title: Blastocysts, MT-treated, rep3

description:
Library name: M3
column name in RNA-Seq_TPM.csv : M3


title: MEC-1 cell line- RP11-161H23.5 Gapmer 2 treatment - rep3

status: Public on Aug 15 2026

type: RNA

city: Barcelona

first: Lluís

last: Hernández

state: Barcelona

address: Rossello 153

department: Area 5

country: Spain

institute: IDIBAPS

hyb_protocol: The ss-cDNA was fragmented and labeled and hybridized onto the  Affymetrix Human Clariom D, for 16hr at 45ºC and 60rpm, using Affymetrix Hybridization 645 oven. Afterwards, arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 System

data_processing: The data was analyzed with Transcriptome Expression Console Software (TAC v4.0.2) using (log2)  SST-RMA algorithm normalization.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MEC-1 cell line after RP11-161H23.5 Gapmer 2 treatment by 4 days

label_protocol: Starting from 10ng of purified total RNA , a reverse transcription reaction was initiated at the Poly-A tail as well as throughout the entire length of RNA to capture both coding and multiple forms of non-coding RNA. Complementary RNA (cRNA) amplification was achieved using low-cycle PCR followed by linear amplification using T7 in vitro transcription (IVT) technology. The cRNA was then converted to biotinylated sense-strand DNA hybridization targets for unbiased coverage of the transcriptomeand scanned using the Affymetrix GeneChip Scanner 3000 System.

growth_protocol: RPMI-1640 supplemented with 10% heat-inactivated fetal bovine serum, 100 U/ml penicillin, 0.1 mg/ml streptomycin

extract_protocol: miRNAeasy kit (Qiagen)

treatment_protocol: 1uM of each Gapmer along 4 days

tag: cell line

tag: treatment

value: RP11-161H23.5 silencing Gapmer 2


title: M55 line with Dox-inducible CDK1 transgene, Dox_1000ng/mL, P12, Rep1

type: SRA

city: Boston

first: Alex

last: Plesa

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

country: USA

institute: Harvard Medical School

description:
Library name: A17
Donor age 55, Passage 12

library_source: transcriptomic

data_processing:
To minimize variability arising from differences in sequencing depth, FASTQ files for all libraries (except LIB058979, LIB092645, and LIB083102) were downsampled to 20 million reads using Seqtk-1.3.
Raw RNA-seq reads were aligned to the GRCh38/GRCm39 reference genome using STAR v2.5.2b and checked for quality control using FastQC v0.11.5
Alignment files were indexed using SAMtools v1.3.154 and gene-level counts were obtained using featureCounts from the Subread v2.0.1 package
Assembly: GRCh38, GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: polyA RNA

growth_protocol: NHDFs were maintained in low-glucose DMEM supplemented with 15% fetal bovine serum (FBS) and 1% Pen-strep (P/S) in humidified atmosphere with 5% CO2 and 5% O2, at 37C. iPSCs were maintained in mTESR+supplement in humidified atmosphre with 5% CO2 at 37C.

extract_protocol:
Cells were lysed using the Monarch DNA/RNA Protection Reagent (NEB T2011) and stored at -80°C until RNA extraction. Total RNA was extrqacted using the Monarch Total RNA Miniprep kit (NEB T2010). Mouse tissues were processed by Novogene.
Libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina using the polyA mRNA workflow according to manufacturer's instructions. LIB058979 was genereated using the Tecan MagicPrepRevelo mRNA-seq kit acoording to manufacturare's instructions. LIB083102 was generated by Novogene using a directional mRNA library preparation method.

treatment_protocol: Transgene was induced using doxycycline at the specified concentration for the specified amount of time. Similarly, rapamycin was added to the media at the 100nM for the specified amount of time.

