title: AF cells, Young, id22361

description: Library name: Sample 7

value: Intervertebral disc

value: Young


title: C2_Discovery_54

status: Public on Jan 28 2026

type: genomic

city: Potsdam

first: Amandeep

last: Singh

state: Brandenburg

address: Arthur-Scheunert-Allee 114-116

department: EOD

country: Germany

institute: German Institute of Human Nutrition

hyb_protocol: The bisulfite treatment and hybridisation was carried out by Life & Brain GmbH

scan_protocol: iscan, carried out by Life & Brain GmbH

data_processing: ChAMP package in R environment

label: other

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood cells

label_protocol: Labeling was carried out by Life & Brain GmbH

extract_protocol: precipitation with sodium acetate

treatment_protocol: Genomic DNA was extracted from blood cells.

tag: Sex

value: M

tag: tissue

value: Blood cells


title: Fecal bacterial DNA, AMP, rep4

type: SRA

city: Nam-gu, Pohang-si

first: Haeun

last: Ko

state: Gyeongsangbuk-do

address: 77, Cheongam-ro

department: Life Science

country: South Korea

institute: POSTECH

description: Library name: HE_AMP_4

library_source: transcriptomic

data_processing:
QIIME2 (v2023.02) was used to process and analyze 16S rRNA gene amplicon sequencing data
Paired-end sequences were merged and quality-filtered using Deblur.
The resulting amplicon sequence variants (ASVs) were used for downstream analyses.
Assembly: SILVA
Supplementary files format and content: Read counts are shown in 16S rRNA read count file.

molecule: total RNA

organism: feces metagenome

source_name: Mus musculus feces

extract_protocol:
Fecal DNA DNA was extracted using the NucleoSpin DNA Stool Kit (MACHEREY-NAGEL) following the manufacturer’s protocol.
Metagenomic sequencing was performed on an Illumina MiSeq platform (Illumina), targeting the V3 and V4 regions of the 16S rRNA gene according to the manufacturer's instructions. 16S rRNA gene amplicon sequencing

value: Feces


title: Fecal bacterial DNA, VAN, rep3

description: Library name: HE_VAN_3


title: whole colonic tissue, colitis recovered, T5224-treated, rep 1

city: Cambridge

first: Surya

last: Nagaraja

state: MA

address: 7 Divinity Ave, Bauer 2nd Floor 208

department: HSCRB

country: USA

institute: Harvard University

description: Library name: DSS41prim_M3

library_source: genomic

data_processing:
EM-seq data were processed and aligned to the mm10 reference genome using the nf-core/methylseq pipeline with GPU-enabled bwa-meth.
Methylation calls were obtained with MethylDackel.
bigWig tracks were generated from per-CpG bedGraph outputs of the nf-core/methylseq pipeline by calculating per-CpG methylation fractions (methylated reads / total coverage) using custom scripts and UCSC bedGraphToBigWig.
Assembly: mm10
Supplementary files format and content: bigwig of methylation fraction at CpGs
Library strategy: EM-seq

organism: Mus musculus

source_name: colon

extract_protocol:
Genomic DNA was extracted using the Qiagen DNeasy Blood & Tissue Kit from OCT sections.
For each sample, 200 ng of DNA was resuspended in water to 48 uL, mixed with control DNA from the NEBNext Enzymatic Methyl-seq V2 Kit total and sonicated on a Covaris S220 to 200 and 600 bp. Sonicated DNA was then processed per EM-seq V2 protocol

treatment_protocol: Colitis mice were treated with 1-1.5% DSS in drinking water for 3 cycles of 7 days on/10 days off. Starting 20 days after DSS cessation, T-5224, or equivalent volume DMSO, was administered at 100 mg/kg p.o. once daily for three days. Animals were sacrificed 24 hours following final dose and colon tissue was embedded as a swiss roll in OCT.

value: colon

tag: cell type

value: colonic epithelium

tag: genotype

value: WT

tag: treatment

value: 23 days following DSS cessation, 100 mg/kg T-5224 p.o.


title: GSC-0131_3_RNA1_Lib2

city: Manhasset

first: Nyasha

last: Chambwe

state: NY

address: 350 Community Drive

department: Institute of Molecular Medicine

institute: Feinstein Institutes for Medical Research

description:
Library name: GSC-0131-Rep6
GSC-0131 Replicate 6

data_processing:
Raw (FASTQ) output RNAseq files were analyzed using the nextflow (ver 22.04.3) pipeline nf-core/rnaseq (version 3.7). Read quality control analysis were performed using FastQC, with filtering of ribosomal RNA reads by SortMeRNA. Genomic contaminants were removed by BBSplit prior to read quality assessment and adapter trimming using Trim Galore. STAR was used to align filtered reads to the human reference genome GRCh37. We used SAMtools to sort and index alignments, and Picard to mark duplicate reads. Expression was quantified using RSEM.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes gene-level raw counts across all samples

source_name: brain

extract_protocol:
Total RNA was extracted and purified using the miRNeasy micro kit (Qiagen)
Total RNA was isolated from cells using the miRNeasy micro kit (Qiagen). Library preparation was performed using the rRNA depletion KAPA RNA HyperPrep Kit with RiboErase (HMR)(Roche Sequencing and Life Science).

value: brain

tag: cell line

value: cancer stem cell line

value: glioma stem cell culture

tag: batch


title: GSC-0131_2_RNA1_Lib1

description:
Library name: GSC-0131-Rep2
GSC-0131 Replicate 2


title: C5_Discovery_60

value: F


title: C5_Discovery_59


title: whole colonic tissue, healthy control, T5224-treated, rep 3

description: Library name: DSS41prim_M12

value: healthy control, 100 mg/kg T-5224 p.o.


title: whole colonic tissue, healthy control, DMSO-treated, rep 1

description: Library name: DSS41prim_M7

value: healthy control, DMSO treated


title: C5_Discovery_55


title: C2_Discovery_53


title: Fecal bacterial DNA, VAN, rep4

description: Library name: HE_VAN_4


title: C5_Discovery_56


title: whole colonic tissue, colitis recovered, T5224-treated, rep 3

description: Library name: DSS41prim_M6


title: Fecal bacterial DNA, VANM, rep5

description: Library name: HE_VANM_5


title: whole colonic tissue, colitis recovered, DMSO-treated, rep 1

description: Library name: DSS41prim_M1

value: 23 days following DSS cessation, DMSO treated


title: C2_Discovery_50


title: GBM8_2_RNA1_Lib1

description:
Library name: GBM8-Rep2
GBM8 Replicate 2


title: C5_Discovery_58


title: C6_Discovery_51


title: GSC-0827_2_RNA1_Lib1

description:
Library name: GSC-0827-Rep2
GSC-0827 Replicate 2


title: Fecal bacterial DNA, VAN, rep2

description: Library name: HE_VAN_2


title: Fecal bacterial DNA, VANM, rep4

description: Library name: HE_VANM_4


title: Fecal bacterial DNA, VAN, rep1

description: Library name: HE_VAN_1


title: Fecal bacterial DNA, VAN, rep6

description: Library name: HE_VAN_6


title: whole colonic tissue, colitis recovered, T5224-treated, rep 2

description: Library name: DSS41prim_M5


title: GBM8_3_RNA1_Lib1

description:
Library name: GBM8-Rep3
GBM8 Replicate 3


title: whole colonic tissue, colitis recovered, DMSO-treated, rep 3

description: Library name: DSS41prim_M4


title: GBM8_1_RNA1_Lib1

description:
Library name: GBM8-Rep1
GBM8 Replicate 1


title: GSC-0827_1_RNA1_Lib1

description:
Library name: GSC-0827-Rep1
GSC-0827 Replicate 1


title: whole colonic tissue, colitis recovered, DMSO-treated, rep 2

description: Library name: DSS41prim_M2


title: mouse colonic organoids, healthy controls, rep 3

description: Library name: DSS21orgs_P4_M9

growth_protocol: Colon organoids were grown in WENR media: 50% ENR (Crypt Basal with 50 ng/mL EGF, 100 ng/mL Noggin, 1:100 Rspondin conditioned media) and 50% Wnt conditioned media. Organoids were passaged every 7 to 10 days by mild dissociation in TrypLE.

extract_protocol:
Genomic DNA was extracted using the Qiagen DNeasy Blood & Tissue Kit.
For each sample, 200 ng of DNA was resuspended in water to 48 uL, mixed with control DNA from the NEBNext Enzymatic Methyl-seq V2 Kit total and sonicated on a Covaris S220 to 200 and 600 bp. Sonicated DNA was then processed per EM-seq V2 protocol

treatment_protocol: Colitis mice were treated with 1-1.5% DSS in drinking water for 3 cycles of 7 days on/10 days off. Organoids were derived from whole colonic tissue 10 days following final cycle of DSS.

value: control


title: Fecal bacterial DNA, VANM, rep6

description: Library name: HE_VANM_6


title: mouse colonic organoids, healthy controls, rep 2

description: Library name: DSS21orgs_P4_M8


title: C6_Discovery_52


title: GBM4_3_RNA1_Lib1

description:
Library name: GBM4-Rep3
GBM4 Replicate 3


title: Fecal bacterial DNA, VANM, rep2

description: Library name: HE_VANM_2


title: GBM4_2_RNA1_Lib1

description:
Library name: GBM4-Rep2
GBM4 Replicate 2


title: C6_Discovery_49


title: C6_Discovery_48


title: C6_Discovery_46


title: Fecal bacterial DNA, SPF, rep6

description: Library name: HE_SPF_6


title: GSC-0131_1_RNA1_Lib1

description:
Library name: GSC-0131-Rep1
GSC-0131 Replicate 1


title: mouse colonic organoids, colitis recovered, rep 1

description: Library name: DSS21orgs_P4_M1

value: colitis


title: C3_Discovery_43


title: Fecal bacterial DNA, SPF, rep4

description: Library name: HE_SPF_4


title: Fecal bacterial DNA, VANM, rep1

description: Library name: HE_VANM_1


title: Fecal bacterial DNA, VANM, rep3

description: Library name: HE_VANM_3


title: Biol rep 2 of SH-SY5Y WT cells

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description: Library name: WT_4

data_processing:
Analysis of sequencing data quality, reads repartition (e.g., for potential ribosomal contamination), inner distance size estimation, genebody coverage, strand-specificity of library were performed using FastQC v0.11.2, Picard-Tools v1.119, Samtools v1.0, and RSeQC v2.3.9
Reads were mapped using STAR v2.7.5a12 on the Human hg38 genome assembly
Read count was performed using featureCount from SubRead v1.5.0 and the Rat FAST DB v2021_3 annotations
Differential expression analysis was executed using DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes DESeq2 normalized count with gene annotations

molecule: polyA RNA

extract_protocol:
RNA was extracted from SH-SY5Y WT, SCR, and G2 cells using the Qiagen RNeasy Micro Kit. RNA concentration and integrity were assessed using a NanoDrop system and an Agilent 2100 Bioanalyzer 2100
The libraries were prepared following the Stranded mRNA Prep protocol from Illumina, starting from 500 ng of high-quality total RNA. Paired end (2 × 75 bp) sequencing was performed on an Illumina Nextseq 500 platform.

value: Neuroblastoma


title: mouse colonic organoids, colitis recovered, rep 3

description: Library name: DSS21orgs_P4_M3


title: Biol rep 1 of SH-SY5Y WT cells

description: Library name: WT_2


title: Biol rep 3 of SH-SY5Y cells silenced with control probe through CRISPR/Cas9

description: Library name: SCR_6


title: GBM4_1_RNA1_Lib1

description:
Library name: GBM4-Rep1
GBM4 Replicate 1


title: C3_Discovery_47

value: M


title: C3_Discovery_42

value: Blood cells


title: mouse colonic organoids, colitis recovered, rep 2

description: Library name: DSS21orgs_P4_M2


title: Biol rep 2 of SH-SY5Y cells silenced with control probe through CRISPR/Cas9

description: Library name: SCR_4


title: Fecal bacterial DNA, SPF, rep5

description: Library name: HE_SPF_5

value: Feces


title: mouse colonic organoids, healthy controls, rep 1

description: Library name: DSS21orgs_P4_M7

value: colon


title: Biol rep 1 of SH-SY5Y cells silenced with control probe through CRISPR/Cas9

description: Library name: SCR_5


title: YC_1070 (re-analyzed)

city: Pamplona

first: Francisco

middle: J

last: Novo

address: Irunlarrea 1

department: Biochemistry and Genetics

country: Spain

institute: University of Navarra

description:
Y6
Re-analysis of GSM5928162

data_processing:
QC control of sample sequencing was verified using FastQC software.
Fastq files were mapped to GRCm39 mouse assembly using Rsubread with default parameters.
Gene expression quantification was carried out with featureCounts using countMultiMappingReads = FALSE, GTF.featureType="exon" and  GTF.attrType="gene".
The genome annotation file was GCF_000001635.27_GRCm39_genomic.gff.
Assembly: GRCm39
Supplementary files format and content: Processed data file is tab-delimited text file including raw counts for each annotated gene.

