title: SK-N-DZ, lane 2, scRNAseq

city: Heidelberg

first: Umut

last: Yildiz

address: Meyerhofstraße 1

institute: European Molecular Biology Laboratory

description:
10x Genomics 3' mRNA library. Read1 contains 16 nt cell barcode followed by 12 nt UMI. Read2 file contains transcript insert
lane2

data_processing:
Single-cell reads were mapped to the GRCh 38 reference genome. Count matrices were generated using Cell Ranger (10X Genomoics, version 6.0.1). Single-cell sequencing data from the two lanes were combined using the aggregation function (cellranger aggr). Data normalization and downstream analysis were performed via Seurat (R package, version 4.0.1). Briefly, the count matrix was filtered for genes that were detected in at least 10 cells. UMI counts for each gene were divided by the total number of counts and multiplied by 10,000 and log-transformed. Guide RNA libraries were processed via fba. Briefly, cell barcode - gRNA assignments were made based on mapping the reads to the custom gRNA library and the whitelist of 10X barcode sequences thereby allowing two mismatches.
Assembly: GRCh 38
Supplementary files format and content: Comma-separated, tab-separated values files and matrix files

source_name: Brain

growth_protocol: Cells were maintained in DMEM (Gibco) with 10% FCS (Gibco), 1X HEPES (Gibco) and 100 U/ml penicillin/streptomycin at 37° C and 5 % CO2.

extract_protocol:
Ten days after transduction, puromycin-selected cells were washed twice with PBS and dissociated with accutase (37° C, 5 min). Cells were collected in PBS + 0.04 % BSA, counted and diluted to 10^6 cells/ml
Single-cell libraries were constructed following the manufacter’s instructions (10x Genomics, Single Cell Gene Expression v3.1 protocol). Briefly, 20,000 SK-N-DZ cells per lane were resuspended in the master mix and loaded alongside the gel beads and the partitioning oil into the chip (G) to generate the GEMs. Polyadenylated mRNA in every single GEM was reverse-transcribed to cDNA with a oligo(dT) primer, that contains the illumina TruSeq Read 1 primer sequence, the 10x Barcode and Unique Molecular Identifiers (UMIs). The barcoded cDNA was pooled and cleaned up with Silane DynaBeads. Full-legnth cDNA was amplified by PCR. AFter enzymatic fragmentation, end repair, A-tailing and ligation, the apropiated sized fragments were selected with SPRIselect beads for subsequent library construction. During the final library construction, the Illumina TruSeq Read 2 primer sequence was introduced alongside a sample index (four per lane). Forty nanogram of full-length cDNA was used as input for the construction of gRNA enrichment libraries following a previously published hemi-nested PCR strategy (Hill et al., 2018)

value: Neuroblastoma

value: Brain

value: SK-N-DZ

tag: age

value: 2 years


title: Lining_macrophages_PBS_IRF5KO_5_1st

status: Public on Apr 10 2023

type: SRA

city: Oxford

first: Irina

last: Udalova

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

country: United Kingdom

institute: University of Oxford

description: PolyA RNA

library_source: transcriptomic

data_processing:
Reads were aligned to the reference and quality checked. Resulting data were mapped to the mm10 genome using STAR v2.7.5b with the options: --runMode alignReads --outFilterMismatchNmax 2. Uniquely mapped read pairs were counted over annotated genes using featureCounts v.2.0.0 with the options: -T 18 -s 2 -Q 255. Differential expression was then analysed with DESeq2 v1.24.0 (Love et al., 2014). Variance stabilised counts for all DESeq2 DEGs, likelihood ratio test, and false discovery rate (FDR) <0.01 were used for dimensionality reduction and the heatmaps. GO analysis was performed using one-sided
Assembly: mm10 (GRCm38)
Supplementary files format and content: countdata_FC.csv

molecule: total RNA

organism: Mus musculus

source_name: knee cell suspensions

extract_protocol:
Sorting of synovial macrophages was carried out from the knee cell suspensions stained as paper described. Lining macrophages were defined as CD45+, Linage- (NK1.1, CD3, CD19), CD11b+, F4/80+ and VSIG4+ cells, whereas sublining macrophages were CD45+, Lin-, CD11b+, F4/80+ and VSIG4-. Two hundred macrophages were sorted through 70-µm nozzle directly into 2.2 µl of lysis buffer (composition detailed below) using BD FACS Aria III.
Two hundred lining and sublining macrophages from 3 WT and 3 IRF5KO mice, isolated from PBS and mBSA injected knees, were sorted into PCR tubes containing 2.2 µl lysis buffer (0.8% (vol/vol) Triton X-100 and 2 U/μl RNase inhibitor (Clontech)).
Samples were transferred into 96-well skirted PCR plate, sealed with an adhesive PCR plate seal (Thermo Fisher), and transferred to Oxford Genomics Centre on dry ice to be sequenced. Briefly, the preparation of libraries was done using NEBNext® Ultra-low/single cell (Smarter-like) protocol (New England BioLabs).

tag: cell type

tag: phenotype

tag: treatment

value: PBS

tag: replicate

tag: round of sequencing


title: SK-N-DZ, lane 1, scRNAseq

country: Germany

description:
10x Genomics 3' mRNA library. Read1 contains 16 nt cell barcode followed by 12 nt UMI. Read2 file contains transcript insert
lane1

library_source: transcriptomic single cell

organism: Homo sapiens

tag: tissue

tag: strain


title: Sublining_macrophages_mBSA_IRF5KO_4_1st

description: PolyA RNA

value: mBSA


title: Lining_macrophages_mBSA_IRF5KO_4_1st

description: PolyA RNA


title: Discoid Lupus-NL9 - Non-lesional skin

type: RNA

city: New York

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

country: USA

institute: Hospital for Special Surgery

description: previously unpublished sample generated during original study

hyb_protocol: Biotinylated cDNA samples were hybridized to  the U133A 2.0 gene chips and subsequently washed, stained with streptavidinphycoerythrin, and scanned on an HP GeneArray Scanner (Hewlett-Packard  Company, Palo Alto, CA).

data_processing: Microarray analysis was performed using healthy controls from an existing GEO dataset (GSE52471) obtained from GEO using GEOquery and combined with non-lesional skin sample data kindly provided by the authors of the original study. Microarray data were normalized with gcRMA normalization using the gcrma R package. Differential gene expression analysis was performed with limma using the empirical Bayes method  and controlling for microarray hybridization kit and sex. Batch correction was performed using ComBat.

label: biotin

source_name: skin biopsy

label_protocol: Amplified cDNA was biotinylated with the Encore Biotin  Module (NuGEN Technologies).

growth_protocol: Patient selection, skin sample acquisition, and RNA isolation has been described in detailed in original GEO submissiion -  GSE52471. Non-lesional and lesional skin samples were from the same patients.

extract_protocol: Briefly, total RNA was reverse transcribed and amplified by using the Ovation  RNA Amplification V2 kit and the Ovation WB Reagent (NuGEN Technologies,  Inc., San Carlos, CA).

tag: Sex

value: male


title: Sublining_macrophages_PBS_IRF5KO_4_1st

description: PolyA RNA


title: Discoid Lupus-NL8 - Non-lesional skin

scan_protocol: Biotinylated cDNA samples were hybridized to  the U133A 2.0 gene chips and subsequently washed, stained with streptavidinphycoerythrin, and scanned on an HP GeneArray Scanner (Hewlett-Packard  Company, Palo Alto, CA).

value: female


title: Lining_macrophages_PBS_IRF5KO_4_1st

description: PolyA RNA


title: week 1_patient.41

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

hyb_protocol: standard Affymetrix protocols

scan_protocol: standard Affymetrix protocols

data_processing: Raw signal intensites were normalized using the RMA algorithm implemented with R 3.5.2 and Bioconductor oligo library.

source_name: skin

label_protocol: standard Affymetrix protocols

growth_protocol: not applicable

extract_protocol: standard Affymetrix protocols

treatment_protocol: subcutaneous injections of ixekizuma 80mg Q2W

tag: visitid

value: Ixekizumab 80mg Q2W

tag: pasi

tag: time

value: Gene expression data at week 1.

value: skin

tag: disease state

value: chronic plaque psoriasis


title: Discoid Lupus-rNL4 - Non-lesional skin


title: Discoid Lupus-NL3 - Non-lesional skin


title: week 1_patient.37


title: week 2_patient.49

value: Gene expression data at week 2.


title: baseline_patient.45

value: Gene expression data at baseline.


title: week 2_patient.55


title: week 1_patient.40


title: Sublining_macrophages_mBSA_wt_3_1st

description: PolyA RNA

value: wild-type


title: week 2_patient.12


title: baseline_patient.21


title: Lining_macrophages_mBSA_wt_3_1st

description: PolyA RNA


title: Sublining_macrophages_PBS_wt_3_1st

description: PolyA RNA


title: Discoid Lupus-NL5 - Non-lesional skin


title: baseline_patient.34


title: Discoid Lupus-L9 Lesional skin

description: originally deposited as GSE52471


title: week 4_patient.14

value: Gene expression data at week 4.


title: Discoid Lupus-NL1 Non-lesional skin


title: week 2_patient.45


title: Lining_macrophages_PBS_wt_3_1st

description: PolyA RNA


title: week 4_patient.27


title: Sublining_macrophages_mBSA_wt_2_2nd

description: PolyA RNA


title: Discoid Lupus-rNL2 - Non-lesional skin


title: Discoid Lupus-L8 Lesional skin

description: originally deposited as GSE52471


title: Lining_macrophages_mBSA_wt_2_2nd

description: PolyA RNA


title: Lining_macrophages_PBS_wt_2_2nd

description: PolyA RNA


title: week 4_patient.49


title: Sublining_macrophages_PBS_wt_2_2nd

description: PolyA RNA


title: week 2_patient.32


title: Discoid Lupus-L5 Lesional skin

description: originally deposited as GSE52471


title: Sublining_macrophages_mBSA_wt_1_2nd

description: PolyA RNA


title: Discoid Lupus-L4 Lesional skin

description: originally deposited as GSE52471


title: Sublining_macrophages_PBS_wt_1_2nd

description: PolyA RNA


title: Lining_macrophages_mBSA_wt_1_2nd

description: PolyA RNA


title: Discoid Lupus-L3 Lesional skin

description: originally deposited as GSE52471


title: Discoid Lupus-L2 Lesional skin

description: originally deposited as GSE52471


title: Discoid Lupus-L1 Lesional skin

description: originally deposited as GSE52471


title: week 2_patient.24


title: week 4_patient.35


title: atac_Mature_LA_161521

city: Vienna

first: Jingkui

last: Wang

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

description: To find ACRs in mature limb cells, ATAC-seq library with FACSed Cherry positive cells was prepared with in-house Tn5.

library_source: genomic

data_processing:
The pair-ended ATAC-seq reads were trimmed with cutadapt (v1.18) and aligned to axolotl genome (AmexG_v6) with bowtie2 (v2.3.5.1).
Multimappers and duplicated reads in the aligned bam files were discarded respectively with samtools (v1.10) and picard (v2.20.6). ATAC-seq narrow peaks were called by macs2 (v2.2.5) with default parameters.
The processing workflow was wrapped with nextflow. For the purpose of reproducibility, peaks were retained only if they were called in at least two biological replicates with p-value < 10^-6;
they were merged into a list of peak consensuses for all samples. Read counts were quantified within those peaks with feature counts from subread (v2.0.1).
After low-signal peaks were filtered with less than 50 read counts, the read counts within peaks across all samples were normalized using the scaling factors from DESeq2 (v1.26.0). These scaling factors were also used to make bigwig files with deeptools (v3.1.2) for the data visualization.
Assembly: AmexG_6
Supplementary files format and content: bigwigs and genomic tracks

molecule: genomic DNA

organism: Ambystoma mexicanum

source_name: Mature LA

extract_protocol:
The sample was performed from 20,000 cells isolated from transgenic animals. Limb connective tissue cells were used for FACS, and then used for library preparation immediately.
We performed ACR profiling analysis using data obtained from ATAC-seq libraries of developmental limb buds (stage 40/41, stage 46 proximal and distal parts), and mature limb at different segments (mature UA vs LA vs hand). Therefore, we also performed libraries from the mature arm and 5, 9, 13 dpa (13 dpa blastema data have two different positions like proximal and distal parts) regenerating arm blastema.

