title: 28_IL23R_IL23_20hr

first: The Gene Lay Institute of

last: Immunology and Inflammation

address: 60 Fenwood Road,

institute: Brigham and Women's Hospital

description: Library name: 28_IL23R_IL23_20hr_AGTTCC

data_processing:
Raw read data quality was checked using tools provided by the ArrayStudio v6.1 program (Omicsoft Corporation). Quality filters including a minimum sequencing base quality score of Q20 and the exclusion of singletons (non-paired reads) or any reads which mapped to multiple locations on the genome were used for subsequent trimming and alignment. Genome alignment and annotation was based on USCS Human Genome B37.3 reference model.  The aligned data profile was assessed using the RNA-Seq QC metrics provided by the ArrayStudio program. All sequencing libraries contained a minimum of 40 million reads with an average of 74 million reads with 84% of reads uniquely mapped to the reference model. To analyze IL-23 induced (or IL-12 induced) differentially expressed genes in the tested samples, read mapping and expression estimation is analyzed using methodology as described in (Li et al., 2010).  The number of reads for each transcript from each sample was converted to fragments per kilo base per million (FPKM) (Trapnell et al., 2010).
Assembly: GRCh37

source_name: T cell

extract_protocol:
Human memory T cells were transduced with lentiviral vectors encoding either IL-23R or IL-12Rβ2. Following transduction, IL-23R⁺ or IL-12Rβ2⁺ cells were isolated and stimulated with IL-23 or IL-12, respectively, for 4 or 12 hours, in the presence or absence of anti-CD3/CD28 co-stimulation. Cells were subsequently harvested for RNA-seq analysis.
Twenty-eight RNA samples derived from T cells were provided for this study. Each RNA sample was quantitated by spectrophotometry (NanoDrop, ND-1000, ThermoScientific, DE) and fluorometry (Quant-iT™ PicoGreen® dsDNA reagent,Cat # P7589, Invitrogen, Eugene, OR).  To check for quality, RNA samples were run using RNA6000 Nano Kit (Cat# 5067-1511, Agilent Technologies, Waldbronn, Germany) on an Agilent 2100 Bioanalyzer.  Illumina fragment libraries were constructed using Illumina TruSeq Stranded mRNA kits and protocols (Illumina, Hayward CA).  A unique adapter index sequence, provided in the kit, was used for each sample.  Samples were checked for accurate library sizing using Agilent High Sensitivity DNA Kit (Cat# 5067-4626, Agilent Technologies, Waldbronn, Germany) on an Agilent 2100 Bioanalyzer.  To accurately quantitate the library, qPCR was performed using Kapa Library Quantification Kit for Illumina (KK4835, KapaBioSystems, Boston, MA) on the Quantstudio 12k Flex real-time PCR instrument (Life Technologies, Carlsbad, CA).  Each library was quantitated in triplicate. Samples were diluted to a final dilution of 3 nM, normalized and pooled into 6 separate pools containing 4 or 5 samples each.  Libraries were diluted to a final dilution on average of 10 pM. To check for proper cluster density and sample normalization, a MiSeq single plex 1 x 26 bp +6 bp index sequencing was performed using the MiSeq instrument.  Flow cell clustering was performed using TruSeq PE Cluster Kit v2 (Illumina, Hayward CA) on the Illumina cBot to prepare for HiSeq sequencing. The Illumina HiSeq 2500 sequencer instrument, reagents, and flow cell (Illumina, Hayward CA) were prepared according to Illumina TruSeq PE SBS Kit v5 protocols. Sequencing was performed in paired-end multiplex 2 x 100 bp mode. Basecalling and demultiplexing were performed on the HiSeq 2500 sequencing system (Illumina) using Illumina’s Real Time Analysis (RTA) v1.18.61 program.

value: T cell

tag: time


title: WT_EB_3_RNA

status: Public on Jun 12 2026

type: SRA

city: Bethesda

first: HeungSun

last: Kwon

state: MD

address: 50 South Drive Building 50

department: NIDDK

country: USA

institute: NIH

library_source: genomic

data_processing:
RNA-seq fastq files were trimmed using the cutadapt program (v2.7)
Preprocessed reads were aligned to the mouse reference genome Gencode M18 using hisat2 (v2.1.0) with default parameters.
Aligned reads were then mapped to gene features using subread featureCounts (v1.6.4) with parameters “-p -s 0 -T 1”.
Differential expression between groups of samples was tested using R (v3.5.1) with DESeq2 package (v1.22.1).
Transcript quantitation was performed with salmon (v0.14.2) with parameters “--libType=A --gcBias --seqBias --validateMappings".
Assembly: mm10 (Gencode M18)
Supplementary files format and content: tab-delimited text file of featurecounts.

molecule: genomic DNA

organism: Mus musculus

growth_protocol: ESC were maintained and differentiated as described, with modifications (Carotta et al. 2004). Undifferentiated ESC were cultured on 0.1% gelatin-coated plates in EmbryoMax DMEM (MilliporeSigma, SLM-220-M supplemented with 10% fetal bovine serum (MilliporeSigma), 2-β-mercaptoethanol (MilliporeSigma, ES-007-E), GlutaMax, penicillin/streptomycin, non-essential amino acids, and ESGRO-2i (MilliporeSigma, cat# SF016-200. To generate EB, cultures were adjusted to 1 × 10^5 cells/ml and incubated in EB medium (STEMCELL TECH, Aggrewell EB formation medium) for 3 to 5 days in Aggrewell plates (STEMCELL TECH, 34421). After 4 days, EB were pooled and grown in suspension in non-adherent plates, with media changed daily. EB were collected on days 3 and 5.

extract_protocol:
RNA was extracted by RNeasy plus kit (Quiagen, 74134).
RNA sequencing libraries were prepared from 1ug of total RNA from ESC, EB or differentiated cells using NEBNext Ultra TM RNA library Prep Kit (NEB, Cat #7770) for Illumina following manufacturer’s

treatment_protocol: gRNAs targeting Ldb1 were cloned into the CRISPR-Cas9 and gRNA expression vector pSpCas9(BB)-2A-GFP (PX458) (Addgene, cat #48138). ES cells were transfected with Mouse ES Cell Nucleofector® Kit (Lonza, cat # VPH-1001) according to the manufacturer’s instructions. Fluorescent cells were sorted 48 hours later and plated at limiting dilution to isolate single clones harboring the LDB1 gene knockout.

tag: cell line

tag: cell type

value: mEB


title: RNA serum, early gastric cancer, GC0086

city: Punta Arenas

first: Yolanda

last: Espinosa-Parrilla

state: Magallanes

address: Manuel Bulnes 01855

country: Chile

institute: Universidad de Magallanes

description:
Library name: SV18664_0009
Column name in exceRpt_miRNA_ReadCounts:  SV18664_0009_S8_R1_001.fastq

library_source: transcriptomic

data_processing:
Data proccesing was perfomed with Norgen Biotek's pipelin based on exceRpt: Cutadapt for trimming and filtering, fastqc for QC, STAR for alignment and featurecounts for quantification.
miRNA Analysis used trimmed mean of M-values (TMM) normalization method for the statistical analysis (Robinson and Oshlack, 2010).
Assembly: hg38
Supplementary files format and content: comma-separated text file (CSV) miRNA read counts per sample

molecule: total RNA

organism: Homo sapiens

source_name: serum

extract_protocol:
RNA was isolated from 250 ul of serum  using Plasma/Serum RNA Purification Mini Kit (Cat. 55000, Norgen Biotek)
RNA libraries were prepared using Norgen Biotek Small RNA Library Prep Kit for Illumina (Cat. 63600, 63620)

tag: tissue

value: serum


title: RNAseq_Rh30_sgChr2.2_rep2

city: Boston

first: Susu

last: Zhang

state: MA

address: 360 Longwood Ave, LC6102

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description:
Library name: RNAseq_Rh30_sgChr2.2_rep2
RNASeq_Rh30_sgCDK8_vs_sgChr2_raw_counts.txt

data_processing:
FastQC was used to evaluate read quality on raw RNA-seq reads. Reads were aligned to the human genome (hg38) using STAR (v2.7.2b) (Dobin et al., 2013). Transcript-level quantifications were calculated using RSEM (v1.3.1) (Li et al. 2011). Gene counts from STAR were then used to quantify differentially expressed genes between the experimental and control conditions using the R Bioconductor package DESeq2 (Anders, et al., 2010) using the approximate posterior estimation for GLM coefficients (apeglm) method for effect size. Normalized expression values for individual samples were obtained from RSEM log2 TPM values with the RSEM log2(TPM+1) values used for GSEA and producing RNA-seq heat map plots.
Assembly: hg38

growth_protocol: Rh30 is cultured in DMEN containing 10% FBS, 1% L-Glutamin, and 1% P.S.

extract_protocol:
Trizol
Novogene library prep pipeline

treatment_protocol: DMSO or BI1347 were added to cell after adhering.

value: Rhabdomyosarcoma

tag: genotype

value: PAX3::FOXO1 fusion


title: 27_IL23R_antiCD3_28_4hr

description: Library name: 27_IL23R_antiCD3_28_4hr_CTTGTA

molecule: polyA RNA


title: RNA serum, early gastric cancer, GC0001

description:
Library name: SV18664_0008
Column name in exceRpt_miRNA_ReadCounts:  SV18664_0008_S7_R1_001.fastq


title: RNAseq_Rh30_sgChr2.2_rep1

description:
Library name: RNAseq_Rh30_sgChr2.2_rep1
RNASeq_Rh30_sgCDK8_vs_sgChr2_raw_counts.txt


title: 26_IL12Rb2_IL12_4hr

description: Library name: 26_IL12Rb2_IL12_4hr_GCCAAT


title: RNA serum, intestinal metaplasia, GC0147

description:
Library name: SV18664_0006
Column name in exceRpt_miRNA_ReadCounts:  SV18664_0006_S6_R1_001.fastq


title: RNAseq_Rh30_BI1347_D7_rep3

description:
Library name: RNAseq_Rh30_BI1347_D7_rep3
RNAseq_Rh30_BI1347_vs_DMSO_raw_counts.txt


title: 25_IL12Rb2_IL12_20hr

description: Library name: 25_IL12Rb2_IL12_20hr_ACAGTG


title: RNA serum, intestinal metaplasia, GC0300

description:
Library name: SV18664_0005
Column name in exceRpt_miRNA_ReadCounts:  SV18664_0005_S5_R1_001.fastq


title: LDB1KO_ESC_3_RNA

value: mESC


title: RNAseq_Rh30_BI1347_D7_rep2

description:
Library name: RNAseq_Rh30_BI1347_D7_rep2
RNAseq_Rh30_BI1347_vs_DMSO_raw_counts.txt


title: 24_IL12Rb2_antiCD3_28_20hr

description: Library name: 24_IL12Rb2_antiCD3_28_20hr_CCGTCC


title: LDB1KO_ESC_1_RNA


title: RNA serum, intestinal metaplasia, GC0271

description:
Library name: SV18664_0004
Column name in exceRpt_miRNA_ReadCounts:  SV18664_0004_S4_R1_001.fastq


title: RNAseq_Rh30_BI1347_D7_rep1

description:
Library name: RNAseq_Rh30_BI1347_D7_rep1
RNAseq_Rh30_BI1347_vs_DMSO_raw_counts.txt


title: WT_ESC_3_RNA


title: 23_IL23R_IL23_antiCD3_28_20hr

description: Library name: 23_IL23R_IL23_antiCD3_28_20hr_CAGATC


title: RNA serum, control, GC0289

description:
Library name: SV18664_0003
Column name in exceRpt_miRNA_ReadCounts:  SV18664_0003_S3_R1_001.fastq


title: RNAseq_Rh30_Bi1347_D3_rep3

description:
Library name: RNAseq_Rh30_Bi1347_D3_rep3
RNAseq_Rh30_BI1347_vs_DMSO_raw_counts.txt


title: RNA serum, advanced gastric cancer, GC0308

description:
Library name: SV18664_0010
Column name in exceRpt_miRNA_ReadCounts:  SV18664_0010_S9_R1_001.fastq


title: 22_IL23R_IL23_antiCD3_28_4hr

description: Library name: 22_IL23R_IL23_antiCD3_28_4hr_TGACCA


title: WT_ESC_2_RNA


title: RNA serum, control, GC0351

description:
Library name: SV18664_0002
Column name in exceRpt_miRNA_ReadCounts:  SV18664_0002_S2_R1_001.fastq


title: RNAseq_Rh30_BI1347_D3_rep1

description:
Library name: RNAseq_Rh30_BI1347_D3_rep1
RNAseq_Rh30_BI1347_vs_DMSO_raw_counts.txt