source_name: FACS-sorted B220+GFP+ cells from spleen

extract_protocol:
Murine spleens were submitted to cellular disaggregation, followed by lysis of erythrocytes using ACK buffer. Then, single-cell preparations were stained with B220 and submitted to fresh cellular sorting in a FACSAria Ilu sorter (BD) after exclusion of dead cells with 7AAD. Total RNA was extracted from sorted cells using TRIzol (Invitrogen) as described in manufacturer´s protocol and quality control of extracted RNA was measured using Agilent 2100 Bioanalyzer.
SE50 sequencing of oligo dT-based mRNA enrichment (polyA RNA)
DNBseq SE50 20M reads

treatment_protocol: Fresh murine spleens were collected from moribund mice.

value: female

tag: strain

tag: murine model

value: Normal control

value: YC controls (YFPstopF/+Cg1Cre/+)

value: spleen

value: splenic lymphoma B cells (B220+GFP+)


title: C6_Discovery_44


title: C6_Discovery_45


title: Fecal bacterial DNA, SPF, rep3

description: Library name: HE_SPF_3


title: Fecal bacterial DNA, SPF, rep2

description: Library name: HE_SPF_2


title: YC_1671 (re-analyzed)

description:
Y3
Re-analysis of GSM5928160


title: C5_Discovery_40


title: Fecal bacterial DNA, SPF, rep1

description: Library name: HE_SPF_1


title: Biol rep 3 of SH-SY5Y cells with PRPF40B gene silencing through CRISPR/Cas9

description: Library name: G2_6


title: C3_Discovery_41


title: pBIC_1521 (re-analyzed)

description:
P11
Re-analysis of GSM5928143

value: ABC-DLBCL lymphoma (pBIC)


title: YC_1067 (re-analyzed)

description:
Y4
Re-analysis of GSM5928161

value: male


title: C6_Discovery_39

value: F


title: pBIC_1761 (re-analyzed)

description:
P9
Re-analysis of GSM5928141


title: Biol rep 2 of SH-SY5Y cells with PRPF40B gene silencing through CRISPR/Cas9

description: Library name: G2_5


title: C3_Discovery_38


title: P12

city: Beijing

first: Tingyang

last: Li

address: No. 16 Dongzhimen Inner South Street, Dongcheng District

department: Institute of Chinese Materia Medica

country: China

institute: China Academy of Chinese Medical Sciences

description: Library name: P12

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM 1-3 516 R44 (v6.1)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes gene counts for each sample

source_name: health people, blood sample

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: blood

tag: disease

value: health


title: C3_Discovery_37


title: P13

description: Library name: P13


title: YC_1669 (re-analyzed)

description:
Y2
Re-analysis of GSM5928159


title: P19

description: Library name: P19


title: C3_Discovery_36


title: pBIC_1766 (re-analyzed)

description:
P10
Re-analysis of GSM5928142


title: C3_Discovery_35


title: H9

description: Library name: H9

source_name: HCC patient, blood sample

value: HCC


title: P17

description: Library name: P17


title: Biol rep 1 of SH-SY5Y cells with PRPF40B gene silencing through CRISPR/Cas9

description: Library name: G2_2


title: H10

description: Library name: H10


title: L14_pBIC10_1734

value: IL-10-deficient ABC-DLBCL lymphoma (pBIC10)

value: pBIC10 (p53F/F Blimp1F/F IKK2castopF/stopF Cg1Cre/+ IL-10F/F)


title: L13_pBIC10_1733


title: Multiome, e14.5 lung B6 BMS, GEX

city: College Station

first: Masako

last: Suzuki

state: TX

address: 498 Olsen Blvd, Norman E. Borlaug Building 202C

department: Nutrition

institute: Texas A&M University

description: Library name: B6_BMS_RNA

library_source: transcriptomic single cell

data_processing:
Preprocessing: Raw FASTQ files were processed using the Cell Ranger ARC pipeline (version 2.0.2, 10x Genomics) to align reads to the mm10 reference genome (2020-A release). This process yielded unique molecular identifier (UMI) counts for gene expression, and ATAC-seq fragment counts for chromatin accessibility. Subsequent analyses were conducted using a standardized snMultiome workflow implemented in R (version 4.4.1), leveraging the Seurat (version 5.0.1)  and Signac (version 1.14.0) packages. Seurat objects were created using the matrix.h5 and fragment.tsv.gz files annotated with EnsDb.Mmusculus.v79. ATAC-seq peaks were identified using MACS2 (ver. 2.2.7.1) and quantified counts in each peak using the FeatureMatrix function in Signac, which was used for downstream analyses of chromatin accessibility. Chromosome nomenclature was standardized to the UCSC style to ensure compatibility with the Cell Ranger ARC output. Quality control measures were applied to exclude low-quality cells from the analysis. Cells were filtered based on the following criteria: low total RNA counts (nfeature_RNA >300, except AJ control >750), low total ATAC-seq counts (nfeature_ATAC>300), high mitochondrial gene expression percentage (<0.2), nucleosome signal > 2, and transcription start site (TSS) enrichment score < 1. These stringent filters ensured the retention of high-quality cells for downstream analyses.
Data processing and analysis: Single-cell multiome data were processed using Seurat v4 and Signac packages in R. For RNA analysis, data were normalized using NormalizeData(), followed by identification of 3,000 highly variable features using FindVariableFeatures(), data scaling with ScaleData(), principal component analysis (PCA) with 50 components, and UMAP dimensionality reduction using the first 30 PCs. For ATAC-seq data, accessible chromatin features were identified using FindTopFeatures() with a minimum cutoff of 50, followed by term frequency-inverse document frequency (TF-IDF) normalization and singular value decomposition (SVD) with 50 components. Integration across samples was performed using FindIntegrationAnchors() with reciprocal latent semantic indexing (rLSI) reduction on dimensions 2-30, followed by IntegrateEmbeddings() to create integrated LSI embeddings. Weighted nearest neighbor (WNN) analysis was performed using FindMultiModalNeighbors() combining RNA and ATAC modalities, followed by WNN-UMAP embedding and graph-based clustering at resolution 0.5 using FindClusters(). One low-quality cluster (cluster 16) was removed from downstream analysis. Differential gene expression analysis was performed using MAST algorithm via FindMarkers() for pairwise comparisons and Wilcoxon rank-sum test via FindAllMarkers() for cluster marker identification.
Assembly: mm10 (GRCm38) - Cell Ranger reference genome 2020-A release
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 file containing filtered feature-barcode matrices for both RNA and ATAC modalities following 10X Genomics Multiome specifications. Includes gene expression counts, ATAC peak accessibility counts, feature annotations (gene IDs, symbols, chromosome locations), and cell barcodes. atac_fragments.tsv.gz: Compressed tab-delimited file containing ATAC-seq fragment coordinates with columns for chromosome, start position, end position, cell barcode, and duplicate count. Represents all high-quality fragments used for peak calling and accessibility analysis. atac_fragments.tsv.gz.tbi: Tabix index file for the compressed fragments file, enabling rapid genomic region queries.

source_name: Lung

extract_protocol:
Pooled E14.5 male mouse lungs of control and BMS493 treatment groups in A/J and B6 strains were used for the analysis. To collect enough single nuclei, embryonic lungs from four (B6) or six (A/J) mice were pooled and mechanically dissociated using the gentleMACS Octo Dissociator (Miltenyi Biotech, MD) with the “4C _nuclei_1” program.
After dissociation, the sample was incubated on ice for 5 minutes, filtered through a 30 µm filter to remove larger particles, and centrifugated at 4°C 300xg for 5 minutes. The pellet was resuspended in 500 µl of cold resuspension buffer (1X PBS, 0.1% BSA, 0.2 U/µl RNase inhibitor) and then centrifugated at 4°C 300xg for 5 minutes. Eventually, the pellet was resuspended in 300 µl of cold resuspension buffer. To further purify and concentrate the nuclei suspension, the 300 µl of nuclei suspension was gently mixed with an equal volume of 50% OptiPrep (MilliporeSigma, MA) in a 2 ml tube and applied gently on top of a 29% OptiPrep (600 µl) cushion in another 2 ml tube followed by centrifugation at 4°C 10000xg for 30minutes. The OptiPrep supernatant was poured out in a single motion, and the pellet was resuspended in 0.1X lysis buffer (0.1X nuclei extraction buffer with 0.2 U/µl RNase inhibitor) for permeabilization according to the 10X Genomics nuclei permeabilization step (CG000375). Nuclei were then collected and resuspended in Diluted Nuclei Buffer (1X Nuclei Resuspension Buffer, 1mM DTT, and 1 U/µl RNase inhibitor). Single nuclei were counted with AO/PI staining using a DeNovix CellDrop FL (D.A.I. Scientific Equipment, IL). The integrity of isolated nuclei was inspected under a microscope at 100x magnification. The Multiome libraries were prepared according to the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC +Gene Expression user guide (CG000338). The library quality was evaluated using the Agilent 4200 TapeStation (Agilent Technologies, CA), and the library concentration was determined by the Qubit Fluorometer (Invitrogen, CA). The single-nuclei ATAC-seq (snATAC-seq) and single-nuclei RNA-seq (snRNA-seq) libraries were sequenced on the Illumina NextSeq 2000 using the 50-8-24-49 and 28-10-10-90 formats, respectively, aiming for 25000 snATAC-seq and 20000 snRNA-seq reads per cell to ensure data coverage.

treatment_protocol: Pregnant mice were orally administered the inverse pan retinoic acid receptor (RAR) agonist, BMS493 (BMS) (3.75 µg/g/day) (B6688, Sigma-Aldrich) or corn oil from E9.5 to E14.5. Dams were sacrificed for embryonic lung analyses at E14.5.

value: Lung

tag: age


title: L15_pBIC10_1740


title: C6_Discovery_34

value: Blood cells


title: H8

description: Library name: H8


title: Multiome, e14.5 lung AJ BMS, GEX

description: Library name: AJ_BMS_RNA

value: A/J


title: Multiome, e14.5 lung B6 BMS, ATAC

description: Library name: B6_BMS_ATAC

library_source: genomic single cell


title: C3_Discovery_32


title: Multiome, e14.5 lung B6 control, GEX

description: Library name: B6_Control_RNA

value: Control


title: Multiome, e14.5 lung AJ BMS, ATAC

description: Library name: AJ_BMS_ATAC


title: H6

description: Library name: H6


title: H7

description: Library name: H7


title: Multiome, e14.5 lung AJ control, GEX

description: Library name: AJ_Control_RNA


title: H5

description: Library name: H5


title: C3_Discovery_30

value: M


title: C3_Discovery_33


title: Multiome, e14.5 lung B6 control, ATAC

description: Library name: B6_Control_ATAC


title: C3_Discovery_31


title: C6_Discovery_27


title: H3

description: Library name: H3


title: C3_Discovery_29


title: PBS_PBS_46_H3K27Ac

city: Pittsburgh

first: Bokai

last: Zhu

state: PA

address: Bridgeside Point 1, 5th Floor, 100 Technology Drive

institute: Aging Institute of UPMC/University of Pittsburgh School of Medicine

description: Library name: 46_H3K27Ac

data_processing:
FastQC + Trimmomatic for initial QC
Burrows-Wheeler Alignment tool for alignment
SAMtools + Picard tools for filtering
MACS for peak calling
DiffBind and ChIPseeker for differential peak calling and annotation
Assembly: mm10
Supplementary files format and content: bigwig files for each condition

source_name: liver tissue harvested from mice injected with PBS 2x/day for 5 days

extract_protocol:
SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology #9003)
NEBNext Ultra II DNA prep kit (NEB: E7645S)

