, ProteinTech, 10528-1-AP; anti-DDX21, Novus Biologicals, NBP1-83310; IgG, CST, #2729; anti-H3K27me3, Active Motif, 39055), washed, and incubated with 2.5 µL pAG-MNase (EpiCypher, 15-1016) per sample for 1 hour at 4°C with rocking, washed, digested for 15-30 minutes, and reactions quenched with EpiCypher STOP buffer for 30 minutes at 37°C according to the manufacturer’s protocol. Nuclei and beads were centrifuged for >4,800 rcf at 4°C for 5-15 minutes, placed on a magnet, and supernatant containing released fragments was removed. Cross-links were then reversed by the addition of SDS to ~0.2% and proteinase K to ~0.4 µg/mL (final concentrations), incubating for 55°C in a thermomixer for 4 hours to overnight. DNA was extracted by a Zymo DNA Clean and Concentrator (Zymo Research, D4014), eluting in 27 µL water.
Library was prepared using the NEB Ultra II DNA library prep kit (NEB, E7103S) following the manufacturer’s protocol with modifications according to published research (Liu et al., 2018).

treatment_protocol: Progenitor cells were not cross-linked, while differentiated cells were cross-linked, as this yielded a reduction in bead aggregation after nuclear extraction. Keratinocytes were washed with PBS, harvested with trypsin and cross-linked in media with 0.1% formaldehyde for 1 minute before quenching with 125 mM glycine. After quenching, cells were placed on ice, centrifuged at 4°C, washed with cold PBS + 0.1% BSA, and maintained afterwards at 4°C.

value: Primary human keratinocytes

value: keratinocytes

value: HA-DDX21 integrated by lentivirus

value: normal glucose


title: H3K27me3, Progenitor, donor 4

description: donor 4


title: IgG, Progenitor, donor 4

description: donor 4

value: IgG


title: H3K27me3, Differentiating, low glucose, donor 4

description: donor 4

value: low glucose


title: IgG, Progenitor, donor 3

description: donor 3


title: IgG, Progenitor, donor 2

description: donor 2


title: IgG, Differentiating, normal glucose, donor 4

description: donor 4


title: IgG, Differentiating, low glucose, donor 3

description: donor 3


title: IgG, Differentiating, low glucose, donor 4

description: donor 4


title: IgG, Differentiating, low glucose, donor 1

description: donor 1


title: IgG, Differentiating, low glucose, donor 2

description: donor 2


title: IgG, Differentiating, normal glucose, donor 3

description: donor 3


title: HA-DDX21 epitope, Progenitor, donor 3

description: donor 3


title: HA-DDX21 epitope, Progenitor, donor 1

description: donor 1


title: IgG, Differentiating, normal glucose, donor 1

description: donor 1


title: HA-DDX21 epitope, Differentiating, low glucose, donor 3

description: donor 3


title: HA-DDX21 epitope, Differentiating, low glucose, donor 2

description: donor 2


title: HA-DDX21 epitope, Differentiating, low glucose, donor 1

description: donor 1


title: HA-DDX21 epitope, Differentiating, normal glucose, donor 3

description: donor 3


title: HA-DDX21 epitope, Differentiating, normal glucose, donor 2

description: donor 2


title: H3K27me3, Differentiating, low glucose, donor 3

description: donor 3


title: HA-DDX21 epitope, Differentiating, normal glucose, donor 1

description: donor 1


title: H3K27me3, Differentiating, low glucose, donor 1

description: donor 1


title: H3K27me3, Differentiating, normal glucose, donor 3

description: donor 3


title: H3K27me3, Differentiating, normal glucose, donor 2

description: donor 2


title: DDX21 epitope, Progenitor, donor 4

description: donor 4


title: DDX21 epitope, Differentiating, normal glucose, donor 4

description: donor 4


title: IgG, Differentiating, normal glucose, donor 2

description: donor 2


title: IgG, Progenitor, donor 1

description: donor 1


title: DDX21 HA-DDX21 epitope, Progenitor, donor 4

description: donor 4


title: DDX21 epitope, Differentiating, low glucose, donor 4

description: donor 4


title: DDX21 HA-DDX21 epitope, Differentiating, low glucose, donor 4

description: donor 4


title: XBP1_3 CUTNRUN

city: Madison

first: Allan

last: brasier

state: WI

address: 715 HIghland

institute: University of Wisconsin-Madison

description: RSV infected bioreplicate 3

data_processing:
library strategy: CUT&RUN
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Reads were trimmed from 3' end until the final base had a quality score > 30
Reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called using SEACR keeping top 20% of peaks.  These are saved as .bed files
Assembly: hg38
Supplementary files format and content: SEACR bed files

source_name: Lung

growth_protocol: Immortalized primary hSAECs were obtained from commercial repository and grown in SAGM small airway epithelial cell growth medium (Lonza, Walkersville, MD, USA) in 5% CO2.