title: WT_EB_2_RNA


title: 21_IL12Rb2_antiCD3_28_4hr

description: Library name: 21_IL12Rb2_antiCD3_28_4hr_CGATGT


title: WT_ESC_1_RNA


title: RNA serum, control, GC0069

description:
Library name: SV18664_0001
Column name in exceRpt_miRNA_ReadCounts: SV18664_0001_S1_R1_001.fastq


title: WT_EB_1_RNA


title: RNAseq_Rh30_BI1347_D1_rep3

description:
Library name: RNAseq_Rh30_BI1347_D1_rep3
RNAseq_Rh30_BI1347_vs_DMSO_raw_counts.txt


title: Tet1 knockout (KO) mice, m1A pull-down 3

city: Beijing

first: Liang

last: Xue

state: Beijing

address: Bldg.3, NO.9, YIKE Rd, Zhongguancun Life Science Park, Changping District, Beiji

country: China

institute: Chinese Institute for Brain Research, Beijing(CIBR)

description:
Tet1KO_IP3
Tet1KO_3_peaks.txt

data_processing:
rRNAs were excluded utilizing the mouse rRNA reference sequence (Mus_musculus.GRCm38.dna.primary_assembly.fa) obtained from NCBI.
Adapter sequences were removed using Cutadapt (v2.8) . Additionally, the first ten nucleotides from the 5’ ends were trimmed to eliminate potentially low-quality bases.
The reads were mapped and aligned using Hisat2 (v2.1.0), followed by peak calling with MACS2 (v2.2.6).
Subsequent data processing and visualization were performed using the R programming language (v4.2.3).
The Guitar package (v2.14.0) was utilized to create m1A distribution plots.
Assembly: GRCm38
Supplementary files format and content: Excel files include peak information generated by m1A-RIP seq of 3 biological replicates for Tet1 KO (Tet1 delta/delta) and Tet1 control (Tet1 fl/fl) mouse brain CPu regions.

source_name: caudate putamen (CPu)

growth_protocol: Adult male Tet1 fl/fl mice were used for virus injection experiments. Animals were housed in a 12-hour light/12-hour cycle, at constant temperature and under enrichment environmental conditions with ad libitum access to sterile food and water.

extract_protocol:
Total RNA was extracted from the CPu of adult mice with TRIzol reagent, and was then digested by DNase I and was further purifed by the Qiagen RNeasy kit. For RNA fragmentation, each sample was incubated for 4 minutes at 94ºC in fragmentation buffer. The fragmentation reaction was stopped with EDTA, followed by standard isopropanol precipitation. For m1A-RIP, ImmuProtein A and G Dynabeads were washed with IP buffer, preincubated with the a m1A antibody, and subsequently allowed to interact with 90% of the RNA in IP buffer for 3hrs at 4ºC. 10% of the sample was put aside to obtain an input control. After washwith IP buffer, methylated RNA was extracted from beads using TRIzol, followed by standard isopropanol precipitation.
Ribosomal RNAs (rRNAs) were removed using  Abclonal rRNA Depletion module, cDNA synthesis was performed using random hexamers, followed by end repair, dA-tailing, adapter ligation, amplification, and purification using Abclonal Fast RNA-seq Lib Prep Kit V2.

treatment_protocol: For CPu targeted TET1 depletions, AAV-Cre-EGFP virus and AAV-EGFP virus were stereotaxically injected into the CPu region of Tet1 fl/fl mice respectively. CPu regions were extracted 2 weeks after all viral injections for downstream processing.

value: caudate putamen (CPu)

value: Tet1 delta/delta

tag: treatment

value: m1A pull-down


title: 20_IL12Rb2_Unstim_0hr

description: Library name: 20_IL12Rb2_Unstim_0hr_GTGAAA


city: Jingzhou

first: Feng

last: Chen

address: No. 88 Jingmi Road, Jingzhou District

department: College of Animal Science and Technology

institute: Yangtze University

description:
Library name: Siniperca_chuatsi
snRNA-Seq of mandarin fish ovary at late stage IV

library_source: other

data_processing:
Reads were processed using the DNBc4tools v2.1.2 pipeline with default and recommended parameters.
Assembly: ASM2008510v1
Supplementary files format and content: Tab-separated values files and matrix files

molecule: other

organism: Siniperca chuatsi

source_name: ovary

extract_protocol:
Frozen Siniperca chuatsi ovary were cut into pieces <0.5 cm and homogenized using a glass Dounce tissue grinder (Sigma, cat. no. D8938). The tissue was homogenized 25 times with pestle A and 25 times with pestle B in 2 ml of ice-cold nuclei EZ lysis buffer. The sample was then incubated on ice for 5 min, with an additional 3 ml of cold EZ lysis buffer. Nuclei were centrifuged at 500g for 5 min at 4 C, washed with 5 ml ice-cold EZ lysis buffer and incubated on ice for 5 min. After centrifugation, the nucleus pellet was washed with 5 ml nuclei suspension buffer (NSB; consisting of 1 PBS, 0.01% BSA and 0.1% RNase inhibitor (Clontech, cat. no. 2313A)). Isolated nuclei were resuspended in 2 ml NSB, filtered through a 35 μm cell strainer (Corning-Falcon, cat. no. 352235) and counted.
The SC libraries were constructed according to the instructions of the DNA Nanoball (DNB) elab C4 scRNA Preparation Kit.  Briefly,  the cells were diluted to a concentration of 1,000 cells/mL and loaded into the cell reservoir of the microfluidic chip.  Barcoded beads  and droplet-generation oil were successively added to the beads and oil reservoirs.  Encapsulated droplets were generated and  collected using a DNBelab C4 system.  Beads that captured the mRNA were recovered for reverse transcription (RT).  Following  polymerase chain reaction (PCR) amplification by polymerase chain reaction, complementary DNA (cDNA) was purified and quantified using a Qubit dsDNA kit (Invitrogen, #Q32854).  Libraries of 30 -end transcripts were subsequently constructed through cDNA  fragmentation, size selection, end repair and A-tailing, adapter ligation, PCR for indexing libraries, and cyclisation of sequencing  libraries, according to the manufacturer’s instructions.  Sequencing libraries were purified and quantified using the Qubit ssDNA  kit (Thermo Fisher Scientific, #Q10212).The sequencing library was performed on DNBSEQ-T7 platform(PE150) using DNBSEQ-T7RS Reagent Kit (FCL PE150) version 3.0. The sequencing and bioinformatic analysis were performed on platform of Majorbio Co., Ltd (Shanghai, China).

value: ovary

tag: age

tag: Sex

value: female

value: Frozen

tag: collection date

tag: geo loc_name


title: RNAseq_Rh30_BI1347_D1_rep2

description:
Library name: RNAseq_Rh30_BI1347_D1_rep2
RNAseq_Rh30_BI1347_vs_DMSO_raw_counts.txt


title: 19_IL23R_IL23_4hr

description: Library name: 19_IL23R_IL23_4hr_AGTTCC


title: Tet1 knockout (KO) mice, m1A pull-down 2

description:
Tet1KO_IP2
Tet1KO_2_peaks.txt


title: RNAseq_Rh30_BI1347_D1_rep1

description:
Library name: RNAseq_Rh30_BI1347_D1_rep1
RNAseq_Rh30_BI1347_vs_DMSO_raw_counts.txt


title: Day_5_Kidney_tamoxifen_ILY_treated

city: New Orleans

first: Xuebin

last: Qin

state: LA

address: 1430 Tulane Avenue

department: Pathology

institute: Tulane University

description: Library name: Sample 5

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using Cell Ranger version 7.1.0 (10× Genomics) to perform alignment to the mouse reference genome, read counting, and the generation of cell-specific gene expression matrices.
Assembly: mm10
Supplementary files format and content: filtered feature-barcode matrices in HDF5 format

source_name: Kidney

extract_protocol:
Kidneys were harvested post-perfusion and processed for single-cell suspension preparation. Tissue dissociation was initiated by mechanical disruption of the kidney, followed by enzymatic digestion. The dissected kidney was incubated in 10 mL of Hank's Balanced Salt Solution (HBSS), containing 0.75 mg/mL collagenase IV (Worthington Biochemical) and 20 µg/mL DNase I (Sigma-Aldrich), for 40 minutes at 37°C. After digestion, the cell suspension was passed through a 40 µm cell strainer to remove debris and larger tissue fragments, and the resulting single-cell suspension was maintained on ice. The cell suspension was then washed twice with PBS by centrifugation at 500 x g for 10 minutes. To enrich hematopoietic cells, the cells were subjected to density gradient centrifugation using Percoll. The pellet obtained from the previous wash was resuspended in 10 mL of 30% Percoll solution and carefully layered over 3 mL of 70% Percoll solution. The gradient was centrifuged at 500 x g for 30 minutes without the application of a brake. Following centrifugation, the interphase layer between the 30% and 70% Percoll solutions, containing enriched single cells, was carefully collected. The collected cells were washed twice with 10 mL of PBS (500 x g, 10 minutes). The final cell pellet was resuspended in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) for downstream single-cell RNA sequencing (scRNA-seq) analysis. Cell number and viability were assessed using an automated cell counter, yielding a viability rate of approximately 84%, suitable for scRNA-seq.
scRNA-seq was performed using the 10× Genomics Chromium platform to analyze transcriptomic profiles of kidney cells. A target of 5000 viable cells per sample was set based on prior optimization using 10× Genomics Single Cell 3′ RNAseq technology (10x Genomics). Live cells were quantified and sorted before processing, ensuring the cell viability exceeded 80% for downstream analysis. Following cell capture, full-length barcoded cDNA libraries were generated from each sample according to the manufacturer's protocol. Briefly, individual cells were partitioned into droplets containing reagents for reverse transcription, generating unique cDNA barcodes for each cell. The cDNAs were then amplified via polymerase chain reaction (PCR) to obtain sufficient material for library preparation. The cDNA libraries were pooled and diluted to a final concentration of 1.8 pM for sequencing. The pooled libraries were sequenced using an Illumina NextSeq 2000 platform, with paired-end single index reads. Sequencing output was analyzed to ensure adequate coverage and depth for each sample.

value: Kidney

value: Tamoxifen(100 μg/g,i.p) for 3 consecutive days+ ILY(120 ng/g,i.v) single dose

value: Day 7


title: Tet1 knockout (KO) mice, m1A pull-down 1

description:
Tet1KO_IP1
Tet1KO_1_peaks.txt


title: 18_IL12Rb2_antiCD3_28_20hr

description: Library name: 18_IL12Rb2_antiCD3_28_20hr_CTTGTA


title: Day_3_Kidney_tamoxifen_ILY_treated

description: Library name: Sample 4

value: Day 3


title: RNAseq_Rh30_DMSO_D7_rep3

description:
Library name: RNAseq_Rh30_DMSO_D7_rep3
RNAseq_Rh30_BI1347_vs_DMSO_raw_counts.txt


title: 17_IL12Rb2_antiCD3_28_4hr

description: Library name: 17_IL12Rb2_antiCD3_28_4hr_GCCAAT


title: ESC_H3K27me3_KO_rep2

description: Cut and Tag

data_processing:
Paired-end fastq reads were preprocessed using cutadapt (v2.7)
Preprocessed reads were aligned to the mouse genome Gencode M18 using Bowtie2 (v2.3.5) with the settings reported for CUT&Tag (Kaya-Okur et al. 2019)..
Duplicated reads were cleaned using picard MarkDuplicates (v2.21.4) with “REMOVE_DUPLICATES=true”.
Peaks were called from bam files using MACS2 (v2.2.7.1) using default settings.
Browser track files were generated using the deepTools bamCoverage with “--minMappingQuality 20 --ignoreDuplicates --normalizeUsing CPM --extendReads 300”.
Assembly: mm10 (Gencode M18)
Supplementary files format and content: bigwig
Library strategy: Cut&Tag

extract_protocol:
Genomic DNA was extracted by Cut&tag-it assay kit(Activemotif, 53170)
CUT&Tag library preparation was performed with the CUT&Tag-IT™ Assay Kit (Active Motif, 53170) according to manufacturer’s protocol. H3K27ac(Active motif, 39085), H3K4me3 (Active motif, 39016) and H3K27me3(Active motif, 39055) were used for IP.