value: Liver

value: Male

value: WT C57BL6/J

value: PBS 2x/day for 5 days


title: N.furzeri_ID8480_old_heart

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

description: WGBS

data_processing:
Raw reads were subjected to adapter and quality trimming using cutadapt (v2.4; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read.
The trimmed reads were aligned to the Nothobranchius furzeri and Nothobranchius orthonotus reference genomes using using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). A sorted BAM file was obtained and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10).
Methylation rates were called for autosomes only using mcall from the MOABS package (v1.3.2; default parameters).
Supplementary files format and content: bigWig file of 10-200X coverage filtered methylation rate BED file (<chr> <start> <end> <methylation rate>)

organism: Nothobranchius furzeri

source_name: heart

extract_protocol:
Genomic DNA was extracted using the PureLink Genomic DNA Mini Kit.
gDNA was sheared by sonication and then bisulfite converted using the Zymo EZ DNA Methylation Gold Kit. Bisulfite converted DNA was then immediately processed using the Swift Biosciences Accel-NGS Methyl-Seq library kit according to manufacturer's instructions

value: heart

tag: age group

value: old

value: GRZ


title: 3944 TCR library

description:
10X GENOMICS
P32

data_processing:
Raw-count gene-cell matrices were generated using Cell Ranger count (v.3.0.1) for creating the unfiltered gene expression matrix (GEX), and cell multi (commands from Cell Ranger multi, v.5.0.1) for combined analysis of GEX and TCR data.
Assembly: GRCm39
Supplementary files format and content: Tab-separated value files and matrix files
Supplementary files format and content: clonotypes.csv and filtered_contig_annotations.csv files
Library strategy: scTCR-seq

source_name: spleen

extract_protocol:
Fresh murine spleens were submitted to mechanic disaggregation with a syringe plunger through a 70 µm cell strainer, followed by lysis of erythrocytes with ACK buffer (NH4Cl 150 mM KHCO3 10 mM EDTA 0.1 mM). Cell suspensions were sorted in a FACSAria II sorter to obtain a final cell suspension of 20% live lymphoma 7AAD- GFP+ cells and 80% microenvironment 7AAD- GFP- cells.
For each sample, 17,000-19,000 cells were loaded on a Chromium Single-Cell Instrument (10X Genomics) at a concentration of 721 cells/µL to generate single-cell gel bead-in-emulsions (GEMs) of approximately 10,000 cells per sample. The Chromium Next GEM Single Cell 5' Reagent Kit v2 (Dual Index) from 10X Genomics was used to produce libraries for both sequencing-ready Gene Expression and T cell V(D)J libraries.

value: female

value: spleen


title: N.furzeri_ID8367_old_heart

description: WGBS


title: H2

description: Library name: H2

value: blood

value: HCC


title: 3944 gene expression library

description:
10X GENOMICS
P31

data_processing:
Raw-count gene-cell matrices were generated using Cell Ranger count (v.3.0.1) for creating the unfiltered gene expression matrix (GEX), and cell multi (commands from Cell Ranger multi, v.5.0.1) for combined analysis of GEX and TCR data.
Assembly: GRCm39
Supplementary files format and content: Tab-separated value files and matrix files
Supplementary files format and content: clonotypes.csv and filtered_contig_annotations.csv files


title: 3571 TCR library

description:
10X GENOMICS
P29

value: pBIC


title: PBS_PBS_45_H3K27Ac

description: Library name: 45_H3K27Ac


title: PBS_PBS_23_H3K27Ac

description: Library name: 23_H3K27Ac


title: C6_Discovery_26

value: F


title: PBS_PBS_21_H3K27Ac

description: Library name: 21_H3K27Ac


title: C6_Discovery_28

value: Blood cells


title: Multiome, e14.5 lung AJ control, ATAC

description: Library name: AJ_Control_ATAC

value: Lung

value: A/J


title: H4

description: Library name: H4


title: N.furzeri_ID8357_old_heart

description: WGBS


title: C3_Discovery_24


title: C6_Discovery_25


title: 3571 gene expression library

description:
10X GENOMICS
P28


title: P8

description: Library name: P8

value: health


title: N.furzeri_ID8365_young_heart

description: WGBS

value: young


title: C3_Discovery_22

value: M


title: H1

description: Library name: H1


title: N.furzeri_ID8465_old_heart

description: WGBS


title: PBS_PBS_46_input

description: Library name: 46_02input

value: Liver

value: Male

value: WT C57BL6/J


title: BCAA_PBS_24_H3K27Ac

description: Library name: 42_H3K27Ac

source_name: liver tissue harvested from mice injected with BCAA 2x/day for 5 days

value: BCAA 2x/day for 5 days


title: P3

description: Library name: P3


title: C2_Discovery_21


title: PBS_PBS_45_input

description: Library name: 45_02input

value: PBS 2x/day for 5 days


title: N.furzeri_ID8619_young_heart

description: WGBS

value: heart

value: GRZ


title: P10

description: Library name: P10

value: blood


title: P2

description: Library name: P2


title: P1

description: Library name: P1


title: N.furzeri_ID8364_young_heart

description: WGBS


title: N.furzeri_ID8360_old_heart

description: WGBS

value: old


title: P5

description: Library name: P5


title: C3_Discovery_23


title: N.furzeri_ID8359_young_heart

description: WGBS


title: BCAA_PBS_17_H3K27Ac

description: Library name: 17_H3K27Ac


title: BCAA_PBS_24_input

description: Library name: 42_02input


title: PBS_PBS_23_input

description: Library name: 23_02input


title: N.furzeri_ID8480_old_liver

description: WGBS

source_name: liver

value: liver


title: C3_Discovery_17


title: N.furzeri_ID8367_old_liver

description: WGBS


title: C6_Discovery_18


title: C3_Discovery_20

value: F


title: N.furzeri_ID8465_old_liver

description: WGBS


title: PBS_PBS_46_IgG

description: Library name: 46_IgG


title: PBS_PBS_21_input

description: Library name: 21_02input


title: Virgin schistosomes, BATT 2d, rep2

city: Shanghai

first: Mengjie

last: Gu

address: 2005, Songhu Rd

institute: Fudan University

description:
Library name: virgin_BATT_2d_biol rep 2
10x Genomics

data_processing:
Reads were quality-checked with FastQC, filtered, and processed with Cell Ranger [26] for genome alignment, barcodes demultiplexing, PCR duplicates removal, and unique molecular identifiers (UMIs)-based gene barcode matrices generation.
Assembly: WormBasa ParaSite: Sm_V10
Supplementary files format and content: Tab-seperated values files and metrix files

organism: Schistosoma mansoni

source_name: whole worm

extract_protocol:
Single-cell suspensions were prepared as described by James J Collins (Science, 2020) , and only samples with > 85% (fluorescence-based counting) were used. Suspensions were adjusted to 1,000 cells/μL, and ~10,000 cells per sample were loaded onto the 10x Genomics Chromium platform.
Steps in GEM Creation & Thermal cycling: GEMs (Gel Bead in Emulsion) were constructed for single cell separation according to the number of cells to be harvested. After GEMs were normally formed, GEMs were collected for reverse transcription in a PCR machine for labeling.  Post Cycling Cleanup & cDNA Amplication: The GEMs were oil-treated, and the amplified cDNA was purified by magnetic beads, and then subjected to cDNA amplification and quality inspection.  Library Preparation & Quantification: The 3ʹ Gene Expression Library was constructed with the quality-qualified cDNA. After fragmentation,  adaptor ligation, sample index PCR, etc., the library is finally quantitatively examined.  Sequencing: The final library pool was sequenced on the Illumina HiSEq instrument using 150-base-pair paired-end reads.

value: whole worm


title: Adult schistosomes, 7 weeks post infection, rep1

description:
Library name: adult_females
10x Genomics


title: BCAA_PBS_17_input

description: Library name: 17_02input


title: Virgin schistosomes, BATT 2d, rep3

description:
Library name: virgin_BATT_2d_biol rep 3
10x Genomics


title: BCAA_PBS_24_IgG

description: Library name: 42_IgG


title: C6_Discovery_15

value: Blood cells


title: C6_Discovery_19


title: Virgin schistosomes, BATT 2d, rep1

description:
Library name: virgin_BATT_2d_biol rep 1
10x Genomics


title: N.furzeri_ID8360_old_liver

description: WGBS


title: PBS_PBS_45_IgG

description: Library name: 45_IgG


title: C6_Discovery_16


title: N.furzeri_ID8357_old_liver

description: WGBS


title: N.furzeri_ID8365_young_liver

description: WGBS


title: Virgin schistosomes, DMSO 2d, rep3

description:
Library name: virgin_DMSO_2d_biol rep 3
10x Genomics


title: Sample Met 6

city: London

first: Yong-Jie

last: Lu

address: Barbican

country: United Kingdom

institute: Queen Mary University of London

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: Signal intensity data from SNP arrays were analyzed using allele-specific copy number analysis of tumors (ASCAT) software

label: Biotin

source_name: Prostate cancer metastasis  to bone

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: A standard phenol/chloroform method was used to extract DNA from fresh frozen bone metastases

value: male

value: bone


title: C2_Discovery_12


title: PBS_PBS_23_IgG

description: Library name: 23_IgG


title: Virgin schistosomes, DMSO 2d, rep1

description:
Library name: virgin_DMSO_2d_biol rep 1
10x Genomics


title: BCAA_PBS_17_IgG

description: Library name: 17_IgG


title: C5_Discovery_10


title: N.furzeri_ID8619_young_liver

description: WGBS

value: young


title: high-fat diet + low protein (HF+LP) animal 5

city: Baton Rouge

first: Jaroslaw

last: Staszkiewicz

state: LA

address: 6400 Perkins Rd

department: Genomics Core Facility

institute: Pennington Biomedical Research Center

description: Library name: HF_LP_3.20

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, 3.5.2(2018-12-2), Rstudio V1.2.1511 and biomaRt V2.38.0
DESeq2  V1.22.2 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Assembly: mouse- GRCm38.84
Supplementary files format and content: tab-delimited text file, raw counts

source_name: hear

extract_protocol:
Heart (left ventricular) samples were removed, fresh frozen on liquid nitrogen and RNA was harvested using Trizol and RNAeasy Mini Kit (Cat#ID-74104).
Quant-Seq  3' mRNA-Seq Library Prep Kit

treatment_protocol: Different diets were used as a treatment in this diet

value: hear

value: 18 months

tag: weight

tag: diet


title: C6_Discovery_9

value: M


title: Sample Met 5


title: N.furzeri_ID8362_young_liver

description: WGBS


title: N.furzeri_ID8367_old_brain

description: WGBS

value: brain


title: high-fat diet + low protein (HF+LP) animal 2

description: Library name: HF_LP_2.17


title: C3_Discovery_14


title: PBS_PBS_21_IgG

description: Library name: 21_IgG

value: Liver

value: Male

value: WT C57BL6/J


title: high-fat diet + low protein (HF+LP) animal 4

description: Library name: HF_LP_3.19


title: Virgin schistosomes, DMSO 2d, rep2

description:
Library name: virgin_DMSO_2d_biol rep 2
10x Genomics


title: N.furzeri_ID8359_young_liver

description: WGBS

value: GRZ


title: C6_Discovery_11


title: high-fat diet + low protein (HF+LP) animal 1

description: Library name: HF_LP_1.16


title: C6_Discovery_6


title: Sample Met 4


title: N.furzeri_ID8357_old_brain

description: WGBS


title: C6_Discovery_13


title: 144-13_KDM4A ChIP

city: Houston

first: Guocan

last: Wang

address: 1515 Holcombe Blvd, T7.3900

institute: MD Anderson Cancer Center

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Peaks were called uing MACS v2.1.2
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: 144-13 cells were cultured in HITES medium supplemented with 5% fetal bovine serum using ATCC-formulated RPMI-1640 Medium (Catalog No.30-2001) with the following components to the base medium: 0.005 mg/ml Insulin, 0.01 mg/ml Transferrin, 30 nM Sodium selenite (final conc.), 10 nM Hydrocortisone (final conc.), 10 nM beta-estradiol (final conc.), extra 2mM L-glutamine (final conc. of 4 mM).