extract_protocol: 4 x 10^6 trypsinized cells were aliquoted and incubated on ice for 10 minutes in 1 ml of nuclear extraction buffer (20 mM HEPES, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 1x cOmplete proteinase inhibitor, 1x protein phosphatase inhibitor cocktail and 0.5 mM spermidine), the released nuclei were pelleted at 600x g, 5 minutes at 4 oC. A basic wash buffer (WB) consisting of 20 mM HEPES, pH7.5, 150 mM NaCl, 0.05% Triton X-1000, 0.1% BSA, 1x cOmplete proteinase inhibitor, 1x protein phosphatase inhibitor cocktail and 0.5 mM spermidine was used throughout. Between incubation steps, the nuclei were pelleted at 600x g, 3 minutes at 4 oC. Prior to antibody binding, the isolated nuclei were incubated with nutation at 4 oC for 5 minutes in WB containing 2 mM EDTA, followed by nutation at 4 oC for 25 minutes in WB. The nuclei were resuspended in antibody buffer produced by diluting 5 mg of FLAG-M2 in 500 ml of Triton X-100-free WB, and incubated with nutation overnight at 4 oC.  After washing three times in 500 ml of WB on ice (10 minutes each time), the nuclei were incubated at 4 oC for 1 h in 50 ml of WB containing 2.5 ml of EpiCypher pAG-MNase 20x stock (EpiCypher, NC). Washing as above, targeted chromatin cleavage was then conducted by incubating the nuclei on ice for 1 h in 150 ml of BSA-free WB containing 2 mM CaCl2. The cleavage was terminated by adding 150 ml of stop buffer (300 mM NaCl, 20 mM EDTA, 4 mM EGTA and 0.5 ng of E. coli Spike-in DNA (EpiCypher, NC) per 150 ml).  The samples were further incubated with nutation at 4 oC for 1 h, centrifuged at 16,000x g for 5 min at 4 oC and the supernatant was collected. Phenol-chloroform DNA precipitation with 80 mg of glycogen was performed and the Cut&Run-enriched DNA was dissolved in 20 ml of 0.1x TE buffer. Following DNA quantitation by a Qubit fluorometer, Cut&Run DNA libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, MA) per the manufacturer’s instruction, with modification in SPRI bead clearance of adaptor ligation and library amplification reactions to retain small-sized DNA fragments (down to ~170 bp in post-library amplification size). The quality of the resultant DNA libraries was confirmed by Agilent TapeStation HS DNA assay (Agilend, CA), and paired-end Illumina NGS was carried out on NovaSeq 6000 with 5 million reads per sample.

treatment_protocol: Sucrose cushion purified RSV Long was prepared and tittered using methylcellulose plaque assay.  hSAECs were treated in triplicate replicates with or without RSV infection (MOI = 1.0, 24 h).

value: Lung

value: hSAEC

value: lung epithelial

value: RSV infected


title: CON1 CUTNRUN

description: control bio replicate 1

value: control


title: XBP1_2 CUTNRUN

description: RSV infected bioreplicate 2


title: CON3 CUTNRUN

description: control bio replicate 3


title: XBP1_1 CUTNRUN

description: RSV infected bioreplicate 1


title: Primary human neutrophils, Control, 6h, biol rep 1

value: Primary human neutrophils


title: H3K27me3, Progenitor, donor 3

description: donor 3


title: IP_rep2_WTdeg_8h

city: Rehovot

first: Anna

last: Uzonyi

address: 234 Herzl street

department: Department of Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
The reads were aligned with STAR/2.7.9a to the hg19 genome. For further analysis, the bam files were filtered for uniquely aligned reads and processed by the bam2Endreads Rscript (Garcia-Campos et al. 2019) for RNA fragment coverage in transcript space.
Assembly: hg19
Supplementary files format and content: Rdata files output of the bam2ReadEnds script of txtools.