title: Tet1 knockout (KO) mice, input 3

description:
Tet1KO_Input3
Tet1KO_3_peaks.txt

value: Input control


title: ATACseq_Rh30-BI1347-4hr-rep2

description: Library name: ATACseq_Rh30-BI1347-4hr-rep2

data_processing:
Raw FASTQ data were trimmed by Trimmomatic-v0.39, and paired end reads were aligned to a concatenated human genome hg38 using Bowtie2 (v2.3.5) ((--dovetail --phred33 -I 0 -X 2000 -N 1 --very-sensitive). Peaks were called using Genrich (v. 0.6.1) (https://github.com/jsh58/Genrich) with the following options -j -y -r -e chrM -q 0.05 -a 20. Peaks were annotated to the nearest TSS using HOMER. Differential analysis was performed using DiffBind and DESeq2. Significantly changed peaks were defined by a 1.5-fold change threshold and FDR<0.05. Bigwig files were generated and normalized using the DESeq2 size factors using Deeptools. Heatmaps were created by Deeptools using the normalized bigwig files.
Assembly: hg38
Supplementary files format and content: bigwig files

extract_protocol:
ATAC-seq kit (cat# 53150) column extraction
ATAC-seq kit (cat# 53150) library prep


title: Day_1_Kidney_tamoxifen_ILY_treated

description: Library name: Sample 3

value: Day 1


title: RNAseq_Rh30_DMSO_D7_rep2

description:
Library name: RNAseq_Rh30_DMSO_D7_rep2
RNAseq_Rh30_BI1347_vs_DMSO_raw_counts.txt


title: 16_IL23R_antiCD3_28_20hr

description: Library name: 16_IL23R_antiCD3_28_20hr_ACAGTG

value: T cell


title: ESC_H3K27me3_WT_rep2

description: Cut and Tag


title: ESC_H3K27me3_WT_rep1

description: Cut and Tag


title: Tet1 knockout (KO) mice, input 2

description:
Tet1KO_Input2
Tet1KO_2_peaks.txt


title: RNAseq_Rh30_DMSO_D7_rep1

description:
Library name: RNAseq_Rh30_DMSO_D7_rep1
RNAseq_Rh30_BI1347_vs_DMSO_raw_counts.txt


title: 15_IL23R_Unstim_0hr

description: Library name: 15_IL23R_Unstim_0hr_GTCCGC


title: Day_0_Kidney_tamoxifen_treated_control

description: Library name: Sample 2

value: Tamoxifen(100 μg/g,i.p) for 3 consecutive days

value: Day 0


title: Tet1 knockout (KO) mice, input 1

description:
Tet1KO_Input1
Tet1KO_1_peaks.txt


title: RNAseq_Rh30_DMSO_D3_rep2

description:
Library name: RNAseq_Rh30_DMSO_D3_rep2
RNAseq_Rh30_BI1347_vs_DMSO_raw_counts.txt

value: Rhabdomyosarcoma

value: PAX3::FOXO1 fusion


title: Normal_Kidney_untreated_control

description: Library name: Sample 1

value: untreated


title: 14_IL23R_antiCD3_28_4hr

description: Library name: 14_IL23R_antiCD3_28_4hr_CCGTCC


title: Tet1 floxed mice, m1A pull-down 3

description:
Tet1Con_IP3
Tet1Con_3_peaks.txt

value: caudate putamen (CPu)

value: Tet1 fl/fl


title: PROseq_Rh30-BI1347-72hr-rep1

description: Library name: PROseq_Rh30-BI1347-72hr-rep1

data_processing:
The sequences were aligned to hg38 using bowtie2 before using the Nascent RNA Sequencing Analysis (NRSA) pipeline31 to determine the gene body and eRNA changes.
Assembly: hg38
Supplementary files format and content: bedGraph files
Library strategy: PRO-Seq

extract_protocol:
ProNex Chemistry beads extraction
PROseq run-on library prep


title: Hindpaw DBA/1_SpAD ossification, biological rep5

type: RNA

city: Chihuahua

first: Susana

middle: Aideé

last: González-Chávez

state: Chihuahua

address: Circuito Universitario Campus II

department: Facultad de Medicina

country: Mexico

institute: Universidad Autónoma de Chihuahua

description: Gene expression data from hindpaw tissue of DBA/1 mice with spondyloarthritis, ossification score 4-4.5 (moderate-to-severe)

hyb_protocol: After fragmentation, 5500 ng of labeled ss-cDNA was hybridized to GeneChip Clariomª D Mouse Arrays for 16Ð18 hours at 45_¡C. Arrays were washed and stained using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Raw data were analyzed using the Transcriptome Analysis Console (TAC, Affymetrix) with default parameters. Global scaling was applied as the normalization method.

label: biotin

source_name: DBA/1 mice with Spontaneous arthritis, confined at 11 week of age, euthanasia at 21 weeks of age, histological ossification score 4-4.5 (moderate-to-severe)

label_protocol: Biotinylated cRNA was prepared from 200 ng total RNA using the Affymetrix GeneChip WT PLUS Reagent Kit, following the manufacturerÕs protocol (User Guide: GeneChip Whole Transcript [WT] Expression Arrays).

extract_protocol: Total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen) according to the manufacturerÕs protocol, optimized for lipid-rich and pulverized frozen tissues.

treatment_protocol: Dissected hindpaw tissues (tarsus to phalanges) were aseptically processed using sterile surgical instruments. Skin and nails were removed. Tissues were immediately snap-frozen in liquid nitrogen and manually pulverized using a stainless steel Biopulverizer (BioSpec Products) prior to RNA extraction.

tag: strain

tag: gender

value: male

tag: age of confinment

value: 11 weeks

tag: age of euthanasia

value: 21 weeks

tag: condition

value: Spondyloarthritis (diseased)

value: Distal hindpaws (tarsus to phalanges), including joints, bone, cartilage, muscle; skin and nails removed


title: input_ChIPmentation

description: input for LDB1 ChIPmentation

data_processing:
Raw fastq reads were preprocessed using cutadapt (v2.7)
Preprocessed reads were aligned to the mouse genome Gencode M18 using Bowtie2 (v2.3.5) with the “--no-unal” option.
Duplicated reads were cleaned using picard MarkDuplicates (v2.21.4) with “REMOVE_DUPLICATES=true”.
Peaks were called from bam files using MACS2 (v2.2.7.1) using default settings.
Browser track files were generated using the deepTools bamCoverage with “--minMappingQuality 20 --ignoreDuplicates --normalizeUsing CPM --extendReads 300”.
Assembly: mm10 (Gencode M18)
Supplementary files format and content: bigwig
Library strategy: ChIPmentation

extract_protocol:
Genomic DNA was extracted by QIAquick PCR purification kit (Quiagen 28104).
ChIPmentation libraries were prepaired as described (Nat Methods. 2015 Oct;12(10):963-965). LDB1 Ab(Abcam: ab 96799) was used for IP.

value: mESC


title: RNAseq_Rh30_DMSO_D3_rep1

description:
Library name: RNAseq_Rh30_DMSO_D3_rep1
RNAseq_Rh30_BI1347_vs_DMSO_raw_counts.txt


title: ko-Trdn_1_input

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

description: Library name: Sample 18

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm39 (Ensembl release 109) with STAR 2.7.11b (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.1.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 3.0.0a7 with FDR < 0.001 and enrichment versus input > 2x (Zhang et al., Model-based Analysis of ChIP-Seq).
Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
Remaining peaks were unified to represent a common set of regions for all samples.
Counts were produced with featureCounts (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Peaks were annotated with the promoter (TSS +- 5000 nt) of the nearest gene based on Ensembl release 109.
Assembly: mm39
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.

source_name: heart

extract_protocol:
Precipitated DNA samples were purified and quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).
Max. 10ng of DNA per sample was used as input for TruSeq ChIP Library Preparation Kit (Illumina) with following modifications. Instead of gel-based size selection before final PCR step, libraries were size selected by SPRI-bead based approach after final PCR with 18 cycles. In detail, samples were 1st cleaned up by 1x bead:DNA ratio to eliminate residuals from PCR reaction, followed by 2-sided-bead cleanup step with initially 0.6x bead:DNA ratio to exclude larger fragments. Supernatant was transferred to new tube and incubated with additional beads in 0.2x bead:DNA ratio for eliminating smaller fragments, like adapter and primer dimers. Bound DNA samples were washed with 80% ethanol, dried and resupended in TE buffer. Library integrity was verified with LabChip Gx Touch 24 (Perkin Elmer). Sequencing was performed on NextSeq2000 platform (Illumina) using P3 flowcell with 72bp single-end setup.

value: heart

value: trdn-as KO

tag: chip antibody


title: 13_IL12Rb2_IL12_antiCD3_28_4hr

description: Library name: 13_IL12Rb2_IL12_antiCD3_28_4hr_CAGATC


title: Tet1 floxed mice, m1A pull-down 2

description:
Tet1Con_IP2
Tet1Con_2_peaks.txt

value: m1A pull-down


title: Hindpaw DBA/1_SpAD ossification, biological rep3

description: Gene expression data from hindpaw tissue of DBA/1 mice with spondyloarthritis, ossification score 2 (moderate)

source_name: DBA/1 mice with Spontaneous arthritis, confined at 11 week of age, euthanasia at 21 weeks of age, histological ossification score 2 (moderate)


title: RNAseq_Rh30_DMSO_D1_rep3

description:
Library name: RNAseq_Rh30_DMSO_D1_rep3
RNAseq_Rh30_BI1347_vs_DMSO_raw_counts.txt


title: ko-Mettl3_1_input

description: Library name: Sample 17


title: LDB1KO_DIF_3_RNA

value: Differntiated cells


title: 12_IL23R_IL23_antiCD3_28_20hr

description: Library name: 12_IL23R_IL23_antiCD3_28_20hr_TGACCA

value: T cell


title: LDB1KO_DIF_2_RNA


title: WT_1_input

description: Library name: Sample 16

value: WT


title: RNAseq_Rh30_DMSO_D1_rep2

description:
Library name: RNAseq_Rh30_DMSO_D1_rep2
RNAseq_Rh30_BI1347_vs_DMSO_raw_counts.txt

value: Rhabdomyosarcoma


title: Tet1 floxed mice, m1A pull-down 1

description:
Tet1Con_IP1
Tet1Con_1_peaks.txt


title: 11_IL12Rb2_IL12_20hr

description: Library name: 11_IL12Rb2_IL12_20hr_CGATGT


title: Tet1 floxed mice, input 3

description:
Tet1Con_Input3
Tet1Con_3_peaks.txt

value: Input control


title: LDB1KO_DIF_1_RNA


title: IgG-ko-Trdn_1

description: Library name: Sample 15

value: part of Diagenode Kit #C01010055


title: Tet1 floxed mice, input 2

description:
Tet1Con_Input2
Tet1Con_2_peaks.txt

value: caudate putamen (CPu)


title: 10_IL23R_IL23_antiCD3_28_4hr

description: Library name: 10_IL23R_IL23_antiCD3_28_4hr_GTGAAA


title: RNAseq_Rh30_DMSO_D1_rep1

description:
Library name: RNAseq_Rh30_DMSO_D1_rep1
RNAseq_Rh30_BI1347_vs_DMSO_raw_counts.txt

value: PAX3::FOXO1 fusion


title: U87 cells, compound 5, 3

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

description: Library name: J3

data_processing:
Adapters were trimmed during demultiplexing by the core facility and trimmed reads were aligned to the genome using STAR version 2.7.10a for alignment to the mouse genome (GRCh38) and to generate count tables using default settings.
Differential expression analysis of count tables was performed using the default settings of DESeq2 version 1.30.1 (Benjamini-Hochberg FDR correction).
Assembly: Gencode GRCh38
Supplementary files format and content: Microsoft Excel Worksheet (.xlsx). Contains normalized counts generated by DESeq2.

growth_protocol: Human U87MG glioblastoma cells (U87 cells) were purchased from ATCC and cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Coring, USA) supplemented with 10% fetal bovine serum (FBS) and 1% Antibiotic/Antimycotic solution (Gibco, USA). Cells were maintained at 37 degrees C in a humidified, 5% CO2 atmosphere with media changes every 48 h.

extract_protocol:
Total RNA was extracted using DNA/RNA/Protein extraction kit (IBI Scientific, Dubuque Iowa) and Dnase-treated using Dnase I (RNase-free, New England Biolabs, Ipswich, MA) and further purified using RNA clean and concentrator kit (Zymo Research, Irvine, CA). Three independent biological replicates were prepared for each treatment group.
A next generation sequencing library was prepared for each sample using NEBNext Poly(A) mRNA Magnet Isolation Module followed by NEBNext Ultra II RNA Library Kit for Illumina. Libraries were barcoded for multiplexing with NEBNext Multiplex Oligos for Illumina. Each multiplexed library was sequenced as a paired-end, 50 base pair sequencing run on an Illumina NovaSeq 6000, located in the Translational Science Laboratory at FSU College of Medicine

treatment_protocol: Human glioblastoma U87 cells at 60–70% density were dosed with 1, 4, and 5 at 30, 10, and 5 micromolar, respectively. After 72 h, cells were harvested, washed with cold PBS.