value: Mature LA

value: Connective tissue cells

tag: genotype

value: Cells were isolated and FACSorted. OMNI-ATAC-seq protocol with in-house Tn5 was used for processing the tagmentation.


title: week 4_patient.8


title: week 4_patient.55


title: baseline_patient.55


title: Lining_macrophages_PBS_wt_1_2nd

description: PolyA RNA


title: Sublining_macrophages_mBSA_IRF5KO_6_2nd

description: PolyA RNA


title: Lining_macrophages_mBSA_IRF5KO_6_2nd

description: PolyA RNA


title: abt_responder_21

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

department: Allergy and Clinical Immunology

country: Japan

institute: Chiba University

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
S09.0P

hyb_protocol: Agilent one-color Quick Amp Labeling Kit protocol

scan_protocol: Agilent one-color gene expression hyb/wash protocol

data_processing:
Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 micron resolution.
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014850_D_F_20110819) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: PBMC from responder21

label_protocol: DNA microarray anasysis was performed using a Quick Amp labeling kit.

extract_protocol: PBMCs were isolated using Ficoll-Paque Premium 1.073. CD4+ T cells. RNA was prepared using the RNeasy Mini Kit (QIAGEN) following the manufacturer's recommendations.

value: rheumatoid arthritis

value: PBMC


title: Sublining_macrophages_PBS_IRF5KO_6_2nd

description: PolyA RNA

value: PBS


title: baseline_patient.24


title: abt_responder_20

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
S07.0P

source_name: PBMC from responder20


title: abt_responder_18

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
M25.0P

source_name: PBMC from responder18


title: abt_responder_19

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
M30.0P

source_name: PBMC from responder19


title: week 4_patient.46


title: OVCAR8-siTEAD4-1

city: Guangzhou

first: Peng

last: Deng

address: Panyu

country: China

institute: SYSUCC

data_processing:
Raw reads were filtered and cleaned by fastp software.
Aliments were performed followed by bowtie2 and STAR instruction
MACS2 were used for the binding profile
RSEM were used for counting
IGV and R were used for visualization
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

growth_protocol: OVCAR8 cellls were cultured in RPMI1640 medium supplemented with 10% FBS and 1% P/S.

extract_protocol:
Lysates were clarified from sonicated nuclei and protien/histone-DNA complexes were isolated with antibody. RNA was harvested using Trizol reagent (Invitrogen).
ChIP-seq libraries were prepared according to NEB ChIP-Seq Library Prep Kit (E6240). RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: OVCAR8 cells were plated into 6-well plate 20 h before transfection with indicated siRNA.

value: high grade serous ovarian cancer (HGSOC)

tag: cell line


title: Sublining_macrophages_mBSA_IRF5KO_5_2nd

description: PolyA RNA

value: mBSA


title: abt_responder_16

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
K09.0P

source_name: PBMC from responder16


title: Lining_macrophages_PBS_IRF5KO_6_2nd

description: PolyA RNA


title: abt_responder_17

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
M23.0P

source_name: PBMC from responder17


title: abt_responder_14

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
E13.0P

source_name: PBMC from responder14


title: OVCAR8-siTEAD4-2


title: baseline_patient.2


title: atac_HEAD_161519

source_name: Head without lower jaw (>10 cm nose to tail)


title: week 1_patient.43


title: baseline_patient.41


title: OVCAR8-NC2

value: siNC


title: abt_responder_13

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
E11.0P

source_name: PBMC from responder13


title: HEK293T_15.5K_RIP_PEN_seq_rep2

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing:
Cutadapt (v2.8) was used to cut the adapters of the paired-end reads and single-end reads. These reads without adapter were subsequently mapped to the human reference genome (hg38) with STAR software with the following parameters: ‘--alignEndsType EndToEnd --outFilterType Normal --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.03  --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 15  --outFilterMatchNminOverLread 0.8 --alignIntronMin 20 --alignIntronMax 1 --alignMatesGapMax 1000  --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --seedSearchLmax 0 --seedMultimapNmax 20000 --seedPerReadNmax 1000 --seedPerWindowNmax 100 --seedNoneLociPerWindow 20 --alignSJDBoverhangMin 1000’. Reads mapping to more than twenty locations were discarded and only sequences in which both ends were aligned to the reference genomes were further analyzed.
We clustered the overlapping paired-end reads that mapped to the genomes. Specifically, we defined the start and end sites with the highest abundance in the cluster as the transcription start site (TSS) and transcription terminal site (TTS), respectively. The sequences between TSSs and TTSs co-occurring within 500 bp were extracted as candidate transcripts. Each candidate transcript with a precise TSS and TTS was input to kturnSeeker. A new software, kturnSeeker, was developed to discover ncRNAs with forward and backward kturn structure. kturnSeeker searches A•G, G•A and G-C basepairs (N-C stem), three-nucleotide bulge and a section of regular basepairing (C stem) step-by-step in candidate sequences, and scores the C stem with a strict score scheme (G-C pair is bonus 3, A-U pair is bonus 2 and mismatch minus 5). Only the total score (C stem) large than 7 was kept as candidate ktRNAs. To identify novel ktRNAs, ktRNAs overlapped known annotation were discarded.
The genome sequence of humans (hg38) was downloaded from the UCSC Genome Browser site. Human gene annotations were acquired from GENCODE on August 2018. The repeat elements in RepeatMasker were downloaded from the UCSC Genome Browser site. Sequences and annotation data for human snoRNAs were downloaded from snoRNA-LBME-db, deepBase, GENCODE, snoRNAome and Refseq in August 2018.  All novel ktRNAs were intersected with these gene annotations using bedtools software.
Genome_build: hg38
Supplementary_files_format_and_content: RPM

growth_protocol: HEK293T-FLAG-15.5K stable cells were cultured in DMEM (Gibico) with 10% fetal bovine serum (FBS, Gibico), 1% penicillin-streptomycin solution (Gibico) and 1μg/mL puromycine (MCE) at 37℃ at 5% CO2.

extract_protocol:
Cell lysate was prepared and incubated with anti-FLAG. Afterwards, the RNA-protein complexes were immunoprecipitated with Dynabeads protein G and the RNA fraction was extracted using RNAzol reagent.
For RIP-PEN-seq, RIP RNA was subjected to rRNA removal (Ribo-Zero rRNA Removal Kit, Illumina, MRZH11124) and further used to generate the library using the TruSeq Samll RNA sample preparation kit (Illumina) following the manufacturer’s instructions.

value: Stable overexpression of 15.5K

tag: antibody

value: anti-FLAG [Proteintech, cat# 66008-3-Ig]


title: abt_responder_15

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
E16.0P

source_name: PBMC from responder15


title: Lining_macrophages_PBS_IRF5KO_5_2nd

description: PolyA RNA


title: Lining_macrophages_mBSA_IRF5KO_5_2nd

description: PolyA RNA


title: Sublining_macrophages_PBS_IRF5KO_5_2nd

description: PolyA RNA


title: abt_responder_12

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
E10.0P

source_name: PBMC from responder12


title: week 4_patient.51

value: Ixekizumab 80mg Q2W

value: skin


title: week 1_patient.35

value: Gene expression data at week 1.

value: chronic plaque psoriasis


title: Sublining_macrophages_mBSA_IRF5KO_4_2nd

description: PolyA RNA


title: HEK293T_15.5K_RIP_PEN_seq_rep1


title: week 2_patient.51

value: Gene expression data at week 2.


title: week 4_patient.41

value: Gene expression data at week 4.


title: week 1_patient.12


title: HEK293T_Cytoplasm

data_processing:
Cutadapt (v2.8) was used to cut the adapters of the paired-end reads and single-end reads. These reads without adapter were subsequently mapped to the human reference genome (hg38) with STAR software with the following parameters: ‘--alignEndsType EndToEnd --outFilterType Normal --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.03  --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 15  --outFilterMatchNminOverLread 0.8 --alignIntronMin 20 --alignIntronMax 1 --alignMatesGapMax 1000  --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --seedSearchLmax 0 --seedMultimapNmax 20000 --seedPerReadNmax 1000 --seedPerWindowNmax 100 --seedNoneLociPerWindow 20 --alignSJDBoverhangMin 1000’. Reads mapping to more than twenty locations were discarded and only sequences in which both ends were aligned to the reference genomes were further analyzed.
We clustered the overlapping paired-end reads that mapped to the genomes. Specifically, we defined the start and end sites with the highest abundance in the cluster as the transcription start site (TSS) and transcription terminal site (TTS), respectively. The sequences between TSSs and TTSs co-occurring within 500 bp were extracted as candidate transcripts. Each candidate transcript with a precise TSS and TTS was input to kturnSeeker. A new software, kturnSeeker, was developed to discover ncRNAs with forward and backward kturn structure. kturnSeeker searches A•G, G•A and G-C basepairs (N-C stem), three-nucleotide bulge and a section of regular basepairing (C stem) step-by-step in candidate sequences, and scores the C stem with a strict score scheme (G-C pair is bonus 3, A-U pair is bonus 2 and mismatch minus 5). Only the total score (C stem) large than 7 was kept as candidate ktRNAs. To identify novel ktRNAs, ktRNAs overlapped known annotation were discarded.
The genome sequence of humans (hg38) was downloaded from the UCSC Genome Browser site. Human gene annotations were acquired from GENCODE on August 2018. The repeat elements in RepeatMasker were downloaded from the UCSC Genome Browser site. Sequences and annotation data for human snoRNAs were downloaded from snoRNA-LBME-db, deepBase, GENCODE, snoRNAome and Refseq in August 2018. All novel ktRNAs were intersected with these gene annotations using bedtools software.
Genome_build: hg38
Supplementary_files_format_and_content: human_ktRNA.csv

molecule: cytoplasmic RNA

growth_protocol: Cells were cultured in complete medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin solution (Gibco) at 37°C under 5% CO2.

