title: Rad21_0H_4C-seq_rep2

description:
Library name: Rad21_0H_rep2
raw_fragment_counts_depletions.rds

value: untreated


title: Ctr_D_2

status: Public on Apr 15 2026

type: SRA

city: Hefei

first: Jianhua

last: Qin

state: Anhui

address: No.96 JinZhai Road Baohe District

department: School of Biomedical engineering

country: China

institute: University of Science and Technology of China

description: Library name: Ctr_D_2

library_source: transcriptomic

data_processing:
STAR software (version 2.5.3a) with default parameters
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
Assembly: GRCh38_release110
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Brain

extract_protocol:
Total RNA was extracted from iBMECs and brain cells separately using TRizol reagent (Invitrogen) . cDNA synthesis was performed using PrimeScript RT Master Mix kit (TaKaRa; Cat #: RR036A) .
2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

tag: tissue

value: Brain

tag: cell line

value: human induced pluripotent stem cells

tag: cell type

value: iPSC-derived brain microvascular endothelial cells

tag: treatment

value: Control


title: Ctr_D_1

description: Library name: Ctr_D_1


title: SL IP rep1

city: Dallas

first: Zheng

last: Xing

state: TX

address: 5323 Harry Hines Blvd.

country: USA

institute: UT Southwestern

description: Library name: Sample 7

data_processing:
Reference genome Saccharomyces cerevisiae (R64-1-1) and gene model annotation files were downloaded from ensembl. Index of the reference genome was built, and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: Saccharomyces cerevisiae (R64-1-1)
Supplementary files format and content: Read count normalized by ERCC spike-in in excel format

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: yeast

extract_protocol:
Total RBA was extracted using acidic phenol extraction and polyA RNA was putified with oligo dT dynabeads.
Library was constructed by Novogene using the SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input as intructed by the manufacturer.

value: yeast

tag: genotype

value: MATa CEN.PK

value: SL 1h


title: Ctr_U_1

description: Library name: Ctr_U_1

value: iPSC-derived pericytes and astrocytes


title: Rad21_0H_4C-seq_rep1

city: Amsterdam

first: Elzo

last: de Wit

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description:
Library name: Rad21_0H_rep1
raw_fragment_counts_depletions.rds

library_source: genomic

data_processing:
Restriction fragment maps for the DpnII and Csp6I digestion were created using the R/Bioconductor package Biostrings.
Viewpoints were demultiplexed by scanning raw reads for viewpoint-specific primer sequences.
For the allele-resolved 4C, the reads were further split into alleles based on the sequenced bases at the SNP positions located downstream from the reverse primers.
Reads were aligned to the mm10 genome using bwa-aln (v0.7.17-r1188) and filtered for paired and uniquely mapped reads using samtools (v1.19.2).
Fragment counts were generated by counting the reads with exact matches of start or end positions to fragment boundaries. The fragment counts were scaled to the total library counts per million and smoothed using a rolling mean with a window size of 21 fragments.
Assembly: mm10
Supplementary files format and content: rds files contain raw fragment counts as a RangedSummarizedExperiment object
Library strategy: 4C-Seq

molecule: genomic DNA

organism: Mus musculus

source_name: Embryo

growth_protocol: Mouse embryonic stem cell lines were cultured as described previously (Liu et al., 2021, 2025; van Schaik et al., 2022). Briefly, the degron-tagged cell lines and the 129/Castaneus F1 hybrid methylation reporter cell lines were cultured on 0.1% gelatin-coated plates in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1) supplemented with N-2 (Gibco), B-27 (Gibco), BSA (0.05%, Gibco), 10 4 U of Leukaemia Inhibitory Factor (LIF) (Millipore), MEK inhibitor PD0325901 (1 μM, Selleckchem), GSK3-β inhibitor CHIR99021 (3 μM, Cayman Chemical) and 1-Thioglycerol (1.5 × 10-4 M, Sigma-Aldrich). The cell lines were passaged every 2  days in daily culture.

extract_protocol:
10 million cells were collected per sample. Cells were crosslinked, lysed, and chromatin was digested with the primary restriction enzyme DpnII. After ligation, crosslinks were reversed and DNA was purified according to established 4C-seq protocols (van de Werken et al., 2012; Haarhuis et al., 2017).
Purified 4C DNA was digested with the secondary restriction enzyme Csp6I and religated to generate small circular DNA fragments. These fragments were amplified by PCR using viewpoint-specific primers. Libraries were indexed using a two-step PCR method to enable multiplexed sequencing. For allele-resolved 4C-seq, a reverse primer specific to a single nucleotide variant was used. Final PCR products were purified and quantified prior to sequencing.

value: Embryo

value: RAD21-AID mESC

value: Embryonic stem cells


title: ratlungN

city: Milwaukee

first: Masaki

last: Lin

state: Wisconsin

address: 8701 W Watertown Plank Rd

institute: Medical College of Wisconsin

description:
Library name: Sample 2
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: rn6
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rattus norvegicus

source_name: lung

extract_protocol:
Freshly obtained rat whole lungs were finely chopped before treatment with 0.1 mg/mL collagenase-D in DMEM and 100ug/mL DNase-I for 1 h. The treated tissue was mashed through a 100 µm cell strainer and washed with 20 mL DMEM containing 10% FBS and 1% antibiotics. The cell suspension was centrifuged for 5 min at 300g to pellet the cells. Red cells were removed by the lysis buffer at room temperature for 60 seconds. The suspension was then serially washed with PBS containing 0.01% BSA before centrifuging at 300 g for 5 min and went through a 70 µm cell strainer once and 40 µm cell strainers twice.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)

value: lung

tag: strain

value: Outbred

value: all lung cell types

tag: age

value: room air (NOX)

value: PBS


title: ratlungHtaurine

description:
Library name: Sample 3
10x Genomics

value: >90% oxygen (HOX)

value: taurine (100 mg/kg)


title: hippocampus, EtOH+UA, rep7

city: Xian yang

first: Hongbo

last: Zhang

state: Shannxi

address: Xi nong road

department: College of Food Science and Engineering

institute: Northwest A&F University

data_processing:
Data filtering:The raw data was filtered with SOAPnuke (v1.5.2)  by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 10%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 50%, afterwards clean reads were obtained and stored in FASTQ format.
Reference genome mapping：The clean data were mapped to the reference genome by HISAT (v2.1.0)
Reference gene mapping:The clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5). The expression level of genes was calculated by RSEM (v1.2.8).
The gene expression FPKM values were calculated using StringTie based on the consensus transcript.
Differential Gene Expression: Within-group differential gene analysis was performed using DESeq under the conditions of Fold Change ≥ 2 and Adjusted P value ≤ 0.001. PossionDis was performed between-group differential gene analysis under the conditions of Fold Change ≥ 2 and FDR ≤ 0.001. Using the pheatmap function on the differential gene set to draw a heatmap of differential gene clusters. According to the GO and KEGG annotation results and classifications, the differentially expressed genes were functionally classified, the phyper in R software was used for KEGG enrichment analysis, and the TermFinder package was used for GO Enrichment analysis (https://metacpan.org/pod/GO::TermFinder). With a Q value of ≤ 0.05 as the threshold, candidate genes that met this condition were defined as significantly enriched.
Gene-set enrichment analysis (GSEA) was performed on genes ranked by their differential expression Signal2Noise using GSEA software (4.3.0 from Broad Institute). KEGG pathway database were downloaded from https://www.kegg.jp/kegg .bin/search_pathway_text?map=mmu&keyword=&mode=1&viewImage=truehttps://www.kegg.jp/kegg .
Assembly: The clean data were mapped to the reference genome by HISAT (v2.1.0)
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: hippocampus

extract_protocol:
A phenol-chloroform extraction
RNA libraries were prepared for sequencing using standard MGISEQ-2002RS protocols

value: hippocampus

value: WT

value: alcohol diet + urolithin A


title: ratlungNtaurine

description:
Library name: Sample 4
10x Genomics


title: JQ1_18h_dTAG_3h_4C-seq_rep2

description:
Library name: JQ1_18h_dTAG_3h_rep2
raw_fragment_counts_ibet.rds

value: 129/CAST F1 hybrid SCR methylation reporter mESC

value: JQ1 18h + dTAG-13 3h


title: YPL IP rep1

description: Library name: Sample 5

value: yeast

value: MATa CEN.PK

value: YPL


title: YPL IP rep2

description: Library name: Sample 6


title: SL IN rep2

description: Library name: Sample 4

value: SL 1h


title: ratlungH

description:
Library name: Sample 1
10x Genomics


title: hippocampus, EtOH+UA, rep4


title: JQ1_18h_dTAG_3h_4C-seq_rep1

description:
Library name: JQ1_18h_dTAG_3h_rep1
raw_fragment_counts_ibet.rds

value: Embryo

value: Embryonic stem cells


title: hippocampus, EtOH+UA, rep5


title: cup-4_mRNA_R3

city: Tel Aviv

first: Hila

last: Gingold

address: 30 Haim Levanon Street

country: Israel

institute: Tel-Aviv University

description:
Library name: Sample 11
cup4-3_S6
Count_table_mrna.csv

data_processing:
small RNA: fastq output files were first assessed for quality, using FastQC
The files were then assigned to adapters clipping using Cutadapt
Next, the clipped reads were aligned against the ce11 version of the C. elegans genome using ShortStack
We counted reads which align in antisense orientation to genes, using the python-based script HTSeq-count and the corresponding Ensembl-provided gff file (release-95)
We then assigned the summarized counts for differential expression analysis using the R package DESeq2 and limited the hits for genes which were shown to have an FDR < 0.1
mRNA: mRNA libraries were first assessed for quality using  FastQC
libraries were then aligned to ce11 version of the genome using HISAT2
The aligned reads were then counted using the python-based script HTSeq-count and the Ensembl-provided gff file (release-95).
Next, the samples were compared for differential expression using the R package DESeq2. Genes were regarded as differentially expressed if they pass the criterion of FDR < 0.1
Assembly: ce11 version of the C. elegans genome
Supplementary files format and content: csv files containing read counts per gene per sample

organism: Caenorhabditis elegans

source_name: Germline

extract_protocol:
RNA extraction: 3 freeze/thaw cycles - -80 ˚C for 30 minutes followed by 15 minutes vortex at room temperature. 1 volume of chloroform was added to 5 volumes of Trizol+gonads. The mix was put in a pre-spun 2mL Heavy Phase-Lock tube and centrifuged at 16000 g for 5 minutes at 4 ˚C. The aqueous phase was transferred to new pre-spun 2mL Heavy Phase-Lock tube, and 1 volume of Phenol:Chloroform:Isoamyl alcohol (sigma) was added per 1 volume of aqueous phase. The tube was centrifuged at 16000 g at room temperature. Aqueous phase was transferred to Eppendorf tube and precipitated with 1 volume of isopropanol and 1.3 μL glycogen (20 μg/μL). the tubes were put for 30 minutes at -20 ˚C before centrifugation at 16000 g at 4˚C. Pellet was washed with 900μL of cold 70% EtOH, and left at room temperature for 20 minutes before being left at -20˚C over night. The next morning, the tube was centrifuged at 16000 g for 10 minutes, and the pellet was washed again with cold 70% EtOH. Tubes were centrifuged at 16000 g for 10 minutes, all EtOH was removed and pellet was resuspended in 12 μL of warm (70˚C) ddH2O. RNA concentration was determined using Qbit and RNA quality was tested using Agilent 2200 TapeStation.
The NEBNext® Multiplex Small RNA Library Prep Set for Illumina® from New England Biolabs® was used for small RNA library preparation. The NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® from New England Biolabs® was used for mRNA library preparation.