value: Human Glioblastoma

value: Compound 5


title: 9_IL23R_IL23_20hr

description: Library name: 9_IL23R_IL23_20hr_AGTTCC


title: IgG-ko-Mettl3_1

description: Library name: Sample 14


title: Tet1 floxed mice, input 1

description:
Tet1Con_Input1
Tet1Con_1_peaks.txt

value: Tet1 fl/fl


title: IgG-WT_1

description: Library name: Sample 13


title: 8_IL12Rb2_IL12_antiCD3_28_20hr

description: Library name: 8_IL12Rb2_IL12_antiCD3_28_20hr_CTTGTA


title: U87 cells, compound 5, 2

description: Library name: J2


title: RRBS of CMs, DNMT3A OE, replicate 5

first: Dogacan

last: Yucel

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

description:
Library name: DNMT3A5
RRBS of cardiomyocyte nuclei from mouse heart, DNMT3A overexpression, replicate 5

data_processing:
FASTQ files were mapped using mm10 assembly.
Bam files were processed using bismark to identify differentially methylated regions between samples.
Assembly: mm10
Supplementary files format and content: Supplementary files format and content: processed data includes bismark coverage files.

source_name: Heart

growth_protocol: Mice were maintained on a standard chow diet in a pathogen-free facility under a 12-hour light/dark cycle with ad libitum access to food and water.

extract_protocol:
Cardiomyocyte nuclei were isolated and purified using MACS.
250 ng of DNA was used to generate libraries according to Zymo-seq RRBS Library Kit.

value: Heart

value: Cardiomyocyte

value: DNMT3A AAV

tag: batch


title: 7_IL12Rb2_IL12_4hr

description: Library name: 7_IL12Rb2_IL12_4hr_GCCAAT

tag: time


title: Polr2a-ko-Trdn_2

description: Library name: Sample 12

value: heart

value: Diagenode #C15200253


title: RRBS of CMs, DNMT3A OE, replicate 4

description:
Library name: DNMT3A4
RRBS of cardiomyocyte nuclei from mouse heart, DNMT3A overexpression, replicate 4


title: Polr2a-ko-Trdn_1

description: Library name: Sample 11

value: trdn-as KO


title: U87 cells, compound 4, 3

description: Library name: T3

tag: cell line

value: Compound 4


title: U87 cells, compound 5, 1

description: Library name: J1

tag: cell type


title: Polr2a-ko-Mettl3_2

description: Library name: Sample 10

tag: tissue


title: RRBS of CMs, DNMT3A OE, replicate 3

description:
Library name: DNMT3A3
RRBS of cardiomyocyte nuclei from mouse heart, DNMT3A overexpression, replicate 3

tag: genotype


title: 6_IL23R_Unstim_0hr

description: Library name: 6_IL23R_Unstim_0hr_ACAGTG

value: T cell


title: U87 cells, compound 4, 2

description: Library name: T2

tag: treatment


title: 5_IL23R_IL23_4hr

description: Library name: 5_IL23R_IL23_4hr_GTCCGC


title: RRBS of CMs, DNMT3A OE, replicate 2

description:
Library name: DNMT3A2
RRBS of cardiomyocyte nuclei from mouse heart, DNMT3A overexpression, replicate 2

value: WT


title: U87 cells, compound 4, 1

description: Library name: T1


title: Polr2a-WT_2

description: Library name: Sample 8


title: 4_IL12Rb2_IL12_antiCD3_28_4hr

description: Library name: 4_IL12Rb2_IL12_antiCD3_28_4hr_CCGTCC


title: U87 cells, compound 1, 3

description: Library name: A3

value: Compund 1


title: RRBS of CMs, DNMT3A OE, replicate 1

description:
Library name: DNMT3A1
RRBS of cardiomyocyte nuclei from mouse heart, DNMT3A overexpression, replicate 1


title: 3_IL12Rb2_Unstim_0hr

description: Library name: 3_IL12Rb2_Unstim_0hr_CAGATC


title: RRBS of CMs, GFP control, replicate 5

description:
Library name: GFP5
RRBS of cardiomyocyte nuclei from mouse heart, control (GFP), replicate 5

value: GFP AAV


title: Polr2a-WT_1

description: Library name: Sample 7


title: U87 cells, compound 1, 2

description: Library name: A2


title: 2_IL23R_antiCD3_28_20hr

description: Library name: 2_IL23R_antiCD3_28_20hr_TGACCA


title: Ctcf-WT_2

description: Library name: Sample 6

value: part of Diagenode Kit #C01010055


title: 1_IL12Rb2_IL12_antiCD3_28_20hr

description: Library name: 1_IL12Rb2_IL12_antiCD3_28_20hr_CGATGT


title: RRBS of CMs, GFP control, replicate 3

description:
Library name: GFP3
RRBS of cardiomyocyte nuclei from mouse heart, control (GFP), replicate 3


title: Ctcf-WT_1

description: Library name: Sample 5


title: U87 cells, vehicle, 3

description: Library name: V3

value: Vehicle


title: Serum CAF+Serum DEX_3

city: hirakata

first: Yuko

last: Emoto

country: Japan

institute: Kansai Medical University

description: Library name: Sample12

data_processing:
The libraries were sequenced on a NextSeq 2000 sequencer (Illumina, Inc., California, USA) to generate 75-nt single reads. Duplicate reads were removed from the raw reads using Seqkit (ver. 2.0.0), and adapter sequence was trimmed with Cutadapt (ver. 3.7). The trimmed reads were mapped to rat genome assembly (rn6) using STAR (ver. 2.7.10a) with the following parameters: --alignEndsType EndToEnd -- outFilterMismatchNmax 1 --outFilterMultimapScoreRange 0 --outReadsUnmapped None --outSAMtype BAM Unsorted --outFilterMultimapNmax 10 --outSAMunmapped Within --outFilterScoreMinOverLread 0 -- outFilterMatchNminOverLread 0 --outFilterMatchNmin 16 --alignSJDBoverhangMin 1000 --alignIntronMax 1. Reads mapped to miRNA genes were quantified using featureCounts of the Subread package (ver. 2.0.1) with the following parameters: -s 1 -O -M -p -C -B -T. Differential gene expression analysis was performed using DESeq2(ver. 1.20.0).
Assembly: Rnor_6
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

organism: Rattus norvegicus

source_name: Serum

growth_protocol: Six-week-old male Sprague-Dawley rats (Jcl:SD) were purchased from CLEA Japan, Inc. (Tokyo, Japan). They were housed in plastic cages with paper-chip bedding in an air-conditioned room at 22 ± 2°C and 60 ± 10% relative humidity under a 12-h light/dark cycle. The animals had free access to food and water (CLEA Rodent Diet CE-2 for Mice, Rats, and Hamsters; CLEA Japan, Inc.).

extract_protocol:
The serum were transferred to -80 °C until use. Total RNA, including the small RNA fraction, was isolated from 200 uL  using the miRNeasy Micro Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s instructions.
The miRNA-seq library was prepared using the QIAseq miRNA Library Kit (Qiagen), following the manufacturer’s instructions. In brief, a pre-adenylated DNA adapter was ligated to the 3' ends of all miRNAs, followed by ligation of an RNA adapter to the 5' ends of mature miRNAs. Reverse-transcription (RT) was then performed using an RT primer containing Unique Molecular Indices (UMIs). Finally, the library was amplified with sample-specific index primers.

treatment_protocol: fter the acclimatization period, the 7-week-old rats were divided into four groups: control, caffeine, dextromethorphan, and caffeine plus dextromethorphan (n = 5 per group). The rats were administered a single oral dose of the drug, as described below. The caffeine group (CAF) received 180 mg/kg caffeine, the dextromethorphan group (DEX) received 200 mg/kg dextromethorphan hydrobromide monohydrate, and the combination group (CAF + DEX) received 180 mg/kg caffeine and 200 mg/kg dextromethorphan hydrobromide monohydrate. All drugs were dissolved in sterile distilled water. Age-matched control groups (control) were treated with vehicle (sterile distilled water) only.

value: Serum

value: Caffeine and Dextromethorphan administration


title: Ctcf-ko-Trdn_2

description: Library name: Sample 4


title: Serum CAF+Serum DEX_2

description: Library name: Sample11


title: RRBS of CMs, GFP control, replicate 1

description:
Library name: GFP1
RRBS of cardiomyocyte nuclei from mouse heart, control (GFP), replicate 1


title: U87 cells, vehicle, 1

description: Library name: V1

value: Human Glioblastoma


title: Ctcf-ko-Trdn_1

description: Library name: Sample 3


title: Serum CAF+Serum DEX_1

description: Library name: Sample10


title: DMPA_10 meningioma, methylation EPIC v2.0

type: genomic

city: Pittsburgh

first: Sakibul

last: Huq

state: PA

address: 200 Lothrop St, Suite B-400

department: Neurological Surgery

institute: University of Pittsburgh Medical Center

hyb_protocol: Bisulfite-converted DNA hybridized to the Infinium MethylationEPIC v2.0 BeadChip per Illumina protocol.

scan_protocol: Scanning/processing on the Illumina NextSeq 550; QC reviewed in GenomeStudio.

data_processing: Raw IDATs read in R with minfi; per-sample noob normalization. Deposited processed file = DMPA-only noob-normalized beta matrix. (Cross-cohort ComBat harmonization with Baylor/Heidelberg was a downstream analysis step, not part of this series' processing.) Manifest build hg38.

label: Cy3 and Cy5

source_name: meningioma

label_protocol: Standard Illumina Infinium protocol.

extract_protocol: Genomic DNA isolated from microdissected FFPE tumor (50-70% neoplastic cellularity).

value: meningioma

value: female

tag: who grade

tag: histologic subtype

value: Secretory

tag: mutation status (ngs panel)

tag: traf7 group

tag: baylor meng subgroup

value: MenG-A

tag: heidelberg methylation class

tag: ucsf methylation group

value: Merlin-intact


title: NL106

city: Guangzhou

first: Ren

last: Mao

address: 58 Zhongshan Road 2nd, Guangzhou

institute: The First Affiliated Hospital, Sun Yat-Sen University

description: 10× Genomics

data_processing:
Human mesenteric tissue single-nucleus RNA-seq data were processed using Cell Ranger software (v3.1.0; 10x Genomics). Raw sequencing reads were converted to FASTQ files, aligned to the human reference genome, and quantified to generate gene-barcode expression matrices for each sample. Low-quality barcodes and UMIs were filtered out. Reads uniquely mapped to the transcriptome and intersecting exonic regions were counted. UMI sequences were corrected for sequencing errors, and valid cell/nucleus barcodes were identified for downstream matrix generation. Cell-by-gene count matrices were generated by UMI counting and cell barcode calling. The filtered feature-barcode matrices for each sample, including barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz, are provided as processed data.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Normal mesenteric adipose tissue in Non-IBD control

extract_protocol:
The samples were chopped on ice into 1-2 mm³ pieces, transferred to cryovials, snap-frozen in liquid nitrogen for 5 minutes, and then stored in an ultra-low temperature freezer and liquid nitrogen.. Then transfer the tissue from the cryovial to a Dounce homogenizer and add 500 μl of pre-chilled lysis buffer to thaw. Use a small and a tight pestle to press the tissue 15-20 times and 5-10 times, respectively, to create a homogenate. Add 700 μl of nuclear wash buffer, mix, and filter through a 70 μm cell strainer. Add 1 ml of 50% iodixanol to the filtrate, mix gently, and layer onto a gradient solution of 30% and 33% iodixanol. Centrifuge at 10,000×g for 20 minutes at 4°C. Extract the white nuclear layer at the interface, add nuclear wash buffer, mix, and centrifuge at 500×g for 8 minutes at 4°C. Transfer the supernatant, resuspend the nuclei, and repeat the wash. Filter through a 40 μm filter, centrifuge, resuspend the nuclei, and adjust the concentration to 700-1200 nuclei/μl using a microscope.
Cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Libraries were generated and equenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1.