extract_protocol:
Total RNA was isolated from cells using RNAzol. For subcellular RNA isolation, cells were trypsinized, centrifuged at 500 g for 3 min at 4 °C, washed with ice-cold PBS and recentrifuged. The cell pellet was resuspended in Hypotonic lysis buffer (10 mM Tris, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.3% NP-40 and 10% Glycerol) supplemented with 1 mM DTT, 100 U/mL RNase inhibitor and 400 μM RVC (NEB) and incubated on ice for 30 min. The resuspension was centrifuged at 1,000 g for 3 min at 4 °C. Approximately 70% volume of the supernatant was carefully removed without disturbing the nuclear pellet and precipitated by RNA precipitation solution (5% 3M sodium acetate, pH 5.5 and 95% ethanol), followed by RNA isolation using RNAzol; this was the cytoplasmic fraction. The remaining nuclear pellet was washed with Hypotonic lysis buffer three times. After centrifugation at 200 g for 2 min at 4 °C, the pellet was resuspended in Modified Wuarin-Schibler buffer (10 mM Tris, pH 7.0, 4 mM EDTA, 0.3 M NaCl, 1 M Urea and 1% NP-40) supplemented with 1 mM DTT, 100 U/mL RNase inhibitor and 400 μM RVC (NEB) and incubated on ice for 5 min. The sample was then centrifuged at 1,000g for 3 min at 4 °C and the supernatant was taken and precipitated by RNA precipitation solution, followed by RNA isolation using RNAzol; this was the nucleoplasmic fraction. For nucleoli isolation, the cell pellet volume was estimated for the next steps. The nuclear pellet was isolated and washed as described above. The pellet was resuspended in ten cell packed pellet volumes of ice-cold S1 buffer (0.25 M Sucrose, 10 mM MgCl2) supplemented with 1 mM DTT, 100 U/mL RNase inhibitor and 400 μM RVC (NEB) and then layered on ten cell packed pellet volumes of ice-cold S3 buffer (0.88 M Sucrose, 5 mM MgCl2) supplemented with 1 mM DTT, 100 U/mL RNase inhibitor and 400 μM RVC (NEB) and pelleted at 1,200g for 5 min at 4 °C. The pellet was then resuspended in ten cell packed pellet volumes of ice-cold S2 buffer (0.34 M Sucrose, 5 mM MgCl2) supplemented with 1 mM DTT, 100 U/mL RNase inhibitor and 400 μM RVC (NEB) and sonicated by using VibraCell Sonicator VCX130PB (Sonics & Materials, Inc.). The suspension was layered on ten cell packed pellet volumes of ice-cold S3 buffer (0.88 M Sucrose, 5 mM MgCl2) supplemented with 1 mM DTT, 100 U/mL RNase inhibitor and 400 μM RVC (NEB) and pelleted at 2,000g for 20 min at 4 °C. The supernatant was discarded, and the pellet was washed with S2 buffer and then centrifuged at 2,000g for 5 min at 4 °C. The pellet constituted the nucleolar fraction.
RNA was treated with RQ1 DNase (Promega) and purified by RNA Clean & Concentrator-5 (Zymo Research). The samples were then ligated to 3’ randomized RNA adaptor (/rApp/NNNNTGGAATTCTCGGGTGCCAAGG/3SpC3/) with T4 RNA ligase 2 truncated KQ (NEB) in 1× T4 RNA ligase reaction buffer supplemented with 12.5% PEG 8000 at 16 °C for 18 h. The excessive adaptors were digested with 100 U 5’ Deadenylase (NEB) at 30 °C for 1 h, incubated with 2 μg E. coli Single-strand DNA-binding protein (Promega) on ice for 30 min and followed by adding 60 U RecJf (NEB) for ssDNA digestion at 37 °C for another hour. The ligated RNA was ligated to 5’ randomized RNA adaptor (GUUCAGAGUUCUACAGUCCGACGAUCNNNN) using T4 RNA Ligase 1 (NEB) in 1× T4 RNA ligase reaction buffer supplemented with 1 mM ATP at 16 °C for 18 h. The ligated RNA was column-purified by RNA Clean & Concentrator-5 (Zymo Research) and subjected to RNase H-based ribosomal RNA depletion according to the standard protocol with some modification5. For rRNA probe digestion, DNase I was replaced by RecJf exonuclease to prevent the digestion of 3’ randomized RNA adaptor. After column-based purification, the rRNA-depleted RNA was reverse-transcribed using SuperScript IV reverse transcriptase (Invitrogen) in 1× RT buffer with truncated RT primer (GCCTTGGCACCCGAGAAT) to eliminate mispriming artifacts. The cDNA was amplified using Phusion High-Fidelity DNA Polymerase (Thermo Scientific) in 1× Phusion HF buffer (Thermo Scientific) with primers (RP1 forward primer and RPI-X reverse primer). The PCR-amplified cDNA was gel-purifed using a 4% NuSieve 3-1 Agarose gel (Lonza) to remove adapter dimers.
small RNA-seq

value: human embryonic kidney cell

tag: rna fraction

value: Cytoplasm RNA


title: Sublining_macrophages_PBS_IRF5KO_4_2nd

description: PolyA RNA


title: Lining_macrophages_PBS_IRF5KO_4_2nd

description: PolyA RNA


title: Lining_macrophages_mBSA_IRF5KO_4_2nd

description: PolyA RNA


title: abt_responder_10

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
E06.0P

source_name: PBMC from responder10


title: HEK293T_Nucleoplasm

molecule: nuclear RNA

value: Nucleoplasm RNA


title: abt_responder_11

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
E09.0P

source_name: PBMC from responder11

value: rheumatoid arthritis


title: HEK293T_Nucleolus

value: Nucleolus RNA


title: OVCAR8-siYAP-2

tag: knock down

value: siYAP


title: abt_responder_8

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
C97.0P

source_name: PBMC from responder8

tag: cell type

value: PBMC


title: abt_responder_7

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
C83.0P

source_name: PBMC from responder7


title: abt_responder_9

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
C105.3P

source_name: PBMC from responder9


title: baseline_patient.40

source_name: skin

value: Gene expression data at baseline.


title: week 2_patient.37


title: baseline_patient.14


title: week 2_patient.50


title: Sublining_macrophages_mBSA_wt_3_2nd

description: PolyA RNA

source_name: knee cell suspensions

tag: phenotype

value: wild-type

value: mBSA


title: Lining_macrophages_mBSA_wt_3_2nd

description: PolyA RNA

tag: treatment


title: abt_responder_6

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
C76.3P

source_name: PBMC from responder6


title: Sublining_macrophages_PBS_wt_3_2nd

description: PolyA RNA

value: PBS

tag: replicate


title: OVCAR8-siYAP-1

value: high grade serous ovarian cancer (HGSOC)


title: week 2_patient.57

value: Ixekizumab 80mg Q2W

value: skin


title: OVCAR8-NC3

value: NC


title: Lining_macrophages_PBS_wt_3_2nd

description: PolyA RNA

tag: round of sequencing


title: OVCAR8-siRAD21-2

tag: tissue


title: abt_responder_3

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
C59.0P

source_name: PBMC from responder3


title: abt_responder_2

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
C48.9P

source_name: PBMC from responder2


title: abt_responder_4

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
C66.0P

source_name: PBMC from responder4


title: bone marrow-derived macrophages, Znrf1 knockout#1, poly(I:C)

city: Taipei

first: You-Sheng

last: Lin

state: Not US or Canada

address: No.7.Chung San South Road, Taipei 10002( Institute of Molecular Medicine, College of Medicine, National Taiwan University)

country: Taiwan

data_processing:
The qualified libraries were then sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads generated by Genomics, BioSci & Tech Co., New Taipei City, Taiwan.
The bases with low quality and sequences from adapters in raw data were removed using the program Trimmomatic (version 0.39).
The filtered reads were aligned to the reference genomes using Bowtie2 (version 2.3.4.1).
A user-friendly software RSEM (version 1.2.28) was used for quantification of the transcript abundance.
Assembly: hg19/mm10
Supplementary files format and content: tab-delimited text files include count, tpm, fpkm  values for each Sample

source_name: BMDMs

growth_protocol: BMDMs cells were differentiated in DMEM supplemented with 10% fetal bovine serum (FBS) containing L929 conditional medium and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNAs were prepared from BMDMs and further purified by the TruSeq Stranded mRNA Library Prep Kit following the manufacturer’s recommendations. Briefly, one mg total RNAs was subjected to oligo(dT) magnetic beads, fragmented and reverse transcribed to synthesize the first strand cDNA using random primers. After the generation of double-strand cDNA and adenylation on the 3' ends of the DNA fragments, the adaptors were ligated and purified with the AMPure XP system.
The quality of the libraries was assessed on the Agilent Bioanalyzer 2100 system and a Real-Time PCR system.

treatment_protocol: WT and Znrf1 knockout BMDMs after 4 hours treatment with poly(I:C) (30 mg/ml)

tag: agent

value: BMDMs

value: macrophage

value: Znrf1 knockout

value: macrophage differentiation


title: bone marrow-derived macrophages, Znrf1 knockout#2, poly(I:C)

institute: Institute of Molecular Medicine, College of Medicine, National Taiwan University


title: OVCAR8-siRAD21-1


title: OVCAR8-NC4


title: week 1_patient.17

value: Gene expression data at week 1.

value: chronic plaque psoriasis


title: OVCAR8-NC2


title: bone marrow-derived macrophages, wild-type#1, poly(I:C)

value: WT


title: OVCAR8-NC1


title: abt_responder_1

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
A63.0P

source_name: PBMC from responder1

value: rheumatoid arthritis


title: ADT_allsamples

city: Cambridge

first: Radhika

last: Goenka

state: MA

address: 200 Sidney St.

institute: Abbvie

description:
single cell ADT
Miltenyi Biotec Lamina Propria Dissociation Kit (130-097-410). Chromium with Next GEM technology and Chromium Single Cell Gene Expression Reagents V2 (10X Genomics)

data_processing:
10x cell ranger mkfastq
10x cell ranger count
CITE-seq Count version 1.4.2
Genome_build: mm10
Supplementary_files_format_and_content: data matrix generated by 10x cell ranger count
Supplementary_files_format_and_content: data matrix generated by CITE-seq Count

source_name: Colon

growth_protocol: FVB/NJ mice were purchased from Jackson Laboratory (Stock number 001800) and housed in a specific-pathogen-free animal facility. 10-week-old female FVB/NJ mice were subjected to fasting 14 hours and infected with C. rodentium (~1×108 colony-forming units (CFUs) of C. rodentium in 200 μl PBS by oral gavage).

extract_protocol:
Single cell suspension from mouse colon was obtained by enzymatic digestion following the Miltenyi Biotec Lamina Propria Dissociation Kit (130-097-410). Cells then were stained with both flow cytometry and CITEseq (HTO and ADTs) antibodies prior sorting to enrich for CD45+ population (80% CD45+B220-, 10% CD45+B220+, 10% CD45-) for each treatment group. Sorted cells then were loaded in the Chromium 10x genomics controller following manufacturer V2 protocol.
A single cell library from each experimental group was prepared following the 10x genomics V2 protocol. Material was QC and quantified by TapeStation D5000 (Agilent) prior to sequencing using a NextSeq 500 (Illumina).
The final library was a combination of each sublibrary in a proportion 21.5:1.25:2.5 (Transcriptome: HTO: ADT) from each one.

treatment_protocol: FVB/NJ mice were  infected with Citrobacter rodentium, and then left either untreated or received prophylactic treatment with PBS vehicle or IL22.Fc. Also, included is a naïve non-infected FVB mouse control

value: Colon

tag: strain

value: FVB/NJ

tag: gender

value: Female

tag: hto

value: non-demultiplexed sample:all treatments


title: bone marrow-derived macrophages, Znrf1 knockout#2, untreated

value: untreated


title: week 4_patient.19

tag: visitid

tag: pasi

tag: time

value: Gene expression data at week 4.


title: bone marrow-derived macrophages, wild-type#2, poly(I:C)

tag: genotype


title: abt_responder_5

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
C75.0P

source_name: PBMC from responder5

tag: disease state

value: PBMC


title: abt_nonresponder_8

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
M20.0P

source_name: PBMC from nonresponder_8


title: week 4_patient.2

value: Ixekizumab 80mg Q2W

value: skin


title: week 4_patient.40


title: week 1_patient.19


title: week 4_patient.45


title: IL22Fc_gene expression

description:
Single cell RNA
Miltenyi Biotec Lamina Propria Dissociation Kit (130-097-410). Chromium with Next GEM technology and Chromium Single Cell Gene Expression Reagents V2 (10X Genomics)

value: Citrobacter rodentium infected and treated with IL22.Fc


title: bone marrow-derived macrophages, wild-type#1, untreated

value: BMDMs

value: macrophage


title: Untreated_gene expression

value: Citrobacter rodentium infected


title: PBS_gene expression

value: Citrobacter rodentium infected and treated with PBS vehicle


title: Naïve_gene expression

value: non-infected


title: bone marrow-derived macrophages, wild-type#2, untreated

value: WT

value: macrophage differentiation


title: bone marrow-derived macrophages, Znrf1 knockout#1, untreated

value: Znrf1 knockout


title: week 1_patient.51

value: Gene expression data at week 1.