value: Germline

tag: developmental stage

value: day one adult nematodes

tag: batch


title: hippocampus, EtOH+UA, rep6


title: cup-4_mRNA_R2

description:
Library name: Sample 10
cup4-2_S3
Count_table_mrna.csv


title: cup-4_mRNA_R1

description:
Library name: Sample 9
cup4-1_S1
Count_table_mrna.csv


title: hippocampus, EtOH+UA, rep3


title: JQ1_18h_DMSO_3h_4C-seq_rep1

description:
Library name: JQ1_18h_DMSO_3h_rep1
raw_fragment_counts_ibet.rds

value: JQ1 18h + DMSO 3h


title: JQ1_18h_DMSO_3h_4C-seq_rep2

description:
Library name: JQ1_18h_DMSO_3h_rep2
raw_fragment_counts_ibet.rds


title: SL IN rep1

description: Library name: Sample 3


title: YPL IN rep1

description: Library name: Sample 1


title: iBet_18h_dTAG_3h_4C-seq_rep2

description:
Library name: iBet_18h_dTAG_3h_rep2
raw_fragment_counts_ibet.rds

value: iBET151 18h + dTAG-13 3h


title: YPL IN rep2

description: Library name: Sample 2


title: N2_WT_mRNA_R3

description:
Library name: Sample 8
wt-3_S13
Count_table_mrna.csv


title: hippocampus, EtOH+UA, rep2


title: iBet_18h_dTAG_3h_4C-seq_rep1

description:
Library name: iBet_18h_dTAG_3h_rep1
raw_fragment_counts_ibet.rds


title: N2_WT_mRNA_R2

description:
Library name: Sample 7
wt-2_S5
Count_table_mrna.csv


title: Callus, 12DAC

city: Seoul

first: Soon Hyung

last: Bae

state: South Korea

address: Gwanak-ro 1, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
Raw reads from the scRNA-seq were processed, mapped, and quantified using the 10x Genomics CellRanger (v7.0.0) pipeline.
Assembly: TAIR10
Supplementary files format and content: Tab-separated values files and matrix files for each sample
Supplementary files format and content: rds file

organism: Arabidopsis thaliana

source_name: leaf explant-derived callus

extract_protocol:
After harvesting and chopping calli with scissors, the calli were incubated in digestion buffer at 25°C for 1 hour at 55 rpm on an orbital shaker in the dark. Then calli were gently digested with brushes or syringe needles to let protoplasts loose from the tissues for 15-20 minutes. After additional digestion at 25°C for 1 hour at 55 rpm, protoplasts were filtered twice through 40 µm cell strainers. Filtered protoplasts were centrifuged for 10 minutes at 100 g, then washed 8% mannitol twice. After centrifugation, the pellet was resuspended with 8% mannitol and 0.04% BSA.
The protoplast solution prepared from callus was loaded into 10x Genomics Chromium Controller to generate Gel Bead-in-Emulsions (GEMs). Library construction with these GEMs was performed with the Chromium Single Cell 3’ Gel Bead and Library Kit v3.1 (PN-1000269) following the user guide (CG000315).

value: leaf explant-derived callus


title: Callus, 7DAC


title: hippocampus, EtOH+UA, rep1


title: cup-4_sRNA_R3

description:
Library name: Sample 6
antisense orientation
R3-Gonads-cup4-TAP_S1
Count_table_srna_as.csv


title: iBet_18h_DMSO_3h_4C-seq_rep2

description:
Library name: iBet_18h_DMSO_3h_rep2
raw_fragment_counts_ibet.rds

value: iBET151 18h + DMSO 3h


title: cup-4_sRNA_R2

description:
Library name: Sample 5
antisense orientation
R2-Gonads-cup4-TAP_S5
Count_table_srna_as.csv


title: hippocampus, EtOH, rep7

value: hippocampus

value: alcohol diet


title: iBet_18h_DMSO_3h_4C-seq_rep1

description:
Library name: iBet_18h_DMSO_3h_rep1
raw_fragment_counts_ibet.rds


title: tts-2(cdb550) mir-35(cdb2 cdb6), L1, rep 2

city: Bethesda

first: Katherine

last: McJunkin

state: Maryland

address: 50 South Dr, Building 50 Room 3148

institute: NIDDK/ NIH

description:
Library name: sAG700
new_tts-2_rawcounts.csv

library_source: other

data_processing:
Adaptor trimming with cutadapt(ver 5.0) with the -q 20 flag
Mapping with bowtie2 (ver. 2.5.3) with --no-unal --end-to-end –sensitive -U flags
BAM indexing with samtools (ver 1.21)
Raw counts generated from htseq (ver. 2.0.4) with --mode union --nonunique fraction -a 0 flags
Assembly: WS280
Supplementary files format and content: Matrix of raw counts from Htseq output

molecule: other

source_name: Whole worm

growth_protocol: C. elegans were grown at 20C on NGM plates.

extract_protocol:
Total RNA was extracted using Trizol.
Libraries were prepared using the NEB small RNA kit with a modified protocol.

value: Whole worm

value: tts-2(seed_mut); mir-35(seed_mut)


title: hippocampus, EtOH, rep6

value: WT


title: GFP_SCR_only_4C-seq_rep2

description:
Library name: GFP_SCR_only_rep2
raw_fragment_counts_methyl_undepleted.rds

value: 129/CAST F1 hybrid SCR methylation reporter mESC


title: GFP_prom_only

description:
Library name: GFP_prom_only
raw_fragment_counts_methyl_undepleted.rds


title: N2_WT_sRNA_R2

description:
Library name: Sample 2
antisense orientation
R2-Gonads-WT-TAP_S7
Count_table_srna_as.csv


title: tts-2(cdb550) mir-35(cdb2 cdb6), embryo, rep 3

description:
Library name: sNC91
new_tts-2_rawcounts.csv


title: N2_WT_sRNA_R3

description:
Library name: Sample 3
antisense orientation
R3-Gonads-WT-TAP_S3
Count_table_srna_as.csv


title: tts-2(cdb550) mir-35(cdb2 cdb6), embryo, rep 2

description:
Library name: sAG696
new_tts-2_rawcounts.csv


title: hippocampus, EtOH, rep4


title: tts-2(cdb550) mir-35(cdb2 cdb6), L1, rep 3

description:
Library name: sNC94
new_tts-2_rawcounts.csv


title: N2_WT_sRNA_R1

description:
Library name: Sample 1
antisense orientation
R1-Gonads-WT-TAP_S11
Count_table_srna_as.csv


title: hippocampus, EtOH, rep3


title: cup-4_sRNA_R1

description:
Library name: Sample 4
antisense orientation
R1-Gonads-cup4-TAP_S9
Count_table_srna_as.csv


title: hippocampus, EtOH, rep2


title: tts-2(cdb550) mir-35(cdb2 cdb6), embryo, rep 1

description:
Library name: sAG695
new_tts-2_rawcounts.csv


title: GFP_SCR_only_4C-seq_rep1

description:
Library name: GFP_SCR_only_rep1
raw_fragment_counts_methyl_undepleted.rds


title: GFP_dTAG_3h_4C-seq_rep2

description:
Library name: GFP_dTAG_3h_rep2
raw_fragment_counts_methyl_depleted.rds

value: 129/CAST F1 hybrid SCR methylation reporter/RAD21-FKBP mESC

value: dTAG-13 3h


title: tts-2(cdb550) mir-35(cdb2 cdb6), L1, rep 1

description:
Library name: sAG699
new_tts-2_rawcounts.csv


title: 5 month tert -/- testes, fish 51

city: Boston

first: Kavita

last: Venkataramani

state: MA

address: 100 Morrissey Blvd

department: Biology

institute: University of Massachusetts

description:
Library name: 5M-M51
5 month tert -/- zebrafish testis RNAs

data_processing:
The reads were aligned to the GRCzv11 assembly of the zebrafish genome (Ensembl) using the program Salmon and the gene annotations published by the Lawson lab
Deseq2 was used for counting with a cut off value for fold change of >1.5 and false discovery rate (FDR) of >0.05.
Clusterprofiler was used for gene ontology (GO) analysis and visualization.
The pheatmap package was used for heatmap generation
Assembly: Ens99/GRCzv11
Supplementary files format and content: salmon quant.sf files

organism: Danio rerio

source_name: Testis

growth_protocol: Zebrafish were raised and maintained in a recirculating system under standard conditions. Animal Care and Use Committee approval was received prior to carrying out all procedures on animals

extract_protocol:
RNeasy micro kit (Qiagen), with the second RPE Buffer wash replaced with an 80% ethanol wash
RNA was sent to Genewiz at Azenta Life Sciences, NJ for library preparation and sequencing. The samples underwent library preparation with the poly-A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform

value: Testis

value: tert-/-, Mut

value: 5 month


title: hippocampus, EtOH, rep5


title: 5 month tert -/- testes, fish 47

description:
Library name: 5M-M47
5 month tert -/- zebrafish testis RNAs


title: mir-35(cdb2 cdb6), L1, rep 3

description:
Library name: sNC92
new_tts-2_rawcounts.csv


title: GFP_dTAG_3h_4C-seq_rep1

description:
Library name: GFP_dTAG_3h_rep1
raw_fragment_counts_methyl_depleted.rds

value: Embryo

value: Embryonic stem cells


title: hippocampus, EtOH, rep1


title: hippocampus, Ctrl, rep9

value: control diet


title: 5 month tert -/- testes, fish 46

description:
Library name: 5M-M46
5 month tert -/- zebrafish testis RNAs


title: GFP_DMSO_3h_4C-seq_rep3

description:
Library name: GFP_DMSO_3h_rep3
raw_fragment_counts_methyl_depleted.rds

value: DMSO 3h


title: GFP_dTAG_3h_4C-seq_rep3

description:
Library name: GFP_dTAG_3h_rep3
raw_fragment_counts_methyl_depleted.rds


title: hippocampus, Ctrl, rep8


title: mir-35(cdb2 cdb6), L1, rep 1

description:
Library name: sAG697
new_tts-2_rawcounts.csv


title: hippocampus, Ctrl, rep7


title: GFP_DMSO_3h_4C-seq_rep2

description:
Library name: GFP_DMSO_3h_rep2
raw_fragment_counts_methyl_depleted.rds


title: 5 month tert -/- testes, fish 49

description:
Library name: 5M-49
5 month tert -/- zebrafish testis RNAs


title: mir-35(cdb2 cdb6), embryo, rep 3

description:
Library name: sNC89
new_tts-2_rawcounts.csv


title: mir-35(cdb2 cdb6), L1, rep 2

description:
Library name: sAG698
new_tts-2_rawcounts.csv


title: hippocampus, Ctrl, rep6


title: GFP_DMSO_3h_4C-seq_rep1

description:
Library name: GFP_DMSO_3h_rep1
raw_fragment_counts_methyl_depleted.rds


title: mir-35(cdb2 cdb6), embryo, rep 2

description:
Library name: sAG694
new_tts-2_rawcounts.csv


title: hippocampus, Ctrl, rep5


title: GFP_both_VP

description:
Library name: GFP_both_VP
raw_fragment_counts_methyl_undepleted.rds


title: mir-35(cdb2 cdb6), embryo, rep 1

description:
Library name: sAG693
new_tts-2_rawcounts.csv


title: 5 month tert +/+ testes, fish 56

description:
Library name: 5m-C56
5 month tert +/+ zebrafish testis RNAs

value: tert+/+; WT


title: 5 month tert +/+ testes, fish 54

description:
Library name: 5m-C54
5 month tert +/+ zebrafish testis RNAs


title: hippocampus, Ctrl, rep4


title: DP_SCR_only_4C-seq_rep2

description:
Library name: DP_SCR_only_rep2
raw_fragment_counts_methyl_undepleted.rds


title: 5 month tert +/+ testes, fish 53

description:
Library name: 5m-C53
5 month tert +/+ zebrafish testis RNAs


title: tts-2(cdb491), L1 stage, rep 3

description:
Library name: sAG687
new_tts-2_rawcounts.csv


title: hippocampus, Ctrl, rep3


title: 3 month tert -/- testes, fish 3

description:
Library name: 3m-M3
3 month tert -/- zebrafish testis RNAs

value: 3 month


title: 5 month tert +/+ testes, fish 58

description:
Library name: 5m-C58
5 month tert +/+ zebrafish testis RNAs


title: DP_prom_only

description:
Library name: DP_prom_only
raw_fragment_counts_methyl_undepleted.rds


title: DP_SCR_only_4C-seq_rep1

description:
Library name: DP_SCR_only_rep1
raw_fragment_counts_methyl_undepleted.rds


title: tts-2(cdb491), L1 stage, rep 1

description:
Library name: sAG666
new_tts-2_rawcounts.csv


title: tts-2(cdb491), L1 stage, rep 2

description:
Library name: sAG683
new_tts-2_rawcounts.csv


title: hippocampus, Ctrl, rep2

value: hippocampus


title: 3 month tert -/- testes, fish 2

description:
Library name: 3m-M2
3 month tert -/- zebrafish testis RNAs


title: hippocampus, Ctrl, rep1


title: tts-2(cdb489), L1 stage, rep 3

description:
Library name: sAG686
new_tts-2_rawcounts.csv


title: 3XFLAG::ALG-2;ebax-1(null), embryos, crosslinked, rep 4

description:
Library name: sKM360
C.elegans_CLASH_counts.csv

data_processing:
Cutadapt v2.10with the parameters -a TGGAATTCTCGGGTGCCAAG -A GATCGTCGGACTGTAGAACT
Paired-end reads were merged using PEAR v0.9.6
deduplication with fastx_collapser v0.0.14
Unique molecular identifiers (UMIs) were trimmed using Cutadapt (-u 4 -u -4 -m 18)
Processed reads were analyzed with Hyb
Assembly: WBcel235
Supplementary files format and content: csv with raw counts per library and matching genomic features

extract_protocol:
RNA was isolated via phenol:choloroform extraction after proteinase K treatment of immunoprecipitated protein
eCLIP libraries were prepared according to Manakov et al. bioRxiv, (2022).