title: Serum DEX_3

description: Library name: Sample9

value: Dextromethorpan administration


title: Ctcf-ko-Mettl3_2

description: Library name: Sample 2

value: heart


title: DMPA_09 meningioma, methylation EPIC v2.0

tag: gender

value: Metaplastic


title: Serum DEX_2

description: Library name: Sample8


title: Scramble-LR-4

city: Winnipeg

first: Athanasios

last: Zovoilis

state: MB

address: 745 Bannatyne Ave

department: Biochemistry and Medical Genetics

country: Canada

institute: University of Manitoba

description:
Library name: Sample 8
Illumina_RNA-seq

data_processing:
FASTQ files were aligned against Ensembl release 102 Mus musculus genome GRCm38 using hisat2 v2.2.0 with the --dta option
For calculating gene/transcript abundances Stringtie v2.2.1 was used with -G -A -B -e -x parameters. For gene/transcript annotation we used the ensemble release 102 version of the Mus Musculus genome in conjunction with transcriptome gtf’s of the same release.
For calculating editrate tables, samples are aligned against the sequences of unique B2 with bwa aln v0.7.19 using options -n 10. The sense-aligning fraction of the bam files was extracted using samtools v1.21 with options -F 16. The sense aligning component was run with reditools v1.2.1 REDItoolDenovo script with options -c 1 -q 1 -m 1 -O 0 -V 1 -n 0. Edit rate was computed using custom method as detailed in the assocaited with this GSE series published manuscript.
Nanopore samples were concatonated group-wise and aligned against Ensembl release 102 GRCm38 mouse genome using Minimap2 v2.24 with the options -ax sr -uf --secondary=yes. Nanopore samples were additionally aligned against the sequences of unique B2 elements (>=125 bp in length) using Minimap2 v2.24 with the same options. The first alignment (on genome) was used with nanopolish v0.14.0 to produce eventalign files, which were then intersected with the coordinates of known B2 mm1a using bedtools v2.31.1. The second alignment (on unique B2ome) was used with nanopolish v0.14.0 and xpore v2.0 to produce the xpore tables.
Assembly: GRCm38
Supplementary files format and content: Normalized abundance measurements generated from stringtie in a tab delimited format depicting FPKM and TMP for  genes/transcripts in the annotation file.
Supplementary files format and content: Editrate tables generated from reditools in a tab delimited format with additional columns added as described in publication. Nanopolish and xpore tables are generated from their respective programs and stored in a tab delimited format. Nanopolish tables contain additional columns representing the B2 loci which they intersected with.

growth_protocol: The HT-22 hippocampal cell line was grown as a monolayer up to 70% confluency in DMEM, 1%pen/strep, 10%Calf Serum (heat inactivated)

extract_protocol:
Trizol RNA extraction: 1mL trizol added to pelleted cells, dissolved 5min. 200uL chloroform added to trizol treated cells, incubate 2min. Centrifuged at 12 000xg 4C. Aqueous layer treated with 500uL isopropanol, incubate -20C 1hour, centrifuged at 12 000xg 10min 4C, pellet washed with 75% ethanol and centrifuged at 7 500xg 5min 4C. Pellet dried 1min, resuspended in 30uL pure H2O. For the Nanopore direct RNA-seq RNA experiment of the HT-22 anti Adar treatment, samples were pooled from n=4 biological replicates prior to library preparation.
Illumina_RNA-seq: Libraries for directional RNA-seq were prepared according to manufacturer's instructions with a size enrichment for longer RNAs >100nt by MiRvana size selection kit preceeding the library construction using NEBNext rRNA depletion kit and NEBNext Ultra RNA Library Prep Kit for Illumina (E7530). Nanopore_Direct_RNA-seq: The libraries were prepared using the vendor recommended protocol for the SQK_RNA002 direct RNA sequencing kit from 1ug of starting material. Briefly, 9.5uL of RNA was mixed with 1uL RTA adaptor (Nanopore), 1.5uL T4 DNA ligase (NEB, M0202M) and 3uL NEBNext quick ligation buffer (NEB, B6058S), and incubated for 15min at room temperature. The first-strand synthesis reaction was constructed from the ligation product by adding 9uL H2O, 2uL dNTP mix (NEB, N0447S), 8uL FS buffer (Invitrogen, 18080093), 4uL 0.1M DTT (Invitrogen, 18080093) and 2uL Superscript III reverse transcriptase (Invitrogen, 18080093) and incubated at 50C for 50min, 70C for 10min, then placed immediately on ice. The sample was then subjected to a 1.8X bead clean up using the vendor recommended protocol with Mag-Bind TotalPure NGS beads (Omega Bio-Tek, M1378), eluting in 23uL H2O. 6uL of the RMX adaptor (Nanopore), 8uL of the NEBNext quick ligation buffer and 3uL of T4 DNA ligase were added to the eluted RNA:DNA hybrid and incubated for another 15min at room temperature, concluded by a 1X bead cleaning reaction. The prepared libraries were loaded and sequenced on a R9.4.1 PromethION flow cell using a PromethION 24 Beta instrument as per manufacturer suggestions.

treatment_protocol: Anti-Adar 1 and 2 siRNA treatment: A pool of siRNAs  targeting Adar1 and Adar 2 (Anti-ADAR) or a control scramble siRNA with no known targets (scramble) were transfected to  500 000 cells for 36h. siRNA was transfected using the Qiagen hiperfect transfecting reagent, according to manufacturers instructions. siRNA incubation occurred at a final concentration of 10nM. siRNA and hiperfect were incubated for 20min before being added to the culture media dropwise. Cells grown in 6 well plates (1mL growth media).

value: Hippocampal cell line

value: Scramble siRNA


title: DMPA_08 meningioma, methylation EPIC v2.0

value: Transitional

value: PIK3CA; FGFR1


title: Mut_4 (boe57 dataset)

description: Library name: Sample 8

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm39 (Ensembl release 109) with STAR 2.7.11a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.1.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: mm39
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.

extract_protocol:
For RNA-seq, RNA was isolated by miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and library preparation integrity were verified with LabChip Gx Touch (Perkin Elmer).
RNA amounts were normalized and 1¬µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit HI Mammalian (Takara Bio). Sequencing was performed on the NextSeq2000 platform (Illumina) using P4 flowcell with 72bp single-end setup.


title: Serum DEX_1

description: Library name: Sample7


title: DMPA_07 meningioma, methylation EPIC v2.0

value: Meningothelial


title: Mut_3 (boe57 dataset)

description: Library name: Sample 7


title: Scramble-LR-2

description:
Library name: Sample 6
Illumina_RNA-seq


title: Serum CAF_3

description: Library name: Sample6

value: Caffeine administration


title: DMPA_06 meningioma, methylation EPIC v2.0

value: Meningothelial with myxoid features


title: Mut_2 (boe57 dataset)

description: Library name: Sample 6


title: Serum CAF_2

description: Library name: Sample5

value: Serum


title: Scramble-LR-1

description:
Library name: Sample 5
Illumina_RNA-seq


title: Mut_1 (boe57 dataset)

description: Library name: Sample 5


title: AntiAdar-LR-4

description:
Library name: Sample 4
Illumina_RNA-seq

value: Adar1&Adar2 siRNA knockdown


title: Serum CAF_1

description: Library name: Sample4


title: DMPA_04 meningioma, methylation EPIC v2.0

value: meningioma

value: Transitional with myxoid features


title: WT_4 (boe57 dataset)

description: Library name: Sample 4


title: AntiAdar-LR-3

description:
Library name: Sample 3
Illumina_RNA-seq


title: DMPA_03 meningioma, methylation EPIC v2.0

value: female


title: WT_3 (boe57 dataset)

description: Library name: Sample 3


title: Serum Control_2

description: Library name: Sample2


title: DMPA_02 meningioma, methylation EPIC v2.0

value: MenG-A

value: unclassified


title: WT_2 (boe57 dataset)

description: Library name: Sample 2


title: Serum Control_1

description: Library name: Sample1


title: AntiAdar-LR-2

description:
Library name: Sample 2
Illumina_RNA-seq


title: DMPA_01 meningioma, methylation EPIC v2.0

value: Merlin-intact


title: WT_1 (boe57 dataset)

description: Library name: Sample 1

value: heart


title: UM_Chor1_IDH1Inhibitor_2

status: Public on Jun 11 2026

city: Ann Arbor

first: Sriram

last: Venneti

state: Michigan

address: 1500 E Medical Center Dr

institute: University of Michigan

description: Library name: Sample 12

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files
Assembly: Reads were mapped to the reference genome GRCh38 (ENSEMBL) using Kallisto (v0.46.0). Alignment options followed ENCODE standards for RNA-seq
Supplementary files format and content: .xls file for the counts for each of the samples

growth_protocol: CH22, UM-Chor1 and JHC7 were cultured in a 4:1 preparation of IMDM:RPMI with 10% FBS and 1% of L-glutamine with 1% antibiotic- antimycotic solution, 0.2% prophylactic Plasmocin®.

extract_protocol:
RNA was isolated using Trizol  (Qiagen 79306)
Libraries were generated using KAPA RNA HyperPrep Kit with RiboErase (HMR).

treatment_protocol: 3uM IDH1 inhibitor 2

value: Chordoma Cell line

value: WT

value: IDH1 inhibitor


title: UM_Chor1_IDH1Inhibitor_1

description: Library name: Sample 11


title: UM_Chor1_DMSO_1

description: Library name: Sample 9

value: DMSO


title: JHC7_IDH1Inhibitor_1

description: Library name: Sample 7


title: JHC7_DMSO_2

description: Library name: Sample 6


title: JHC7_IDH1Inhibitor_2

description: Library name: Sample 8


title: CH22_IDH1Inhibitor_1

description: Library name: Sample 3


title: CH22_DMSO_2

description: Library name: Sample 2


title: CH22_DMSO_1

description: Library name: Sample 1


title: smrd1Null_3

city: Seattle

first: Vaishnavi

last: Jadhav

state: WA

address: VA Puget Sound 1660 South Columbian Way

institute: University of Washington

description: Library name: N3

data_processing:
Feature counts, RNASTAR, DESeq2
Assembly: Caenorhabditis_elegans.WBcel235.112.gtf
Supplementary files format and content: RNASTAR BAM files, feature counts .txt file, Differential gene expression .csv file.

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: All strains were maintained at 20 °C on NGM plates seeded with OP50 Escherichia coli

extract_protocol:
RNA was extracted from L4 snap-frozen C. elegans pellets using TRIzol Reagent (Thermo Fisher Scientific, Inc.) per manufacturer’s protocol. RNA was resuspended in 50 μL sterile water and concentration was assessed using NanoPhotometer® NP80 spectrophotometer (Implen GmbH). DNA contamination was then removed from the RNA sample using the DNA-free™ Kit (Thermo Fisher).
Novogene PolyA enrichment. Quantified libraries are pooled and sequenced on Illumina NovaSeqXPlus-Directional

value: whole body


title: smrd1Null_4

description: Library name: N4


title: smrd1Null_2

description: Library name: N2


title: smrd1Null_1

description: Library name: N1


title: Control_4

description: Library name: C4


title: Control_3

description: Library name: C3


title: Control_1

description: Library name: C1


title: SpheroidsDiff_3

city: Urbana

first: Hao-Chun

last: Fan

address: 1207 West Gregory Drive

department: College of Agricultural, Consumer and Environmental Sciences

institute: University of Illinois Urbana-Champaign

description: Library name: SpheroidsDiff_3

data_processing:
Reads were filtered and trimmed using fastp v0.24.0, and aligned to the Large_White_v1_114 using STAR v2.7.11, followed by coordinate-sorting using samtools v1.22.1.
PCR and optical duplicates were removed using UMIcollapse v1.1.0. Alignment and read-distribution metrics were assessed using RSeQC v5.0.4 and Qualimap v2.3. Gene-level counts were generated using featureCounts from subread v2.1.1. Counts were assigned to exons and 3′ UTRs and grouped by gene_id. Gene counts were annotated using metadata from the reference GTF file
Assembly: Large_White_v1_114
Supplementary files format and content: Tab-delimited text file containing raw counts and counts per million (CPM) for each sample.

organism: Sus scrofa

source_name: Oviduct

extract_protocol:
Cells were collected and lysed/preserved in 1X Zymo DNA/RNA Shield according to the Plasmidsaurus RNA-Seq sample preparation instructions.
Poly(A)+ mRNA was captured using oligo-dT priming, followed by reverse transcription, second-strand cDNA synthesis, tagmentation, library indexing with unique dual indices, and PCR amplification to add Illumina P5/P7 adapter sequences.