tag: cell type

value: Fibroblast

tag: genotype

value: Dox_1000ng/mL, 3days

tag: batch


title: M55 line with Dox-inducible CDK1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A18
Donor age 55, Passage 12


title: YF1-IP-5_210930N_S51_L002_R1R2_001.fastq.gz

city: Shanghai

first: Lijun

last: Wang

address: 333 Nan Chen Road

country: China

institute: Shanghai University

description: Library name: Sample6

data_processing:
Basecalls were performed usina bcl2fasta y2.17 for Novaseq output.
RIP-seq reads were trimmed from 3' end until the final base had a quality score > 30using skewer-0.2.2, discarding reads left with< 50 bp.
RIP-seq reads were aligned to the mouse mm10 genome using Bowtie version 2-2.2.3. Only uniquely mapping reads with at most two mismatches were retained.
To create RIP-seq coverage plots, the locations of the mapped RIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads permillion, rm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the sianifcance cutoff p-value <=1e-3.
Assembly: Mouse mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Mus musculus

source_name: heart

extract_protocol:
RNA was extracted with miRNeasy Mini Kit (Qiagen) and send for sequencing.
RIP-seq

tag: tissue

value: heart

value: adult mouse cardiac myocytes


title: M55 line with Dox-inducible HDAC6 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A50
Donor age 55, Passage 12


title: OCUG-1 Sorafenib 1.25 uM + IACS-010759 1 uM biological replicate 3

first: Yingbin

last: Liu

state: Shanghai

address: Dongfang Road1630

institute: Department of Biliary-Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description:
Library name: OCUG1_Sora1.25uM_IACS1uM_Rep3
Bulk RNA-seq of OCUG-1 gallbladder cancer cells after sorafenib 1.25 uM plus IACS-010759 1 uM for 72 h, biological replicate 3.

data_processing:
Illumina base-call files were demultiplexed into lane- and library-specific paired-end FASTQ files using bcl2fastq. The resulting gzip-compressed, unfiltered FASTQ files were deposited as raw sequencing data.
For OCUG-1-S10-2, OCUG-1-S125-2, OCUG-1-S125-3, and OCUG-1-S125-I-2, the corresponding L2 and L3 paired-end FASTQ files were combined by read direction before alignment and expression quantification. All original lane-specific FASTQ files are deposited.
Raw RNA-seq data were subjected to quality control and filtering using fastp (v1.3.2) to remove adapter sequences and low-quality reads. Reads with low-quality bases (quality score < Q20) exceeding 30% of total bases were removed, and reads shorter than 36 bp after trimming were discarded. Basic sequencing metrics, including base quality profiles, Q30, and GC content, were assessed. Clean high-quality reads were aligned to the human reference genome GRCh38 using HISAT2 (v2.2.2) with Ensembl release 113 annotation. Gene-level quantification was performed using featureCounts (Subread v2.1.1) based on exon annotations to generate raw count matrices. Sequencing quality, alignment performance, and read assignment statistics were summarized using MultiQC (v1.33).
All downstream analyses were performed in R (v4.4.1). To minimize the impact of lowly expressed genes, only genes with non-zero expression in at least 75% of samples were retained for subsequent analyses. Principal component analysis (PCA) was used to evaluate overall sample relationships and data quality. Differential expression analysis was conducted on raw counts using DESeq2 (v1.42.1). Differentially expressed genes (DEGs) were defined as |log2 fold change| > 1 and Benjamini-Hochberg-adjusted P value (FDR) < 0.05 and were visualized using volcano plots and heatmaps. Heatmaps were generated from DESeq2 size-factor-normalized counts with row-wise Z-score scaling; displayed genes met FDR < 0.05 and |log2 fold change| > 1 in at least one relevant contrast.
GO Biological Process (BP) enrichment analysis was performed on DEGs using clusterProfiler (v4.10.1); multiple-testing-adjusted P values were calculated, and representative terms with P value < 0.05 were selected for display. Gene set enrichment analysis was performed using the GSEA() function in clusterProfiler (v4.10.1). Before GSEA, genes were not filtered by P value, adjusted P value, or absolute log2 fold change. All genes with non-missing gene symbols and available log2 fold change values from the differential expression analysis were included. For duplicated gene symbols, one representative record was retained. Genes were ranked by log2 fold change in decreasing order to generate a preranked gene list. Gene sets were obtained from the MSigDB C5 collection, version 2025.1, using human gene symbols, and gene sets containing 10 to 500 genes were retained. Enrichment score, normalized enrichment score, P value, and Benjamini-Hochberg-adjusted P value were calculated for each pathway, and the complete GSEA results were retained; representative pathways with P value < 0.05 were selected for display.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files containing gene-level raw read counts generated by featureCounts based on Ensembl release 113 annotation for the GRCh38 human reference genome. Rows represent Ensembl gene IDs and columns represent individual RNA-seq samples. Count values are unnormalized integer read counts and were used as input for downstream differential expression analysis with DESeq2.