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor (Diagenode)
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Human NEPC cell line

tag: chip antibody

value: anti-KDM4A antibody (#5766, lot 021110, Schuele Laboratory)


title: high-fat diet + low protein (HF+LP) animal 3

description: Library name: HF_LP_3.18


title: N.furzeri_ID8364_young_liver

description: WGBS

value: liver


title: high-fat diet (HF) animal 4

description: Library name: HF_3.14

value: HF


title: C6_Discovery_7


title: high-fat diet (HF) animal 3

description: Library name: HF_3.13


title: C2_Discovery_4

value: F


title: high-fat diet (HF) animal 5

description: Library name: HF_3.15


title: N.furzeri_ID8480_old_brain

description: WGBS

value: old


title: C2_Discovery_8

value: Blood cells


title: high-fat diet (HF) animal 2

description: Library name: HF_2.12


title: C2_Discovery_5


title: C2_Discovery_2


title: N.furzeri_ID8364_young_brain

description: WGBS


title: grouped zebrafish whole-larvae 5 dpf, wild-type, rep6

city: Madison

first: Andrew

middle: H

last: Miller

state: WI

address: 1111 Highland Ave

department: Neuroscience

institute: University of Wisconsin-Madison

description: Library name: WT5-6

data_processing:
RNA sequencing was carried out by the Biotechnology Center Gene Expression Center at the University of Wisconsin Madison on an Illumina HiSeq 2500 platform. Transcriptomic data processing adhered to ENCODE Consortium guidelines and best practices for RNA-Seq (ENCODE Project Consortium, 2016). Raw (2×150 bp) Illumina reads were adapter-trimmed using Skewer (v0.1.123; Jiang et al. 2014). Trimmed reads were aligned to the Danio rerio GRCz11 reference genome (NCBI Assembly: GCA_000002035.4) using STAR (v2.5.3a; Dobin et al. 2013), a splice-aware aligner, with gene annotation from Ensembl release 102. Gene- and isoform-level expression quantification was performed with RSEM (v1.3.1; Li and Dewey 2011), which estimates transcript abundance using expectation-maximization. For downstream differential gene expression analysis, expected read counts from RSEM were rounded to the nearest integer and imported into edgeR (v3.28.0; Robinson, McCarthy, and Smyth 2010), run within the R statistical environment (v3.6.2) Library size normalization across samples was performed using the trimmed mean of M-values (TMM) method (Robinson and Oshlack 2010). Genes were retained for statistical testing if they exceeded a count-per-million (CPM) threshold in a minimum number of samples, defined by the number of biological replicates per condition, with a minimum read count of 10. This independent filtering step reduced noise and increased statistical power.
Assembly: Danio rerio GRCz11 reference genome (NCBI Assembly: GCA_000002035.4)
Supplementary files format and content: RSEM files contain expected read counts, TPM, and FPKM for each sample

organism: Danio rerio

source_name: whole-larvae

extract_protocol:
RNA was isolated from groups of 20 whole-larvae at 5 dpf using TRIzol Reagent (Invitrogen) following the manufacturer’s instructions
RNA libraries for RNA-seq were prepared by the Biotechnology Center Gene Expression Center at the University of Wisconsin Madison using commercial kits following the manufacturer's instructions

value: whole-larvae

value: wild-type


title: Sample Met 3

value: male

value: bone


title: Sample Met 1


title: N.furzeri_ID8465_old_brain

description: WGBS


title: N.furzeri_ID8360_old_brain

description: WGBS


title: low protein (LP) animal 5 sample 2

description: Library name: LP_3.10

value: hear

value: 18 months

value: LP


title: 6W_Tail3

city: Fuzhou

first: Jinyan

last: Chen

address: No.7 Wusi Road

institute: Fufian Academy of Medical Sciences

description: Library name: Tail-6

data_processing:
Raw sequencing reads were assessed for quality using FastQC v0.11.7.
Low-quality reads and adapter sequences were removed from the raw data using Cutadapt v1.14. Bowtie was used to align the filtered reads to the reference genome (Rnor6) with default parameters.
miRNA expression levels were quantified and novel miRNAs were predicted using miRDeep2 v0.0.8. Differential expression analysis was performed using edgeR v3.18.1 to identify differentially expressed miRNAs between experimental conditions.
Functional annotation and enrichment analysis were conducted using DAVID to interpret the biological significance of differentially expressed miRNAs.
Assembly: Rnor6
Supplementary files format and content: xlsx file include  CPM values for all samples.

organism: Rattus norvegicus

source_name: islet

extract_protocol:
RNA was harvested using TRIzol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencingn using standard Illumina protocols.

value: islet


title: 144-13_input


title: grouped zebrafish whole-larvae 5 dpf, wild-type, rep5

description: Library name: WT5-5


title: N.furzeri_ID8362_young_brain

description: WGBS

value: brain

value: young


title: N.furzeri_ID8619_young_brain

description: WGBS

value: GRZ


title: Sample Met 2


title: grouped zebrafish whole-larvae 5 dpf, wild-type, rep7

description: Library name: WT5-7


title: C2_Discovery_1

data_processing: ChAMP package in R environment

source_name: Blood cells

extract_protocol: precipitation with sodium acetate

value: M


title: C2_Discovery_3


title: grouped zebrafish whole-larvae 5 dpf, wild-type, rep4

description: Library name: WT5-4


title: grouped zebrafish whole-larvae 5 dpf, wild-type, rep8

description: Library name: WT5-8


title: grouped zebrafish whole-larvae 5 dpf, wild-type, rep3

description: Library name: WT5-3


title: low protein (LP) animal 15

description: Library name: LP_3.9


title: RBOHD S39A/S339A/S343A, botrytis 48 hpi, biol rep 3

city: Kaiserslautern

first: Alejandra

last: VIelba Fernández

state: Rhineland-Palatinate

address: Paul-Ehrlich-Straße 22

department: BIology

institute: RPTU

description: Library name: 1224-12_S12

data_processing:
CLC Genomics Workbench Version 24.0.1
QC Tool: QC for sequencing reads 0.2
Read trimming: trim reads 3.0
RNA-Seq analysis: RNA-Seq Analysis 2.8
DGE: Differential Expression for RNA-Seq 2.8
Assembly: Expression browser: create expression browser 1.1
Supplementary files format and content: Excel file with gene information and total count, RPKM, TPM and CPM per sample

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
Total RNA was extracted with the RNeasy Plant Mini Kit (QIAGEN), treated with DNase I, and assessed on a Bioanalyzer.
Libraries were prepared using the TruSeq Stranded mRNA kit (Illumina) and sequenced on a NovaSeq 6000 (paired-end 150 bp). Reads were mapped to TAIR10 using STAR; differential expression was analyzed with DESeq2 (FDR < 0.05).

value: leaf

value: RBOHD S39A/S339A/S343A

value: Infection with Botrytis cinerea, 48 hpi


title: low protein (LP) animal 20

description: Library name: LP_2.8


title: 6W_Tail1

description: Library name: Tail-4


title: N.furzeri_ID8359_young_brain

description: WGBS

source_name: brain


title: 24W_Tail3

description: Library name: Tail-3


title: grouped zebrafish whole-larvae 5 dpf, wild-type, rep2

description: Library name: WT5-2


title: 6W_Tail2

description: Library name: Tail-5


title: RBOHD S39A/S339A/S343A, mock, biol rep 3

description: Library name: 1224-11_S11

value: Mock


title: low protein (LP) animal 2

description: Library name: LP_1.6


title: grouped zebrafish whole-larvae 5 dpf, nf1 mutant, rep7

description: Library name: N5-7


title: normal protein (NP) animal 6

description: Library name: NP_2.4

value: NP


title: low protein (LP) animal 13

description: Library name: LP_1.7


title: normal protein (NP) animal 8

description: Library name: NP_3.5


title: normal protein (NP) animal 3

description: Library name: NP_2.3


title: grouped zebrafish whole-larvae 5 dpf, wild-type, rep1

description: Library name: WT5-1

value: whole-larvae


title: Col-0, botrytis 48hpi, biol rep 3

description: Library name: 1224-10_S10


title: RBOHD S39A/S339A/S343A, botrytis 48 hpi, biol rep 2

description: Library name: 1224-8_S8


title: 24W_Tail2

description: Library name: Tail-2


title: RBOHD S39A/S339A/S343A, mock, biol rep 2

description: Library name: 1224-7_S7


title: Col-0, botrytis 48hpi, biol rep 2

description: Library name: 1224-6_S6


title: high-fat diet (HF) animal 1

description: Library name: HF_1.11

value: HF


title: grouped zebrafish whole-larvae 5 dpf, nf1 mutant, rep8

description: Library name: N5-8


title: 6W_Head3

description: Library name: Head-6


title: grouped zebrafish whole-larvae 5 dpf, nf1 mutant, rep6

description: Library name: N5-6


title: Col-0, mock, biol rep 3

description: Library name: 1224-9_S9


title: normal protein (NP) animal 4

description: Library name: NP_1.1


title: 24W_Tail1

description: Library name: Tail-1


title: grouped zebrafish whole-larvae 5 dpf, nf1 mutant, rep5

description: Library name: N5-5


title: 6W_Head2

description: Library name: Head-5


title: 24W_Head3

description: Library name: Head-3


title: Col-0, mock, biol rep 2

description: Library name: 1224-5_S5


title: grouped zebrafish whole-larvae 5 dpf, nf1 mutant, rep3

description: Library name: N5-3


title: 24W_Head2

description: Library name: Head-2


title: Col-0, mock, biol rep 1

description: Library name: 1224-1_S1


title: grouped zebrafish whole-larvae 5 dpf, nf1 mutant, rep2

description: Library name: N5-2


title: 6W_Head1

description: Library name: Head-4


title: Small intestine, Muscle, rep1

city: Boston

first: Meenakshi

last: Rao

address: 300 Longwood Ave

department: Pediatrics-Division of Gastroenterology

institute: Boston Children's Hospital

data_processing:
Read depth was calculated using CellRanger and was ~16,000 reads per cell. Single cell analyses were conducted using Seurat 4.3.0 and subpackages
Assembly: mm10
Supplementary files format and content: comma separated values files and matrix files

source_name: small intestinal muscle

extract_protocol:
Single cell suspensions of GFP+ muscularis cells were stained with trypan blue to assess viability and cell concentration. Approximately 4,000 cells per sample were then loaded onto the 10X chromium controller.
Libraries were prepped according to the manufacturer’s protocols (Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 and dual index). Samples were pooled 1:1 prior to sequencing using the Illumina NextSeq 500 150 cycle kit.

value: small intestinal muscle

value: Postnatal Day 21

value: muscularis glia

value: GFP+

value: male


title: Small intestine, Muscle, rep2


title: normal protein (NP) animal 5

description: Library name: NP_3.2

value: hear

value: 18 months


title: N.furzeri_ID8365_young_brain

description: WGBS

value: brain

value: young


title: grouped zebrafish whole-larvae 5 dpf, nf1 mutant, rep1

description: Library name: N5-1


title: Col-0, botrytis 48hpi, biol rep 1

description: Library name: 1224-2_S2


title: grouped zebrafish whole-larvae 5 dpf, nf1 mutant, rep4

description: Library name: N5-4


title: Across PZ and TZ H1-1

status: Public on Jan 27 2026

first: xiao

last: kai

address: YueYang Road 420

institute: SIBCB

description:
Library name: H1-1
10X Genomics

data_processing:
Raw reads were processed using the Seurat v4 and Cell Ranger v2.1 pipelines. Low‑quality nuclei and doublets were removed (nFeature_RNA > 200 < 2500, percent.mt < 20). Batch correction was performed by canonical correlation analysis (CCA). Dimension reduction and clustering were conducted with UMAP and PCA. Differential gene expression and pathway enrichment were analyzed using Seurat and clusterProfiler packages in R 4.2.2.
Assembly: Human reference genome GRCh38 (10x Genomics).
Supplementary files format and content: Processed data include Seurat object (RDS)

molecule: nuclear RNA

source_name: Prostate

extract_protocol:
Formalin‑fixed paraffin‑embedded (FFPE) prostate tissues were deparaffinized, rehydrated, and homogenized in pre‑chilled lysis buffer (CST, Sigma‑Aldrich). Nuclei were isolated and subjected to partial crosslink reversal at 25 °C for 30 min and 80 °C for 15 min in buffer containing 2.4 U/ml Proteinase K and 0.1% SDS. After washing in PBS, nuclei were resuspended for in‑situ reverse transcription with a mixture of random and oligo‑dT primers.
Single‑nucleus cDNA libraries were generated using the SeekOne® Digital Droplet system (SeekGene Biosciences) following the snFLARE‑seq workflow. In‑nucleus reverse transcription products were ligated with barcoded hydrogel beads inside droplets, then template‑switched and amplified by index PCR. Libraries were purified with AMPure XP beads and sequenced on Illumina NovaSeq 6000 or MGI DNBSEQ‑T7 platforms using PE150 chemistry.