value: chronic plaque psoriasis


title: Blood, not active, animal 11 [11_B_NA]

city: Zaragoza

first: Kenza

last: Lakhssassi

state: Zaragoza

address: Av Montañana, 930,

country: Spain

institute: CITA

data_processing:
All transcripts were analysed with bioinformatics tools implemented within OmicsBox v2.0.36 from BioBam
Checking quality control of the sequence with FastQC
Sequence reads were trimmed for adaptor sequence/low-quality sequence using the Sliding Window Trimming option with a window size of 40 and a required quality of 20. The filtering configuration of reads was set to 20 and 35 for the average quality and the minimum length respectively
Clean reads were mapped against the ovine reference genome  using STAR v2.7.8a
Mapped reads were assembled by HTSeq. Gene quantification levels were analysed using the Union model.
Identification of differentially expressed genes with EdgeR
Assembly: Oar_rambouillet 1.0 (GCA_002742125.1)
Supplementary files format and content: Raw_gene_counts_matrix.txt: tab-delimited text file with raw gene counts for every gene and every sample

organism: Ovis aries

source_name: Blood

extract_protocol:
Blood samples were taken in Tempus tubes (Applied Biosystems, Thermofisher, UK) and stored at -80 °C, The TempusTM Spin RNA Isolation Reagent Kit was used to extract the total RNA from peripheral blood (Applied Biosystems, Thermofisher, UK) according to the manufacturer´s instructions.
Sequencing was carried out at the CNAG (Centro Nacional de Análisis Genómico, Spain; https://www.cnag.crg.eu/). The RNA-Seq library was prepared with KAPA Stranded mRNA-Seq Illumina Platforms Kit (Roche) following the manufacturer´s recommendations using Illumina platform compatible adaptors with unique dual indexes and unique molecular identifiers (Integrated DNA Technologies). The final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on NovaSeq 6000 (Illumina) with a read length of 2x151bp following the manufacturer’s protocol for dual indexing.

value: Blood

tag: age

value: Adult ram

tag: breed

value: Rasa Aragonesa

tag: sexual behavior

value: Not Active


title: Blood, not active, animal 12 [12_B_NA]


title: week 2_patient.35

value: Ixekizumab 80mg Q2W

value: Gene expression data at week 2.


title: week 2_patient.54

value: skin


title: week 4_patient.29

value: Gene expression data at week 4.


title: abt_nonresponder_9

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
M45.0P

source_name: PBMC from nonresponder_9

value: rheumatoid arthritis

tag: cell type

value: PBMC


title: Blood, not active, animal 9 [9_B_NA]


title: abt_nonresponder_4

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
C113.0P

source_name: PBMC from nonresponder_4


title: abt_nonresponder_2

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
C79.0P

source_name: PBMC from nonresponder_2


title: abt_nonresponder_3

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
C86.0P

source_name: PBMC from nonresponder_3


title: abt_nonresponder_1

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
C58.0P

source_name: PBMC from nonresponder_1


title: week 2_patient.19

source_name: skin

tag: treatment


title: abt_nonresponder_5

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
E05.0P

source_name: PBMC from nonresponder_5


title: Blood, not active, animal 8 [8_B_NA]


title: abt_nonresponder_7

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
M05.9P

source_name: PBMC from nonresponder_7


title: week 4_patient.15


title: baseline_patient.29

value: Gene expression data at baseline.


title: week 2_patient.15


title: abt_nonresponder_6

description:
Gene expression before abatacept treatment from a rheumatoid arthritis patient
K07.0P

source_name: PBMC from nonresponder_6


title: Blood, not active, animal 7 [7_B_NA]


title: SWAT_HFD_5

city: New Haven

first: Matthew

middle: S

last: Rodeheffer

state: Connecticut

address: 316 Cedar St.

department: Comparative Medicine

institute: Yale University

data_processing:
Reads were aligned to reference genome mm9 with TopHat discarding alignments with more than 2 mismatches and not specifying library type as this sets the default library type.
The python module HTSeq was used specifying for an unstranded RNA analysis with preset parameters to quantify gene expression.
Assembly: mm9
Supplementary files format and content: tab-delimited text file matrix includes unnormalized reads per gene

molecule: polyA RNA

source_name: inguinal WAT (SWAT)

growth_protocol: All animals were kept in temperature and humidity-controlled rooms on a 12-hour:12-hour light:dark cycle, with lights on from 7:00 a.m. to 7:00 p.m.

extract_protocol:
RNA was isolated using Direct-zol RNA Miniprep Kit (Zymo Research).
mRNA was purified from approximately 200ng of total RNA with oligo-dT beads and sheared by incubation at 94C in the presence of Mg2+  (Roche Kapa mRNA Hyper Prep Cat# KR1352).  Following first-strand synthesis with random primers, second strand synthesis and A-tailing was performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ dTMP overhangs were ligated to library insert fragments.  Library amplification amplified fragments carrying the appropriate adapter sequences at both ends.  Strands marked with dUTP were not amplified. Indexed libraries were quantified by qRT-PCR using a commercially available kit (Roche KAPA Biosystems Cat# KK4854) and insert size distribution determined by either the Agilent Bioanalyzer. Samples with a yield of ≥ 0.5 ng/ul and a size distribution of 150-300bp were used for sequencing.  For flow cell preparation and sequencing, sample concentrations were normalized to 15 pM and loaded onto an Illumina HiSeq 2500 V4 flow cell at a concentration that yields 25 million passing filter clusters per sample. Samples were sequenced using 75 bp single-end sequencing according to Illumina protocols. The 6 bp index is read during additional sequencing reads that automatically follow the completion of read 1.  Data generated during sequencing runs are simultaneously transferred to the YCGA high-performance computing cluster. A positive control (prepared bacteriophage Phi X library) provided by Illumina was spiked into every lane at a concentration of 0.3% to monitor sequencing quality in real time. Signal intensities were converted to individual base calls during a run using the system's Real Time Analysis (RTA) software.  Base calls were transferred from the machine's dedicated personal computer to the Yale High Performance Computing cluster via a 1 Gigabit network mount for downstream analysis.  Primary analysis - sample de-multiplexing and alignment to the mouse genome - was performed using Illumina's CASAVA 1.8.2 software suite. Only samples with an error rate less than 2 % and with a distribution of reads per sample in a lane within reasonable tolerance were further processed.

treatment_protocol: Female C57Bl6/J mice 8-11 weeks old were kept on standard diet (SD- Harlan Laboratories 2018S) or fed 60% lard high-fat diet (HFD- Research Diets D12492) for 3 days before perigonadal (VWAT) and inguinal subcutaneous (SWAT) tissue collection. Each sample is pooled from tissues from 3 female mice. APCs were isolated via FACS as lineage negative (CD45-/CD31-), CD29+, CD34+, Sca1+, and CD24 -/+.

value: inguinal WAT (SWAT)

value: Adipocyte precursor cells

value: Female

tag: diet

value: 60percent lard high-fat diet (HFD)

tag: time point

value: Day 3


title: Blood, active, animal 6 [6_B_A]

tag: tissue

value: Active


title: SWAT_HFD_4


title: week 1_patient.14

value: Gene expression data at week 1.

value: chronic plaque psoriasis


title: Blood, not active, animal 10 [10_B_NA]

value: Blood

value: Adult ram

value: Rasa Aragonesa


title: SWAT_HFD_2


title: week 2_patient.43

value: Ixekizumab 80mg Q2W

value: Gene expression data at week 2.


title: SWAT_HFD_3


title: Blood, active, animal 5 [5_B_A]


title: Hepa1-6_15.5K_RIP_PEN_seq_rep1

data_processing:
Cutadapt (v2.8) was used to cut the adapters of the paired-end reads and single-end reads. These reads without adapter were subsequently mapped to the mouse reference genome (mm10) with STAR software with the following parameters: ‘--alignEndsType EndToEnd --outFilterType Normal --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.03  --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 15  --outFilterMatchNminOverLread 0.8 --alignIntronMin 20 --alignIntronMax 1 --alignMatesGapMax 1000  --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --seedSearchLmax 0 --seedMultimapNmax 20000 --seedPerReadNmax 1000 --seedPerWindowNmax 100 --seedNoneLociPerWindow 20 --alignSJDBoverhangMin 1000’. Reads mapping to more than twenty locations were discarded and only sequences in which both ends were aligned to the reference genomes were further analyzed.
We clustered the overlapping paired-end reads that mapped to the genomes. Specifically, we defined the start and end sites with the highest abundance in the cluster as the transcription start site (TSS) and transcription terminal site (TTS), respectively. The sequences between TSSs and TTSs co-occurring within 500 bp were extracted as candidate transcripts. Each candidate transcript with a precise TSS and TTS was input to kturnSeeker. A new software, kturnSeeker, was developed to discover ncRNAs with forward and backward kturn structure. kturnSeeker searches A•G, G•A and G-C basepairs (N-C stem), three-nucleotide bulge and a section of regular basepairing (C stem) step-by-step in candidate sequences, and scores the C stem with a strict score scheme (G-C pair is bonus 3, A-U pair is bonus 2 and mismatch minus 5). Only the total score (C stem) large than 7 was kept as candidate ktRNAs. To identify novel ktRNAs, ktRNAs overlapped known annotation were discarded.
The genome sequence of mice (mm10) was downloaded from the UCSC Genome Browser site. Mouse gene annotations were acquired from GENCODE on August 2018. The repeat elements in RepeatMasker were downloaded from the UCSC Genome Browser site. Sequences and annotation data for mouse snoRNAs were downloaded from snoRNA-LBME-db, deepBase, GENCODE, snoRNAome and Refseq in August 2018. All novel ktRNAs were intersected with these gene annotations using bedtools software.
Genome_build: mm10

growth_protocol: Hepa1-6-FLAG-15.5K stable cells were cultured in DMEM (Gibico) with 10% fetal bovine serum (FBS, Gibico), 1% penicillin-streptomycin solution (Gibico) and 1μg/mL puromycine (MCE) at 37℃ at 5% CO2.

extract_protocol:
Cell lysate was prepared and incubated with anti-FLAG. Afterwards, the RNA-protein complexes were immunoprecipitated with Dynabeads protein G and the RNA fraction was extracted using RNAzol reagent.
For RIP-PEN-seq, RIP RNA was subjected to rRNA removal and further used to generate the library using the TruSeq Samll RNA sample preparation kit (Illumina) following the manufacturer’s instructions.

value: Stable overexpression of 15.5K

tag: antibody

value: anti-FLAG [Proteintech, cat# 66008-3-Ig]


title: Blood, active, animal 3 [3_B_A]


title: Hep3B_SpdCas9-TET1-CD MS2-MCP-p65-HSF1 NO G_repL3

type: genomic

city: Clayton

first: Joe

last: Cursons

state: VIC

address: 19 Innovation Walk

department: Biomedicine Discovery Institute

country: Australia

institute: Monash University

description:
205762850073_R07C01
Hep3B (pediatric hepatocellular carcinoma) cell line

hyb_protocol: Bisulphite converted DNA was amplified, fragmented, and hybridised to Illumina Infinium MethylationEPIC BeadChip Kit using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Methylation data analysis were conducted using the minfi R package to read.idat files into R (version 3.6.3), and the missMethyl R package was used for data processing and normalization. Specifically, we identified low quality probes and removed them from the data normalized by SWAN. We then extracted β and M-values (with an offset of 100 for calculating M values). Data quality control was performed using PCA and MDS plots as well as histograms of β values, probe-level differential methylation analysis was performed on M-values using limma, and probes with an adjusted p-value < 0.05 and absolute log fold change > 0.5 were considered as differentially methylated probes (DMPs). To map probes to their associated genes and gene regions, we used the IlluminaHumanMethylationEPICanno.ilm10b2.hg19 R package.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

growth_protocol: Hep3B cells were cultured in DMEM low glucose-pyruvate supplemented containing 10% HyClone fetal bovine serum (FBS) (GE Healthcare Life Sciences, Cat. No. SH30084.03) and 1% antibiotic-antimycotic (Gibco, Cat. No. 15240062).