value: alg-2(cdb12 cdb51) II; ebax-1(tm2321) IV


title: 3 month tert -/- testes, fish 10

description:
Library name: 3m-M10
3 month tert -/- zebrafish testis RNAs


title: tts-2(cdb489), L1 stage, rep 2

description:
Library name: sAG682
new_tts-2_rawcounts.csv

value: Whole worm


title: DP_dTAG_3h_4C-seq_rep2

description:
Library name: DP_dTAG_3h_rep2
raw_fragment_counts_methyl_depleted.rds


title: DP_dTAG_3h_4C-seq_rep3

description:
Library name: DP_dTAG_3h_rep3
raw_fragment_counts_methyl_depleted.rds


title: 3 month tert -/- testes, fish 15

description:
Library name: 3m-M15
3 month tert -/- zebrafish testis RNAs


title: DP_DMSO_3h_4C-seq_rep3

description:
Library name: DP_DMSO_3h_rep3
raw_fragment_counts_methyl_depleted.rds


title: wild type, embryos, crosslinked, rep 2

description:
Library name: sKM358
C.elegans_CLASH_counts.csv

value: wild type


title: DP_dTAG_3h_4C-seq_rep1

description:
Library name: DP_dTAG_3h_rep1
raw_fragment_counts_methyl_depleted.rds


title: 3XFLAG::ALG-2, embryos, crosslinked, rep 4

description:
Library name: sKM359
C.elegans_CLASH_counts.csv

value: alg-2(cdb12 cdb51) II


title: 3XFLAG::ALG-2;ebax-1(null), embryos, crosslinked, rep 3

description:
Library name: sKM357
C.elegans_CLASH_counts.csv


title: 3 month tert +/+ testes, fish 17

description:
Library name: 3m-C17
3 month tert +/+ zebrafish testis RNAs


title: wildtype, L1 stage, rep 3

description:
Library name: sAG685
new_tts-2_rawcounts.csv


title: 3 month tert +/+ testes, fish 12

description:
Library name: 3m-C12
3 month tert +/+ zebrafish testis RNAs


title: tts-2(cdb489), L1 stage, rep 1

description:
Library name: sAG665
new_tts-2_rawcounts.csv


title: wildtype, L1 stage, rep 2

description:
Library name: sAG681
new_tts-2_rawcounts.csv


title: DP_DMSO_3h_4C-seq_rep2

description:
Library name: DP_DMSO_3h_rep2
raw_fragment_counts_methyl_depleted.rds


title: DP_both_VP

description:
Library name: DP_both_VP
raw_fragment_counts_methyl_undepleted.rds

value: 129/CAST F1 hybrid SCR methylation reporter mESC


title: alg-1(gk214) X , L1, rep 3

description: Library name: sBD585


title: 3 month tert +/+ testes, fish 1

description:
Library name: 3m-C1
3 month tert +/+ zebrafish testis RNAs


title: DMSO_6h_DMSO_3h_4C-seq_rep2

description:
Library name: DMSO_6h_DMSO_3h_rep2
raw_fragment_counts_ibet.rds

value: DMSO 9h


title: DMSO_6h_dTAG_3h_4C-seq_rep1

description:
Library name: DMSO_6h_dTAG_3h_rep1
raw_fragment_counts_ibet.rds

value: DMSO 6h + dTAG-13 3h


title: 3XFLAG::ALG-2, embryos, crosslinked, rep 3

description:
Library name: sKM356
C.elegans_CLASH_counts.csv


title: alg-1(gk214) X , embryo, rep 3

description: Library name: sBD582


title: wild type, embryos, crosslinked, rep 1

description:
Library name: sKM355
C.elegans_CLASH_counts.csv


title: splenic B220+ (Miz-1WT) replicate 2

city: Montréal

first: Tarik

last: Moroy

address: 110 Pine Ave W, Montreal

country: Canada

institute: IRCM

description: Library name: MIZ-1WT Rep2

data_processing:
Reads were mapped on the GRCm38 v77 genome using Tophat v2.1.0
Raw counts were obtained using the HTSeqCount software
Assembly: GRCm38
Supplementary files format and content: Comma-separated file that contains the raw counts

source_name: spleen

extract_protocol:
For RNA isolation, B220+ splenocytes were lysed in TRI Reagent (Sigma) and isolated RNA was cleaned using the RNeasy Mini Kit (Qiagen). For RNA sequencing (RNA-seq), a biological duplicate of sequencing libraries was prepared from RNA extracts.
Ribosomal RNA were depleted (Ribo-Zero™ Magnetic Gold Kit, Epicentre) and library was prepared using KAPA Stranded RNA-Seq Kit with RiboErase. NGS sequencing (pair-end 50 cycles) was done on HiSeq 2000/2500 System (Illumina).

value: spleen

value: WT


title: alg-1(gk214) X, embryo, rep 2

description: Library name: sBD576


title: wildtype, L1 stage, rep 1

description:
Library name: sAG664
new_tts-2_rawcounts.csv


title: alg-1(gk214) X, L1, rep 2

description: Library name: sBD579


title: splenic B220+ (Miz-1DPOZ) replicate 2

description: Library name: MIZ-1DPOZ Rep2

value: Miz-1 deltaPOZ


title: splenic B220+ (Miz-1DPOZ) replicate 1

description: Library name: MIZ-1DPOZ Rep1


title: DMSO_6h_dTAG_3h_4C-seq_rep2

description:
Library name: DMSO_6h_dTAG_3h_rep2
raw_fragment_counts_ibet.rds

value: Embryo


title: ChIP splenic B220+ (Miz-1DPOZ)

description: Library name: MIZ-1DPOZ ChIP

data_processing:
Reads were mapped on the UCSC mm10 reference genome using bowtie2 v.2.2.6
Peaks were called using MACS v2.1.0 with a q-value cutoff of 0.01
Assembly: mm10
Supplementary files format and content: narrowPeak (except for Input samples)

extract_protocol:
10 million cells were fixed with 1% Formaldehyde for 10 minutes with agitation at room temperature. Fixation was blocked by the addition of 125 mM glycine for 5 minutes with agitation at room temperature.
Protein-chromatin complexes were collected using dynabeads overnight with agitation at 4°C. Complexes bound beads were then washed and eluted from beads for 4h at 65°C. RNAse and proteinase K were added to the mix for 1h at 42°C. DNA was extracted using QIAquick kit (Qiagen). DNA was then used to prepare librairies (KAPA Hyper Kit) for NGS sequencing (pair-end, 50 cycles) on HiSeq 2000/2500 System (Illumina).

value: Miz-1 delta POZ

tag: chip antibody


title: DP_DMSO_3h_4C-seq_rep1

description:
Library name: DP_DMSO_3h_rep1
raw_fragment_counts_methyl_depleted.rds

value: 129/CAST F1 hybrid SCR methylation reporter/RAD21-FKBP mESC

value: Embryonic stem cells


title: alg-1(gk214) X, L1, rep 1

description: Library name: sBD573


title: Input splenic B220+ (Miz-1DPOZ)

description: Library name: MIZ-1DPOZ Input


title: splenic B220+ (Miz-1WT) replicate 1

description: Library name: MIZ-1WT Rep1


title: 3XFLAG::ALG-2;ebax-1(null), embryos, crosslinked, rep 2

description:
Library name: sKM282
C.elegans_CLASH_counts.csv


title: 3XFLAG::ALG-2;ebax-1(null), embryos, crosslinked, rep 1

description:
Library name: sKM278
C.elegans_CLASH_counts.csv


title: 3XFLAG::ALG-2, embryos, crosslinked, rep 1

description:
Library name: sKM277
C.elegans_CLASH_counts.csv


title: 3XFLAG::ALG-2, embryos, crosslinked, rep 2

description:
Library name: sKM281
C.elegans_CLASH_counts.csv


title: DMSO_6h_DMSO_3h_4C-seq_rep1

description:
Library name: DMSO_6h_DMSO_3h_rep1
raw_fragment_counts_ibet.rds


title: Ctcf_6H_4C-seq_rep2

description:
Library name: Ctcf_6H_rep2
raw_fragment_counts_depletions.rds

value: CTCF-AID mESC

value: auxin 6h


title: ChIP splenic B220+ (Miz-1WT)

description: Library name: MIZ-1WT ChIP


title: alg-2(ok304) II, L1, rep 3

description: Library name: sBD584

value: alg-2(ok304) II


title: alg-1(gk214) X, embryo, rep 1

description: Library name: sBD570


title: S2

type: other

city: Cincinnati

first: Yunguan

last: Wang

state: oh

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

data_processing: Spatial gene expression was decoded using the MERlin pipeline on the VizGen MERSCOPE platform (software version 234b). Cell segmentation was performed using a VizGen-optimized implementation of the Cellpose algorithm on the DAPI and cell boundary images.

source_name: Liver

extract_protocol: Needle biopsies from two PSC patients with early stage of disease were collected under IRB protocol IRB#2017-2284 and IRB#2016-7388. Freshly cut, unstained sections from archived FFPE liver biopsies of these two patients were mounted to slides provided by VizGen for hybridization according to the vendor’s instructions.

tag: subject status

value: 12-year-old male with elevated liver function tests and abnormal liver imaging who was diagnosed with PSC based on biopsy findings

value: Liver


title: Ctcf_3H_4C-seq_rep2

description:
Library name: Ctcf_3H_rep2
raw_fragment_counts_depletions.rds

value: auxin 3h


title: miRNA_BM39W_3

city: Guangzhou

first: ling

last: ma

state: Guangdong

address: No. 9 Jinsui Road, Tianhe District, Guangzhou City, Guangdong province

institute: Guangzhou Women and Children’s Medical Center

description: Library name: miRNAsample7

data_processing:
scRNA-seq data, raw reads were processed using Cell Ranger (v8.0.0) for filtering and alignment to the GRCh38 reference genome. Raw sequencing reads were processed using Cell Ranger (v8.0.0) with default parameters for alignment to the GRCh38 reference genome and gene quantification
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: breast milk

extract_protocol:
The intact cells are immediately processed on a dedicated platform. The workflow begins with precise quantification and viability assessment of the suspension, which is then promptly loaded into a microfluidic system, such as the 10x Genomics Chromium controller, where individual cells are co-encapsulated with uniquely barcoded gel beads in nanoliter-scale droplets. Within these droplets, the cells are lysed, releasing their RNA, which is then captured by the barcoded beads and reverse-transcribed on-site to generate cell-specific cDNA. This is followed by cDNA amplification, library construction with sequencing adapters, and final quality control, such as fragment analysis, before high-throughput sequencing.
The workflow for preparing scRNA-seq libraries using the 10x Genomics Chromium Single Cell 3' v3 reagent kit (commonly run on Illumina sequencers) involves four key phases. First, a viable single-cell suspension is mixed with gel beads and partitioning oil, then loaded onto a Chromium chip to generate Gel Bead-in-Emulsions (GEMs) where reverse transcription occurs, adding cell barcodes and UMIs. Second, the emulsion is broken, and cDNA is purified and amplified via PCR. Third, the amplified cDNA undergoes enzymatic fragmentation, end-repair, A-tailing, and adapter ligation to construct the final Illumina-compatible library, followed by cleanup with SPRIselect beads. Finally, the library is quantified and quality-checked (e.g., Bioanalyzer) before sequencing on Illumina platforms, typically with a 28-10-91 cycle configuration for Read 1, i7 index, and Read 2, respectively.