value: Oviduct

value: Epithelial cells

value: Spheroids formed in Incubation Medium


title: SpheroidsDiff_4

description: Library name: SpheroidsDiff_4


title: SpheroidsDiff_2

description: Library name: SpheroidsDiff_2


title: SpheroidsDiff_1

description: Library name: SpheroidsDiff_1


title: SpheroidsFBS_4

description: Library name: SpheroidsFBS_4

value: Spheroids formed in DMEM/F12


title: SpheroidsFBS_3

description: Library name: SpheroidsFBS_3


title: SpheroidsFBS_2

description: Library name: SpheroidsFBS_2


title: Cell 3

description: Library name: Cell 3

value: Scraped single cells


title: Cell 2

description: Library name: Cell 2


title: non-tuberculous cutaneous ulcer tissue sample from human 3

city: Nanjing

first: Jiayan

last: Qian

address: Affiliated of Nanjing University of Chinese Medicine to Nanjing Integrated Traditional Chinese and Western Medicine Hospital

institute: Nanjing Integrated Traditional Chinese And Western Medicine Hospital

description: The gene expression status of the wound tissue in patients with non-tuberculous ulcers

hyb_protocol: Labeled cRNAs were hybridized onto the Human lncRNA V6 microarray (Agilent Technologies, design ID: 084410) according to the manufacturer's standards. After hybridization, the microarrays were washed with phosphate-buffered saline (PBS).

scan_protocol: After washing, the microarrays were imaged by a scanner (G2505C; Agilent Technologies).

data_processing: Feature Extraction 10.7.1.1 (Agilent Technologies) and GeneSpring 13.1 (Agilent Technologies) were used to process the original image and extract the original data. Differentially expressed genes/lncRNAs were identified using the screening criteria of fold change (FC) ≥ 2.0 and P < 0.05.

source_name: Human non-tuberculous cutaneous ulcer tissue sample

label_protocol: Sample labeling was performed based on Human lncRNA V6 (4*180K; design ID: 084410) chip standards (Agilent Technologies). Briefly, total RNA was transcribed to double-stranded complementary DNA (cDNA), then synthesized into complementary RNA (cRNA), and labeled with cyanine-3-CTP (Cy3).

growth_protocol: The samples were human wound tissues collected from patients diagnosed with UCT and NCTUs. The tissues were obtained through standard surgical procedures at the hospital. No in vitro cell culture or animal growth conditions were applied, as the samples were directly derived from clinical patients.

extract_protocol: Total RNA was extracted from the tissues of patients with UCT and those with NCTUs. Total RNA was quantified by a spectrophotometer (NanoDrop ND-2000; Thermo Scientific, Waltham, MA). RNA integrity was assessed using a bioanalyzer (2100; Agilent Technologies, Santa Clara, CA).

treatment_protocol: The tissue samples were divided into two groups based on the clinical diagnosis: the UCT group and the NCTUs group. The samples were processed for total RNA extraction immediately after surgical collection to assess the differential gene/lncRNA expression profiles between the two clinical conditions.

value: male

tag: age


title: Control_2

description: Library name: C2


title: non-tuberculous cutaneous ulcer tissue sample from human 2


title: non-tuberculous cutaneous ulcer tissue sample from human 1


title: Polr2a-ko-Mettl3_1

description: Library name: Sample 9

tag: chip antibody

value: Diagenode #C15200253


title: SpheroidsFBS_1

description: Library name: SpheroidsFBS_1


title: RRBS of CMs, GFP control, replicate 4

description:
Library name: GFP4
RRBS of cardiomyocyte nuclei from mouse heart, control (GFP), replicate 4

value: Heart

tag: strain

value: Cardiomyocyte

value: GFP AAV

tag: batch


title: Cell 4

description: Library name: Cell 4


title: Tuberculous ulcer tissue sample from human 3

description: The gene expression status of the wound tissue in patients with tuberculous ulcers

source_name: Human tuberculous ulcer tissue sample


title: U87 cells, compound 1, 1

description: Library name: A1

tag: cell line

value: Human Glioblastoma

value: Compund 1


title: Tuberculous ulcer tissue sample from human 2


title: RRBS of CMs, GFP control, replicate 2

description:
Library name: GFP2
RRBS of cardiomyocyte nuclei from mouse heart, control (GFP), replicate 2

tag: cell type


title: U87 cells, vehicle, 2

description: Library name: V2

value: Vehicle


title: OE-MSD1 strain, YPD, Replicate #3

city: Nanchang

first: Fanglin

last: Zheng

state: Jiangxi

address: 1519 Dongyue Avenue, Nanchang County, Jiangxi Province

department: The First Affiliated Hospital of Nanchang University

institute: Nanchang University

description:
Library name: Sample 24
OE-MSD1_YPD-3

data_processing:
The clean reads were mapped to the reference strain JEC21α genome using HISAT2.
FPKM  of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Differential expression analysis was performed using the DESeq2.
The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).
Assembly: ASM9104v1 (JEC21α)
Supplementary files format and content: Tab-delimited text fle includes raw counts for each Sample
Supplementary files format and content: Text files include FPKM values for each Sample

organism: Cryptococcus deneoformans

source_name: Yeast and hyphae cells

growth_protocol: The wild type XL280 strain and msd1 mutant were cultured under mating inducing (V8) condition for 24, 48 and 72 h respectively, the MSD1 overexpression and XL280 cultured under mating repressing (YPD) condition for 24 h.

extract_protocol:
RNA was extracted using a commercial Ultrapure RNA kit (CWBIO, CW0581S) according to the manufacturer’s protocol. 1 μg total RNA of each samples were used for the construction of sequencing libraries.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit following the manufacturer’s instructions. The libraries were sequenced on an Illumina Novaseq 6000  platform and 150 bp paired-end reads were generated.

value: Yeast and hyphae cells

value: MATalpha, PGPD1-MSD1-HYG

value: Mating repressing


title: Cell 1

description: Library name: Cell 1

tag: tissue


title: OE-MSD1 strain, YPD, Replicate #1

description:
Library name: Sample 22
OE-MSD1_YPD-1

tag: genotype


title: OE-MSD1 strain, YPD, Replicate #2

description:
Library name: Sample 23
OE-MSD1_YPD-2

tag: treatment


title: XL280 strain, YPD, Replicate #2

description:
Library name: Sample 20
WT_YPD-2

source_name: Yeast cells

value: Yeast cells

value: MATalpha, wild type


title: XL280 strain, YPD, Replicate #1

description:
Library name: Sample 19
WT_YPD-1


title: XL280 strain, YPD, Replicate #3

description:
Library name: Sample 21
WT_YPD-3


title: Ctcf-ko-Mettl3_1

description: Library name: Sample 1

value: heart

value: part of Diagenode Kit #C01010055


title: msd1 strain, V8 72h, Replicate #3

description:
Library name: Sample 18
msd1_72h-3

value: MATalpha, msd1::NAT

value: Mating inducing


title: msd1 strain, V8 72h, Replicate #2

description:
Library name: Sample 17
msd1_72h-2


title: Tuberculous ulcer tissue sample from human 1

value: female


title: msd1 strain, V8 72h, Replicate #1

description:
Library name: Sample 16
msd1_72h-1


title: Scramble-LR-3

description:
Library name: Sample 7
Illumina_RNA-seq

value: Hippocampal cell line

value: Scramble siRNA


title: msd1 strain, V8 48h, Replicate #3

description:
Library name: Sample 15
msd1_48h-3


title: msd1 strain, V8 48h, Replicate #2

description:
Library name: Sample 14
msd1_48h-2


title: msd1 strain, V8 48h, Replicate #1

description:
Library name: Sample 13
msd1_48h-1


title: msd1 strain, V8 24h, Replicate #3

description:
Library name: Sample 12
msd1_24h-3


title: msd1 strain, V8 24h, Replicate #2

description:
Library name: Sample 11
msd1_24h-2


title: msd1 strain, V8 24h, Replicate #1

description:
Library name: Sample 10
msd1_24h-1


title: XL280 strain, V8 72h, Replicate #3

description:
Library name: Sample 9
WT_72h-3


title: XL280 strain, V8 72h, Replicate #2

description:
Library name: Sample 8
WT_72h-2


title: XL280 strain, V8 72h, Replicate #1

description:
Library name: Sample 7
WT_72h-1


title: DMPA_05 meningioma, methylation EPIC v2.0

value: meningioma

tag: who grade

value: Metaplastic

value: MenG-A

value: Merlin-intact


title: XL280 strain, V8 48h, Replicate #1

description:
Library name: Sample 4
WT_48h-1


title: XL280 strain, V8 48h, Replicate #3

description:
Library name: Sample 6
WT_48h-3


title: XL280 strain, V8 24h, Replicate #3

description:
Library name: Sample 3
WT_24h-3


title: XL280 strain, V8 48h, Replicate #2

description:
Library name: Sample 5
WT_48h-2


title: XL280 strain, V8 24h, Replicate #2

description:
Library name: Sample 2
WT_24h-2


title: XL280 strain, V8 24h, Replicate #1

description:
Library name: Sample 1
WT_24h-1


title: Serum Control_3

description: Library name: Sample3

value: Serum


title: LD79-Fam-Hist-120

city: Hong Kong

first: Daniele

last: Romeo

address: Pok Fu Lam Rd, Lung Fu Shan

country: Hong Kong

institute: The University of Hong Kong

description: Library name: LD79-Fam-Hist-120_peaks.broadPeak

data_processing:
Paired-end CUT&RUN FASTQ files were adapter- and quality-trimmed with Trimmomatic v0.39 (Bolger et al., 2014) in PE mode using 8 threads and the following settings:  ILLUMINACLIP:AdaptorsCPOS.fa:2:30:1  SLIDINGWINDOW:4:20  MINLEN:30
Read quality before and after trimming was assessed with FastQC (Andrews, 2010).
Reads were aligned to the Labroides dimidiatus reference genome (Kang et al., 2023/2024) after building the genome index with Bowtie2 bowtie2-build.
Trimmed reads were aligned with Bowtie2 (Langmead et al., 2009) using: --very-sensitive -p 8
Alignments were converted to BAM, sorted, and indexed using SAMtools (Li et al., 2009) (e.g., samtools view, samtools sort, samtools index). Read group information was added using Picard AddOrReplaceReadGroups (Picard Toolkit), specifying:  RGPL=ILLUMINA  RGLB=KAPA_Hyper_Prep  RGSM=<sample-specific ID> (plus sample-specific RG identifiers).  PCR duplicates were marked but not removed using Picard MarkDuplicates with:  REMOVE_DUPLICATES=false  VALIDATION_STRINGENCY=SILENT  CREATE_INDEX=true Duplicates were retained because the observed duplication rate (~25%) was considered acceptable for CUT&RUN data and removing them could reduce biological signal. Peak calling was performed with MACS2 using each H3K27ac BAM as treatment and the matched input BAM as control:  treatment/control: -t (antibody) vs -c (input)  paired-end mode: -f BAMPE  effective genome size: -g 7.2e8  significance threshold: -q 0.01  broad peaks: --broad  signal tracks: --bdg.
Assembly: Reference sequence used for read alignment: Labroides dimidiatus reference genome (GenBank assembly GCA_030710495.1, ASM3071049v1; BioProject PRJNA937036), generated by Kang et al., 2023 (https://doi.org/10.1186/s12915-023-01682-3)
Supplementary files format and content: .broadPeak — BED-like, tab-delimited text file containing broad peak regions called by MACS2 for each sample. Each row reports genomic coordinates (chrom, start, end) plus peak statistics (name, score, strand, signalValue, pValue, qValue).
Library strategy: CUT&RUN

organism: Labroides dimidiatus

source_name: Forebrain

extract_protocol:
CUT&RUN experiments were performed on adult Labroides dimidiatus brain tissue following the Cell Signaling Technology CUT&RUN protocol (#86652) using H3K27ac antibody. Input DNA was processed according to Cell Signaling guidelines for Input DNA by MNase digestion. Library preparation and Illumina sequencing were performed by the Genomics Core (Centre for PanorOmic Sciences, HKU) using the KAPA Hyper Prep Kit (KR0961) with xGen® Dual Index UMI Adapters. To optimize yield and quality, the post-ligation cleanup bead ratio was increased from 0.8× to 1.1×. Libraries were validated by Agilent Fragment Analyzer, Qubit and qPCR, and sequenced on an Illumina NovaSeq 6000 platform (paired-end 151 bp). An average of 93% bases reached Q30 quality.
CUT&RUN experiments were performed on adult Labroides dimidiatus brain tissue following the Cell Signaling Technology CUT&RUN protocol (#86652) using H3K27ac antibody. Input DNA was processed according to Cell Signaling guidelines for Input DNA by MNase digestion. Library preparation and Illumina sequencing were performed by the Genomics Core (Centre for PanorOmic Sciences, HKU) using the KAPA Hyper Prep Kit (KR0961) with xGen® Dual Index UMI Adapters. To optimize yield and quality, the post-ligation cleanup bead ratio was increased from 0.8× to 1.1×. Libraries were validated by Agilent Fragment Analyzer, Qubit and qPCR, and sequenced on an Illumina NovaSeq 6000 platform (paired-end 151 bp). An average of 93% bases reached Q30 quality.