extract_protocol: Cells were washed in DPBS, collected, and centrifuged at 1,000 rpm for 5 minutes at room temperature. Pelleted cells were washed in DPBS and centrifuged again. Cells pellets were then processed using a Monarch Genomic DNA Purification Kit (NEB, Cat. No. T3010L) according to the manufacturer's protocol. After QC, 500ng of purified genomic DNA was processed using Illumina Methylation EPIC 850K microarray.

treatment_protocol: Hep3B cells were seeded in complete culture medium at 350,000 cells in 6-well plates 18 hours prior to transfection. The next day, the cells were transfected with 250 μL transfection mix consisting of 5 μL Lipofectamine 3000, 5 μL P3000 reagent (Invitrogen, Cat. No. L3000001), and 2.55 μg of plasmid DNA in Opti-MEM (Gibco), according to the manufacturer’s protocol. Culture medium containing the transfection mix was removed after 4 hours and exchanged for fresh culture medium. Cells were collected 96-hours post-transfection for RNA extraction (to confirm HHIP transcriptional upregulation) and for genomic DNA extraction for DNA methylation analysis.

tag: cell line

tag: contstruct

value: SpdCas9-TET1-CD MS2-MCP-p65-HSF1 and no targeting gRNA

value: Male


title: week 2_patient.17

value: skin


title: Blood, active, animal 1 [1_B_A]


title: Blood, active, animal 4 [4_B_A]


title: VWAT_HFD_5

source_name: perigonadal WAT (VWAT)

value: perigonadal WAT (VWAT)

value: Adipocyte precursor cells

tag: strain

tag: gender


title: Hep3B_SpdCas9-TET1-CD MS2-MCP-p65-HSF1 NO G_repL1

description:
205762850073_R05C01
Hep3B (pediatric hepatocellular carcinoma) cell line


title: Hep3B_SpdCas9-TET1-CD MS2-MCP-p65-HSF1_ HHIP G4_rep4

description:
205762850073_R04C01
Hep3B (pediatric hepatocellular carcinoma) cell line

value: SpdCas9-TET1-CD MS2-MCP-p65-HSF1 and a gRNA targeting the HHIP pro


title: VWAT_HFD_2

value: Female

value: 60percent lard high-fat diet (HFD)

value: Day 3


title: HS14, day3, rep2

city: Saint-Petersburg

first: Margarita

last: Sorokina

address: Akkuratova 2

country: Russia

institute: Almazov National Medical Research Centre

data_processing:
Read quality was checked for each sample using FastQC v0.11.9.
Sequenced reads were mapped to the mouse genome using mapper STAR v2.7 with rat reference genome Rnor_6.0 (Ensembl release 104) and annotation Rnor_6.0.104.chr.gtf
Aligned reads were count with featureCounts program v1.6.4.
Further analysis were made using DESeq2, fgsea и clusterProfiler R packages, as well as MSigDB and phantasus online tools.
Assembly: Genome Rnor_6.0 (Ensembl release 104)
Supplementary files format and content: tab-delimited text file includes matrix of raw counts for each of 12 Samples

organism: Rattus norvegicus

growth_protocol: Fibro-adipogenic progenitor cells (FAPs) were cultured in DMEM supplemented with 1% penicillin-streptomycin, 1% L-glutamine, 10% FBS (HyClone, USA) on cell culture dishes. Adipogenic differentiation of FAPs was stimulated by replacing the culture media with adipocyte induction medium composed of culture medium supplemented with 1 μM insulin, 1 μM dexamethasone, and 0,5 μM 3-isobutyl-1-methylxanthine.

extract_protocol:
Total RNA was isolated from the cells with an Extract RNA kit (Evrogen, Russia)
Libraries were constructed using TruSeq Stranded mRNA library prep kit

treatment_protocol: Cells were isoleted and cultured to subconfluent state.

value: m. soleus

value: fibro-adipogenic progenitor cells

value: primary cells

value: Hindlimb suspension (HS)

tag: day of_hs

tag: day of_differentiation


title: Hep3B_SpdCas9-TET1-CD MS2-MCP-p65-HSF1 NO G_repL2_2

description:
205762850073_R08C01
Hep3B (pediatric hepatocellular carcinoma) cell line


title: HS14, day3, rep1


title: HS14, day0, rep1


title: Hep3B_SpdCas9-TET1-CD MS2-MCP-p65-HSF1_HHIP G4_rep1

description:
205762850073_R01C01
Hep3B (pediatric hepatocellular carcinoma) cell line


title: SWAT_SD_4

value: inguinal WAT (SWAT)

value: Standard diet (SD)

value: Day 0


title: week 4_patient.50

tag: visitid

value: Ixekizumab 80mg Q2W

tag: pasi

tag: time

value: Gene expression data at week 4.

value: chronic plaque psoriasis


title: SWAT_HFD_1


title: SWAT_SD_3


title: Blood, active, animal 2 [2_B_A]

value: Blood

tag: age

value: Adult ram

tag: breed

value: Rasa Aragonesa

value: Active


title: Hep3B_SpdCas9-VPR MS2-MCP-p65-HSF1_NO G_rep3

description:
205762850028_R07C01
Hep3B (pediatric hepatocellular carcinoma) cell line

value: SpdCas9-VPR MS2-MCP-p65-HSF1 and no targeting gRNA

value: Male


title: VWAT_HFD_4

value: perigonadal WAT (VWAT)

tag: cell type

value: Adipocyte precursor cells

value: Female

value: 60percent lard high-fat diet (HFD)

value: Day 3


title: HS7, day0, rep1

value: m. soleus

value: fibro-adipogenic progenitor cells

value: primary cells

tag: treatment

value: Hindlimb suspension (HS)


title: VWAT_HFD_1

tag: diet


title: VWAT_SD_5

value: Standard diet (SD)

tag: time point

value: Day 0


title: VWAT_HFD_3

tag: tissue


title: HS14, day0, rep2


title: HS7, day0, rep2


title: VWAT_SD_4


title: Hep3B_SpdCas9-VPR MS2-MCP-p65-HSF1_HHIP G4_rep4

description:
205762850028_R04C01
Hep3B (pediatric hepatocellular carcinoma) cell line

value: SpdCas9-VPR MS2-MCP-p65-HSF1 and a gRNA targeting the HHIP pro


title: Hep3B_SpdCas9-TET1-CD MS2-MCP-p65-HSF1_HHIP G4_rep2

description:
205762850073_R02C01
Hep3B (pediatric hepatocellular carcinoma) cell line

value: SpdCas9-TET1-CD MS2-MCP-p65-HSF1 and a gRNA targeting the HHIP pro


title: Hep3B_SpdCas9-TET1-CD MS2-MCP-p65-HSF1 NO G_repL2_1

description:
205762850073_R06C01
Hep3B (pediatric hepatocellular carcinoma) cell line

value: SpdCas9-TET1-CD MS2-MCP-p65-HSF1 and no targeting gRNA


title: Control, day3, rep2

value: Control


title: Hep3B_SpdCas9-VPR MS2-MCP-p65-HSF1_HHIP G4_rep3

description:
205762850028_R03C01
Hep3B (pediatric hepatocellular carcinoma) cell line


title: baseline_patient.57

value: Ixekizumab 80mg Q2W

value: Gene expression data at baseline.

value: skin

tag: disease state

value: chronic plaque psoriasis


title: VWAT_SD_2

value: perigonadal WAT (VWAT)

value: Adipocyte precursor cells

value: Female


title: Hep3B_SpdCas9-TET1-CD MS2-MCP-p65-HSF1 _HHIP G4_rep3

description:
205762850073_R03C01
Hep3B (pediatric hepatocellular carcinoma) cell line

tag: cell line

value: Male


title: SWAT_SD_5

value: inguinal WAT (SWAT)


title: Control, day0, rep1

value: m. soleus

value: fibro-adipogenic progenitor cells

value: primary cells


title: HS7, day3, rep2

value: Hindlimb suspension (HS)


title: Hep3B_SpdCas9-VPR MS2-MCP-p65-HSF1_NO G_rep4

description:
205762850028_R08C01
Hep3B (pediatric hepatocellular carcinoma) cell line

tag: contstruct

value: SpdCas9-VPR MS2-MCP-p65-HSF1 and no targeting gRNA


title: Hep3B_SpdCas9-VPR MS2-MCP-p65-HSF1_HHIP G4_rep1

description:
205762850028_R01C01
Hep3B (pediatric hepatocellular carcinoma) cell line

value: SpdCas9-VPR MS2-MCP-p65-HSF1 and a gRNA targeting the HHIP promoter


title: SWAT_SD_2

tag: strain

value: Standard diet (SD)

value: Day 0


title: HS7, day3, rep1


title: Hep3B_SpdCas9-VPR MS2-MCP-p65-HSF1_NO G_rep2

description:
205762850028_R06C01
Hep3B (pediatric hepatocellular carcinoma) cell line

tag: gender


title: GFP

city: College Station

first: Fei

last: Liu

address: 206 Olsen Blvd

institute: Texas A&M University Health Science Center

data_processing:
The Cell Ranger Suite version 2.0.2 software was used to perform sample barcode processing and single-cell gene UMI (unique molecular index) counting Alignment, filtering, barcode counting and unique molecular identifier counting were performed using Cell Ranger 3.1.0 with default parameters. Reads were aligned to mouse reference mm10.
Genome_build: mm10
Supplementary_files_format_and_content: Hierarchical Data Format. Matrix containing features, cell-barcodes and read.

source_name: submandibular glands

extract_protocol: scRNA-seq libraries were generated using the 10x Chromium platform and the version 3 Chromium Single Cell 3` reagent kit following the manufacturers instructions (10x Genomics).

treatment_protocol: Retroductal instillation of adenoviral vectors (1x10^9 particles per gland) carrying GFP or rat Shh gene

tag: protocol

value: 7 days after GFP gene transfer

value: submandibular glands

tag: developmental stage

value: adult


title: SWAT_SD_1


title: Hep3B_SpdCas9-VPR MS2-MCP-p65-HSF1_NO G_rep1

description:
205762850028_R05C01
Hep3B (pediatric hepatocellular carcinoma) cell line


title: OsWRKY65-2 rep1

status: Public on Apr 09 2023

city: Jeonju-si

first: Sang ryeol

last: Park

state: Jeollabuk-do

address: 370, Nongsaengmyeong-ro, Deokjin-gu

country: South Korea

institute: Rural Development Administration

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to RAP-DB_IRGSP-1.0 whole genome by using HISAT2 version 2.1.0 with parameter -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
FPKM were calculated by using StringTie version 2.1.3b, with parameter --rf -l -o -G -A -e
Assembly: RAP-DB_IRGSP-1.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Oryza sativa Japonica Group

source_name: rice leaf

growth_protocol: The 2-week-old WT, WRKY65-2 plants were grown in MS medium 16h light / 8h dark 28℃.