value: breast milk


title: alg-2(ok304) II, embryo, rep 2

description: Library name: sBD575

value: Whole worm


title: Ctcf_3H_4C-seq_rep1

description:
Library name: Ctcf_3H_rep1
raw_fragment_counts_depletions.rds


title: Input splenic B220+ (Miz-1WT)

description: Library name: MIZ-1WT Input


title: Ctcf_6H_4C-seq_rep1

description:
Library name: Ctcf_6H_rep1
raw_fragment_counts_depletions.rds


title: BM31W_2

description: Library name: Sample3


title: alg-2(ok304) II, embryo, rep 3

description: Library name: sBD581


title: Ctcf_0H_4C-seq_rep2

description:
Library name: Ctcf_0H_rep2
raw_fragment_counts_depletions.rds

value: untreated


title: S1

value: 10-year-old female with newly diagnosed PSC, possible PSC-AIH overlap, and a history of autoimmune pancreatitis and IBD


title: BM35W

description: Library name: Sample4


title: alg-2(ok304) II, L1, rep 2

description: Library name: sBD578


title: miRNA_BM39W_1

description: Library name: miRNAsample5


title: Hep3B siSBNO1#2 replicate 4

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: Library name: KG188-12

data_processing:
trimmed with ktrim version 1.6.0 Parameters: -s 26 -t 6
Reads were mapped to the genome with STAR Version 2.7.11b; Parameters:  --outSAMstrandField intronMotif --outSAMunmapped Within --outSAMattributes NH HI AS nM NM XS
raw count table were created with featureCounts Version 2.0.2. CPM estimates, generated with cpm function from edgeR version 4.6.2
Assembly: GRCh38.p14
Supplementary files format and content: raw counts created with featureCounts
Supplementary files format and content: CPM estimates, generated with cpm function from edgeR version 4.6.2

growth_protocol: Hep3B cells were cultured in Minimum Essential Medium

extract_protocol:
Total RNA was extracted using the Macherey-Nagel RNA Extraction Kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols, strand specific mRNA sequencing on DNBSEQ platform PE100bp

treatment_protocol: siRNA-mediated knockdown was performed using Lipofectamine RNAiMAX Transfection Reagent (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s instructions.

value: transfected with siSBNO1#2


title: RFP_ATAC-seq_rep2

description: Library name: RFP_rep2

data_processing:
Reads were mapped to the mm10 genome using bwa-mem (v0.7.17-r1188) and filtered for paired and uniquely mapped reads using samtools (v1.19.2).
Reads were assigned to 129 or CAST allele by mapping to assembled 129 and CAST genomes and assigning each reads to the allele with a better alignment score (AS bam tag).
Coverage peaks were called using macs2 and read counts in peaks were generated using the “summarizeOverlaps” function from the R/Bioconductor package GenomicAlignments.
Assembly: mm10
Supplementary files format and content: bigwig files contain normalized coverage tracks for allele-resolved and ambiguous reads.

growth_protocol: Mouse embryonic stem cell lines were cultured as described previously (Liu et al., 2021, 2025; van Schaik et al., 2022). Briefly, the 129/Castaneus F1 hybrid methylation reporter cell lines were cultured on 0.1% gelatin-coated plates in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1) supplemented with N-2 (Gibco), B-27 (Gibco), BSA (0.05%, Gibco), 10 4 U of Leukaemia Inhibitory Factor (LIF) (Millipore), MEK inhibitor PD0325901 (1 μM, Selleckchem), GSK3-β inhibitor CHIR99021 (3 μM, Cayman Chemical) and 1-Thioglycerol (1.5 × 10-4 M, Sigma-Aldrich). The cell lines were passaged every 2  days in daily culture.

extract_protocol:
ATAC-seq on the sorted methylation reporter populations was carried out following a previously described protocol (Buenrostro et al., 2013). Cells were sorted based on their fluorescence signal into independent tubes and 50.000 cells were used for ATAC. The Tn5 transposase was purified in-house by the NKI protein facility as described in Braccioli et al., 2025. Cells were collected, washed 1x in cold PBS and nuclei were lysed in 2× lysis buffer (1 M Tris–HCl pH 7.5, 5 M NaCl, 1 M MgCl2, 10% IGEPAL). The nuclei isolation buffer was removed by centrifugation and nuclei were resuspended in tagmentation buffer (20 mM Tris (hydroxymethyl)aminomethane; 10 mM MgCl2, 20% dimethylformamide, adjusted to pH 7.6 with acetic acid) containing the Tn5 and incubated for 1 hour at 37°C.
Two rounds of PCR were performed using the KAPA kit to incorporate sequencing adapters and to amplify the library DNA. Libraries were size-selected with AMPure XP (Bechman) beads to retain fragments smaller than 700 bp.

value: 129/CAST F1 hybrid SCR methylation reporter mESC

tag: sample group

value: RFP


title: Ctcf_0H_4C-seq_rep1

description:
Library name: Ctcf_0H_rep1
raw_fragment_counts_depletions.rds

value: Embryo


title: BM31W_1

description: Library name: Sample2


title: alg-2(ok304) II, embryo, rep 1

description: Library name: sBD569


title: miRNA_BM35W

description: Library name: miRNAsample4


title: Hep3B siSBNO1#2 replicate 3

description: Library name: KG188-11


title: alg-2(ok304) II, L1, rep 1

description: Library name: sBD572


title: miRNA_BM39W_2

description: Library name: miRNAsample6


title: miRNA_BM31W_2

description: Library name: miRNAsample3


title: miRNA_BM31W_1

description: Library name: miRNAsample2


title: RFP_ATAC-seq_rep1

description: Library name: RFP_rep1


title: GFP_ATAC-seq_rep2

description: Library name: GFP_rep2

value: GFP


title: ebax-1(tm2321) IV, embryo, rep 3

description: Library name: sBD557

value: ebax-1(tm2321) IV


title: Hep3B siSBNO1#2 replicate 2

description: Library name: KG188-10


title: Hep3B siSBNO1#2 replicate 1

description: Library name: KG188-09


title: miRNA_BM27W

description: Library name: miRNAsample1


title: Hep3B siSBNO1#1 replicate 4

description: Library name: KG188-08


title: ebax-1(tm2321) IV, L1, set 1, rep 2

description: Library name: sBD555


title: DP_ATAC-seq_rep2

description: Library name: DP_rep2

value: Embryonic stem cells

value: DP


title: ebax-1(tm2321) IV, embryo, rep 2

description: Library name: sBD553


title: DP_ATAC-seq_rep1

description: Library name: DP_rep1


title: ebax-1(tm2321) IV, L1, set 1, rep 3

description: Library name: sBD559


title: Hep3B siSBNO1#1 replicate 3

description: Library name: KG188-07

value: transfected with siSBNO1#1


title: BM39W_1

description: Library name: Sample5


title: BM39W_3

description: Library name: Sample7


title: Hep3B siSBNO1#1 replicate 1

description: Library name: KG188-05


title: Lungs_FPB2_6-hours

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

description: Library name: 192

data_processing:
Adapters were trimmed and low-quality reads (N20 threshold) were filtered using a custom quality control pipeline. FASTQC was used to evaluate read quality metrics.
Trimmed reads were mapped to mature miRNAs in miRBase v21 using Bowtie v1.0.0, allowing one mismatch.
Reads were also mapped to the mm9 reference genome (UCSC) for validation. Only reads mapping to annotated miRNAs were retained.
Read counts were normalized using TMM (Trimmed Mean of M-values) via edgeR (Bioconductor).
Differential expression was assessed using two-way ANOVA across dose and timepoint groups. PCA and clustering were used for exploratory analysis.
Assembly: Mus musculus mm9 (UCSC)
Supplementary files format and content: Processed data includes normalized miRNA counts for each sample across cortex, heart, and lung tissues. File format: .xlsx  with miRNAs as rows and samples as columns.

source_name: Lungs

growth_protocol: Adult male SKH-1 Elite mice (Charles River, strain code 477) were housed in standard vivarium conditions with food and water provided ad libitum. All procedures were conducted in AAALAC-accredited facilities under IACUC-approved protocols.

extract_protocol:
Tissues were homogenized in TRIzol Reagent (Invitrogen) and total RNA, including small RNAs, was extracted using the miRNeasy Mini Kit (QIAGEN) following the manufacturer’s protocol. RNA quality was assessed using NanoDrop, Qubit, and Agilent Tapestation 2200.
Small RNA libraries were prepared using the Illumina TruSeq Small RNA Sample Prep Kit. 3′ and 5′ adapters were ligated to RNA, followed by reverse transcription, PCR amplification, and gel-based size selection. Libraries were pooled and sequenced on an Illumina NextSeq 500 to generate 50 bp single-end reads.

treatment_protocol: Mice were administered subcutaneous fentanyl citrate at one of three doses: HNLD (62 mg/kg), LD10 (110 mg/kg), or LD50 (135 mg/kg). Sham controls received vehicle only. Mice were euthanized at 0h (40 min), 6h, 24h, or 7d post-injection for tissue collection.

value: Lungs

value: SKH-1 Elite

tag: dose

tag: timepoint

value: 6 hours


title: GFP_ATAC-seq_rep1

description: Library name: GFP_rep1


title: ebax-1(tm2321) IV, embryo, rep 1

description: Library name: sAG62


title: ebax-1(tm2321) IV, L1, set 2, rep 3

description: Library name: sAG379


title: Hep3B NTC replicate 4

description: Library name: KG188-04

value: transfected with NTC


title: Lungs_FP96_0-hour

description: Library name: 191

value: 200uL Ringer's

value: Control

value: 0 hour


title: Lungs_FP95_0-hour

description: Library name: 190


title: BM39W_2

description: Library name: Sample6

value: breast milk


title: Hep3B NTC replicate 3

description: Library name: KG188-03


title: SM002 CITE-seq antibody-derived tag library (Feature Barcode)

city: Tucson

first: Bao

last: Thai

state: AZ

address: 1656 E Mabel St

institute: University of Arizona

description:
Library name: SM002-ADT
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
SM002_Features_Reference.csv

data_processing:
Raw sequencing data were processed using the Cell Ranger pipeline (10x Genomics). FASTQ files were aligned to the human reference genome (GRCh38) to generate gene expression count matrices. Antibody-derived tag (ADT) counts were quantified using the Feature Barcode pipeline. V(D)J sequencing data were processed using the Cell Ranger VDJ pipeline to assemble and annotate B cell receptor sequences. Filtered count matrices were generated for downstream analysis. All analyses were performed using default parameters unless otherwise specified.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data are provided as sparse count matrices in Matrix Market format, including barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files generated by Cell Ranger. These files contain gene expression and antibody-derived tag (ADT) counts for each cell. The features.tsv.gz file includes feature annotations distinguishing gene expression and antibody capture modalities. Each row corresponds to a feature (gene or antibody), and each column corresponds to a single cell barcode.

molecule: protein

source_name: bone marrow

extract_protocol:
Human bone marrow cells were isolated and processed into a single-cell suspension. Cells were washed, filtered to remove debris, and counted prior to downstream applications. For CITE-seq, cells were incubated with oligonucleotide-conjugated antibodies targeting surface markers including IgD and IgM according to manufacturer protocols. Following staining, cells were washed to remove unbound antibodies and resuspended in buffer for single-cell encapsulation.
Single-cell libraries were generated using the 10x Genomics Chromium platform. Cell suspensions were loaded onto the Chromium controller for droplet-based partitioning and barcoding. Gene expression (GEX) libraries were prepared using the Chromium Single Cell 3' Gene Expression kit. Antibody-derived tag (ADT) libraries were generated using the Chromium Single Cell Feature Barcode technology for CITE-seq. In addition, V(D)J libraries were constructed using the Chromium Single Cell Immune Profiling kit to capture B cell receptor sequences. Libraries were prepared according to the manufacturer’s instructions and sequenced on an Illumina platform to generate paired-end reads.

value: bone marrow

value: B cells

value: wild type


title: SM002 single-cell V(D)J sequencing library

description: Library name: SM002-VDJ


title: BM27W

description: Library name: Sample1


title: Hep3B siSBNO1#1 replicate 2

description: Library name: KG188-06


title: ebax-1(tm2321) IV, L1, set 1, rep 1

description: Library name: sAG72

value: Whole worm


title: Lungs_FP94_24-hours

description: Library name: 189

value: 24 hours


title: ebax-1(tm2321) IV, L1, set 2, rep 2

description: Library name: sAG352

value: ebax-1(tm2321) IV


title: ebax-1(tm2321) IV, L1, set 2, rep 1

description: Library name: sAG351


title: SM002 single-cell RNA-seq (10x Genomics 3' Gene Expression)

description:
Library name: SM002-GEX
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
SM002_Features_Reference.csv


title: Hep3B NTC replicate 1

description: Library name: KG188-01


title: si_RNA_2: FLCN-specific siRNA, biological replicate 3

city: Qingdao

first: liu

last: yanjun

state: shangdong

address: No. 1677 Wutaishan Road

department: Department of Pathology

institute: Qingdao University

description:
Library name: si_RNA_3
Paired-end (or single-end) 150 bp RNA sequencing was performed on the Illumina NovaSeq 6001 platform.