treatment_protocol: Patient-derived FFPE tissues were retrospectively collected according to the protocol approved by the Ethics Committee of Nanjing Drum Tower Hospital (ID: 2017-044-02). Informed consent was obtained from all participants.

value: Prostate


title: Across PZ and TZ G1-2

description:
Library name: G1-2
10X Genomics


title: Across PZ and TZ I1-2

description:
Library name: I1-2
10X Genomics


title: 24W_Head1

description: Library name: Head-1

value: islet


title: Across PZ and TZ I1-1

description:
Library name: I1-1
10X Genomics


title: Across PZ and TZ G1-1

description:
Library name: G1-1
10X Genomics


title: Small intestine, Muscle, rep3


title: Across PZ and TZ F1-2

description:
Library name: F1-2
10X Genomics


title: RBOHD S39A/S339A/S343A, mock, biol rep 1

description: Library name: 1224-3_S3

value: leaf

value: RBOHD S39A/S339A/S343A


title: Peripheral zone E1

description:
Library name: E1
10X Genomics


title: Transition_zone D2

description:
Library name: D2
10X Genomics


title: Transition_zone E2-1

description:
Library name: E2-1
10X Genomics


title: RBOHD S39A/S339A/S343A, botrytis 48 hpi, biol rep 1

description: Library name: 1224-4_S4

value: Infection with Botrytis cinerea, 48 hpi


title: Across PZ and TZ H1-2

description:
Library name: H1-2
10X Genomics


title: Transition_zone B1

description:
Library name: B1
10X Genomics


title: MOLM-13 cells, zotatifin, Ribo-seq rep3

first: Peter

last: van Galen

state: Massachusetts

address: 4 Blackfan Circle

department: Hematology

institute: Brigham and Women's Hospital / Broad Institute of MIT and Harvard

description:
Library name: RIBO_ZOT3
RIBO_7_count

library_source: other

data_processing:
RNA-seq: Filter 1 (fastp) - Remove reads containing adapters
RNA-seq: Filter 2 (fastp) - Remove reads containing more than 10% of unknown nucleotides (N)
RNA-seq: Filter 3 (fastp) - Remove reads containing all A Bases
RNA-seq: Filter 4 (fastp) - Remove low quality reads containing more than 50% of low quality (Q-value≤20) bases
RNA-seq: Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were removed. The remaining clean reads were further used in assembly and gene abundance calculation.
RNA-seq: Paired-end clean reads were mapped to the reference genome using HISAT2.2.4 with "-rnastrandness RF" and other parameters set as a default.
Ribo-seq: Filter 1 - Remove reads containing adapter
Ribo-seq: Filter 2 - Remove reads with N ratio greater than 10%
Ribo-seq: Filter 3 - Remove reads that are all A bases
Ribo-seq: Filter 4 - Remove low-quality reads (the number of bases with quality value Q≤20 accounts for more than 50% of the entire read)
Ribo-seq: Only Read 1 data was analyzed since the target RNA fragment of Ribo-seq sequencing is only 30bp
Ribo-seq: The short reads alignment software Bowtie2 (v2.2.8) was used to remove ribosomal RNA, tRNA, snoRNA, snRNA, and miRNA
Ribo-seq: Only the reads with a length of 20bp~40bp were kept
Ribo-seq: The Read 1 data obtained after length filtering were aligned to the reference gene sequence with Star
Assembly: ncbi_GCF_000001405.39_GRCh38.p13
Supplementary files format and content: Tab-delimited text files include raw counts for each sample
Library strategy: Ribo-Seq

molecule: other

growth_protocol: MOLM-13 cells were cultured in RPMI media supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
To prepare samples for ribosome sequencing, 5-10 million cells were pelleted at 500 g for 5 minutes, the supernatant was discarded, and pellets were gently mixed with room temperature culture medium containing cycloheximide (final concentration 0.1 mg/ml). Cells were pelleted again, supernatant discarded, and pellets were gently mixed with pre-cooled PBS containing 0.1 mg/ml cycloheximide. Cells were pelleted again, supernatant discarded, and pellets were snap-frozen in liquid nitrogen for ribosome sequencing.  To prepare samples for RNA sequencing, 5-10 million cells were pelleted and washed with pre-cooled PBS. Cells were pelleted again and TRIzol was added at 1 ml per million cells and pipetted repeatedly until no cell clumps remained. Samples were then snap-frozen in liquid nitrogen and sent to CD Genomics for ribosome sequencing and RNA-sequencing.
At CD Genomics, RNA-seq was performed on the cell pellets. The total RNA-seq protocol included mRNA enrichment by Oligo(dT), RNA fragmentation (200-700 nt), random hexamer primed cDNA synthesis, size selection, PCR amplification, and next generation sequencing.  In parallel, Ribo-seq was performed by processing the ribosome-nascent chain complex (RNC) with RNase to remove ribosome unprotected RNA fragments. Then ribosomes were removed, and finally the small fragments of ~30 bp in-translating RNA protected by ribosomes were detected by next generation sequencing. These ribosome-protected RNA fragments indicate the "footprint" of the ribosome's ongoing translation.

treatment_protocol: Cells were treated for 4 hours with 100 nM of Zotatifin (MedChem Express) or DMSO as control.

value: AML cells

value: Zotatifin


title: Across PZ and TZ F1-1

description:
Library name: F1-1
10X Genomics


title: Peripheral zone D1

description:
Library name: D1
10X Genomics


title: MOLM-13 cells, zotatifin, Ribo-seq rep1

description:
Library name: RIBO_ZOT1
RIBO_5_count


title: Transition_zone E2-2

description:
Library name: E2-2
10X Genomics


title: Peripheral zone A2

description:
Library name: A2
10X Genomics


title: Transition_zone B2

description:
Library name: B2
10X Genomics


title: Transition_zone C1

description:
Library name: C1
10X Genomics


title: Transition_zone A1

description:
Library name: A1
10X Genomics


title: Peripheral zone C2

description:
Library name: C2
10X Genomics


title: MOLM-13 cells, zotatifin, RNA-seq rep3

description:
Library name: RNA_ZOT3
RNA-7_count

data_processing:
RNA-seq: Filter 1 (fastp) - Remove reads containing adapters
RNA-seq: Filter 2 (fastp) - Remove reads containing more than 10% of unknown nucleotides (N)
RNA-seq: Filter 3 (fastp) - Remove reads containing all A Bases
RNA-seq: Filter 4 (fastp) - Remove low quality reads containing more than 50% of low quality (Q-value≤20) bases
RNA-seq: Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were removed. The remaining clean reads were further used in assembly and gene abundance calculation.
RNA-seq: Paired-end clean reads were mapped to the reference genome using HISAT2.2.4 with "-rnastrandness RF" and other parameters set as a default.
Ribo-seq: Filter 1 - Remove reads containing adapter
Ribo-seq: Filter 2 - Remove reads with N ratio greater than 10%
Ribo-seq: Filter 3 - Remove reads that are all A bases
Ribo-seq: Filter 4 - Remove low-quality reads (the number of bases with quality value Q≤20 accounts for more than 50% of the entire read)
Ribo-seq: Only Read 1 data was analyzed since the target RNA fragment of Ribo-seq sequencing is only 30bp
Ribo-seq: The short reads alignment software Bowtie2 (v2.2.8) was used to remove ribosomal RNA, tRNA, snoRNA, snRNA, and miRNA
Ribo-seq: Only the reads with a length of 20bp~40bp were kept
Ribo-seq: The Read 1 data obtained after length filtering were aligned to the reference gene sequence with Star
Assembly: ncbi_GCF_000001405.39_GRCh38.p13
Supplementary files format and content: Tab-delimited text files include raw counts for each sample


title: MOLM-13 cells, zotatifin, RNA-seq rep1

description:
Library name: RNA_ZOT1
RNA-5_count


title: MOLM-13 cells, DMSO, RNA-seq rep1

description:
Library name: RNA_DMSO1
RNA-1_count

value: DMSO


title: DEV16136 12pcw quadriceps tendon (whole)

city: Oxford

first: Sarah

last: Snelling

address: Windmill Road

department: NDORMS

institute: UNIVERSITY OF OXFORD

description:
Library name: Sample 13 (DEV16136-QUAD)
10x Genomics 3' v3.1

data_processing:
Fetal tendon raw sequencing files were aligned with CellRanger153 (v7.0) using 10x Genomics' pre-built GRCh38-2020-A reference (compiled from ENSEMBL's 98th release of the human reference genome) with default settings. Ambient RNA was removed using CellBender154 (v0.2.2) with custom values for expected-cells, total-droplets-included, epochs and low-count-threshold parameters, which were selected based on the properties of individual samples and what was expected. The command was rerun until optimal conditions (training and test loss converging, expected number of cells selected, no error or warning messages in log files) were achieved for each sample. To obtain spliced and unspliced count matrices, velocyto87 (v0.17.17) command line function velocyto run10x was used with the aforementioned reference genome file and a repeat sequences masked gtf file (h38_repeat_mask.gtf) downloaded from UCSC Genome Browser. The resulting loom output files were compared with CellBender output files, then merged using scVelo155 (v0.2.5) function scvelo.utils.merge() to retain overlapping barcodes.
Assembly: GRCh38-2020-A (compiled from ENSEMBL's 98th release of the human reference genome), provided by 10X Genomics
Supplementary files format and content: Gunzipped raw sequencing FASTQ files
Supplementary files format and content: Processed and annotated .h5ad anndata object file containing all samples

source_name: quadriceps tendon

extract_protocol:
Nuclei isolation for fetal and adult tendon samples outlined in Table S1 was carried out following protocols for small tissues developed and published by Mimpen and colleagues from the Tendon Seed Network, found here: https://www.protocols.io/view/adaption-for-small-samples-nuclei-isolation-from-s-rm7vzyx75lx1/v1. Briefly, tendons were cut into ~1 mm pieces on dry ice and dissociated in CST buffer (292 mM NaCl, 20 mM Tris-HCL 7.5 pH, 2 mM CaCl2, 42 mM MgCl2, 0.5% CHAPS, 0.01% BSA, RNase and protease inhibitors) on a rotor for 2 min at 4°C. After addition of PBS with 2% BSA (bovine serum albumin) the suspensions were strained through 20 µm strainers (Greiner Bio-one). The nuclei-containing suspensions were then centrifuged at 500 g for 5 min at 4°C. Following centrifugation, the supernatant was discarded and the nuclei within the pellet were stained with DAPI and counted manually using a haemocytometer (NanoEntek DHC-N01) and fluorescence microscopy.
Nuclear suspensions, diluted in PBS with 1% BSA to a concentration of 200-1000 nuclei/μl, were loaded onto a Chromium Next GEM Chip G (10x Genomics) with the aim of recovering 1,000-10,000 nuclei per sample. The samples were then processed using the Chromium Controller (10x Genomics) and prepared into libraries using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics) following the manufacturer's instructions. Libraries were indexed with the Single Index Kit T Set A (10x Genomics). Quality control assessments for cDNA and final libraries were conducted using D1000 or D5000 High Sensitivity ScreenTape (Agilent) assays on a 4150 TapeStation System (Agilent). The final libraries were pooled together and sequenced using a NovaSeq 6000 (Illumina) by Genewiz (UK) with a minimum sequencing depth of approximately 20,000 read pairs per expected nucleus.