growth_protocol: HEK293T and HEK293T Y14-HA-dTAG cells were maintained in DMEM high glucose (Dutscher) supplemented with 10% of fetal bovine serum (Sigma-Aldrich), and 1% of penicillin and streptomycin (Sigma-Aldrich).

extract_protocol:
RNA was extracted with BIO TRI RNA reagent (Bio-lab)
RNA was poly-A selected with oligo dT-beads (Dynabeads® mRNA DIRECT™ Kit life tech) and subjected to m6Aseq2 according to Dierks et al, 2021 Nature Methods.

treatment_protocol: In 6 well plate, cells were cultivated at 70% confluency and treated with DMSO 1:1000 or 50 nM dTAG13 (Sigma-Aldrich) in DMSO, and harvested after 4, 8, 16 and 24 hours post-treatment.

tag: sample type

value: human

value: human embryonic kidney

value: DMSO, 8h


title: CON2 CUTNRUN

description: control bio replicate 2


title: HaHi02_Gex

city: San Diego

first: Ashu

last: Sethi

address: 9420 Athena Circle

department: Health Sciences

institute: La Jolla Institute for Immunology

description:
Gene expression matrix
Gen expression matrix for each cell

data_processing:
Data processing was done using Cell Ranger software v5.0.0.
The demultiplexing was performed using mkfastq
Alignment with reference GRCh38 (GENCODE v32/Ensembl 98) and gene counting were done using Multi program
R package Seurat(v4.0.2) was used for downstream clustering and UMAP analysis
Seurat's function HTOdemux was used for hashtag demultiplexing and singlet assignment
Assembly: GRCh38 (GENCODE v32/Ensembl 98)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
Cryopreserved PBMC were thawed, stained with live/dead stain, and anti-human CD56, CD19, CD3, CD14 and CD16 antibodies, and TotalSeqTM-C oligonucleotide-conjugated antibodies (Biolegend, one different per sample).CD14+ monocytes were defined as live CD3-CD19-CD56-CD14+ cells. For each sample, 15,000 CD14+CD16+ and 15,000 CD14+CD16- monocytes were sorted using BD Aria 3 cell sorter into low-retention 1.5-ml collection tubes (Thermo Fisher Scientific), containing 0.5 ml of a 1:1 solution of phosphate-buffered saline (PBS):FBS supplemented with ribonuclease inhibitor (1:100; Takara Bio), and pooled together. Following cell sorting, cells were washed with ice-cold PBS, centrifuged for 10 min (600g at 4°C), gently resuspended in ice-cold PBS supplemented with 0.04% ultrapure bovine serum albumin (Sigma-Aldrich).
The library preparation was performed using a 10x Genomics 5′ Tag v2 chemistry kit with dual indexes and feature barcoding technology for cell surface proteins. The amplification of complementary DNA was carried out with 13 cycles of amplification; the 5′ Tag gene expression libraries and the corresponding hashtag libraries were generated separately with 13 and 8 cycles of amplification, respectively. The libraries were sequenced using the Illumina NovaSeq 6000 sequencing platform with the following read lengths: read 1, 101 cycles; read 2, 101 cycles; i7 index, 10 cycles; i5 index, 10 cycles.

treatment_protocol: No specific treatment involved

value: PBMC

value: CD14+ monocytes


title: DDX21 HA-DDX21 epitope, Differentiating, normal glucose, donor 4

description: donor 4

value: Primary human keratinocytes


title: IP_rep2_WTdeg_16h

value: DMSO, 16h


title: IP_rep2_WTdeg_0h

value: DMSO, 0h


title: IP_rep2_WTdeg_24h


title: IP_rep2_Y14deg_4h

value: 50 nM dTAG13,4h


title: IP_rep2_WTdeg_4h

value: DMSO, 4h


title: IP_rep2_Y14deg_8h

value: 50 nM dTAG13, 8h


title: IP_rep2_Y14deg_24h

value: 50 nM dTAG13, 24h


title: IP_rep2_Y14deg_0h

value: 50 nM dTAG13, 0h


title: IP_rep2_Y14deg_16h

value: 50 nM dTAG13,16h


title: IP_rep1_WTdeg_8h


title: NHEK, Golf, differentiated

city: Irvine

first: Bryan

last: Sun

address: 829 Medical Sciences Ct

institute: University of California Irvine

description: Differentiated Sample 2

data_processing:
For RNA-seq, raw reads were uniquely mapped to hg19 using STAR with default parameter. Bedtools were used to transform the mapped bam file into bedGraph. RPKM and raw reads count were calculated by self-designed scripts with ensemble annotation(Homo_sapiens.GRCh37.gtf). The differential expression analysis was performed using DESeq.
Assembly: hg19
Supplementary files format and content: counts.txt