data_processing:
Library quality was verified by Agilent 2100 Bioanalyzer and Qubit 4.0 Fluorometer. Qualified libraries were sequenced on the Illumina NovaSeq 6000 platform (or Illumina HiSeq X Ten) with a paired-end (PE) read length of 150 bp (PE150). The sequencing was performed by Nanjing Personalbio Gene Technology Co., Ltd. (Nanjing, China).
Raw sequencing reads were filtered to remove low-quality reads (Q-score < 20), adapter-contaminated reads, and reads with >10% unknown bases (N) using Trimmomatic (v0.39) or fastp (v0.23.2). Clean reads were mapped to the human reference genome (GRCh38/hg38) using STAR aligner (v2.7.10a) with default parameters. Gene expression levels were quantified as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) using HTSeq (v0.13.5).
Assembly: GRCh38/hg38 (Homo sapiens Assembly 38, GenCode v38 annotation)
Supplementary files format and content: 1. Gene expression matrix: TSV/CSV format, including Ensembl Gene ID, official gene symbol, raw read counts, FPKM and TPM values for each sample. 2. Differentially expressed gene list: TSV/CSV format, including Ensembl Gene ID, official gene symbol, log2(fold change), raw P-value, adjusted P-value (FDR), and up/down regulation annotation. 3. Enrichment analysis results: TSV/CSV format for GO (Molecular Function, Cellular Component, Biological Process) and KEGG enrichment, including term ID, term name, number of enriched genes, P-value, FDR, and gene list for each term. 4. Aligned sequence data: BAM format (sorted and indexed) of clean reads aligned to hg38. 5. Visualization raw data: TSV/CSV format for volcano plots, heatmaps, and enrichment bubble plots (all plotting data).

source_name: thyroid gland

growth_protocol: Human thyroid follicular epithelial cell line Nthy-ori 3-1 was cultured in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1% penicillin-streptomycin (Gibco) at 37°C in a humidified atmosphere containing 5% CO2. Cells were passaged at 80-90% confluence using 0.25% trypsin-EDTA (Gibco) and seeded at a density of 1×10^6 cells per 10 cm cell culture dish 24 h prior to transfection to ensure 70-80% confluence at the time of transfection.

extract_protocol:
Total RNA was isolated from cultured Nthy-ori 3-1 cells (Mock control, FLCN wild-type transfected, FLCN-siRNA knocked down, and FLCN mutant (c.992C>T, c.1179delC, c.1285_1286insC) transfected groups) using a standard TRIzol/chloroform extraction method (or commercial RNA extraction kit). RNA purity and integrity were assessed by Nanodrop and Agilent 2100 Bioanalyzer (RNA Integrity Number, RIN ≥ 8.0 was required for library construction).
cDNA libraries were constructed from qualified total RNA using the Illumina TruSeq Stranded Total RNA Library Prep Kit (Human/Mouse/Rat) (or Personalbio customized library construction kit) following the manufacturer's instructions. Ribosomal RNA (rRNA) was removed prior to cDNA synthesis to enrich for coding and non-coding RNA. The RNA was fragmented, reverse-transcribed into first-strand cDNA, and second-strand cDNA was synthesized with dUTP to achieve strand specificity. cDNA fragments were end-repaired, A-tailed, and ligated with Illumina adaptors, followed by PCR amplification to generate the final cDNA libraries.

treatment_protocol: For FLCN overexpression experiments: Nthy-ori 3-1 cells were transfected with 4 μg of EGFP-tagged FLCN wild-type (WT) plasmid, FLCN c.992C>T (p.S331F) mutant plasmid, FLCN c.1179delC (p.M394Cfs*74) mutant plasmid, FLCN c.1285_1286insC (p.H429Pfs*27) mutant plasmid or empty EGFP vector (Mock control) using Lipofectamine 3000 (Invitrogen, Cat.no.L3000015) according to the manufacturer's standard instructions. For FLCN knockdown experiments: cells were transfected with 100 nM of FLCN-specific siRNA or negative control siRNA using Lipofectamine RNAiMAX (Invitrogen, Cat.no.13778150). Transfection efficiency was verified by fluorescence microscopy (EGFP fluorescent signal) for overexpression groups and qRT-PCR/Western blot for knockdown groups. All cells were harvested 48 h post-transfection for subsequent total RNA extraction.

value: thyroid gland

value: Nthy-ori 3-1

value: thyroid follicular epithelial cell

value: FLCN knockdown

value: FLCN siRNA transfection

value: Batch 1


title: Hep3B NTC replicate 2

description: Library name: KG188-02

value: transfected with NTC


title: mir-35(cdb2 cdb 78) II, L1

description: Library name: sAG71

value: mir-35(cdb2 cdb 78)


title: Lungs_FP93_24-hours

description: Library name: 188

value: Lungs

value: SKH-1 Elite

value: 200uL Ringer's

value: Control


title: mir-35(cdb2 cdb 78) II, embryo

description: Library name: sAG61


title: Lungs_FP92_24-hours

description: Library name: 187


title: Lungs_FP91_24-hours

description: Library name: 186


title: si_RNA_2: FLCN-specific siRNA, biological replicate 2

description:
Library name: si_RNA_2
Paired-end (or single-end) 150 bp RNA sequencing was performed on the Illumina NovaSeq 6000 platform.


title: SNU1079 siSBNO1#2 replicate 3

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
Assembly: GRCh38.p13
Supplementary files format and content: TPM abundance estimates, generated with kallisto quant 0.4.6
Supplementary files format and content: normalized values created with voom of the limma package in R

growth_protocol: SNU1079 cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum (Thermo Fisher Scientific, Offenbach, Germany) and 1% Penicillin-streptomycin (100IU/ml and 100g/ml, respectively).

extract_protocol:
Total RNA was extracted using the Macherey-Nagel RNA Extraction Kit (Macherey-Nagel, Düren, Germany).
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols, strand specific mRNA sequencing on DNBSEQ platform PE100bp

treatment_protocol: To study SBNO1 knockdown, SNU1079 cells were transfected with NTC, siSBNO1#1 or siSBNO1#2 using Lipofectamine RNAiMAX Transfection Reagent.


title: mir-35(cdb2 cdb4) II, L1, set 1

description: Library name: sAG68

value: mir-35(cdb2 cdb4) II


title: si_RNA_1: FLCN-specific siRNA, biological replicate 1

description:
Library name: si_RNA_1
Paired-end (or single-end) 150 bp RNA sequencing was performed on the Illumina NovaSeq 6000 platform.


title: SNU1079 NTC replicate 3

value: NTC


title: mir-35(cdb2 cdb4) II, embryo, set 1

description: Library name: sAG58

value: Whole worm


title: Lungs_FP88_0-hour

description: Library name: 185

value: 0 hour


title: SNU1079 siSBNO1#1 replicate 3


title: C1285_insC_3: FLCN c.1285_1286insC (p.H429Pfs*27) mutant plasmid, biological replicate 3

description:
Library name: C1285_insC_3
Paired-end (or single-end) 150 bp RNA sequencing was performed on the Illumina NovaSeq 6000 platform.

value: FLCN c.1285_1286insC mutant overexpression


title: mir-35(cdb2 cdb4) II, L1, set 2, rep 3

description: Library name: sAG371


title: Lungs_FP87_0-hour

description: Library name: 184


title: C1285_insC_2:  FLCN c.1285_1286insC (p.H429Pfs*27) mutant plasmid, biological replicate 2

description:
Library name: C1285_insC_2
Paired-end (or single-end) 150 bp RNA sequencing was performed on the Illumina NovaSeq 6000 platform.

value: thyroid gland


title: mir-35(cdb2 cdb4) II, L1, set 2, rep 2

description: Library name: sAG346


title: Lungs_FP86_6-hours

description: Library name: 183

value: 6 hours


title: SNU1079 siSBNO1#1 replicate 2


title: mir-35(cdb2 cdb4) II, L1, set 2, rep 1

description: Library name: sAG345


title: C1285_insC_1:  FLCN c.1285_1286insC (p.H429Pfs*27) mutant plasmid, biological replicate 1

description:
Library name: C1285_insC_1
Paired-end (or single-end) 150 bp RNA sequencing was performed on the Illumina NovaSeq 6000 platform.

value: Nthy-ori 3-1

value: thyroid follicular epithelial cell


title: SNU1079 siSBNO1#2 replicate 2


title: C1179_delC_1: FLCN c.1179delC (p.M394Cfs*74) mutant plasmid, biological replicate 1

description:
Library name: C1179_delC_1
Paired-end (or single-end) 150 bp RNA sequencing was performed on the Illumina NovaSeq 6000 platform.

value: FLCN c.1179delC (p.M394Cfs*74) mutant

value: FLCN c.1179delC mutant overexpression


title: SNU1079 siSBNO1#2 replicate 1


title: Lungs_FP84_7-days

description: Library name: 181

value: 7 days


title: mir-35(cdb2 cdb4) II; ebax-1(tm2321) IV, L1, rep 3

description: Library name: sAG97

value: mir-35(cdb2 cdb4) II; ebax-1(tm2321) IV


title: Lungs_FP85_6-hours

description: Library name: 182

value: Lungs


title: C1179_delC_2: FLCN c.1179delC (p.M394Cfs*74) mutant plasmid, biological replicate 2

description:
Library name: C1179_delC_2
Paired-end (or single-end) 150 bp RNA sequencing was performed on the Illumina NovaSeq 6000 platform.

value: Batch 1


title: SNU1079 NTC replicate 2


title: Lungs_FP83_7-days

description: Library name: 180

value: SKH-1 Elite

value: 200uL Ringer's


title: SNU1079 NTC replicate 1


title: SNU1079 siSBNO1#1 replicate 1


title: Lungs_FP82_7-days

description: Library name: 179

value: Control


title: C992_CT_3: FLCN c.992C>T (p.S331F) mutant plasmid, biological replicate 3

description:
Library name: C992_CT_3
Paired-end (or single-end) 150 bp RNA sequencing was performed on the Illumina NovaSeq 6000 platform.

value: FLCN c.992C>T (p.S331F) mutant

value: FLCN c.992C>T mutant overexpression


title: mir-35(cdb2 cdb4) II; ebax-1(tm2321) IV, embryo, rep 3

description: Library name: sAG93

value: Whole worm


title: mir-35(cdb2 cdb4) II; ebax-1(tm2321) IV, L1, rep 2

description: Library name: sAG89


title: C992_CT_2:  FLCN c.992C>T (p.S331F) mutant plasmid, biological replicate 2

description:
Library name: C992_CT_2
Paired-end (or single-end) 150 bp RNA sequencing was performed on the Illumina NovaSeq 6000 platform.


title: Root +Fe+U 3

city: Udine

first: Fabio

last: Marroni

address: Via delle Scienze 208

country: Italy

institute: Università di Udine

description: Library name: 15P

data_processing:
The obtained reads were aligned to the SL4.0 reference genome and ITAG4.0 transcriptome using hisat2
Assembly: SL4.0 reference genome and ITAG4.0 transcriptome
Supplementary files format and content: Tab delimited file includes FPKM for all the samples

organism: Solanum lycopersicum

source_name: Root

extract_protocol:
One gram of root tissue was homogenized in liquid nitrogen, and total RNA was isolated from approximately 60 mg of the resulting powder using the Spectrum Plant Total RNA Kit (Sigma–Aldrich) following the manufacturer's instructions.
Library preparation followed the Illumina TrueSeq 2.0 protocol, using 2 μg of total RNA per sample (Venuti et al., 2019). Libraries were prepared using the Universal Plus mRNA-Seq kit (Tecan Genomics, Redwood City, CA) according to manufacturer instruction.

value: Root


title: Lungs_FP78_6-hours

description: Library name: 177


title: mir-35(cdb2 cdb4) II; ebax-1(tm2321) IV, embryo, rep 2

description: Library name: sAG85


title: Lungs_FP81_7-days

description: Library name: 178


title: WT_3: NFLCN wild-type overexpression plasmid, biological replicate 3

description:
Library name: WT_3
Paired-end (or single-end) 150 bp RNA sequencing was performed on the Illumina NovaSeq 6000 platform.

value: thyroid gland

value: FLCN wild-type overexpression


title: mir-35(cdb2 cdb4) II; ebax-1(tm2321) IV, L1, rep 1

description: Library name: sAG73


title: C992_CT_1: FLCN c.992C>T (p.S331F) mutant plasmid, biological replicate 1

description:
Library name: C992_CT_1
Paired-end (or single-end) 150 bp RNA sequencing was performed on the Illumina NovaSeq 6000 platform.