extract_protocol:
Total RNA was extracted using the Maxwell® 16 LEV plant RNA Purification Kit (Promega, Madison, USA) according to the manufacturer's instructions.   The extracted RNA concentration was calculated by Quant-IT RiboGreen (Invitrogen).   RNA size was confirmed using Agilent RNA 6000 Pico kit on Agilent 2100 Bioanalyzer System. (Agilent Technologies, Böblingen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: rice leaf

value: seedling

tag: genotype

value: OsWRKY65-2 overexpression

value: post planting day 14


title: OsWRKY65-2 rep3


title: VWAT_SD_3

value: perigonadal WAT (VWAT)

value: Adipocyte precursor cells

value: Female


title: Intestine epithelium, drug stimulated rep2

city: Beijing

first: Jing

address: Shuguanghuayuan middle road #9, Haidian district

department: Institute of Animal Husbandry and Veterinary Medicine

institute: Beijing Academy of Agriculture and Forestry Sciences

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trim-galore v0.6.6, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the Ensembl Sus scrofa "Large White" genome(v1.105)  using Bowtie2 (v2.4.2). Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: bigWig files were generated using the bamCoverage in deeptools package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: bigwig, narrowPeak

organism: Sus scrofa

source_name: intestine epithelium

extract_protocol:
Cells were lysed with homogenization buffer for 10 minutes. After lysis, accesible chromatin frgments are separated using Tn5 transpotase and subsequent centrifugation.
Libraries were prepared using TruePrep DNA Library Prep Kit V2 for Illumina from Vazyme. 10ng of DNA was used for input and IP samples. Libraries were amplified using 13 cycles on thermocycler.Amplified libraries were size-selected at 200-300bp in length.

value: intestine epithelium

value: Stimulated


title: Control, day0, rep2

value: m. soleus

value: fibro-adipogenic progenitor cells

value: primary cells

value: Control

tag: day of_hs

tag: day of_differentiation


title: Control, day3, rep1


title: Hep3B_SpdCas9-VPR MS2-MCP-p65-HSF1_HHIP G4_rep2

description:
205762850028_R02C01
Hep3B (pediatric hepatocellular carcinoma) cell line

value: SpdCas9-VPR MS2-MCP-p65-HSF1 and a gRNA targeting the HHIP pro

value: Male


title: Intestine epithelium, control rep3


title: Intestine epithelium, control rep1


title: VWAT_SD_1

value: Standard diet (SD)

value: Day 0


title: OsWRKY65-2 rep2

value: rice leaf

tag: age


title: WT rep3

value: seedling

value: wild type


title: WT rep2

value: post planting day 14


title: WT rep1


title: Shh

value: 7 days after Shh gene transfer

value: submandibular glands

value: adult


title: Intestine epithelium, drug stimulated rep3

value: intestine epithelium


title: C19-specific cells, infected and 1 month post 2nd vaccine, rep.3

city: Rijeka

first: Felix

middle: Martinus

last: Wensveen

address: Braće Branchetta 20

department: Histology & Embryology

country: Croatia

institute: University of Rijeka faculty of medicine

data_processing:
Fastq files were generated using bcl2fastq.
Sequencing reads were aligned to human reference genome hg19 using Hisat2 (v2.0.2), with default parameters.
Count tables were generated using HTseq.
Assembly: Genome_build: hg19 (GRCh37)
Supplementary files format and content: tab delimited text file

source_name: PBMC

extract_protocol:
Cells were lysed and total RNA was extracted using the Qiagen RNeasy Micro Kit according to the manufacturers’ protocol. S
Libraries were constructed using the Illumina Nextera XT kit and analyzed for concentration (Qubit DNA assay and NanoDrop; Thermo Fisher Scientific).

treatment_protocol:
PBMC of HLA:A2+ people were isolated by density gradient using histopaque-1077.
Cells were stained using peptide loaded tetramers, as well as CD3 and CD8 and sorted using a FACSaria 2.

value: PBMC

value: CD8+ T cells

value: SARS-2 specific cells

value: Infected and 1 month after 2nd vaccination (Pfizer)


title: Intestine epithelium, control rep2

value: Control


title: C19-specific cells, infected and 1 month post 2nd vaccine, rep.2


title: C19-specific cells, 1month post 2nd vaccine, rep.5

value: 1 month after 2nd vaccination (Pfizer)


title: C19-specific cells, 1month post 2nd vaccine, rep.3


title: C19-specific cells, 1month post 2nd vaccine, rep.2


title: Intestine epithelium, drug stimulated rep1

value: Stimulated


title: SkMel147 doxycycline biological replica 2

city: Barcelona

first: Mariano

middle: F

last: Zacarias-Fluck

address: Natzaret, 115-117

department: Preclinical and Translational Research Program

institute: Vall d'Hebron Institute of Oncology (VHIO)

hyb_protocol: Total RNA was linearly amplified using WT Plus (Affymetrix). The resulting ssDNA was used to hybridize Affimetrix microarrays. Hybridization data was acquired using the Affimetrix GeneChip/GeneTitan platforms. Transcriptomes were determined on a genome wide Clariom S Human HT (Affimetrix).

scan_protocol: Arrays were scanned on a Affymetrix GeneTitan instrument (ThermoFisher Scientific-Affymetrix) according to the manufacturer’s protocol.

data_processing: Affymetrix CEL files were normalized by RMA preprocessing methodology and analyzed using Bioconductor followed by GSEA 4.10 software from Broad Institute.

label: Biotin

label_protocol: Labeling of samples was carried out according to the manufacturer’s standard protocol

growth_protocol: BALB/c nude mice bearing A375 or SkMel147 s.c. tumors were given doxycycline (or its vehicle) in the drinking water to induce the expression of Omomyc in the tumor cells when tumors were 100 mm3.

extract_protocol: 50-100 mg of tumor tissue was homogenized with a pestle in TRIzol. Total RNA were extracted using TRIzol following manufacturer's procedures. Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: BALB/c nude mice bearing A375 or SkMel147 s.c. tumors were given doxycycline (or its vehicle) in the drinking water to induce the expression of Omomyc in the tumor cells. Mice were euthanized seven days post-treatment and s.c. melanomas were excised and flash frozen at -80ºC until processing.

value: skin melanoma


title: SkMel147 doxycycline biological replica 4


title: C19-specific cells, 6months post infection, rep.3

value: 6 months after infection


title: SkMel147 doxycycline biological replica 3


title: C19-specific cells, infected and 1 month post 2nd vaccine, rep.4


title: SkMel147 vehicle biological replica 4


title: SkMel147 vehicle biological replica 1


title: SkMel147 doxycycline biological replica 1


title: C19-specific cells, 6months post infection, rep.2


title: SkMel147 vehicle biological replica 3


title: A375 doxycycline biological replica 2

description: A375 Doxycycline 2

data_processing: Affymetrix CEL files were normalized by RMA preprocessing methodology and analyzed using Bioconductor followed by GSEA 3.0 software from Broad Institute.


title: A375 doxycycline biological replica 3

description: A375 Doxycycline 3


title: A375 doxycycline biological replica 5

description: A375 Doxycycline 5


title: C19-specific cells, 1month post 2nd vaccine, rep.4


title: C19-specific cells, 6months post infection, rep.1


title: SkMel147 vehicle biological replica 2


title: Flu-specific cells, rep. 4

value: Influenza-specific cells


title: C19-specific cells, 1month post 2nd vaccine, rep.1


title: C19-specific cells, 6months post infection, rep.4


title: A375 vehicle biological replica 5

description: A375 vehicle 5


title: Flu-specific cells, rep. 3


title: Flu-specific cells, rep. 1


title: A375 doxycycline biological replica 4

description: A375 Doxycycline 4


title: A375 vehicle biological replica 2

description: A375 vehicle 2


title: 1114A

city: Xianmen

first: Yuchen

address: Xiangan South Road

institute: Xianmen University

data_processing:
Sequence reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trim_galore (v0.6.7)
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR (v2.7.9a)
Assembly: mm10
Supplementary files format and content: tab-delimited text files with raw counts for each sample

source_name: Expression profile of Mettl3 knockout in CD4+ T cells

extract_protocol:
To isolate CD4+ T cells, mouse dorsal skin was excised and the fat layer was removed using a surgical scalpel. The skin tissue was treated with dispase II (2.5 mg/ml) in Hank’s Balanced Salt Solution for 60 min at 37 °C. The dermal fraction was collected by scraping and then cut into small pieces. Dermal single-cell suspensions were obtained after collagenase IV (1 mg/ml) treatment for 2 h at 37 °C, followed by filtering and centrifugation. Samples were stained for 30 min on ice. The following antibodies were used: anti-CD4-PE (100408, Biolegend) and anti-CD45-FITC (103108, Biolegend).
According to the sample and product requirements, select the corresponding detection method for quality inspection, take a sample no larger than 4 μL, add Oligo-dT Primer, place it on a PCR instrument, and perform RNA denaturation; prepare a reverse transcription system, and use SMART amplification technology to synthesize the first Strand cDNA. Prepare a PCR amplification system for pre-amplification of cDNA; select the corresponding detection method for quality inspection of cDNA; use the transposase method for qualified amplification products for subsequent library construction; select the corresponding detection method according to product requirements for quality inspection of the library After the PCR product is denatured into a single strand, prepare a circularization reaction system and set up a reaction program to obtain a single-stranded circular product and digest the uncircularized linear DNA molecule.

treatment_protocol: 8–12-week-old mice received a daily topical dose of 15 mg or 62.5 mg of 5% IMQ cream (Aldara, 3M Pharmaceuticals) on the  back for 5 consecutive days

value: skin

value: CD4+ T cells from skin

value: Imiquimod

value: Imiquimod-induced psoriasis mouse model


title: A375 vehicle biological replica 4

description: A375 vehicle 4


title: Flu-specific cells, rep. 5


title: Flu-specific cells, rep. 2


title: 1110A


title: A375 vehicle biological replica 3

description: A375 vehicle 3


title: A375 vehicle biological replica 1

description: A375 vehicle 1


title: 1103A


title: 1107A


title: A375 Doxycycline 5

description: Clariom S, human HT

data_processing: Affymetrix CEL files were normalized by RMA preprocessing methodology and analyzed using Bioconductor followed by GSEA 4.10 software from Broad Institute. Due to experimental protocol, the samples were ran in batches, indicated in the cel file name. ComBat was used to batch correct.

source_name: A375 doxycycline biological replica 5

growth_protocol: Cells were grown at 37ºC, 5% CO2 in RPMI1640 supplemented with glutamine and 10% FBS

extract_protocol: Total RNA were extracted using TRIzol following manufacturer's procedures. Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Cells were plated in the presence or not of Docycycline (2 µg/ml) for 4 days


title: KO_IR2

city: WuHan

first: Dong

address: No.5  HangKong Road

institute: Huazhong University of Science and Technology

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10（ensembl_mus_musculus_grcm38_p6_gca_000001635_8） whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: ensembl_mus_musculus_grcm38_p6_gca_000001635_8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: kidney

growth_protocol: Animals were housed in ventilated microisolator cages with free access to water and food under a 12:12 h light/dark cycle in a temperature-controlled room (22 ± 2°C).

extract_protocol:
Total RNA from each sample was extracted using RNAiso Plus (Takara Biotech), and concentration was measured using an ND-1000 NanoDrop (Thermo Scientific, Wilmington, DE).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). Firststrand cDNA wassynthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Mice were anesthetized and underwent midline abdominal incisions with left renal pedicle bluntly clamped for 45 min (unilateral renal occlusion). Reperfusion was recovered by removing the clamps. Wounds in abdomens were sutured. Mice were euthanized at day 3 to harvest blood, injured kidney and non-injured kidney.

value: kidney

value: G9a knockout

value: renal ischemia reperfusion


title: A375 Doxycycline 3

description: Clariom S, human HT

source_name: A375 doxycycline biological replica 3


title: KO_IR1

value: adult


title: WT_IR2

value: wildtype


title: A375 Doxycycline 2

description: Clariom S, human HT

source_name: A375 doxycycline biological replica 2


growth_protocol: BALB/c nude mice bearing SkMel147 s.c. tumors were given doxycycline (or its vehicle) in the drinking water to induce the expression of Omomyc in the tumor cells when tumors were ~750 mm3.