source_name: skin

growth_protocol: Keratinocytes were propagated in a 1:1 mixture of KSFM and 154 media (Thermo Fisher) with recommended manufacturer supplements

extract_protocol:
Trizol (Invitrogen) and Direct-Zol kit (Zymo)
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. The suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using BGISEQ-500.

treatment_protocol: In vitro differentiation was performed by plating keratinocytes to 100% culture confluence with addition of 1.2 mM calcium chloride supplemented into culture media for 96 hours.

value: skin

value: primary cells

value: keratinocyte

value: wild type

value: 1.2 mM calcium x 96 hours


title: NHEK, Hotel, differentiated

description: Differentiated Sample 3


title: HaHi02_CITE

description:
Hashtag/barcode expression matrix
Hashtag/barcode expression matrix for each cell. Each hashtag/barcode corresponds to one sample.


title: IP_rep1_WTdeg_4h

value: human

value: human embryonic kidney


title: NHEK, Hotel, progenitors

description: Undifferentiated Sample 3


title: NHEK, Alpha, progenitors

description: Undifferentiated Sample 1


title: IP_rep1_WTdeg_24h


title: IP_rep1_WTdeg_16h


title: NHEK, Golf, progenitors

description: Undifferentiated Sample 2


title: IP_rep1_WTdeg_0h


title: IP_rep1_Y14deg_4h


title: Mouse TA, uninjured control 3

city: Fayetteville

first: Jeffrey

last: Wolchok

state: AR

address: 700 W. Research Blvd

department: Biomedical Engineering

institute: University of Arkansas

data_processing:
usegalaxy.eu pipeline
Use RNA-STAR for Gapped-read mapper for RNA-seq data ( input 2 pair-end raw files per sample)
Use feature to measure gene expression in RNA-Seq experiments from BAM files ( generated from RNA-Star)
Use edgeR to perform differential expression of count data
Assembly: mm39
Supplementary files format and content: tabular  files include normalized counted reads, per gene for each sample

extract_protocol:
RNA extarction was are performed by comerical lab BGI
RNA libraries were constructed by comerical lab BGI

treatment_protocol: 50 µl of matrix gel (6 mg/ml) on the left TA, and 50 µl of vehicle control (PBS) on the right TA

value: Tibialis anterior muscle

value: uninjured


title: IP_rep1_Y14deg_8h


title: Mouse TA, uninjured control 4


title: IP_rep1_Y14deg_24h


title: Mouse TA, PBS control 4

value: PBS


title: IP_rep1_Y14deg_0h


title: Mouse TA, uninjured control 2


title: NHEK, Alpha, differentiated

description: Differentiated Sample 1


title: IP_rep1_Y14deg_16h


title: input_rep2_WTdeg_8h

value: DMSO, 8h


title: input_rep2_WTdeg_4h


title: Mouse TA, PBS control 1


title: Mouse TA, PBS control 3


title: Mouse TA, PBS control 2


title: input_rep2_WTdeg_24h


title: input_rep2_WTdeg_16h

value: DMSO, 16h


title: SJALCL014724_D1

tag: gender

value: M

tag: age at diagnosis

tag: sample source

value: Lymph node, cervical

tag: histologic subtype

value: SCV


title: Mouse TA, matrix gel treated 4

tag: tissue

tag: treatment

value: matrix gel


title: Mouse TA, matrix gel treated 1


title: Mouse TA, matrix gel treated 2


title: input_rep2_Y14deg_8h

tag: cell line

tag: cell type

value: 50 nM dTAG13, 8h


title: input_rep2_Y14deg_4h

value: 50 nM dTAG13,4h


title: Mouse TA, uninjured control 1


title: input_rep2_Y14deg_16h

value: 50 nM dTAG13,16h