value: quadriceps tendon

value: female

tag: anatomy

value: whole tendon

tag: donor

tag: library prep_batch


title: MOLM-13 cells, DMSO, Ribo-seq rep3

description:
Library name: RIBO_DMSO3
RIBO_3_count


title: DEV16569 17pcw Achilles tendon (whole)

description:
Library name: Sample 14 (DEV16569-ACH)
10x Genomics 3' v3.1

source_name: Achilles tendon

tag: tissue

value: Achilles tendon

tag: Sex


title: MOLM-13 cells, zotatifin, RNA-seq rep2

description:
Library name: RNA_ZOT2
RNA-6_count

tag: cell type


title: Pooled sample of DEV16135 and DEV16171 12pcw quadriceps tendons (whole)

description:
Library name: Sample 11 (DEV16135DEV16171-QUAD)
10x Genomics 3' v3.1

value: male


title: DEV16569 17pcw quadriceps tendon (whole)

description:
Library name: Sample 15 (DEV16569-QUAD)
10x Genomics 3' v3.1


title: MOLM-13 cells, DMSO, RNA-seq rep3

description:
Library name: RNA_DMSO3
RNA-3_count

tag: treatment


title: MOLM-13 cells, DMSO, RNA-seq rep2

description:
Library name: RNA_DMSO2
RNA-2_count

tag: cell line


title: MOLM-13 cells, zotatifin, Ribo-seq rep2

description:
Library name: RIBO_ZOT2
RIBO_6_count


title: DEV16127 17pcw quadriceps tendon (whole)

description:
Library name: Sample 7 (DEV16127-QUAD)
10x Genomics 3' v3.1


title: DEV16136 12pcw Achilles tendon (whole)

description:
Library name: Sample 12 (DEV16136-ACH)
10x Genomics 3' v3.1


title: MOLM-13 cells, DMSO, Ribo-seq rep2

description:
Library name: RIBO_DMSO2
RIBO_2_count


title: DEV16127 17pcw Achilles tendon (whole)

description:
Library name: Sample 6 (DEV16127-ACH)
10x Genomics 3' v3.1


title: DEV15985 20pcw quadriceps tendon (midbody)

description:
Library name: Sample 5 (DEV15985-QUAD)
10x Genomics 3' v3.1

value: midbody


title: DEV16134 12pcw quadriceps tendon (whole)

description:
Library name: Sample 9 (DEV16134-QUAD)
10x Genomics 3' v3.1


title: T1913b2,B2

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description: Library name: T1913b2

data_processing:
trimming using cutadapt implemented in docker4seq version 2.4.8
Mapping on Canis familiaris miRNA precursors (miRBase 22.1), using BWA implemented in docker4seq version 2.4.8
Assembly: Canis familiaris miRNA precursors, miRBase 22.1
Supplementary files format and content: Tab separated file (counts)

organism: Canis lupus familiaris

source_name: Saliva

extract_protocol:
Total RNA was extracted using the MicroRNA Concentrator kit (A&A Biotecnology, Cat. No 035-25C) following the manufacturer’s instructions.
NEBNext Multiplex small RNA Library Prep

value: Saliva

tag: Stage


title: DEV16134 12pcw Achilles tendon (whole)

description:
Library name: Sample 8 (DEV16134-ACH)
10x Genomics 3' v3.1


title: DEV15985 20pcw Achilles tendon (midbody)

description:
Library name: Sample 4 (DEV15985-ACH)
10x Genomics 3' v3.1


title: BT245_RNAseq_CTL.3

first: Jamie

middle: N.

last: Anastas

address: 1 Baylor Plaza

department: Neurosurgery

institute: Baylor College of Medicine

description: Library name: BT245_RNAseq_CTLsg.3

data_processing:
RNAseq reads were aligned to hg38 using STAR
Counts tables were generated using featureCounts
Assembly: hg38
Supplementary files format and content: tab-delimited text files with transcript counts

source_name: glioma

growth_protocol: SU-DIPGXIII cells were maintained as gliomaspheres in DMG media (50:50 DMEM/F12 and Neurobasal A, supplements with B27 minus Vitamin A, heparin, sodium pyruvate, GlutaMAX, MEM non-essential amino acids,  HEPES, Antibiotic-Antimyotic, Heparin, hPDGF-AA, hPDGF-BB, hFGF154, and hEGF) in a humidified chamber with 5% CO2 at 37C

extract_protocol:
RNA was extracted using TRIzol reagent and polyA transcripts were purified.
Paired-end libraries were generated from RNAseq cDNA using an Illumina DNA-Seq library preparation kits (Illumina Technologies).

treatment_protocol: These cells were not treated

value: glioma

value: SU-DIPGXIII

value: diffuse midline glioma

tag: genotype

value: WT


title: Pooled sample of DEV16135 and DEV16171 12pcw Achilles tendons (whole)

description:
Library name: Sample 10 (DEV16135DEV16171-ACH)
10x Genomics 3' v3.1


title: MOLM-13 cells, DMSO, Ribo-seq rep1

description:
Library name: RIBO_DMSO1
RIBO_1_count


title: DEV15984 20pcw quadriceps tendon (midbody)

description:
Library name: Sample 3 (DEV15984-QUAD)
10x Genomics 3' v3.1


title: R2209b1less3,B1<3anni

description: Library name: R2209b1less3


title: DEV15984 20pcw Achilles tendon (midbody)

description:
Library name: Sample 2 (DEV15984-ACH)
10x Genomics 3' v3.1


title: BT245_RNAseq_CTL.1

description: Library name: BT245_RNAseq_CTLsg.1


title: BT245_RNAseq_SGF29sgC.2

description: Library name: BT245_RNAseq_SGF29sgC.2

value: SGF29 KO


title: ACL_iNSCs_PN59

city: Kyoto

first: Makoto

last: Ikeya

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

country: Japan

institute: Kyoto University

description: Library name: ChRN0415

data_processing:
Single cell RNA-seq: The processing, filtration, analysis, and plotting of data were done in Python using Scanpy
Assembly: hg38
Supplementary files format and content: Single cell RNA-seq: filtered feature bc matrix  h5 file

source_name: hindbrain

extract_protocol:
5000 cells from each sample were processed anhd prepared using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 from 10x Genomics
Single cell RNA-seq: sequencing library using the Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 from 10x Genomics, according to the standard procedures recommended by the manufacturer (Dual Index). After cDNA synthesis, size (TapeStation) and concentration (Qubit) measurements were performed. The size (TapeStation) and concentration (qPCR method) were performed after library preparation.

value: hindbrain

value: Stem cells

tag: timepoint


title: DEV15983 20pcw Achilles tendon (midbody)

description:
Library name: Sample 1 (DEV15983-ACH)
10x Genomics 3' v3.1


title: R2209a,A

description: Library name: R2209a

value: A


title: P1940b2,B2

description: Library name: P1940b2


title: R1710b2,B2

description: Library name: R1710b2


title: P1927b1more3,B1>3 anni

description: Library name: P1927b1more3

value: B1>3 anni


title: T1906b1more3,B1>3 anni

description: Library name: T1906b1more3


title: CONDRO_TNB_CTRL_9_L1_R1_001_WAxUZlTj23UF.fastq.gz

city: Bologna

first: Stefania

last: D'Adamo

state: BO

address: Via Irnerio 48

department: DIBINEM

institute: University of Bologna

description:
Library name: Sample 5
Column name in "Primary Chondrocytes_tRF_LPS vs Ctrl_raw counts.csv" and "Primary Chondrocytes_tRF_LPS vs Ctrl_DESeq2 Normalized counts.csv" CONDRO_TNB_CTRL_9_L1_R1_001_WAxUZlTj23UF

data_processing:
CLC Genomics Workbench v23.0.5
3' adapter trimming and UMI reads collpsing with CLC Genomics Workbench v23.0.5  ((Minimum length of miRNA: 15, Maximum length of miRNA: 55, UMI length: 12, Maximum size of small UMI groups: 1, Common sequence: AACTGTAGGCACCATCAAT, Maximum differences in common sequence: 1)
Trimmed reads were mapped and quantified using MINTmap v1.0 (a dedicated tool for tRNA-derived fragment profiling.) in default mode. Mapping was performed against the human genome using a curated tRNA reference set derived from gtRNAdb release v1.0 and including both nuclear- and mitochondrial-encoded tRNAs, as implemented by default in MINTmap.
Low-abundance features were filtered prior to differential expression analysis using the Thresholdseq R package (v1.1). Differential expression analysis was performed using DESeq2 (R package v1.42.1) applying a patients-paired experimental design to compare LPS-treated and non-treated primary chondrocytes.
An annotation metadata file was generated to integrate DESeq2 output with additional information on tRNA-derived fragments, including tRF sequence, structural category, and parental tRNA origin. Annotation was derived from MINTmap results and cross-referenced with MINTbase 2.0.
Assembly: gtRNAdb release v1.0
Supplementary files format and content: Primary Chondrocytes_tRF_LPS vs Ctrl_raw counts.csv File which includes raw counts for all samples
Supplementary files format and content: Primary Chondrocytes_tRF_LPS vs Ctrl_DESeq2 Normalized counts.csv File which includes size factors-adjusted DEseq2 Normalized counts for all samples
Supplementary files format and content: Primary Chondrocytes_tRF_annotation_MINTmap_MINTbase_LPS_vs_CTRL.csv  Annotation file linking MINTmap license plate identifiers to tRNA-derived fragment sequences, structural categories, parental tRNA origin, and corresponding MINTbase 2.0 unique identifiers.

source_name: Cartilage

growth_protocol: Human articular chondrocytes were isolated from femoral condyles and tibial plateaus of OA patients undergoing total knee arthroplasty at the Rizzoli Orthopaedic Institute. Primary chondrocytes at P0–P1 were used for small RNA sequencing and qPCR validation. Primary chondrocytes were plated at high density (250,000 cells/well in 12-well plates) 48–72 h before treatment.

extract_protocol:
Total RNA was isolated from primary chondrocytes using the miRNeasy Micro Kit (Qiagen), following the manufacturer’s instructions. To improve ligation and reverse transcription efficiency of modified tRNA fragments, RNA was pre-treated using the rtStar™ tRF&tiRNA Pretreatment Kit
RNA library preparation was conductuced by the QIAseq miRNA Library Illumina kit (#331502, Qiagen) accordingly to the manufacturer's protocol

treatment_protocol: Inflammatory stress was induced with LPS (10 µg/mL, Sigma) for 6 h

value: Cartilage

value: Chondrocytes

value: Wt

value: Ctrl


title: ACL_iNSCs_PN41

description: Library name: ChRN0414


title: P1933b2,B2

description: Library name: P1933b2


title: CONDRO_TGA_CTRL_7_L1_R1_001_3I58HCgbb9Mo.fastq.gz

description:
Library name: Sample 3
Column name in "Primary Chondrocytes_tRF_LPS vs Ctrl_raw counts.csv" and "Primary Chondrocytes_tRF_LPS vs Ctrl_DESeq2 Normalized counts.csv": CONDRO_TGA_CTRL_7_L1_R1_001_3I58HCgbb9Mo


title: S2010a,A

description: Library name: S2010a


title: S1820b2,B2

description: Library name: S1820b2


title: BT245_RNAseq_CTL.2

description: Library name: BT245_RNAseq_CTLsg.2


title: CONDRO_SCB_LPS_4_L1_R1_001_mQ6i5Qk9l264.fastq.gz

description:
Library name: Sample 2
Column name in "Primary Chondrocytes_tRF_LPS vs Ctrl_raw counts.csv" and "Primary Chondrocytes_tRF_LPS vs Ctrl_DESeq2 Normalized counts.csv": CONDRO_SCB_LPS_4_L1_R1_001_mQ6i5Qk9l264

value: 10 ug/mL LPS for 6h


title: ACL_iNSCs_PN5

description: Library name: ChRN0412


title: BT245_RNAseq_SGF29sgC.1

description: Library name: BT245_RNAseq_SGF29sgC.1


title: K2301b1less3,B1<3anni

description: Library name: K2301b1less3


title: L2320b1less3,B1<3anni

description: Library name: L2320b1less3


title: CONDRO_SCB_CTRL_3_L1_R1_001_sdifJ3zu9GBd.fastq.gz

description:
Library name: Sample 1
Column name in "Primary Chondrocytes_tRF_LPS vs Ctrl_raw counts.csv" and "Primary Chondrocytes_tRF_LPS vs Ctrl_DESeq2 Normalized counts.csv": CONDRO_SCB_CTRL_3_L1_R1_001_sdifJ3zu9GBd


title: ACL_iNSCs_PN21

description: Library name: ChRN0413


title: M2001a,A

description: Library name: M2001a


title: R1709b1more3,B1>3 anni

description: Library name: R1709b1more3


title: G2219a,A

description: Library name: G2219a


title: RfxCas13d-TP53g1-rep1

first: Li

last: Zhixue

address: 320 Yueyang Road, Xuhui District

institute: CAS Center for Excellence in Molecular Cell Science

description:
Library name: RfxCas13d-TP53g1-rep1
RfxCas13d-TP53g1-rep1

data_processing:
Adapters were trimmed from the raw paired-end fastq reads using Trim-Galore (v.0.0.6) with the parameters –quality 20 --stringency=1 --length=35 --paired.
The remaining reads were mapped to the human genome (hg38) using the STAR program (v.2.7.9a).
Gene abundance was normalized as TPM (transcripts per million).
Assembly: hg38
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

source_name: Human embryonic kidney

growth_protocol: Lenti-X 293T cells were maintained in DMEM supplemented with 10% Fetal Bovine Serum at 37℃ with 5% CO2.