growth_protocol: HuCCT1 cells were cultured in RPMI-1640, and OCUG-1 cells were cultured in DMEM, at 37 °C in a humidified incubator with 5% CO2. Media were supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin (Procell). Cells were routinely passaged at a 1:3 ratio, and experiments used cells in logarithmic growth phase.

extract_protocol:
Cells were harvested after 72 h of drug treatment, and total RNA was extracted using the TRIzol method.
RNA-seq libraries were prepared by Berry Genomics using a TruSeq mRNA-seq workflow for eukaryotic RNA samples and sequenced on an Illumina NovaSeq platform as 150-bp paired-end reads.

treatment_protocol: Sorafenib and IACS-010759 were dissolved in DMSO as 10 mM stock solutions and diluted in the corresponding culture medium. Cells were treated for 72 h under four conditions: vehicle control with matched DMSO at no more than 0.1%, 1.25 µM sorafenib, 10 µM sorafenib, or 1.25 µM sorafenib plus 1 µM IACS-010759. Each condition included three independent biological replicates for each cell line.

value: sorafenib 1.25 uM plus IACS-010759 1 uM, 72 h


title: MEC-1 cell line- CYTOR Gapmer 1+2 treatment - rep2

source_name: MEC-1 cell line after CYTOR Gapmer 1+2 treatment by 4 days

value: LINC00152 silencing Gapmer 1+2


title: Blastocysts, MT-treated, rep2

city: Beijing

first: Kui

middle: Wen

last: Ma

address: No.2 Yuanmingyuan West Road, Haidian District

institute: China Agricultural University

description:
Library name: M2
column name in RNA-Seq_TPM.csv : M2

data_processing:
Fastp 0.20.1 and FastQC 0.11.9 were used for data quality control.
Reads were aligned to the bovine reference genome (Bos_taurus.ARS-UCD1.3) with the corresponding genome annotation (Bos_taurus.ARS-UCD1.2.108) using STAR 2.7.9a.
Gene counting was performed with featureCounts (Subread 1.6.3) .
DESeq2 [35] was used to identify differentially expressed genes.
Assembly: Bos_taurus.ARS-UCD1.3
Supplementary files format and content: csv files include TPM values for each sample

organism: Bos taurus

source_name: embryo

growth_protocol: Blastocysts from the MT-treated (n = 3) and control (n = 3) groups were frozen in liquid nitrogen and stored at -80 ℃

extract_protocol:
total RNA was extracted from the embryos using TRIzol reagent (Ambion, USA) and treated with DNase I (Takara, China) to eliminate genomic DNA
RNA-seq libraries were constructed using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA). Double-stranded cDNA was synthesized (SuperScript Kit, Invitrogen, USA), amplified via PCR, and size-fractionated (200–300 bp) using magnetic beads. Libraries were quantified via a TBS380 fluorometer prior to paired-end sequencing (PE150) on an Illumina NovaSeq 6000 platform.