value: Nthy-ori 3-1


title: Root +Fe+U 2

description: Library name: 14P


title: Lungs_FP77_6-hours

description: Library name: 176

value: 6 hours


title: Root +Fe+U 1

description: Library name: 13P


title: mir-35(cdb2 cdb4) II; ebax-1(tm2321) IV, embryo, rep 1

description: Library name: sAG63


title: WT_2:  FLCN wild-type overexpression plasmid, biological replicate 2

description:
Library name: WT_2
Paired-end (or single-end) 150 bp RNA sequencing was performed on the Illumina NovaSeq 6000 platform.

value: thyroid follicular epithelial cell


title: Lungs_FP74_0-hour

description: Library name: 175

value: 0 hour


title: mir-35(cdb2 cdb4) tts-2 (cdb472) II, L1, rep 3

description: Library name: sAG548

value: mir-35(cdb2 cdb4) tts-2 (cdb472) II


title: WT_1： FLCN wild-type overexpression plasmid, biological replicate 1

description:
Library name: WT_1
Paired-end (or single-end) 150 bp RNA sequencing was performed on the Illumina NovaSeq 6000 platform.


title: Lungs_FP73_6-hours

description: Library name: 174


title: mir-35(cdb2 cdb4) tts-2 (cdb472) II, L1, rep 2

description: Library name: sAG547


title: Lungs_FP72_6-hours

description: Library name: 173


title: Root +Fe+A 1

description: Library name: 10P


title: MOCK_3: transfected with empty EGFP vector, biological replicate 3

description:
Library name: MOCK_3
Paired-end (or single-end) 150 bp RNA sequencing was performed on the Illumina NovaSeq 6000 platform.

value: Empty vector control

value: Empty vector transfection


title: mir-35(cdb2 cdb6) II, L1

description: Library name: sAG69

value: mir-35(cdb2 cdb6) II


title: Root +Fe+A 2

description: Library name: 11P


title: Root +Fe+Ni 3

description: Library name: 9P


title: mir-35(cdb2 cdb4) tts-2 (cdb472) II, L1, rep 1

description: Library name: sAG538


title: Lungs_FP71_0-hour

description: Library name: 172

value: Lungs

value: SKH-1 Elite


title: MOCK_1: ransfected with empty EGFP vector, biological replicate 1

description:
Library name: MOCK_1
Paired-end (or single-end) 150 bp RNA sequencing was performed on the Illumina NovaSeq 6000 platform.

value: Batch 1


title: Lungs_FP69_0-hour

description: Library name: 171


title: MOCK_2: s transfected with empty EGFP vector, biological replicate 2

description:
Library name: MOCK_2
Paired-end (or single-end) 150 bp RNA sequencing was performed on the Illumina NovaSeq 6000 platform.


title: Root +Fe+A 3

description: Library name: 12P


title: mir-35(cdb2 cdb6) II; ebax-1(tm2321) IV, L1, rep 3

description: Library name: sAG98

value: mir-35(cdb2 cdb6) II; ebax-1(tm2321) IV


title: Parental Normoxia Regular Media Replicate 3

city: Farmington

first: Yasir

last: Suhail

state: Connecticut

address: 263 Farmington Avenue

department: BME

institute: UCHC

description: Library name: NP3

data_processing:
Alignment using hisat2, and counting to genes using featureCounts
Assembly: Grch38
Supplementary files format and content: Read counts per gene

source_name: cell line

extract_protocol:
Standard total RNA extraction using established laboratory protocols.
Standard RNA-seq library preparation using established commercial kits and manufacturer protocols.

value: cell line

value: Cancer Cell

value: Parental

value: Normoxia

tag: media

value: Regular Media


title: Lungs_FP68_6-hours

description: Library name: 170


title: Root +Fe+Ni 2

description: Library name: 8P

value: Root


title: Parental Normoxia Regular Media Replicate 2

description: Library name: NP2


title: mir-35(cdb2 cdb6) II; ebax-1(tm2321) IV, embryo, rep 3

description: Library name: sAG94

value: Whole worm


title: mir-35(cdb2 cdb6) II, embryo

description: Library name: sAG59


title: Lungs_FP66_24-hours

description: Library name: 168

value: 24 hours


title: Lungs_FP67_0-hour

description: Library name: 169

value: 0 hour


title: Root +Fe-N 3

description: Library name: 6P


title: Root +Fe+Ni 1

description: Library name: 7P


title: Root +Fe-N 2

description: Library name: 5P


title: HE230622-TNA

city: Jinhua

first: QI

last: TU

address: 365 Renmin East Road, Wucheng District

institute: Zhejiang University School of Medicine

description: Library name: Sample1

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: GW23T254D01
Supplementary files format and content: .txt

source_name: Brain

extract_protocol:
1. Experimental Procedures 1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. 1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification. 1.2 DNA Purification 1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube. 1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min. 1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA. 1.3 RNA Purification 1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Brain

value: Ommaya capsule implantation rep1


title: mir-35(cdb2 cdb6) II; ebax-1(tm2321) IV, L1, rep 2

description: Library name: sAG90


title: Parental Normoxia Regular Media Replicate 1

description: Library name: NP1


title: Lungs_FP64_24-hours

description: Library name: 167


title: Parental Hypoxia TIFM Replicate 3

description: Library name: TP3

value: Hypoxia

value: TIFM


title: Root -Fe-N 3

description: Library name: 3P


title: Lungs_FP62_24-hours

description: Library name: 165

value: Lungs


title: mir-35(cdb2 cdb6) II; ebax-1(tm2321) IV, embryo, rep 2

description: Library name: sAG86


title: Parental Hypoxia TIFM Replicate 2

description: Library name: TP2


title: Lungs_FP61_7-days

description: Library name: 164

value: SKH-1 Elite

value: 7 days


title: mir-35(cdb2 cdb6) II; ebax-1(tm2321) IV, L1, rep 1

description: Library name: sAG74

value: mir-35(cdb2 cdb6) II; ebax-1(tm2321) IV


title: mir-35(cdb2 cdb6) II; ebax-1(tm2321) IV , embryo, rep 1

description: Library name: sAG64


title: Lungs_FP63_24-hours

description: Library name: 166


title: Root -Fe-N 2

description: Library name: 2P


title: Parental Hypoxia TIFM Replicate 1

description: Library name: TP1

value: cell line


title: Root +Fe-N 1

description: Library name: 4P


title: Lungs_FP60_7-days

description: Library name: 163


title: mir-35(cdb2 cdb72) II, embryo

description: Library name: sAG60

value: mir-35(cdb2 cdb72)


title: Parental Hypoxia Regular Media Replicate 3

description: Library name: HP3

value: Cancer Cell

value: Parental


title: mir-35(cdb2 cdb72) II, L1

description: Library name: sAG70


title: peony,55day

city: weifang

first: yongqi

last: liu

state: shandong

address: 699 Binhu Road, Xiashan District

institute: Peking University Institute of Advanced Agricultural Sciences

description:
Library name: peony
Tomato callus Spatial Transcriptomics sequencing data

data_processing:
Alignment: Raw reads were mapped to the tomato genome (SL4.0, ITAG4.1) using BSTMatrix (v2.4) for BMKMANU data, SAW (v8.0) for Stereo-Seq, and CellRanger (v7.0.0) for 10x Genomics.
Clustering: Seurat (v5.1.0) filtered cells (>30 genes/cell), normalized counts, and performed PCA/Harmony-based batch correction. UMAP/Louvain clustering identified cell states.
Trajectory & Networks: Monocle2/3 inferred pseudo-time trajectories. RNA velocity (velocyto/dynamo) and co-expression networks (hdWGCNA) analyzed developmental dynamics.
Spatial Visualization: Custom Python scripts mapped gene expression to cell masks using histological images.
Assembly: S_lycopersicum_chromosomes.4.00
Supplementary files format and content: The clustering analysis results were saved as an RDS file containing clustering information for subsequent analysis and data sharing.
Library strategy: Spatial Transcriptomics

source_name: callus

extract_protocol:
Total RNA was extracted from tomato callus tissues using the RNAprep Pure Plant Kit (TIANGEN). For spatial transcriptomics, RNA was isolated from cryosectioned or FFPE-embedded tissues (10-µm sections) after permeabilization (14 min for BMKMANU; 30 min Triton X-100 for ISSeq). RNA integrity was verified via Qubit 4.0.
BMKMANU S1000/S3000 RNA-Seq: Libraries were prepared using BMKMANU S1000/S3000 Gene Expression Assay Kits (ST03002). Tissue sections were permeabilized, reverse-transcribed, and amplified with cDNA denaturation and purification steps. Final libraries were sequenced on Illumina NovaSeq.BGI Stereo-Seq: cDNA was synthesized on Stereo-Seq chips after methanol fixation and FB/ssDNA staining. Amplified cDNA was fragmented and ligated with adapters for DNBSEQ-T10 sequencing.

value: callus


title: Parental Hypoxia Regular Media Replicate 2

description: Library name: HP2

value: Regular Media


title: Lungs_FP59_7-days

description: Library name: 162


title: BMK,16day5

description:
Library name: BMK_16d5
Tomato callus Spatial Transcriptomics sequencing data


title: Root -Fe-N 1

description: Library name: 1P

value: Root


title: Parental Hypoxia Regular Media Replicate 1

description: Library name: HP1


title: Lungs_FP58_24-hours

description: Library name: 161

value: LOEL

value: 24 hours


title: BMK,16day4

description:
Library name: BMK_16d4
Tomato callus Spatial Transcriptomics sequencing data


title: mir-35(cdb2 cdb72) II; ebax-1(tm2321) IV, embryo, rep 3

description: Library name: sAG96

data_processing:
Adaptor trimming with cutadapt(ver 5.0) with the -q 20 flag
Mapping with bowtie2 (ver. 2.5.3) with --no-unal --end-to-end –sensitive -U flags
BAM indexing with samtools (ver 1.21)
Raw counts generated from htseq (ver. 2.0.4) with --mode union --nonunique fraction -a 0 flags
Assembly: WS280
Supplementary files format and content: Matrix of raw counts from Htseq output

extract_protocol:
Total RNA was extracted using Trizol.
Libraries were prepared using the NEB small RNA kit with a modified protocol.

value: Whole worm


title: mir-35(cdb2 cdb72) II; ebax-1(tm2321) IV, L1, rep 3

description: Library name: sAG92


title: ARNT KO Clone B Normoxia Regular Media Replicate 3

description: Library name: N33

value: ARNT KO Clone B

value: Normoxia


title: Lungs_FP56_24-hours

description: Library name: 159


title: BMK,16day2

description:
Library name: BMK_16d2
Tomato callus Spatial Transcriptomics sequencing data


title: ARNT KO Clone B Normoxia Regular Media Replicate 1

description: Library name: N31


title: Lungs_FP57_24-hours

description: Library name: 160


title: mir-35(cdb2 cdb72) II; ebax-1(tm2321) IV, L1, rep 2

description: Library name: sAG76


title: mir-35(cdb2 cdb72) II; ebax-1(tm2321) IV, embryo, rep 1

description: Library name: sAG66


title: BMK,16day1

description:
Library name: BMK_16d1
Tomato callus Spatial Transcriptomics sequencing data


title: Lungs_FP55_0-hour

description: Library name: 158

value: 0 hour


title: BMK,16day3

description:
Library name: BMK_16d3
Tomato callus Spatial Transcriptomics sequencing data


title: Lungs_FP54_24-hours

description: Library name: 157

value: Lungs


title: mir-35(cdb2 cdb72) II; ebax-1(tm2321) IV, embryo, rep 2

description: Library name: sAG88


title: ARNT KO Clone B Hypoxia TIFM Replicate 3

description: Library name: T33

value: Hypoxia

value: TIFM


title: mir-35(cdb2 cdb72) II; ebax-1(tm2321) IV, L1, rep 1

description: Library name: sAG100


title: ARNT KO Clone B Normoxia Regular Media Replicate 2

description: Library name: N32


title: BMK,14day3

description:
Library name: BMK_14d3
Tomato callus Spatial Transcriptomics sequencing data


title: ARNT KO Clone B Hypoxia TIFM Replicate 2

description: Library name: T32


title: Lungs_FP53_7-days

description: Library name: 156

value: SKH-1 Elite

value: 7 days


title: Lungs_FP52_7-days

description: Library name: 155


title: mir-35(cdb2 cdb78) II; ebax-1(tm2321) IV, L1, rep 3

description: Library name: sAG99


title: BMK,14day2

description:
Library name: BMK_14d2
Tomato callus Spatial Transcriptomics sequencing data