extract_protocol:
RNA was isolated by standard Trizol-chloroform extraction according to the manufacturer’s instructions
mRNA libraries were constructed using Smart-seq2 as previously described. Briefly, 10 ng of total RNA was reverse transcribed using ProtoScript II Reverse Transcriptase (NEB, M0368). After PCR pre-amplification, cDNA libraries were purified using Agencourt Ampure XP beads (Beckman Coulter, A63881) and 2 ng of purified cDNA was used for the next tagmentation reaction. The final amplified libraries were purified again by Agencourt Ampure XP beads and sequenced at 2×150 bp on Illumina NovaSeq 6000 platform.

treatment_protocol: Lenti-X 293T cells transfected with the indicated plasmids were treated with 10 ng/ml Doxycycline for the induction of dPspCas13 or dRfxCas13d protein.

value: Human embryonic kidney

value: Epithelial cell


title: G2139b1more3,B1>3 anni

description: Library name: G2139b1more3

value: Saliva


title: RfxCas13d-TP53g1-rep2

description:
Library name: RfxCas13d-TP53g1-rep2
RfxCas13d-TP53g1-rep2


title: CONDRO_TNB_LPS_10_L1_R1_001_jJgM5Ct6K9db.fastq.gz

description:
Library name: Sample 6
Column name in "Primary Chondrocytes_tRF_LPS vs Ctrl_raw counts.csv" and "Primary Chondrocytes_tRF_LPS vs Ctrl_DESeq2 Normalized counts.csv": CONDRO_TNB_LPS_10_L1_R1_001_jJgM5Ct6K9db


title: G2022b1less3,B1<3anni

description: Library name: G2022b1less3


title: RfxCas13d-TP53g1-rep3

description:
Library name: RfxCas13d-TP53g1-rep3
RfxCas13d-TP53g1-rep3


title: G1915b2,B2

description: Library name: G1915b2


title: RfxCas13d-EZH2g2-rep2

description:
Library name: RfxCas13d-EZH2g2-rep2
RfxCas13d-EZH2g2-rep2


title: CONDRO_TGA_LPS_8_L1_R1_001_5AhT0ZyPe2PI.fastq.gz

description:
Library name: Sample 4
Column name in "Primary Chondrocytes_tRF_LPS vs Ctrl_raw counts.csv" and "Primary Chondrocytes_tRF_LPS vs Ctrl_DESeq2 Normalized counts.csv": CONDRO_TGA_LPS_8_L1_R1_001_5AhT0ZyPe2PI


title: G2301b1less3,B1<3anni

description: Library name: G2301b1less3


title: RfxCas13d-gNT-rep3

description:
Library name: RfxCas13d-NT-rep3
RfxCas13d-gNT-rep3


title: RfxCas13d-EZH2g1-rep1

description:
Library name: RfxCas13d-EZH2g1-rep1
RfxCas13d-EZH2g1-rep1


title: RfxCas13d-EZH2g2-rep1

description:
Library name: RfxCas13d-EZH2g2-rep1
RfxCas13d-EZH2g2-rep1


title: sgSLC25A12 SLC25A12-F137S dMTS-DELE1, Antimycin A, biological replicate 2

first: Guan

last: Jialiang

state: Beijing

address: China, Beijing, Haidian district, Peking University, 1000871

institute: Peking University

description: Library name: S5-2

data_processing:
Raw reads were trimmed to remove adaptor sequences and low-quality bases. Cleaned reads were aligned to the mouse reference genome (hg38) using HISAT2 (v2.1.0). Gene expression was quantified using featureCounts (v2.0.6).
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each sample. Rows correspond to genes and columns correspond to samples.

source_name: kidney

growth_protocol: HEK293T cells (ATCC CRL-3216) were cultured in high-glucose Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (Hyclone). Cells were maintained at 37°C in a humidified atmosphere with 5% CO2 and confirmed to be free of mycoplasma contamination.

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent following the manufacturer's protocol.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). A certain amount of RNA are denatured at suitable temperature to open the secondary structure, and mRNA is enriched by oligo (dT) attached magnetic beads. After reacting at a suitable temperature for a fixed time period, RNAs are fragmented with fragmentation reagents. Then First-strand cDNA is generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesized double strand cDNA is subject to end repairment reaction. After cDNA end repairment, a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments through A tailing reaction. Then the reaction system for adaptor ligation configured to ligate adaptors with the cDNAs, and finally, the library products are amplified through PCR reaction and subjected to quality control. Next, the single-stranded library products are produced via denaturation. The reaction system for circularization is set up to get the single-stranded cyclized DNA products. Any uncyclized single stranded linear DNA molecules will be digested. The final single strand circularized library is amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule. The DNBs are loaded into the patterned nanoarray and PE 150 bases reads are generated on T7 platform (BGI-Shenzhen, China).

treatment_protocol: Cells were treated with vehicle or 40 nM Antimycin A for 6 hours.

value: kidney

value: human embryonic kidney 293 cells

value: SLC25A12 knockout

value: Antimycin A


title: F2205a,A

description: Library name: F2205a


title: RfxCas13d-gNT-rep2

description:
Library name: RfxCas13d-NT-rep2
RfxCas13d-gNT-rep2


title: RfxCas13d-EZH2g1-rep2

description:
Library name: RfxCas13d-EZH2g1-rep2
RfxCas13d-EZH2g1-rep2


title: C2324b1less3,B1<3anni

description: Library name: C2324b1less3


title: C2004b1more3,B1>3 anni

description: Library name: C2004b1more3


title: sgSLC25A12 SLC25A12-F137S dMTS-DELE1, Antimycin A, biological replicate 4

description: Library name: S5-4


title: RfxCas13d-gNT-rep1

description:
Library name: RfxCas13d-NT-rep1
RfxCas13d-gNT-rep1


title: sgSLC25A12 SLC25A12-F137S dMTS-DELE1, Antimycin A, biological replicate 1

description: Library name: S5-1


title: sgSLC25A12 SLC25A12-F137S dMTS-DELE1, Antimycin A, biological replicate 3

description: Library name: S5-3


title: RfxCas13d-EZH2g2-rep3

description:
Library name: RfxCas13d-EZH2g2-rep3
RfxCas13d-EZH2g2-rep3


title: sgSLC25A12 SLC25A12-F137S, Antimycin A, biological replicate 4

description: Library name: S4-4


title: F2205b1more3,B1>3 anni

description: Library name: F2205b1more3


title: sgSLC25A12 SLC25A12-F137S, Antimycin A, biological replicate 2

description: Library name: S4-2


title: PspCas13b-TP53g1-rep3

description:
Library name: PspCas13b-TP53g1-rep3
PspCas13b-TP53g1-rep3


title: B2229a,A

description: Library name: B2229a


title: B2229b1more3,B1>3 anni

description: Library name: B2229b1more3


title: PspCas13b-TP53g1-rep2

description:
Library name: PspCas13b-TP53g1-rep2
PspCas13b-TP53g1-rep2


title: RfxCas13d-rep3

description:
Library name: RfxCas13d-rep3
RfxCas13d-rep3


title: PspCas13b-EZH2g2-rep2

description:
Library name: PspCas13b-EZH2g2-rep2
PspCas13b-EZH2g2-rep2


title: PspCas13b-TP53g1-rep1

description:
Library name: PspCas13b-TP53g1-rep1
PspCas13b-TP53g1-rep1


title: PspCas13b-EZH2g2-rep3

description:
Library name: PspCas13b-EZH2g2-rep3
PspCas13b-EZH2g2-rep3


title: sgSLC25A12 SLC25A12-F137S, Antimycin A, biological replicate 3

description: Library name: S4-3


title: RfxCas13d-EZH2g1-rep3

description:
Library name: RfxCas13d-EZH2g1-rep3
RfxCas13d-EZH2g1-rep3


title: sgSLC25A12 SLC25A12-WT, Antimycin A, biological replicate 4

description: Library name: S3-4


title: PspCas13b-EZH2g2-rep1

description:
Library name: PspCas13b-EZH2g2-rep1
PspCas13b-EZH2g2-rep1


title: sgSLC25A12 SLC25A12-WT, Antimycin A, biological replicate 2

description: Library name: S3-2


title: RfxCas13d-rep2

description:
Library name: RfxCas13d-rep2
RfxCas13d-rep2


title: RfxCas13d-rep1

description:
Library name: RfxCas13d-rep1
RfxCas13d-rep1


title: PspCas13b-EZH2g1-rep3

description:
Library name: PspCas13b-EZH2g1-rep3
PspCas13b-EZH2g1-rep3


title: sgSLC25A12 vector, Antimycin A, biological replicate 2

description: Library name: S2-2


title: PspCas13b-EZH2g1-rep2

description:
Library name: PspCas13b-EZH2g1-rep2
PspCas13b-EZH2g1-rep2


title: sgSLC25A12 vector, Antimycin A, biological replicate 1

description: Library name: S2-1


title: sgSLC25A12 vector, Antimycin A, biological replicate 4

description: Library name: S2-4


title: PspCas13b-gNT-rep1

description:
Library name: PspCas13b-NT-rep1
PspCas13b-gNT-rep1


title: PspCas13b-gNT-rep2

description:
Library name: PspCas13b-NT-rep2
PspCas13b-gNT-rep2


title: WT vector, Antimycin A, biological replicate 4

description: Library name: S1-4

value: wild type


title: Control-rep6

description:
Library name: Control-rep6
Control-rep6


title: WT vector, Antimycin A, biological replicate 2

description: Library name: S1-2


title: PspCas13b-rep3

description:
Library name: PspCas13b-rep3
PspCas13b-rep3


title: sgSLC25A12 SLC25A12-F137S dMTS-DELE1, normal, biological replicate 3

description: Library name: N5-3

value: Normal


title: PspCas13b-EZH2g1-rep1

description:
Library name: PspCas13b-EZH2g1-rep1
PspCas13b-EZH2g1-rep1


title: PspCas13b-rep1

description:
Library name: PspCas13b-rep1
PspCas13b-rep1


title: PspCas13b-rep2

description:
Library name: PspCas13b-rep2
PspCas13b-rep2


title: WT vector, Antimycin A, biological replicate 1

description: Library name: S1-1


title: PspCas13b-gNT-rep3

description:
Library name: PspCas13b-NT-rep3
PspCas13b-gNT-rep3


title: sgSLC25A12 SLC25A12-WT, Antimycin A, biological replicate 1

description: Library name: S3-1


title: WT vector, Antimycin A, biological replicate 3

description: Library name: S1-3


title: Control-rep5

description:
Library name: Control-rep5
Control-rep5


title: sgSLC25A12 SLC25A12-F137S dMTS-DELE1, normal, biological replicate 2

description: Library name: N5-2


title: sgSLC25A12 SLC25A12-F137S dMTS-DELE1, normal, biological replicate 4

description: Library name: N5-4


title: sgSLC25A12 vector, Antimycin A, biological replicate 3

description: Library name: S2-3


title: sgSLC25A12 SLC25A12-F137S, normal, biological replicate 4

description: Library name: N4-4


title: sgSLC25A12 SLC25A12-F137S dMTS-DELE1, normal, biological replicate 1

description: Library name: N5-1


title: sgSLC25A12 SLC25A12-F137S, Antimycin A, biological replicate 1

description: Library name: S4-1


title: sgSLC25A12 SLC25A12-F137S, normal, biological replicate 3

description: Library name: N4-3


title: Control-rep4

description:
Library name: Control-rep4
Control-rep4


title: PBL from P3

city: Little Rock

first: Yong-Chen

middle: William

address: 4301 W Markham St

department: Pathology

institute: University of Arkansas for Medical Sciences

description:
Library name: P3-PBL
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger-multi software (v7.1.0 ) for CITEseq (5' RNA, FB and TCR) or Cell-Ranger ATAC software (v2.1.0)
Assembly: scRNAseq (GRCh38-2020-A) scTCRseq(GRCh38-alts-ensembl-7.1.0) scATACseq (GRCh38-r107)
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_contig_annotations.csv.gz
Supplementary files format and content: CellRanger-ATAC output files: filtered_peak_bc_matrix.h5, fragments.tsv.gz, singlecell.csv.gz

source_name: PBL

extract_protocol:
Tumor specimens were dissociated by a gentleMACS dissociator (Miltenyi Biotec) and cryopreserved. After thawing, CD3+ live cells were sorted by FACS and subjected to scATACseq sample preparation. PBL samples from the same patients were also sorted for live cells for scATACseq sample preparation.
Libraries were prepared according to manufactures' instruction (single-cell 5' immune profiling and single-cell ATAC) (10X Genomics)

treatment_protocol: PBMCs from healthy donors were stimulated with CD3/CD28 beads from day 0 to day 10, followed by 5-FU or cisplatin treatment from day 3 to day 7. The stimulation and treatment were repeated for a total of 3 cycles.