value: embryo

value: MT-treated


title: YF1-IP-3_210930N_S50_L002_R1R2_001.fastq.gz

description: Library name: Sample5


title: M65 line with Dox-inducible UBE2I transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: S59
Donor age 65, Passage 10


title: MEC-1 cell line- CYTOR Gapmer 1 treatment - rep2

source_name: MEC-1 cell line after CYTOR Gapmer 1 treatment by 4 days

value: LINC00152 silencing Gapmer 1


title: Blastocysts, control, rep2

description:
Library name: C2
column name in RNA-Seq_TPM.csv : C2

value: control


title: M55 line with Dox-inducible FAU transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A42
Donor age 55, Passage 12

value: FAU


title: Blastocysts, control, rep3

description:
Library name: C3
column name in RNA-Seq_TPM.csv : C3


title: M55 line with Dox-inducible CDC34 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A16
Donor age 55, Passage 12


title: MEC-1 cell line- Scrambled Gapmer treatment (Exp CYTOR) - rep3

source_name: MEC-1 cell line after Scrambled Gapmer treatment by 4 days

value: Control LINC00152 silencing


title: Blastocysts, control, rep1

description:
Library name: C1
column name in RNA-Seq_TPM.csv : C1


title: MEC-1 cell line- CYTOR Gapmer 1+2 treatment - rep1


title: OCUG-1 Sorafenib 10 uM biological replicate 1

description:
Library name: OCUG1_Sora10uM_Rep1
Bulk RNA-seq of OCUG-1 gallbladder cancer cells after sorafenib 10 uM for 72 h, biological replicate 1.

value: sorafenib 10 uM, 72 h


title: WT_BCN1_C

description: Sample from Barcelona

source_name: CLL cells purifided from cryopreserved PBMC and treated by 24h: Condition C

growth_protocol: RPMI-1640 supplemented with 10% heat-inactivated fetal bovine serum, 100 U/ml penicillin, 0.1 mg/ml streptomycin+IL-2 (1.54 ng/ml)+CpG-ODN2006 (0.38 ug/ml)

treatment_protocol: see samples/summary for the different protocols

value: Primary CLL cells

value: Condition C


title: MEC-1 cell line- Scrambled Gapmer treatment (Exp LINC00158) - rep2

value: Control LINC00158 silencing


title: OCUG-1 Sorafenib 1.25 uM + IACS-010759 1 uM biological replicate 2

description:
Library name: OCUG1_Sora1.25uM_IACS1uM_Rep2
Bulk RNA-seq of OCUG-1 gallbladder cancer cells after sorafenib 1.25 uM plus IACS-010759 1 uM for 72 h, biological replicate 2.


title: OCUG-1 Sorafenib 1.25 uM + IACS-010759 1 uM biological replicate 1

description:
Library name: OCUG1_Sora1.25uM_IACS1uM_Rep1
Bulk RNA-seq of OCUG-1 gallbladder cancer cells after sorafenib 1.25 uM plus IACS-010759 1 uM for 72 h, biological replicate 1.


title: MEC-1 cell line- Scrambled Gapmer treatment (Exp CYTOR) - rep2


title: MEC-1 cell line- CYTOR Gapmer 1+2 treatment - rep3


title: MEC-1 cell line- CYTOR Gapmer 1 treatment - rep1


title: OCUG-1 Sorafenib 10 uM biological replicate 3

description:
Library name: OCUG1_Sora10uM_Rep3
Bulk RNA-seq of OCUG-1 gallbladder cancer cells after sorafenib 10 uM for 72 h, biological replicate 3.


title: M55 line with Dox-inducible GART transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: A44
Donor age 55, Passage 13

value: GART


title: OCUG-1 NC biological replicate 3

description:
Library name: OCUG1_NC_Rep3
Bulk RNA-seq of OCUG-1 gallbladder cancer cells after vehicle control for 72 h, biological replicate 3.

value: vehicle control (DMSO <= 0.1%), 72 h


title: M55 line with Dox-inducible CDC20 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A14
Donor age 55, Passage 12

value: Fibroblast

value: Dox_1000ng/mL, 3days


title: OCUG-1 Sorafenib 10 uM biological replicate 2

description:
Library name: OCUG1_Sora10uM_Rep2
Bulk RNA-seq of OCUG-1 gallbladder cancer cells after sorafenib 10 uM for 72 h, biological replicate 2.


title: M55 line with Dox-inducible CDC34 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A15
Donor age 55, Passage 12


title: OCUG-1 Sorafenib 1.25 uM biological replicate 3

description:
Library name: OCUG1_Sora1.25uM_Rep3
Bulk RNA-seq of OCUG-1 gallbladder cancer cells after sorafenib 1.25 uM for 72 h, biological replicate 3.