extract_protocol: The whole lymph node tissue was homogenized with a pestle in TRIzol. Total RNA were extracted using TRIzol following manufacturer's procedures. Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: BALB/c nude mice bearing SkMel147 s.c. tumors were given doxycycline (or its vehicle) in the drinking water to induce the expression of Omomyc in the tumor cells. Mice were euthanized two days post-treatment and lymph nodes metastases were confirmed by IVIS imaging, excised and flash frozen at -80ºC until processing.

value: lymph nodes metastases


title: WT_IR1


title: A375 Doxycycline 4

description: Clariom S, human HT

source_name: A375 doxycycline biological replica 4


title: A375 Doxycycline 1

description: Clariom S, human HT

source_name: A375 doxycycline biological replica 1


title: A375 Control 3

description: Clariom S, human HT

source_name: A375 control biological replica 3


title: A375 Control 4

description: Clariom S, human HT

source_name: A375 control biological replica 4


title: Cells_UHRF1-depleted_rep2

city: Coleraine

first: Colum

middle: Patrick

last: Walsh

state: County Londonderry

address: Cromore Road

department: Life and Health Sciences

institute: Ulster University

description: UH4 replicate two

hyb_protocol: Standard Illumina Protocol

scan_protocol: Completed by commercial provider Cambridge Genomics Services

growth_protocol: The wild-type (hTERT1604) lung fibroblast cell line (Ouellette et al., 2000) and derivatives were cultured in 4.5g/l glucose DMEM with 10% FBS and 2× NEAA (all Thermo-Fisher Scientific, Loughborough, UK).

extract_protocol: RNA was extracted from cells growing in log phase using the RNeasy Mini Kit (Qiagen).  including a DNase step.

treatment_protocol: Depletion of UHRF1 in hTERT1604 (UH4 lines) for this study used GIPz Lentiviral shRNAmir (Thermo-Fisher Scientific) according to the manufacturer’s instructions. Rescue cell lines (WT10/18, PHD1/4/10, TTD9) were generated by transfecting UH4  cells with pCMV plasmids containing full length UHRF1 cDNA which was either intact (WT)  or contained functional mutations in either the PHD or TTD domains as previously described  (28); specifically TTD1 Y188A, PHD1/2/10 D334A/E335A. Individual colonies were selected  in G418 (Sigma-Aldrich)

value: Male

tag: sample type

value: hTERT

value: UHRF1 KD hTERT


title: Cells_UHRF1-rescue_rep1

description: UH+R10 replicate one

data_processing: Completed by commercial provider Cambridge Genomics Services

value: UHRF1 Rescue 10 hTERT


title: Cells_UHRF1-rescue_rep3

description: UH+R10 replicate three


title: A375 Control 2

description: Clariom S, human HT

source_name: A375 control biological replica 2

tag: cell type

value: skin melanoma


title: KO2

tag: treatment


title: KO1


title: WT2


title: WT1


title: Cells_UHRF1-depleted_rep3

description: UH4 replicate three


title: (CT-26 model) Multimer-binding CD8+ CTRL isolated from PBMC

city: Evanston

first: Zongjie

state: Illinois

address: Silverman Hall - Room 4578, 2170 Campus Dr

department: Biomedical Engineering

institute: Northwestern University

description: CT-26_DEG_Non-CTRL vs CTRL

data_processing:
Ribosomal and mitochondrial genome removal
Alignment (STAR v2.7.3a)
Raw counts estimation (HTSeq v0.11.2)
Counts normalization and comparison (DESeq2)
N/A
Assembly: mm10
Supplementary files format and content: Raw and normalized gene counts
Supplementary files format and content: Differentially expressed genes

source_name: Purified PBMC based on multimers

extract_protocol:
MedGenome in-house  protocol
Standard Takara SMART-Seq v4 RNA
Ultra-input RNAseq

value: Purified PBMC based on multimers

value: Primary cells

value: CD8+ lymphocytes

value: WT

value: Multimer-binding


title: (CT-26 model) Residual of CD8+ lymphocyte isolated from PBMC

description: CT-26_DEG_Non-CTRL vs CTRL


title: (B16 model) Residual of CD8+ lymphocyte isolated from PBMC

description: B16_DEG_Non-CTRL vs CTRL


title: SkMel147 vehicle biological replica 3


title: A375 Control 1

description: Clariom S, human HT

source_name: A375 control biological replica 1


title: SkMel147 vehicle biological replica 4


title: A375 Control 5

description: Clariom S, human HT

source_name: A375 control biological replica 5


title: A375 doxycycline biological replica 1

description: A375 Doxycycline 1


title: Cells_wild-type_rep3

description: WThTERT replicate three

source_name: WT

value: WT hTERT


title: Cells_wild-type_rep1

description: WThTERT replicate one


title: Cells_UHRF1-depleted_rep1

description: UH4 replicate one


title: SkMel147 vehicle biological replica 2


title: (B16 model) Multimer-binding CD8+ CTRL isolated from PBMC

description: B16_DEG_Non-CTRL vs CTRL


title: SkMel147 vehicle biological replica 1


title: Cells_UHRF1-rescue_rep2

description: UH+R10 replicate two


title: RING1B-HEK293FT_siNC_rep1

status: Public on Apr 08 2023

city: boston

first: Danesh

last: Moazed

address: 240 longwood avenue

department: cell biology

institute: Harvard medical school

description: ChIP-seq

data_processing:
ChIP-seq reads were quality controlled with fastqc (v0.11.5)
Pooled libraries were demultiplexed using fastx
Reads were aligned to the reference genome using bowtie2 with default parameters.
The mapped reads were normalized to reads per genome content using Deeptools, saved as bw files and visualized in IGV.
ChIP-seq peaks were called with macs2 (v2.1.1.20160309) and broad peak calling option using corresponding input files for background normalization
Assembly: hg19
Supplementary files format and content: The mapped reads were normalized to reads per genome content using Deeptools, saved as bw files and visualized in IGV.

extract_protocol:
Cells for ChIP were cultured in 15 cm plates. Cell were first washed with cold PBS, crosslinked at room temperature with 10 mM DMP (ThermoFisher Scientific) for 30 min, and then 1% formaldehyde (ThermoFisher Scientific) for 15 min. Crosslinking reactions were quenched by addition of 125 mM glycine for 5 min. Crosslinked cells were separated by 3 min treatment of 0.05% trypsin (Gibco), and then washed with cold PBS 3 times. In every wash, cells were centrifuged for 3 min at 1000xg at 4℃.Cell were then resuspended in sonication buffer (pH 7.9, 50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 1% Triton, 0.1% Sodium deoxycholate, and 0.5% SDS) and sonicated to shear chromatin into ~300 bp fragments using a Branson sonicator. Sonicated samples were diluted 5-fold with ChIP dilution buffer (pH 7.9, 50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 1% Triton, 0.1% Sodium deoxycholate) to obtain a final concentration of 0.1% SDS. Diluted samples were centrifuged at13,000 rpm for 10 min. The supernatant was pre-cleared with protein A/G or Dynabeads M-280 Streptavidin beads (ThermoFisher) and immunoprecipitated for 3-12 h using 3 μg antibodies and 40 μl protein A/G or Dynabeads M-280 Streptavidin beads. The beads were washed twicewith high salt wash buffer A (pH 7.9, 50 mM Hepes, 500 mM NaCl, 1 mM EDTA, 1% Triton, 0.1% Sodium deoxycholate, and 0.1% SDS), and once with wash buffer B (pH 7.9, 50 mM Hepes, 250 mM LiCl, 1 mM EDTA, 1% Triton, 0.1% Sodium deoxycholate, 0.5% NP-40). The bound chromatin fragments were eluted with elution buffer (pH 8.0, 50 Mm Tris, 10 mM EDTA, 1% SDS) for 5 min at 65℃. Eluted DNA-proteins complexes were treated with RNase A and crosslinks were reversed overnight at 65℃. Proteinase K was then added to digest proteins for 1 h at 55℃. DNA was further purified using PCR Purification Kit (QIAGEN) and analyzed by PCR on a QuantStudio 7 Flex Real Time PCR System (Applied Biosystem). PCR parameters were 95℃for 2 min and 40 cycles of 95℃ for 15s, 60℃ for 15s, and 72℃ for 15 s, followed by 72℃ for 1 min. All the ChIP-qPCR data presented were at least three biological replicates. Primer sequences are in the table. Error bar represent standard deviation (three biological replicates).
For ChIP-seq, sequencing library was constructed using TruSeq DNA sample Prep Kits (Illumina) and adapter dimers were removed by agarose gels electrophoresis. Sized selected and purified DNA libraries were sequenced on an Illumina Hiseq 2500 machine (Bauer core facility at Harvard University) to obtain 50 bp single-end reads.

tag: sirna

value: siControl

tag: medium

value: DMEM

tag: antibody

value: RING1B (cell signaling technology 5694S)


title: RING1B-HEK293FT_siUSP7_rep2

description: ChIP-seq


title: RING1B-HEK293FT_siUSP7_rep1

description: ChIP-seq


title: BMI1-HEK293FT_siUSP7_rep2

description: ChIP-seq

value: BMI1 (Bethyl, A301-694A-T)


title: PCGF1-HEK293FT_siUSP7_rep2

description: ChIP-seq

value: PCGF1 (Abcam, ab259943)


title: PCGF1-HEK293FT_siUSP7_rep1

description: ChIP-seq


title: PCGF1-HEK293FT_siNC_rep2

description: ChIP-seq


title: PCGF1-HEK293FT_siNC_rep1

description: ChIP-seq


title: BMI1-HEK293FT_siUSP7_rep1

description: ChIP-seq


title: C19-specific cells, infected and 1 month post 2nd vaccine, rep.1

tag: tissue

value: PBMC

value: CD8+ T cells

value: SARS-2 specific cells

value: Infected and 1 month after 2nd vaccination (Pfizer)


title: EZH_DKO_ES_rep2

description: mRNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-seq reads were mapped to the human genome (GRCh37/hg19) with Kallisto (version 1.15.0).
Transcript abundances were normalized with Transcripts Per Million (TPM) mapped reads.
Differentially expressed genes were identified by DESeq2 ((v1.18.1)) with fold change>2 and Benjamini–Hochberg false discovery rate adjusted P < 0.05.
deeptool (v/3.0.2) was used to generate bigwig files for visualization in IGV tool
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file normalized to RPGC for each Sample

source_name: human ES H9

extract_protocol:
For mRNA-seq, total RNA was isolated from human cells with an RNA purification kit (Qiagen, 74134) and genomic DNA was removed by genomic DNA binding columns in the kit.
For RNA-seq, two μg of total RNA was used to start RNA-seq library construction. Poly(A)-containing mRNA was isolated by poly-A selection beads and further reverse transcribed to cDNA. The resulting cDNA was ligated with adapters, amplified by PCR, and further cleaned to obtain the final library. Libraries were sequenced on an Illumina Hiseq machine (Novogene) to obtain 150 bp paired-end reads.

tag: cell line

value: human ES H9

tag: knockout

value: EZH1 and EZH2 double knockout


title: BMI1-HEK293FT_siNC_rep1

description: ChIP-seq


title: EZH_DKO_ES_rep1

description: mRNA-seq


title: siRNF2_ES_rep2

description: mRNA-seq


title: siRNF2_ES_rep1

description: mRNA-seq


title: siSENP3_ES_rep1

description: mRNA-seq


title: siSENP3_ES_rep2

description: mRNA-seq


title: USP7in_rep1

description: mRNA-seq

tag: drug treatment

value: 1 uM FT671 for 2 days

tag: ectopic expression


title: siNC_ES_rep2

description: mRNA-seq


title: siNC_ES_rep1

description: mRNA-seq


title: siSENP3_wtRes_rep2

description: mRNA-seq

value: SENP3 wild-type


title: siUSP7_rep2

description: mRNA-seq


title: RING1B-HEK293FT_siNC_rep2

description: ChIP-seq


title: siSENP3_muRes_rep1

description: mRNA-seq

value: SENP3 C532A


title: siUSP7_rep1

description: mRNA-seq


title: siSENP3_rep2

description: mRNA-seq


title: siSENP3_rep1

description: mRNA-seq


title: TEX10_siSENP3_rep2.bw

description: ChIP-seq

data_processing:
ChIP-seq reads were quality controlled with fastqc (v0.11.5)
Pooled libraries were demultiplexed using fastx
Reads were aligned to the reference genome using bowtie2 with default parameters.
The mapped reads were normalized to reads per genome content using Deeptools, saved as bw files and visualized in IGV.
ChIP-seq peaks were called with macs2 (v2.1.1.20160309) and broad peak calling option using corresponding  input files for background normalization
Genome_build: hg19
Supplementary_files_format_and_content: The mapped reads were normalized to reads per genome content using Deeptools, saved as bw files and visualized in IGV.