value: PBL


title: TIL from  P2

description:
Library name: P2-TIL
10X Genomics

source_name: Metastatic colorectal cancer

value: Metastatic colorectal cancer

value: TIL


title: TIL from  P3

description:
Library name: P3-TIL
10X Genomics


title: sgSLC25A12 SLC25A12-WT, Antimycin A, biological replicate 3

city: Beijing

description: Library name: S3-3


title: sgSLC25A12 SLC25A12-F137S, normal, biological replicate 2

description: Library name: N4-2


title: PBL from P2

description:
Library name: P2-PBL
10X Genomics


title: PBL from P1

description:
Library name: P1-PBL
10X Genomics


title: sgSLC25A12 SLC25A12-WT, normal, biological replicate 4

description: Library name: N3-4


title: T cells from donor D1007, cisplatin(CIS)-treated TMRM low, ATAC

description:
Library name: D1007-CIS-TMRM-Low-ATAC
10X Genomics

source_name: T cells from a healthy donor

value: T cells from a healthy donor

value: T cells

value: Cisplatin-treated


title: sgSLC25A12 SLC25A12-F137S, normal, biological replicate 1

description: Library name: N4-1


title: sgSLC25A12 SLC25A12-WT, normal, biological replicate 3

description: Library name: N3-3


title: sgSLC25A12 vector, normal, biological replicate 4

description: Library name: N2-4


title: sgSLC25A12 SLC25A12-WT, normal, biological replicate 1

description: Library name: N3-1


title: sgSLC25A12 vector, normal, biological replicate 2

description: Library name: N2-2


title: TIL from  P1

description:
Library name: P1-TIL
10X Genomics


title: WT vector, normal, biological replicate 3

description: Library name: N1-3


title: WT vector, normal, biological replicate 2

description: Library name: N1-2


title: T cells from donor D2008, cisplatin(CIS)-treated TMRM low, ATAC

description:
Library name: D2008-CIS-TMRM-Low-ATAC
10X Genomics


title: T cells from donor D2008, cisplatin(CIS)-treated, ATAC

description:
Library name: D2008-CIS-ATAC
10X Genomics


title: T cells from donor D6053, cisplatin(CIS)-treated, ATAC

description:
Library name: D6053-CIS-ATAC
10X Genomics


title: sgSLC25A12 vector, normal, biological replicate 3

description: Library name: N2-3


title: WT vector, normal, biological replicate 4

description: Library name: N1-4


title: WT vector, normal, biological replicate 1

description: Library name: N1-1


title: sgSLC25A12 SLC25A12-WT, normal, biological replicate 2

description: Library name: N3-2


title: T cells from donor D6053, without cisplatin (NC), ATAC

description:
Library name: D6053-NC-ATAC
10X Genomics

value: unstimulated


title: T cells from donor D1007, without cisplatin (NC), ATAC

description:
Library name: D1007-NC-ATAC
10X Genomics


title: T cells from donor D1007, cisplatin(CIS)-treated MASS high, ATAC

description:
Library name: D1007-CIS-MASS-Hi-ATAC
10X Genomics


title: T cells from donor D2008, cisplatin(CIS)-treated TMRM high, ATAC

description:
Library name: D2008-CIS-TMRM-Hi-ATAC
10X Genomics


title: hnRNPF-knockout iCCA cells-2

city: Xi’an

first: Jianlin

state: shaanxi

address: 127 West Changle Street

institute: Fourth Military Medical University

description:
Library name: R_KO_2
Column name in gene_count_matrix.csv: R_KO_2

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GRCh38/hg38 using CLC genomic benchwork (parameters-mismath cost:2insertion cost:3 deletion cost:3 length fraction:0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCh38/hg38
Supplementary files format and content: raw counts for each Sample

source_name: liver

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: liver

value: iCCA cell

value: hnRNPF-knockout


title: sgSLC25A12 vector, normal, biological replicate 1

description: Library name: N2-1


title: T cells from donor D0010, 5-FU-treated, ATAC

description:
Library name: D0010-5FU-ATAC
10X Genomics


title: hnRNPF-knockout iCCA cells-3

description:
Library name: R_KO_3
Column name in gene_count_matrix.csv: R_KO_3


title: T cells from donor D1007, cisplatin(CIS)-treated TMRM high, ATAC

description:
Library name: D1007-CIS-TMRM-Hi-ATAC
10X Genomics


title: T cells from donor D6053, untreated (N), ATAC

description:
Library name: D6053-N-ATAC
10X Genomics


title: T cells from donor D1007, cisplatin(CIS)-treated MASS low, ATAC

description:
Library name: D1007-CIS-MASS-Low-ATAC
10X Genomics


title: T cells from donor D1007, cisplatin(CIS)-treated, ATAC

description:
Library name: D1007-CIS-ATAC
10X Genomics


title: parental iCCA cells-3

description:
Library name: R_NC_3
Column name in gene_count_matrix.csv: R_NC_3

value: parental


title: T cells from donor D0010, untreated (N), ATAC

description:
Library name: D0010-N-ATAC
10X Genomics


title: hnRNPF-knockout iCCA cells-1

description:
Library name: R_KO_1
Column name in gene_count_matrix.csv: R_KO_1


title: parental iCCA cells-1

description:
Library name: R_NC_1
Column name in gene_count_matrix.csv: R_NC_1


title: control_mitosis

city: Sapporo

first: Hideki

last: Tanizawa

state: Hokkaido

address: Kita 15, Nishi 7, Kita-ku

department: Institute for Genetic Medicine

institute: Hokkaido University

data_processing:
In situ Hi-C data were processed using the rfy_hic2 package (https://github.com/rafysta/rfy_hic2)
Processed HiC data were converted to juicer format using the pre command of JUICER program (version 1.22.01)
Assembly: S.pombe (2018)
Supplementary files format and content: Juicer format

organism: Schizosaccharomyces pombe

extract_protocol:
Fission yeast cells (approximately 5 x 108 cells at OD595 = 0.5) were fixed with 3% pFA at 26°C for 10 minutes and disrupted with glass beads using Mini-Beadbeater-16 (BioSpec Products) in lysis buffer [50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1 mM PMSF, and EDTA-free Protease Inhibitor Cocktail (Roche)].  After washing with 1 ml PBS solution, the cells were further fixed with 3 mM disuccinimidyl glutarate (Thermo Fisher Scientific) in 2.5 ml PBS solution at 30°C for 40 minutes.  The fixed cells were incubated at 62°C for 7 minutes with 0.1% SDS and subsequently with 1% Triton-X 100.  The permeabilized cells were incubated with 25 units of MboI, HinfI, and MluCI at 37°C overnight.  The pellet containing restriction enzyme-digested DNA fragments was treated with 150 μM biotin-14-dATP, dCTP, dGTP, and dTTP and incubated with 20 units of Klenow fragment (NEB) at 37°C for 45 minutes, followed by proximity ligation using 2,500 units of T4 DNA ligase (NEB) at room temperature for 4 hours with a gentle rotation.  After ligation, the pellet was subjected to proteinase K treatment at 68°C overnight in the presence of 0.5 M NaCl.
DNA was purified by phenol/chloroform extraction and ethanol precipitation.  The purified DNA was sheared into 100–500 bp fragments by Bioruptor UCD-200 (Diagenode).  Biotin-labeled DNA was purified using Dynabeads MyOne Streptavidin T1 (Thermo Fisher Scientific).  Sequencing adapters were ligated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) while DNA was bound to the beads.  Sequencing libraries were amplified by PCR using the NEBNext Ultra II Q5 Master Mix (NEB) with NEBNext Multiplex Oligos for Illumina (NEB).

tag: strain

tag: restriction enzyme

value: MboI, HinfI, MluCI


title: T cells from donor D6053, 5-FU-treated, ATAC

last: Lu

description:
Library name: D6053-5FU-ATAC
10X Genomics


title: Overexpression of gene atp8 in plant 2 and overexpression group 3

city: Changchun

first: Bo

last: Xu

address: 5268 Renmin Street

department: College of Forestry and Grassland Science

institute: Jilin Agricultural University

description:
Library name: atp8-OE2_3
Column name in gene_count.xls:atp8-OE2-3

data_processing:
Clean reads obtained after quality filtering were aligned to the M.sativa reference genome (Zhongmu No. 4) using HISAT2 (v2.2.1)(Long et al. 2022). Transcript assembly and gene expression quantification were performed based on the reference genome annotation. Differentially expressed genes were identified using DESeq2, with genes showing an adjusted P value < 0.05 considered significantly differentially expressed.
Assembly: M.sativa reference genome (Zhongmu No. 4)
Supplementary files format and content: Excel read count of genes for each sample

organism: Medicago sativa

source_name: flowers

extract_protocol:
Transcriptome sequencing was performed by Wuhan MetWare Biotechnology Co., Ltd. using a standard plant mRNA-seq workflow. Anther samples from wild-type (WT) plants and two atp8 overexpression lines (atp8-OE1 and atp8-OE2) were collected, with three independent biological replicates per genotype. Total RNA was extracted following standard protocols, and RNA quality was assessed prior to library construction.
RNA sequencing was conducted by Illumina platforms based on sequencing-by-synthesis (SBS) technology.

value: flowers


title: T cells from donor D2008, untreated (N), ATAC

description:
Library name: D2008-N-ATAC
10X Genomics


title: HD_mitosis


title: T cells from donor D2008, 5-FU-treated, ATAC

description:
Library name: D2008-5FU-ATAC
10X Genomics


title: T cells from donor D1007, untreated (N), ATAC

description:
Library name: D1007-N-ATAC
10X Genomics


title: Overexpression of gene atp8 in plant 2 and overexpression group 1

description:
Library name: atp8-OE2_1
Column name in gene_count.xls:atp8-OE2-1


title: T cells from donor D1007, 5-FU-treated, ATAC

description:
Library name: D1007-5FU-ATAC
10X Genomics


title: Overexpression of gene atp8 in plant 2 and overexpression group 2

description:
Library name: atp8-OE2_2
Column name in gene_count.xls:atp8-OE2-2


title: T cells from donor D6053, 5-FU-treated, TCR

description:
Library name: D6053-5FU-TCR
10X Genomics


title: T cells from donor D6053, untreated (N), GEX

description:
Library name: D6053-N-GEX
10X Genomics


title: T cells from donor D6053, untreated (N), TCR

description:
Library name: D6053-N-TCR
10X Genomics


title: parental iCCA cells-2

last: Wang

description:
Library name: R_NC_2
Column name in gene_count_matrix.csv: R_NC_2


title: Overexpression of gene atp8 in plant 1, and overexpression group 3

description:
Library name: atp8-OE1_3
Column name in gene_count.xls:atp8-OE1-3


title: Overexpression of gene atp8 in plant 1 and overexpression group 2

description:
Library name: atp8-OE1_2
Column name in gene_count.xls:atp8-OE1-2


title: T cells from donor D2008, 5-FU-treated, TCR

description:
Library name: D2008-5FU-TCR
10X Genomics


title: Wild plant control group 3

description:
Library name: WT_3
Column name in gene_count.xls:WT-3


title: T cells from donor D2008, without cisplatin (NC), ATAC

description:
Library name: D2008-NC-ATAC
10X Genomics


title: Overexpression of gene atp8 in plant 1 and overexpression group 1

description:
Library name: atp8-OE1_1
Column name in gene_count.xls:atp8-OE1-1


title: T cells from donor D2008, 5-FU-treated, GEX

description:
Library name: D2008-5FU-GEX
10X Genomics


title: T cells from donor D6053, 5-FU-treated, GEX

description:
Library name: D6053-5FU-GEX
10X Genomics


title: Wild plant control group 2

description:
Library name: WT_2
Column name in gene_count.xls:WT-2


title: T cells from donor D2008, untreated (N), GEX

description:
Library name: D2008-N-GEX
10X Genomics


title: T cells from donor D1007, 5-FU-treated, GEX

description:
Library name: D1007-5FU-GEX
10X Genomics