value: Forebrain


title: LD78-Con-Hist-120

description: Library name: LD78-Con-Hist-120_peaks.broadPeak


title: LD80-Fam-Hist-120

description: Library name: LD80-Fam-Hist-120_peaks.broadPeak


title: LD72-Fam-Hist-30

description: Library name: LD72-Fam-Hist-30_peaks.broadPeak


title: LD70-Con-Hist-30

description: Library name: LD70-Con-Hist-30_peaks.broadPeak


title: LD71-Fam-Hist-30

description: Library name: LD71-Fam-Hist-30_peaks.broadPeak


title: LD69-Con-Hist-30

description: Library name: LD69-Con-Hist-30_peaks.broadPeak


title: LD58-Fam-Hist-120

description: Library name: LD58-Fam-Hist-120_peaks.broadPeak


title: LD59-Fam-Hist-120

description: Library name: LD59-Fam-Hist-120_peaks.broadPeak


title: LD57-Con-Hist-120

description: Library name: LD57-Con-Hist-120_peaks.broadPeak


title: LD56-Con-Hist-120

description: Library name: LD56-Con-Hist-120_peaks.broadPeak


title: LD55-Con-Hist-120

description: Library name: LD55-Con-Hist-120_peaks.broadPeak


title: LD48-Fam-Hist-30

description: Library name: LD48-Fam-Hist-30_peaks.broadPeak


title: AntiAdar-LR-1

description:
Library name: Sample 1
Illumina_RNA-seq

value: Adar1&Adar2 siRNA knockdown


title: LD46-Fam-Hist-30

description: Library name: LD46-Fam-Hist-30_peaks.broadPeak


title: LD44-Con-Hist-30

description: Library name: LD44-Con-Hist-30_peaks.broadPeak


title: LD43-Con-Hist-30

description: Library name: LD43-Con-Hist-30_peaks.broadPeak


title: LD45-Con-Hist-30

description: Library name: LD45-Con-Hist-30_peaks.broadPeak


title: LD29-Fam-Hist-120

description: Library name: LD29-Fam-Hist-120_peaks.broadPeak


title: UM_Chor1_DMSO_2

description: Library name: Sample 10

value: Chordoma Cell line

value: WT

value: DMSO


title: LD28-Fam-Hist-120

description: Library name: LD28-Fam-Hist-120_peaks.broadPeak


title: LD26-Con-Hist-120

description: Library name: LD26-Con-Hist-120_peaks.broadPeak


title: LD25-Con-Hist-120

description: Library name: LD25-Con-Hist-120_peaks.broadPeak


title: LD17-Fam-Hist-30

description: Library name: LD17-Fam-Hist-30_peaks.broadPeak


title: LD18-Fam-Hist-30

description: Library name: LD18-Fam-Hist-30_peaks.broadPeak


title: Se_CC_mBR_190_1

city: Richland

first: Predictive Phenomics

last: Initiative

address: 902 Battelle Boulevard

institute: Pacific Northwest National Laboratory

description:
Library name: Batch 2 Sample 3 Time 3 biol rep 1
S.e co-culture membrane bioreactor time-series

data_processing:
Rsubread v2.16.1 was used to obtain transcript counts provided in the processed data file.
Assembly: NC_007604.1
Supplementary files format and content: csv, transcript counts

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: axenic

growth_protocol: Synechococcus elongatus PCC 7942 CscB/SPS strain, engineered to overexpress sucrose phosphate synthase (SPS) and sucrose permease (CscB), was obtained from Dr. Daniel Ducat. Rhodotorula toruloides NBRC 0880 (Rhodosporidium toruloides IFO0880) was used as the yeast partner. Axenic S. elongatus and co-cultures with R. toruloides were grown at 30 ± 2°C with 2% CO₂ in nitrogen under ~200 µmol photons m⁻² s⁻¹ provided by LED lighting. Cultures were mixed at ~200 rpm using PTFE magnetic stir bars in BG11 medium supplemented with 0.09 g/L yeast nitrogen base (without amino acids and ammonium sulfate), 0.264 g/L ammonium sulfate, 0.174 g/L potassium phosphate dibasic, and 3 g/L HEPES (pH 8.3). Where applicable, 1 mM IPTG was added to induce CscB/SPS expression. Antibiotics (chloramphenicol 25 mg/L and kanamycin 25 mg/L) were used during routine maintenance but removed prior to experiments. Tube perturbation experiments used 25 mL working volume in 50 mL vented tubes supplemented with 100 mg/L sucrose. Bioreactor experiments used membrane-separated (2-chamber mBR) and mixed co-culture configurations in ~600 mL vessels.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plus Mini Kit. Samples were homogenized using QiaShredder, then processed following the manufacturer's protocol with 70% ethanol addition. RNA quality and quantity were assessed by NanoDrop One spectrophotometry. A total of 2 µg RNA in 40 µL was submitted for RNA sequencing per sample.
Library construction and sequencing was performed by Azenta Life Sciences. Library preparation used the NEBNext Ultra RNA Library preparation kit with rRNA depletion performed using the QIAGEN FastSelect rRNA depletion kit with dual depletion. Sequencing was performed on the Illumina platform using paired-end 2x150bp with single indexing (~350M PE reads, ~105GB per sample).

treatment_protocol: Co-culture perturbation conditions were applied at a single time point and included: oxidative stress (5 mM methyl viologen/5x Fe, 5 mM H₂O₂, 50 µM Cd(NO₃)₂), photosynthesis inhibition (10 µM DCMU), temperature stress (37°C, 14°C), pH stress (pH 6.5, pH 10.5), nutrient limitation (no nitrogen, no phosphorus, no trace elements), alternative nitrogen sources (5x (NH₄)₂SO₄, 5x nitrate), heterotrophic conditions (1–10 g/L sucrose, vented and sealed), vitamin B12 supplementation (0.37 µg/L), vitamin B12 combined with H₂O₂ stress, yeast extract amendment (1 g/L), high salt stress (150 mM NaCl), and reduced gas phase (40 mL in sealed tubes). Membrane bioreactor and mixed co-culture bioreactor samples were collected at ~90, ~140, and ~190 hrs.

value: axenic

value: cscB+ delta-sps

value: S.e MBR co-culture day 8


title: Se_CC_mBR_190_3

description:
Library name: Batch 2 Sample 3 Time 3 biol rep 3
S.e co-culture membrane bioreactor time-series


title: Se_CC_mBR_140_3

description:
Library name: Batch 2 Sample 3 Time 2 biol rep 3
S.e co-culture membrane bioreactor time-series

value: S.e MBR co-culture day 6


title: Se_CC_mBR_190_2

description:
Library name: Batch 2 Sample 3 Time 3 biol rep 2
S.e co-culture membrane bioreactor time-series


title: Se_CC_mBR_140_1

description:
Library name: Batch 2 Sample 3 Time 2 biol rep 1
S.e co-culture membrane bioreactor time-series


title: Se_CC_mBR_140_2

description:
Library name: Batch 2 Sample 3 Time 2 biol rep 2
S.e co-culture membrane bioreactor time-series


title: Se_CC_mBR_90_3

description:
Library name: Batch 2 Sample 3 Time 1 biol rep 3
S.e co-culture membrane bioreactor time-series

value: S.e MBR co-culture day 4


title: Se_CC_mBR_90_1

description:
Library name: Batch 2 Sample 3 Time 1 biol rep 1
S.e co-culture membrane bioreactor time-series


title: Se_CC_mBR_90_2

description:
Library name: Batch 2 Sample 3 Time 1 biol rep 2
S.e co-culture membrane bioreactor time-series


title: Se_ax_mBR_190_3

description:
Library name: Batch 2 Sample 2 Time 3 biol rep 3
S.e axenic membrane bioreactor control time-series

value: S.e MBR axenic day 8


title: JHC7_DMSO_1

description: Library name: Sample 5


title: Se_ax_mBR_190_2

description:
Library name: Batch 2 Sample 2 Time 3 biol rep 2
S.e axenic membrane bioreactor control time-series


title: Se_ax_mBR_190_1

description:
Library name: Batch 2 Sample 2 Time 3 biol rep 1
S.e axenic membrane bioreactor control time-series


title: Se_ax_mBR_140_3

description:
Library name: Batch 2 Sample 2 Time 2 biol rep 3
S.e axenic membrane bioreactor control time-series

value: S.e MBR axenic day 6


title: CH22_IDH1Inhibitor_2

description: Library name: Sample 4

value: IDH1 inhibitor


title: Se_ax_mBR_140_2

description:
Library name: Batch 2 Sample 2 Time 2 biol rep 2
S.e axenic membrane bioreactor control time-series


title: Se_ax_mBR_140_1

description:
Library name: Batch 2 Sample 2 Time 2 biol rep 1
S.e axenic membrane bioreactor control time-series


title: Se_ax_mBR_90_3

description:
Library name: Batch 2 Sample 2 Time 1 biol rep 3
S.e axenic membrane bioreactor control time-series

value: S.e MBR axenic day 4


title: Se_ax_mBR_90_2

description:
Library name: Batch 2 Sample 2 Time 1 biol rep 2
S.e axenic membrane bioreactor control time-series


title: Se_ax_190_3

description:
Library name: Batch 2 Sample 1 Time 3 biol rep 3
S.e axenic control time-series

value: S.e axenic control day 8


title: Se_ax_190_1

description:
Library name: Batch 2 Sample 1 Time 3 biol rep 1
S.e axenic control time-series


title: Se_ax_mBR_90_1

description:
Library name: Batch 2 Sample 2 Time 1 biol rep 1
S.e axenic membrane bioreactor control time-series


title: Se_ax_140_3

description:
Library name: Batch 2 Sample 1 Time 2 biol rep 3
S.e axenic control time-series

value: S.e axenic control day 6


title: Se_ax_190_2

description:
Library name: Batch 2 Sample 1 Time 3 biol rep 2
S.e axenic control time-series


title: Se_ax_140_2

description:
Library name: Batch 2 Sample 1 Time 2 biol rep 2
S.e axenic control time-series


title: Se_ax_140_1

description:
Library name: Batch 2 Sample 1 Time 2 biol rep 1
S.e axenic control time-series


title: Se_ax_90_3

description:
Library name: Batch 2 Sample 1 Time 1 biol rep 3
S.e axenic control time-series

value: S.e axenic control day 4


title: Se_ax_90_2

description:
Library name: Batch 2 Sample 1 Time 1 biol rep 2
S.e axenic control time-series


title: Se_ax_90_1

description:
Library name: Batch 2 Sample 1 Time 1 biol rep 1
S.e axenic control time-series


title: Subject 12

city: Denver

first: Elizabeth

last: Wynn

state: CO

address: 1400 Jackson St.

institute: National Jewish Health

description:
Library name: Subject 12
Bronchoalveolar lavage cells from healthy adult after LPS exposure

data_processing:
Initial pre-processing of the 10 subjects’ 10X scRNA-seq data, including demultiplexing, alignment to the hg38 human genome, and UMI-based gene expression quantification, was performed using Cell Ranger (version 3.0, 10X Genomics)
Assembly: hg38
Supplementary files format and content: comma separated (.csv) matrix of raw counts. Rows are features and columns are cells.
Supplementary files format and content: integrated_all_samples_v5.RDS: Integrated Seurat object containing single-cell RNA-seq data from paired baseline samples (GSE151928) and LPS-treated samples (GSE300946). The object includes all cell types, with processed, normalized, and integrated expression data, as well as annotated metadata including cluster identities and cell type classifications.
Supplementary files format and content: macrophage_recluster_v5.RDS: Subset Seurat object containing macrophage cells extracted from the integrated dataset of paired baseline (GSE151928) and LPS-treated (GSE300946) samples. Macrophages were reclustered to resolve subpopulations, and the object includes integrated expression data, and subcluster identities.

source_name: Bronchoalveolar lavage cells

extract_protocol:
Enrolled subjects underwent flexible fiberoptic bronchoscopy and bronchoalveolar lavage with serial installation and aspiration of normal saline. Lavage fluid was centrifuged to pellet cells. Cell pellet was resuspended at 1x10^6 cells per ml in PBS containing 0.04% bovine serum albumin.
Single cells were captured using The Chromium Box (10x Genomics, Pleasanton, CA). The Chromium Single Cell 3’ GEM, library, and gel bead kit PN-1000075 were used along with Bead Chip B PN-1000092 for cell capture and library construction. Libraries were sequenced with the Illumina NovaSEQ 6000 sequencer (Illumina, Inc., San Diego, CA) using an S4 flow cell.