title: ARNT KO Clone B Hypoxia Regular Media Replicate 3

description: Library name: H33

value: cell line


title: BMK,15day

description:
Library name: BMK_15d
Tomato callus Spatial Transcriptomics sequencing data


title: ARNT KO Clone B Hypoxia TIFM Replicate 1

description: Library name: T31

value: Cancer Cell


title: ARNT KO Clone B Hypoxia Regular Media Replicate 2

description: Library name: H32


title: BMK,14day1

description:
Library name: BMK_14d1
Tomato callus Spatial Transcriptomics sequencing data


title: Lungs_FP51_24-hours

description: Library name: 154


title: BMK,13day

description:
Library name: BMK_13d
Tomato callus Spatial Transcriptomics sequencing data


title: BMK,12day6

description:
Library name: BMK_12d6
Tomato callus Spatial Transcriptomics sequencing data


title: mir-35(cdb2 cdb78) II; ebax-1(tm2321) IV, embryo, rep 3

description: Library name: sAG95


title: ARNT KO Clone B Hypoxia Regular Media Replicate 1

description: Library name: H31


title: Lungs_FP48_0-hour

description: Library name: 152


title: Lungs_FP47_0-hour

description: Library name: 151


title: mir-35(cdb2 cdb78) II; ebax-1(tm2321) IV, L1, rep 2

description: Library name: sAG91


title: ARNT KO Clone A Normoxia Regular Media Replicate 3

description: Library name: N23

value: ARNT KO Clone A


title: Lungs_FP49_6-hours

description: Library name: 153

value: 6 hours


title: mir-35(cdb2 cdb78) II; ebax-1(tm2321) IV, embryo, rep 2

description: Library name: sAG87


title: mir-35(cdb2 cdb78) II; ebax-1(tm2321) IV , L1, rep 1

description: Library name: sAG75


title: BMK,12day3

description:
Library name: BMK_12d3
Tomato callus Spatial Transcriptomics sequencing data

value: callus


title: BMK,12day5

description:
Library name: BMK_12d5
Tomato callus Spatial Transcriptomics sequencing data


title: mir-35(cdb2 cdb78) II; ebax-1(tm2321) IV, embryo, rep 1

description: Library name: sAG65


title: tts-2 (cdb383) II;  ebax-1(tm2321) IV , rep 3

description: Library name: sAG461

value: tts-2 (cdb383) II;  ebax-1(tm2321) IV


title: Lungs_FP45_6-hours

description: Library name: 150

value: LOEL


title: ARNT KO Clone A Normoxia Regular Media Replicate 2

description: Library name: N22

value: Regular Media


title: Lungs_FP44_6-hours

description: Library name: 149


title: BMK,12day4

description:
Library name: BMK_12d4
Tomato callus Spatial Transcriptomics sequencing data


title: ARNT KO Clone A Hypoxia TIFM Replicate 3

description: Library name: T23


title: Lungs_FP42_6-hours

description: Library name: 147


title: Lungs_FP43_7-days

description: Library name: 148


title: ARNT KO Clone A Normoxia Regular Media Replicate 1

description: Library name: N21


title: BMK,12day2

description:
Library name: BMK_12d2
Tomato callus Spatial Transcriptomics sequencing data


title: BMK,10day8

description:
Library name: BMK_10d8
Tomato callus Spatial Transcriptomics sequencing data


title: tts-2 (cdb383) II;  ebax-1(tm2321) IV , rep 2

description: Library name: sAG382

value: Whole worm


title: ARNT KO Clone A Hypoxia TIFM Replicate 2

description: Library name: T22


title: tts-2 (cdb383) II, L1, rep 2

description: Library name: sAG380

value: tts-2 (cdb383)II


title: tts-2 (cdb383) II, L1, rep 1

description: Library name: sAG354


title: tts-2 (cdb383) II;  ebax-1(tm2321) IV , rep 1

description: Library name: sAG357


title: BMK,12day1

description:
Library name: BMK_12d1
Tomato callus Spatial Transcriptomics sequencing data


title: ARNT KO Clone A Hypoxia TIFM Replicate 1

description: Library name: T21


title: tts-2 (cdb383) II, L1, rep 3

description: Library name: sAG527


title: BMK,10day6

description:
Library name: BMK_10d6
Tomato callus Spatial Transcriptomics sequencing data


title: BMK,10day7

description:
Library name: BMK_10d7
Tomato callus Spatial Transcriptomics sequencing data


title: Lungs_FP40_7-days

description: Library name: 145


title: Lungs_FP41_7-days

description: Library name: 146


title: ARNT KO Clone A Hypoxia Regular Media Replicate 3

description: Library name: H23


title: Lungs_FP38_6-hours

description: Library name: 143


title: BMK,10day5

description:
Library name: BMK_10d5
Tomato callus Spatial Transcriptomics sequencing data


title: tts-2 (cdb396 cdb469) II, L1, rep 3

description: Library name: sAG627

value: tts-2 (cdb396 cdb469) II


title: ARNT KO Clone A Hypoxia Regular Media Replicate 2

description: Library name: H22


title: QGP1 Normoxia Control Replicate 3

description: Library name: QN3

data_processing:
Aligned and transcript counts using Salmon
Assembly: Grch38
Supplementary files format and content: Reads estimation per transcript
Supplementary files format and content: Reads per gene

value: Normoxia

tag: medium

value: Control


title: Lungs_FP39_24-hours

description: Library name: 144

value: Lungs

value: 24 hours


title: ARNT KO Clone A Hypoxia Regular Media Replicate 1

description: Library name: H21

value: Hypoxia


title: Lungs_FP33_6-hours

description: Library name: 142

value: SKH-1 Elite


title: tts-2 (cdb396 cdb469) II, L1, rep 1

description: Library name: sAG606


title: Lungs_FP32_0-hour

description: Library name: 141

value: 0 hour


title: BMK,10day4

description:
Library name: BMK_10d4
Tomato callus Spatial Transcriptomics sequencing data


title: BMK,10day3

description:
Library name: BMK_10d3
Tomato callus Spatial Transcriptomics sequencing data


title: tts-2 (cdb396 cdb469) II, L1, rep 2

description: Library name: sAG612


title: Lungs_FP30_0-hour

description: Library name: 140


title: tts-2 (cdb396 cdb471) II, L1, rep 3

description: Library name: sAG564

value: tts-2 (cdb396 cdb471) II


title: BMK,10day2

description:
Library name: BMK_10d2
Tomato callus Spatial Transcriptomics sequencing data


title: QGP1 Normoxia Control Replicate 1

description: Library name: QN1

value: Cancer Cell


title: tts-2 (cdb396 cdb471) II, L1, rep 2

description: Library name: sAG560


title: QGP1 Hypoxia Control Replicate 3

description: Library name: QH3


title: Lungs_FP29_6-hours

description: Library name: 139

value: 6 hours


title: QGP1 Normoxia Control Replicate 2

description: Library name: QN2


title: BMK,10day1

description:
Library name: BMK_10d1
Tomato callus Spatial Transcriptomics sequencing data

value: callus


title: QGP1 Hypoxia Control Replicate 1

description: Library name: QH1


title: BMK,6day2

description:
Library name: BMK_6d2
Tomato callus Spatial Transcriptomics sequencing data


title: tts-2 (cdb407); sqt-1(cdb412 cdb415) II, L1, rep 3

description: Library name: sAG492


title: QGP1 Hypoxia Control Replicate 2

description: Library name: QH2


title: Lungs_FP27_7-days

description: Library name: 138

value: 7 days


title: Panc1 Normoxia TIFM Replicate 3

description: Library name: C6

value: TIFM


title: tts-2 (cdb407); sqt-1(cdb412 cdb415) II, L1, rep 2

description: Library name: sAG485


title: BMK,6day1

description:
Library name: BMK_6d1
Tomato callus Spatial Transcriptomics sequencing data


title: BMK,8day

description:
Library name: BMK_8d
Tomato callus Spatial Transcriptomics sequencing data


title: tts-2 (cdb396 cdb471) II, L1, rep 1

description: Library name: sAG542


title: BMK,2,4day

description:
Library name: BMK_2_4d
Tomato callus Spatial Transcriptomics sequencing data


title: Lungs_FP23_24-hours

description: Library name: 135


title: Panc1 Normoxia TIFM Replicate 2

description: Library name: C2


title: tts-2 (cdb407); sqt-1(cdb412 cdb415) II, L1, rep 1

description: Library name: sAG466


title: Lungs_FP25_0-hour

description: Library name: 137

value: LOEL


title: Panc1 Normoxia TIFM Replicate 1

description: Library name: C10


title: Lungs_FP22_6-hours

description: Library name: 134


title: Lungs_FP24_7-days

description: Library name: 136


title: BMK,0day2

description:
Library name: BMK_0d2
Tomato callus Spatial Transcriptomics sequencing data

source_name: cotyledon

value: cotyledon


title: BMK,0day1

description:
Library name: BMK_0d1
Tomato callus Spatial Transcriptomics sequencing data


title: Panc1 Normoxia Control Replicate 3

description: Library name: C9


title: tts-2(cdb376) II, L1, rep 1

description: Library name: sAG274

value: Whole worm

value: tts-2(cdb376) II


title: Lungs_FP21_0-hour

description: Library name: 133


title: Panc1 Normoxia Control Replicate 2

description: Library name: C5

value: Normoxia


title: tts-2(cdb376) II, L1, rep 2

description: Library name: sAG275


title: Lungs_FP20_0-hour

description: Library name: 132


title: 16day,BMK_DG1000,scRNA-seq,rep1

description:
Library name: BMK_DG1000_16d1
Tomato callus single cell sequencing data

data_processing:
Raw sequencing data quality assessment: The quality of raw sequencing data was evaluated using Fastp to ensure accuracy and reliability.
Data alignment and matrix generation: The sequencing reads were aligned to the tomato reference genome using Cell Ranger and BMKDG1000MANU software, generating a gene expression matrix.
Clustering analysis: The generated gene expression matrix was imported into the R environment, and clustering analysis was performed using the Seurat package to identify different cell types and subpopulations.
Assembly: S_lycopersicum_chromosomes.4.00
Supplementary files format and content: The clustering analysis results were saved as an RDS file containing clustering information for subsequent analysis and data sharing.

growth_protocol: Seeds of Solanum lycopersicum cv. Micro-Tom (MT, LA3911) were sterilized in 75% EtOH for 60 sec, followed by 1% NaOCl with 0.02% Triton X-100 for 15 min, then rinsed eight times with sterile distilled water and dried. Seeds were germinated on 1/2 MS medium (4.33 g L−1 MS basal salt mixture, 1% sucrose, 3.5% phytagel, pH 5.8) in the dark for 3 days, then transferred to long-day conditions (16-h light/8-h dark) at 25°C with 70% relative humidity.

extract_protocol:
For RNA extraction, fresh callus tissues were collected and processed using the RNeasy mini plus kit (Qiagen). Approximately 1.3 µg of total RNA was used for library construction
Fresh callus tissues were dissociated into single cells using enzymatic digestion.Single-cell suspensions were prepared and loaded onto the 10x Chromium platform.Gel Bead-In-Emulsion (GEM) reactions were performed to encapsulate single cells with gel beads.Reverse transcription was conducted within the GEMs to generate cDNA.cDNA was amplified, purified, and fragmented.Sequencing libraries were constructed using the 10x Chromium Single Cell Library Kit.