value: TEX10 (ThermoFisher 720257)


title: TEX10_siNC_rep2.bw

description: ChIP-seq


title: BMI1-HEK293FT_siNC_rep2

description: ChIP-seq


title: siCtrl_rep2

description: mRNA-seq

value: siNC


title: NC_rep2

description: mRNA-seq


title: H2AK119ub1-HEK293FT_siNC_rep2.bw

description: ChIP-seq

value: WT

value: H2AK119ub1 (cell signaling technology 8240S)


title: NC_rep1

description: mRNA-seq

value: DMEM


title: CBX2-HEK293FT_siNC_rep2.bw

description: ChIP-seq

value: siControl

value: CBX2 (Proteintech, 15579-1-AP)


title: TEX10_siSENP3_rep1.bw

description: ChIP-seq


title: CBX2-HEK293FT_siUSP7_rep1.bw

description: ChIP-seq


title: TEX10_siNC_rep1.bw

description: ChIP-seq


title: H2AK119ub1-HEK293FT_siUSP7_rep2.bw

description: ChIP-seq


title: H2AK119ub1-HEK293FT_siUSP7_rep1.bw

description: ChIP-seq


title: siCtrl_rep1

description: mRNA-seq


title: H2AK119ub1-HEK293FT_siNC_rep1.bw

description: ChIP-seq


title: Cells_wild-type_rep2

description: WThTERT replicate two

tag: gender

value: Male

value: hTERT

tag: disease state

value: WT hTERT


title: USP7in_rep2

description: mRNA-seq


title: HT1080-H4WT-S4-IP

city: Chaoyang

first: Liting

last: Lan

state: Beijing

address: Datun 15 Road

department: Institute of biophysics

institute: University of Chinese Academy of Sciences

data_processing:
Paired-end reads were trimmed for adaptor sequence using cutadapt (Martin 2011) with parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -e 0.1 -n 2 -m 35 -q 30 –pairfilter = any, and then mapped to hg38 using Bowtie2 (Langmead, Trapnell et al. 2009) with parameters: -I 10 -X 1000 -3 5 --local --no-mixed --no-discordant --no-unal. Duplicates were marked using picard MarkDuplicates (https://broadinstitute.github.io/picard/) with default parameters and removed using samtools view (Li, Handsaker et al. 2009) with parameters: -f 2 -F 1024 -q 10. Replication timing profile and timing domain were analyzed as described in (Ryba, Battaglia et al. 2011, Marchal, Sasaki et al. 2018). Briefly, in each 50 kb genome window, replication timing were calculated as log2((S1+S2)/(S3+S4))), then normalized with R function normalize.quantiles.use.target() from R package ‘preprocessCore’. The quantile normalized replication timing value were used for replication timing domain segmentation by R function CNA() from R package ‘DNAcopy’ and for timing domain annotation using HOMER (Heinz, Benner et al. 2010). Heatmap was produced using Java Treeview (Saldanha 2004). For IGV (Integrative Genomics Viewer) (Robinson, Thorvaldsdóttir et al. 2011) visualization, the normalized value was Loess-smoothed using R function loess() from R package ‘stats’.
Assembly: hg19, mm10
Supplementary files format and content: bedGraph
Library strategy: Repli-seq

source_name: Connective tissue

extract_protocol: HEK293T and HT1080 cells were cultured in the presence of 100 μM BrdU (sigma) for 2 h. To obtain four sub-populations of S phase cells, including S1, S2, S3 and S4, cells were fixed, stained with PI and sorted by FACS according to their DNA content. Next, isolated cells were lysed immediately in lysis buffer (50 mM Tris, pH 8.0, 10 mM EDTA, 1 M NaCl, 0.5% SDS, 0.1 mg/mL RNase A, 0.2 mg/mL Protease K) and incubated at 37 °C for 3 h, then at 55 °C for 8 h. Genomic DNA was extracted with phenol: chloroform: isoamyl (25:24:1) and chloroform: Isoamyl alcohol (24:1) and precipitated with 75% ethanol and 300 mM NaAc. DNA pellet was dissolved in TE (10 mM Tris, pH 8.0, 1 mM EDTA) before being sonicated using Bioruptor to 200-500 bp. The sonicated DNA was end-repaired, dA-tailed, and adapter-ligated. The adapter-ligated DNA was boiled for 10 min and cooled on ice immediately for 2 min. DNA solution was incubated with BrdU antibody (BD Bioscience, BD44) and rotated at 4 °C overnight. The mixture was incubated with protein G Dynabeads (Life Technology, 10009D) and rotated at 4 °C for another 8 h. After washing five times with washing buffer (PBS with 0.05% (v/v) Triton-X100) and once with TE, the beads were eluted by elution buffer (TE with 0.5% (w/v) SDS) at 65 °C for 10 min. After extraction with DNA Clean & Concentrator-5 kit (ZYMO, D4014), DNA was subjected to library amplification using Next Q5 Hot Start HiFi PCR Master Mix (NEB, M0543) and NEBNext Multiplex Oligos for Illumina (NEB, E7600). The libraries were purified with Ampure beads (0.9 ×) (Beckman, A633881) and sequenced using DNBSEQ-T7 platforms.

value: Connective tissue

value: epithelial cell

tag: genotype

value: H4WT overexpression


title: PAEC, siControl rep1

city: 咸阳

first: yangfan

last: jia

state: 陕西

address: 中国陕西省杨凌区

institute: 西北农林科技大学

data_processing:
Cleaned raw data were aligned to the rat reference genome (NCBI: GCA_000001895.4) using Hisat2 (v2.0.5). FeatureCounts (v2.0.3) was used to count the reads numbers mapped to each gene.
Genes showing an adjusted P value < 0.05 and |log2 (fold change) | > log2 (1.5) identified by the DESeq2 R package (1.32.0) were assigned as differential expressed genes. Data processing and visualization using Tidyverse R Package (1.3.1).

source_name: lung

growth_protocol: Primary rat pulmonary artery endothelial cells (PAEC) and smooth muscle cells (PASMC) were  respectively cultured in Endothelial Cell Growth Medium-2(Catalog#CC-3162, LONZA, Basel, Switzerland) and Smooth Muscle Cell Medium (Catalog#1101, ScienCell, Carlsbad, CA, USA). Both cell types were maintained in a humidity incubator at 37°C, 5% CO2.

extract_protocol:
RNA was harvested using Trizol (TaKara).
RNA libraries for RNA-seq were prepared using the Next UltraTM Directional RNA Library Prep Kit for Illumina (NEB, MA, USA)following manufacturer's protocols.

value: lung

value: PASMC

value: control siRNA


title: siSENP3_wtRes_rep1

description: mRNA-seq

value: SENP3 wild-type


title: PAEC, siNRF2 rep3

value: Nrf2 siRNA


title: CBX2-HEK293FT_siNC_rep1.bw

description: ChIP-seq


title: PASMC, siNRF2 rep2


title: HT1080-H4WT-S2-IP


title: HT1080-H4WT-S1-IP


title: siSENP3_muRes_rep2

description: mRNA-seq

value: SENP3 C532A


title: PAEC, siNRF2 rep1

value: WT


title: PAEC, siNRF2 rep2


title: HT1080-H4WT+PUG-S4-IP

description: HT1080-H4WT+PUG_target_qnor.Loess.bedGraph

value: PUGNAc


title: PAEC, siControl rep2


title: HT1080-H4WT+PUG-S3-IP


title: PAEC, siControl rep3


title: epi2

city: Hong Kong

first: Zilong

last: WEN

address: Rm6319, HKUST, Clear water bay, Kowloon

department: Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

data_processing:
Raw reads were aligned to zebrafish reference genome (genome reference: GRCz11; annotation reference: GRCz11.103) combined with the sequences for DsRedx using the Cell Ranger pipelines (v6.0).
Downstream analysis of unique molecular identifiers (UMI) count matrix was conducted in R using the Seurat pipeline (v4.0.5).
Pseudotime analysis was performed with the Monocle3 package in R.
Assembly: danRer11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: epidermis

extract_protocol:
Six adult Tg(spic:EGFP) fish were sacrificed, 8,000 EGFP+ cells, and 50,000 singlet cells from the single-cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter (Invitrogen).
10x scRNA-seq library was carried out with a 10X Chromium single cell platform. In brief, after the cell sorting, single-cell suspensions were prepared according to the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single-cell Gel Beads-in-emulsion (GEMs). Libraries were prepared using Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System, followed by sequencing on Illumina Novaseq 6000 system (Illumina) for a targeting average depth of around 100,000 read pairs per cell.

value: epidermis

tag: development stage

value: 6 months old

value: spic:EGFP+ and singlet cells

tag: strain


title: HT1080-H4S47A-S4-IP

description: HT1080-H4S47A_target_qnor.Loess.bedGraph

value: H4S47A overexpression


title: PASMC, siNRF2 rep3


title: PASMC, siNRF2 rep1


title: PASMC, siControl rep3


title: CBX2-HEK293FT_siUSP7_rep2.bw

description: ChIP-seq

value: DMEM

value: CBX2 (Proteintech, 15579-1-AP)


title: HT1080-H4S47A-S1-IP

value: Connective tissue


title: mutant_gill_7

description:
mut_gill_7
data_TPM_progenitor_mut_sib.csv

data_processing:
Reads were aligned to the GRCz11.94 (danRer11) zebrafish reference genome using the STAR package, and gene counts were calculated using feature Counts.
The count tables were normalized to produce transcripts per million (TPM) tables.
Principal component analysis (PCA) was carried out using the R Stats package.
Differential expression genes (DEGs) were assessed with the R DESeq2 package.
Assembly: danRer11
Supplementary files format and content: comma-separated values file of TPM values for each sample

source_name: gill

extract_protocol:
The EGFP+DsRedx- progenitor cells for RNA-seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted.
cDNA library was prepared according to the standard Smart-seq2 protocol with minor modifications. Briefly, 30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo-dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase (18064071, Invitrogen). The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit (50-196-5217, Roche) for 23 cycles and purified with the Ampure XP beads (A63881, Beckman). The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina (TD501, Vazyme).

value: gill

value: Tg(spic:EGFP; mpeg1:DsRedx)

value: spic:EGFP+mpeg1:DsRedx- cells

value: mutant

tag: Stage

value: adult


title: HT1080-H4S47A+PUG-S4-IP

description: HT1080-H4S47A+PUG_target_qnor.Loess.bedGraph

value: epithelial cell


title: PASMC, siControl rep2

value: lung

value: PASMC

value: control siRNA


title: HT1080-H4WT+PUG-S2-IP

value: H4WT overexpression

value: PUGNAc


title: PASMC, siControl rep1

value: WT


title: mutant_gill_8

description:
mut_gill_8
data_TPM_progenitor_mut_sib.csv


title: epi1

value: epidermis

value: 6 months old

value: spic:EGFP+ and singlet cells


title: HT1080-H4S47A-S3-IP

value: H4S47A overexpression