tag: Sex

value: male

value: Bronchoalveolar lavage cells

tag: diagnosis

value: healthy

tag: timepoint

value: day 2 post-LPS

tag: paired baseline_gsm


title: CHB donor Hu-P-005522 single nucleus transcriptomics

city: Foster City

first: Ricardo

last: Ramirez

state: CA

address: 333 Lakeside Drive

institute: Gilead Sciences

description:
Library name: P5522
snRNA-Seq.RDS.gz

data_processing:
Illumina Fastq files were aligned to 10x Visium human transcriptome probe set v2.0_GRCh38-2020-A using Spaceranger-3.0.1 or CellRanger-8.0.0 for spatial transcriptomics and single-nucleus RNA-Seq, respectively
Count data were merged in R using the Seurat package and normalized using SCTransform
Cell-type estimation was performed using RCTD from spacexr version 2.2.1
Cell-type annotations in snRNA-Seq data were performed using SingleR package
Assembly: hg38
Supplementary files format and content: compressed Seurat R data objects.
Supplementary files format and content: For human samples: chb_ST_pre-processed_Seurat.RDS.gz includes is a list of individual samples and includes corresponding H&E images used by Visium while chb_ST_processed_Seurat.RDS.gz includes the merged and filtered data object. .

source_name: Liver

extract_protocol:
10X Visium FFPE Kit
FFPE sections of 5µm thickness were prepared using a Leica RM2255 microtome and placed on Superfrost Plus glass slides (Epredia, Cat#22-042-941), as per guidance outlined in 10X Genomics Visium CytAssist Tissue preparation guide (CG000518). Slides were subjected to H&E staining as outlined in guidance provided by 10X Genomics (CG000518). Following H&E staining, slides were imaged using Aperio AT2 DX scanner (Leica Biosystems, Cat#23AT2100) at 40X magnification. Following imaging, coverslips were removed, and tissues were decrosslinked. Library construction was conducted as described in 10X Genomics, CG000495. Post library construction QC was performed on the 2100 Bioanalyzer Instrument (Agilent) with the High Sensitivity DNA Kit (Agilent Technologies, Cat#5067-4626). Library concentrations were measured using the Qubit dsDNA High Sensitive Assay Kit (Invitrogen, Cat#Q32854). Sequencing was performed on the Illumina NovaSeq6000, following the guidance outlined in the 10X Genomics Visium CytAssist Spatial Gene Expression User Guide (CG000495). Sequencing was performed to meet a targeted sequencing depth of 50,000 read pairs per tissue-covered spot.

value: Liver

value: CHB


title: CHB donor Hu-P-005521 single nucleus transcriptomics

description:
Library name: P5521
snRNA-Seq.RDS.gz


title: CHB donor Hu-P-005524  single nucleus transcriptomics

description:
Library name: P5524
snRNA-Seq.RDS.gz


title: healthy donor Hu-P-003749 single nucleus transcriptomics

description:
Library name: P3749
snRNA-Seq.RDS.gz


title: NCMT2

city: Suzhou

first: Wenbo

last: Jia

state: Jiangsu Province

address: No.199 Ren'ai Road

institute: Soochow University

description: Library name: 5

data_processing:
Rawdata were generated after sequencing, image analysis, base calling and quality filtering on sequencer.
Firstly, Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.3).
The trimmed reads were aligned to the merged pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch. The numbers of mature miRNAmapped tags were defined as the raw expression levels of that miRNA. The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach.
Then, trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs. Differentially expressed miRNA between two groups were filtered by Fold Change and P-value.
miRNA targets were performed by popular miRNA target prediction softwares, miRNA-targets networks were plotted by cytoscape software (v2.8.0), and the GO and KEGG pathway analysis were performed based on the top 10 differentially expressed miRNA target genes.
Assembly: HG38
Supplementary files format and content: count

source_name: colon

extract_protocol:
Total RNA was extracted using Trizol reagent
The small RNA libraries were constructed with GenSeq® Small RNA Library Prep Kit (GenSeq, Inc.) by following the manufacturer’s instructions. Briefly, 3’ and 5’ adaptors were successively ligated to RNA samples. Then, the adaptor-ligated RNA was reversely transcribed into cDNA, followed by PCR amplification. After amplification, the cDNA libraries were size-selected for miRNA fractions before sequencing and then sequenced in platform.

value: colon


title: NCMT3

description: Library name: 6


title: NCMT1

description: Library name: 4


title: CA3

description: Library name: 3


title: CA2

description: Library name: 2


title: umbilical cord blood hematopoietic stem cells (CD34+) cells, DMSO rep3

city: Shanghai

first: Yu

last: Li

state: Shanghai

address: No.600 Yishan Road

department: Department of Obstetrics and Gynecology

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: Library name: sample6

data_processing:
The sequence reads were aligned to GRCm38/M25 using STAR (2.7.10a).
Uniquely mapped sequencing reads were assigned to Gencode M25 gene using featureCounts (v2.0.1)
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files of ’gene_fpkm‘ include log2RPKM values for all Sample.

source_name: cord blood

growth_protocol: Cells were cultured in Stemline II Hematopoietic Stem Cell Expansion Medium (Sigma, S0912) supplemented with 100 ng/mL stem cell factor (SCF) (R&D Systems, #7466 - SC - 010/CF), 100 ng/mL thrombopoietin (TPO) (R&D Systems, #288 - TP - 200/CF), and 50 ng/mL Fms - like tyrosine kinase 3 ligand (Flt3L) (BioLegend, #710802) in the presence of 50 IU/mL penicillin and 50 μg/mL streptomycin.

extract_protocol:
Total RNA was isolated from  umbilical cord blood hematopoietic stem cells (CD34+) ex vivo cultured for 7 days treated with DMSO and 8-Me-PIQ using FastPure Cell/Tissue Total RNA Isolation Kit (Vazyme).
mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then RNA was digested with RNase H. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. 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 amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. Each group was sequenced in replicates by Illumina NovaSeq 6000 with single end 150 bp read length.

treatment_protocol: PBS

value: cord blood

value: Primary cells

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

value: ex vivo cultured for 7 days


title: umbilical cord blood hematopoietic stem cells (CD34+) cells, DMSO rep2

description: Library name: sample5


title: umbilical cord blood hematopoietic stem cells (CD34+) cells, DMSO rep1

description: Library name: sample4


title: umbilical cord blood hematopoietic stem cells (CD34+) cells, 8-Me-PIQ rep1

description: Library name: sample1


title: CA1

description: Library name: 1


title: FMM-PVBP-Spatial

city: London

first: Theodoros

last: Xenakis

address: 20 Guilford Street

country: United Kingdom

institute: UCL

description:
Library name: FMM-sp-AB-gex
Preeclamptic

data_processing:
Spatial transcriptomics: Fast files were processed using 10X Genomics' SpaceRanger v2.1.0. Fastq files were generated with `mkfastq`, and processed files with `count`.
Single cell Transcriptomics:Fastq files were processed using 10X Genomics CellRanger 3.1.0 with "cellranger multit".
Assembly: Spatial transcriptomics: 10X Genomics' genome build: GRCh38-2020-A. Single-cell transcriptomics: Pre-built human reference 3.0.0, GRCh38 (Ensembel release 93)
Supplementary files format and content: Spatial transcriptomics: Spaceranger count spatial directory. Paraphrased from https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/spatial-outputs: aligned_fiducials.jpg: shows which fiducial spots on the slide were detected by spaceranger; detected_tissue_image.jpg: shows the section of tissue detected by spaceranger; scalefactors_json.json: relative scales of user-supplied images; spatial_enrichment.csv: Moran's I values for each expressed feature; tissue_hires_image.png: high-resolution image of the tissue; tissue_lowres_image.png: low-resolution image of the tissue; tissue_positions.csv: table with information about each spot; barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz: gene expression matrix files.
Supplementary files format and content: Single-cell transcriptomics: CellRanger count output with the files accounting for filtered feature-barcode matrices for each GEM well in "gz" compressed format.
Library strategy: Spatial Transcriptomics

source_name: Placenta

extract_protocol:
For spatial transcriptomics: Fresh frozen tissue were OCT embedded, and 10µm frozen sections were cut with cryostat. For single-cell and nuclei transcriptomics: samples were freshly dissociated using custom protocol. Nuclei were isolated using 10X Genomics nuclei isolation kit according to manufacturers recommended protocol.
For spatial transcriptomics: Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction. For single-cell an nuclei transcriptomics: single cell or nuclei suspensions were prepared and processed using the Chromium Single Cell 5’ Reagent Kits v3.1

value: Placenta


title: FMM-Myometrium-Spatial

description:
Library name: FMM-sp-CD-gex
Preeclamptic

source_name: Myometrium

value: Myometrium


title: FMM-CAM-Spatial

description:
Library name: FMM-sp-CAM-gex
Preeclamptic

source_name: Chorioamniotic membranes

value: Chorioamniotic membranes


title: FSH-PVBP-Spatial

description:
Library name: FSH-sp-AB-gex
Preeclamptic


title: FSH-CAM-Spatial

description:
Library name: FSH-sp-CAM-gex
Preeclamptic


title: FNS-PVBP-Spatial

description:
Library name: FNS-sp-AB-gex
Control


title: FNS-CAM-Spatial

description:
Library name: FNS-sp-CAM-gex
Control


title: FNS-Myometrium-Spatial

description:
Library name: FNS-sp-CD-gex
Control


title: FYI-PVBP-Spatial

description:
Library name: FYI-sp-AB-gex
Control


title: FJD-PVBP-Spatial

description:
Library name: FJD-sp-AB-gex
Control


title: umbilical cord blood hematopoietic stem cells (CD34+) cells, 8-Me-PIQ rep3

description: Library name: sample3


title: FYI-CAM-Spatial

description:
Library name: FYI-sp-CAM-gex
Control


title: FYI-Myometrium-Spatial

description:
Library name: FYI-sp-CD-gex
Control


title: HV_7_PBMC

city: Bethesda

first: Stephen

middle: R

last: Brooks

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 or v6.0.2
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
Skin biopsy from Degos disease patients and healthy volunteers were washed with PBS and digested enzymatically using whole skin dissociation kit (Miltenyi Biotec).  Following mechanical dissociation and filteration, cells were resuspended in 500 μL of complete RPMI-1640 with 10% FBS before sorting. Skin live cells were enriched by fluorescence-activated cell sorting (FACS) using Sytox green. PBMCs from blood were isolated according to desity centrifugation method. PBMCs and CSF samples were subjected to ACK lysis treatment to remove RBCs. Finally, single cell suspensions prepared from skin, PBMCs and CSF were counted and and cell concentration was adjusted in the range of 700-1200 cells/ul with the viability of > 70% before being used for single-cell RNA-sequencing.
Library construction was performed in accordance with 10X Genomics protocol (10X Chromium 5' v2 or 5'-HT kit).

value: PBMC


title: HV_6_PBMC

description: 10x Genomics


title: FJD-Myometrium-Spatial

description:
Library name: FJD-sp-CD-gex
Control


title: C&R_Rh30_MED13_BI1347-24hr_rep1

city: Boston

first: Susu

last: Zhang

address: 360 Longwood Ave, LC6102

institute: Dana-Farber Cancer Institute

description: Library name: C_R_Rh30_MED13_BI1347-24hr_rep1

data_processing:
Sequencing read quality was examined using FastQC (http://www.bioinformatics.babraham.ac.uk) (v0.11.9). Raw FASTQ data were trimmed using Trimmomatic-v0.38 and paired end reads were aligned to human hg38 genome using Bowtie2 (v2.3.5) in very sensitive local mode --dovetail --phred33 -I 0 -X 2000 -N 1 --very-sensitive). Peaks were called using MAXS2 (v2.1.4) with a threshold of q<0.01 and peak were annotated to the nearest TSS using HOMER. Differential analysis was performed using DiffBind and DESeq2. Significantly changed peaks were defined by a 1.5-fold change threshold and FDR<0.05. Bigwig files were normalized and generated using Deeptools. Heatmaps were created by Deeptools using the normalized bigwig files.
Assembly: hg38
Supplementary files format and content: Bigwig file
Library strategy: CUT&Run

extract_protocol:
CUT&RUN+NEB DNA clean up
NEB Next Ultra II library prep kit

value: Rhabdomyosarcoma

value: PAX3::FOXO1 fusion