value: sorafenib 1.25 uM, 72 h


title: HuCCT1 Sorafenib 1.25 uM + IACS-010759 1 uM biological replicate 2

description:
Library name: HuCCT1_Sora1.25uM_IACS1uM_Rep2
Bulk RNA-seq of HuCCT1 intrahepatic cholangiocarcinoma cells after sorafenib 1.25 uM plus IACS-010759 1 uM for 72 h, biological replicate 2.

value: sorafenib 1.25 uM plus IACS-010759 1 uM, 72 h


title: M65 line with Dox-inducible SUMO1 transgene, Dox_1000ng/mL, Rep1

description:
Library name: S43
Donor age 65, Passage 11


title: M55 line with Dox-inducible CCNB1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A12
Donor age 55, Passage 12


title: OCUG-1 Sorafenib 1.25 uM biological replicate 1

description:
Library name: OCUG1_Sora1.25uM_Rep1
Bulk RNA-seq of OCUG-1 gallbladder cancer cells after sorafenib 1.25 uM for 72 h, biological replicate 1.


title: M55 line with Dox-inducible CDC20 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A13
Donor age 55, Passage 12


title: HuCCT1 Sorafenib 10 uM biological replicate 3

description:
Library name: HuCCT1_Sora10uM_Rep3
Bulk RNA-seq of HuCCT1 intrahepatic cholangiocarcinoma cells after sorafenib 10 uM for 72 h, biological replicate 3.


title: M55 line with Dox-inducible ATG5 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A8
Donor age 55, Passage 12


title: HuCCT1 Sorafenib 1.25 uM + IACS-010759 1 uM biological replicate 3

description:
Library name: HuCCT1_Sora1.25uM_IACS1uM_Rep3
Bulk RNA-seq of HuCCT1 intrahepatic cholangiocarcinoma cells after sorafenib 1.25 uM plus IACS-010759 1 uM for 72 h, biological replicate 3.


title: HuCCT1 Sorafenib 10 uM biological replicate 1

description:
Library name: HuCCT1_Sora10uM_Rep1
Bulk RNA-seq of HuCCT1 intrahepatic cholangiocarcinoma cells after sorafenib 10 uM for 72 h, biological replicate 1.


title: HuCCT1 Sorafenib 1.25 uM + IACS-010759 1 uM biological replicate 1

description:
Library name: HuCCT1_Sora1.25uM_IACS1uM_Rep1
Bulk RNA-seq of HuCCT1 intrahepatic cholangiocarcinoma cells after sorafenib 1.25 uM plus IACS-010759 1 uM for 72 h, biological replicate 1.


title: OCUG-1 NC biological replicate 1

description:
Library name: OCUG1_NC_Rep1
Bulk RNA-seq of OCUG-1 gallbladder cancer cells after vehicle control for 72 h, biological replicate 1.


title: M55 line with Dox-inducible AKT1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A6
Donor age 55, Passage 12


title: OCUG-1 NC biological replicate 2

description:
Library name: OCUG1_NC_Rep2
Bulk RNA-seq of OCUG-1 gallbladder cancer cells after vehicle control for 72 h, biological replicate 2.


title: M55 line with Dox-inducible CCNA2 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A9
Donor age 55, Passage 12


title: HuCCT1 Sorafenib 10 uM biological replicate 2

description:
Library name: HuCCT1_Sora10uM_Rep2
Bulk RNA-seq of HuCCT1 intrahepatic cholangiocarcinoma cells after sorafenib 10 uM for 72 h, biological replicate 2.


title: M55 line with Dox-inducible ATG5 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A7
Donor age 55, Passage 12


title: SK-N-MC_CIAP1_noDOX, 1 biologial Rep, 96h

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

country: Germany

institute: German Cancer Research Center (DKFZ)

description: Gene expression data

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Clariom D™ Arrays. Microarrays were washed and stained with Affymetrix GeneChip® 3000 Fluidics Station.