treatment_protocol: Cotyledons of 6-day-old seedlings were excised and placed onto SIM medium (4.33 g L−1 MS basal salt mixture, 3% sucrose, 1 mg L−1 Zeatin, 0.1 mg L−1 IAA, 3.5% phytagel, pH 5.8) to induce shoot regeneration. Cultures were maintained under 70% relative humidity and light at approximately 50 µmol m−2 s−1 (16/8 h light/dark cycle) at 25°C


title: Panc1 Normoxia Control Replicate 1

description: Library name: C1

value: Control


title: Lungs_FP19_24-hours

description: Library name: 131

value: Lungs


title: tts-2(cdb396 cdb473) II, L1, rep 1

description: Library name: sAG607

value: tts-2(cdb396 cdb473) II


title: tts-2(cdb396 cdb473) II, L1, rep 3

description: Library name: sAG628


title: 16day,10x_Chromium,scRNA-seq,rep2

description:
Library name: 10x_Chromium_16d2
Tomato callus single cell sequencing data


title: tts-2(cdb396 cdb473) II, L1, rep 2

description: Library name: sAG613


title: tts-2(cdb396) II, L1, rep3

description: Library name: sAG460

value: tts-2(cdb396) II


title: Lungs_FP17_7-days

description: Library name: 130

value: SKH-1 Elite


title: Panc1 Hypoxia TIFM Replicate 2

description: Library name: C4

value: Hypoxia


title: Lungs_FP16_7-days

description: Library name: 129


title: tts-2(cdb396) II, L1, rep2

description: Library name: sAG421


title: Heart_FPB2_6-hours

description: Library name: 128

source_name: Heart

value: Heart


title: 14day,BMK_DG1000,scRNA-seq,rep2

description:
Library name: BMK_DG1000_14d2
Tomato callus single cell sequencing data


title: 14day,BMK_DG1000,scRNA-seq,rep1

description:
Library name: BMK_DG1000_14d1
Tomato callus single cell sequencing data


title: Panc1 Hypoxia TIFM Replicate 1

description: Library name: C12

value: Cancer Cell


title: Panc1 Hypoxia TIFM Replicate 3

description: Library name: C8


title: 16day,10x_Chromium,scRNA-seq,rep1

description:
Library name: 10x_Chromium_16d1
Tomato callus single cell sequencing data


title: tts-2(cdb396) II, L1, rep1

description: Library name: sAG399


title: 14day,10x_Chromium,scRNA-seq,rep1

description:
Library name: 10x_Chromium_14d1
Tomato callus single cell sequencing data


title: Heart_FP95_0-hour

description: Library name: 126

value: 200uL Ringer's

value: 0 hour


title: Panc1 Hypoxia Control Replicate 2

description: Library name: C3


title: tts-2(cdb467) II, L1, rep 3

description: Library name: sAG626

value: tts-2(cdb467) II


title: Panc1 Hypoxia Control Replicate 3

description: Library name: C7


title: tts-2(cdb467) II, L1, rep 2

description: Library name: sAG611


title: Panc1 Hypoxia Control Replicate 1

description: Library name: C11


title: 12day,BMK_DG1000,scRNA-seq,rep1

description:
Library name: BMK_DG1000_12d1
Tomato callus single cell sequencing data

value: callus


title: tts-2(cdb467) II, L1, rep 1

description: Library name: sAG605


title: Heart_FP96_0-hour

description: Library name: 127


title: 12day,BMK_DG1000,scRNA-seq,rep2

description:
Library name: BMK_DG1000_12d2
Tomato callus single cell sequencing data


title: Heart_FP93_24-hours

description: Library name: 124

value: 24 hours


title: wildtype, L1 stage, set 2, rep 3

description: Library name: sBD583

value: wild type


title: MiaPaCa Normoxia TIFM Replicate 2

description: Library name: MT2

source_name: MiaPaCa

value: MiaPaCa

value: TIFM


title: Heart_FP94_24-hours

description: Library name: 125


title: MiaPaCa Normoxia TIFM Replicate 1

description: Library name: MT1

value: Normoxia


title: Heart_FP92_24-hours

description: Library name: 123

value: Control


title: wildtype, embryro, set 2, rep 3

description: Library name: sBD580

value: Whole worm


title: Heart_FP91_24-hours

description: Library name: 122


title: wildtype, L1 stage, set 2, rep 2

description: Library name: sBD577


title: MiaPaCa Normoxia TIFM Replicate 3

description: Library name: MT3


title: MiaPaCa Normoxia Control Replicate 3

description: Library name: MN3


title: Lysine 96h late phase C

type: RNA

city: Saarbruecken

first: Michael

last: Kohlstedt

address: Campus A1.5

institute: Saarland University

description: Lys lateC6

hyb_protocol: Agilent hybridisation kit

scan_protocol: Agilent SureScan S2600D Microarray Scanner

data_processing: Feature extraction and statistical analysis were performed using the limma R package (moderated t-test, p adj < 0.05, Benjamini–Hochberg correction, ≥1-fold change)

organism: Yarrowia lipolytica

source_name: cell biomass

label_protocol: Agilent labeling kit (one color)

growth_protocol: baffled 500 mL shake flask, 50 mL yeast nitrogen base (YNB) minimal medium with different nutrient concentrations (20 g L-1 glycerol, 5 g L-1 ammonium sulfate, MES buffer pH = 6.8), 28°C, 230 rpm, initial OD600 = 0.1

extract_protocol: mRNA extracted from harvested cell pellets using RiboPure Yeast RNA extraction kit

treatment_protocol: Cells (2 mL) were harvested via centrifugation (30 sec, 4°C, 13.000 x g) and snap-frozen in liquid nitrogen

value: The Hyb6 strain at 96 h in the late stationary phase after 15 mM lysine addition

tag: growth phase

value: late stationary phase


title: Heart_FP88_0-hour

description: Library name: 121

tag: tissue

value: SKH-1 Elite


title: wildtype, embryro, set 2, rep 2

description: Library name: sBD574


title: Heart_FP87_0-hour

description: Library name: 120


title: wildtype, L1 stage, set 2, rep 1

description: Library name: sBD571


title: MiaPaCa Normoxia Control Replicate 1

description: Library name: MN1

tag: cell line


title: Lysine 96h late phase B

description: Lys lateB6


title: Heart_FP86_6-hours

description: Library name: 119

value: 6 hours


title: Lysine 48h early phase B

description: Lys earlyB5

value: The Hyb6 strain at 48 h in the early stationary phase after 15 mM lysine addition

value: early stationary phase


title: wildtype, embryro, set 2, rep 1

description: Library name: sBD568


title: MiaPaCa Normoxia Control Replicate 2

description: Library name: MN2

tag: cell type

value: Cancer Cell


title: MiaPaCa Hypoxia TIFM Replicate 3

description: Library name: MR3

tag: treatment

value: Hypoxia


title: wildtype, L1 stage, set 1, rep 3

description: Library name: sBD558

tag: genotype


title: Heart_FP85_6-hours

description: Library name: 118

value: Heart

tag: strain

value: 200uL Ringer's


title: MiaPaCa Hypoxia TIFM Replicate 2

description: Library name: MR2


title: Lysine 96h late phase A

description: Lys lateA6


title: Lysine 48h early phase A

description: Lys earlyA5


title: Lysine 10h exp phase C

description: Lys expC4

value: The Hyb6 strain at 10 h in the exponential phase before 15 mM lysine addition

value: exponential growth


title: MiaPaCa Hypoxia TIFM Replicate 1

description: Library name: MR1

value: MiaPaCa


title: Lysine 10h exp phase B

description: Lys expB4


title: Heart_FP83_7-days

description: Library name: 116

value: 7 days


title: Heart_FP84_7-days

description: Library name: 117


title: wildtype, embryro, set 1, rep 3

description: Library name: sBD556

value: wild type


title: Heart_FP82_7-days

description: Library name: 115

value: Control


title: MiaPaCa Hypoxia Control Replicate 2

description: Library name: MH2


title: MiaPaCa Hypoxia Control Replicate 3

description: Library name: MH3


title: Heart_FP81_7-days

description: Library name: 114


title: wildtype, L1 stage, set 1, rep 2

description: Library name: sBD554

value: Whole worm


title: wildtype, L1 stage, set 5, rep 3

description: Library name: sAG625


title: wildtype, embryro, set 1, rep 2

description: Library name: sBD552


title: Heart_FP78_6-hours

description: Library name: 113


title: JP8 Normoxia TIFM Replicate 3

description: Library name: FN6

value: Normoxia

value: TIFM


title: Heart_FP77_6-hours

description: Library name: 112

value: SKH-1 Elite


title: wildtype, L1 stage, set 1, rep 1

description: Library name: sAG67


title: wildtype, L1 stage, set 5, rep 1

description: Library name: sAG604


title: MiaPaCa Hypoxia Control Replicate 1

description: Library name: MH1


title: Heart_FP73_6-hours

description: Library name: 110

value: 6 hours


title: Heart_FP72_6-hours

description: Library name: 109


title: wildtype, L1 stage, set 5, rep 2

description: Library name: sAG610


title: JP8 Normoxia TIFM Replicate 1

description: Library name: FN4


title: JP8 Hypoxia TIFM Replicate 3

description: Library name: FH6


title: wildtype, embryro, set 1, rep 1

description: Library name: sAG57


title: JP8 Hypoxia TIFM Replicate 2

description: Library name: FH5


title: wildtype, L1 stage, set 4, rep 3

description: Library name: sAG562


title: Heart_FP74_0-hour

description: Library name: 111

value: 0 hour


title: JP8 Normoxia TIFM Replicate 2

description: Library name: FN5


title: GLP1R agnoist and Anti-IL17A-ab treated 3, macrophage

city: Indianapolis

first: Santhosh Kumar

last: Pasupuleti

state: Indiana

department: Pediatrics

institute: Indiana University School of Medicine

description: Library name: Combo_3_macrophage

data_processing:
The RNA-seq reads were mapped to the mouse genome mm10 using a STAR (v2.7.2a) RNA-seq aligner with the following parameter: “–outSAMmapqUnique” Uniquely mapped sequencing reads were assigned to GENCODE M22 gene using featureCounts (v2.0.1) with the following parameter: “-s 0 -p -Q 10 -O.”
Assembly: GRCm38/mm10
Supplementary files format and content: readCounts

source_name: Visceral Adipose Tissue

growth_protocol: Leptin-deficient LepOb/Ob (Ob/Ob) mice (stock no. 000632) on a C57BL/6J background was obtained from The Jackson Laboratory. Wild-type (WT) C57BL/6 control mice and Shp2E76K/+;LysM-Cre⁺ mice (C57BL/6 background) were generated at the Indiana University School of Medicine core facility. Mice used in this study were approximately 12–14 weeks of age and included both males and females. Animals were maintained under standard housing conditions (12-hour light/12-hour dark cycle), group-housed by age, sex, and genotype, and provided food and water ad libitum. Experimental groups were matched for age and sex. We did not observe any difference in function or phenotypes between males and females.

extract_protocol:
Total RNA was isolated from bone marrow (BM) cells and adipose tissue macrophages (ATMs) collected from vehicle control and three treatment groups (n = 3 mice per group) using the Qiagen RNeasy Plus Micro Kit, following the manufacturer’s instructions. RNA quality was assessed using an Agilent Bioanalyzer, and samples with RNA integrity number (RIN) > 8 were used for downstream library preparation.
Paired-end RNA-seq libraries were prepared at the Indiana University Genomics Core Facility using standard Illumina protocols. Sequencing was performed on an Illumina NovaSeq X Plus platform. Each experimental group included three biological replicates, with approximately 30 million reads generated per sample. Library type - Unstranded (RSeQC: 1++,1--,2+-,2-+; 1+-,1-+,2++,2--)

treatment_protocol: The CD45.2+ donor BM cells from Shp2E76K/+;LysM-Cre+ mice were mixed with age matched Boy/J CD45.1+ competitor BM donor cells (with an equal number of viable total BM cells, 500K:500K). Recipient mice (Ob/Ob and WT) were lethally irradiated (700 cGy + 400 cGy) one day prior to transplantation (intravenous tail injection) of donor cell. At 8 weeks post-transplantation, the Ob/Ob recipient mice were then randomized and treated for 30 days with Vehicle, Beinaglutide, a GLP-1R agonist (3 mg/kg, s.c.), an anti–IL-17A antibody (200 μg/mouse, i.p., three times weekly), or the combination. Mice were harvested after 30 days of drug treatment.

value: Visceral Adipose Tissue

value: Macrophages

value: GLP1R agnoist and Anti-IL17A-ab treated

value: Batch 1


title: wildtype, L1 stage, set 4, rep 2

description: Library name: sAG557

source_name: Whole worm


title: Heart_FP69_0-hour

description: Library name: 107

value: Heart


title: JP8 Hypoxia TIFM Replicate 1

description: Library name: FH4

value: Cancer Cell

value: Hypoxia


title: GLP1R agnoist and Anti-IL17A-ab treated 1, macrophage

description: Library name: Combo_1_macrophage


title: GLP1R agnoist and Anti-IL17A-ab treated 2, macrophage

description: Library name: Combo_2_macrophage


title: Heart_FP68_6-hours

description: Library name: 106


title: wildtype, L1 stage, set 4, rep 1

description: Library name: sAG541


title: Heart_FP71_0-hour

description: Library name: 108


title: JP7 Normoxia TIFM Replicate 2

description: Library name: FN2


title: Heart_FP67_0-hour

description: Library name: 105