scan_protocol: Microarrays were scanned with Affymetrix GeneChip® 3000 Scanner.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

source_name: re-expression CIAP1

label_protocol: Biotinylated cRNA were prepared using Affymetrix GeneChip® WT PLUS Reagent Kit according to its manufacture's instruction from 6 μg total RNA.

growth_protocol: 1.000.000 cells per flask/T75 flask were cultured for 96h with/without addtion of dox (1μg/ml).

extract_protocol: RNA was extracted by using RNA isolation kit from Macherey-Nagel.

treatment_protocol: Cells were treated with/without dox (1μg/ml) for 96h, with a refreshment after 48h.

value: Ewing sarcoma


title: HuCCT1 Sorafenib 1.25 uM biological replicate 1

description:
Library name: HuCCT1_Sora1.25uM_Rep1
Bulk RNA-seq of HuCCT1 intrahepatic cholangiocarcinoma cells after sorafenib 1.25 uM for 72 h, biological replicate 1.


title: TP53alt6_A

description: Sample from Aviano

source_name: CLL cells purifided from cryopreserved PBMC and treated by 24h: Condition A

value: Condition A


title: HuCCT1 NC biological replicate 3

description:
Library name: HuCCT1_NC_Rep3
Bulk RNA-seq of HuCCT1 intrahepatic cholangiocarcinoma cells after vehicle control for 72 h, biological replicate 3.


title: M55 line with Dox-inducible AKT1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A5
Donor age 55, Passage 12


title: TP53alt6_D

description: Sample from Aviano

source_name: CLL cells purifided from cryopreserved PBMC and treated by 24h: Condition D

value: Condition D


title: M55 line with Dox-inducible ACTL6A transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A3
Donor age 55, Passage 12


title: M55 line with Dox-inducible ACTL6A transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A4
Donor age 55, Passage 12


title: TP53alt6_C

description: Sample from Aviano


title: THP-1, T3+DOX-rabbit-IgG

city: Tian Jin

first: meng

last: yang

state: Tianjin

address: Nanjing Road No.288

institute: State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital

description: Library name: 54-T3+DOX-rabbit-IgG

library_source: genomic

data_processing:
Subsequent analysis followed established computational pipelines detailed in the CUT&Tag Data Processing and Analysis Protocol (Zheng et al., 2020; Protocol.io). Differential peaks analysis was performed using Diff Bind (v3.10.1) with statistically significant peaks identified at p < 0.05.
Assembly: GRCh38/hg38
Supplementary files format and content: bw
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
CUT&Tag experiment in combination with the Hyperactive TM In-Situ ChIP Library Prep Kit for Illumina from Vazyme (TD902-01).
The extracted DNA fragments were extracted and subjected to high-throughput sequencing.

value: AML cell


title: THP-1, T2+DOX-rabbit-IgG

description: Library name: 53-T2+DOX-rabbit-IgG


title: THP-1, FULL+DOX-rabbit-IgG

description: Library name: 56-FULL+DOX-rabbit-IgG


title: TP53alt5_C

description: Sample from Aviano


title: HuCCT1 NC biological replicate 1

description:
Library name: HuCCT1_NC_Rep1
Bulk RNA-seq of HuCCT1 intrahepatic cholangiocarcinoma cells after vehicle control for 72 h, biological replicate 1.


title: THP-1, T6-rabbit-IgG

description: Library name: 51-T6-rabbit-IgG


title: THP-1, T3-rabbit-IgG

description: Library name: 50-T3-rabbit-IgG


title: THP-1, T6+DOX-rabbit-IgG

description: Library name: 55-T6+DOX-rabbit-IgG


title: M55 line with Dox-inducible ACTG1 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A2
Donor age 55, Passage 12


title: TP53alt5_D

description: Sample from Aviano


title: TP53alt5_B

description: Sample from Aviano

source_name: CLL cells purifided from cryopreserved PBMC and treated by 24h: Condition B

value: Condition B


title: THP-1, FULL-rabbit-IgG

description: Library name: 52-FULL-rabbit-IgG


title: PBMC_3-2, VDJ

city: Seoul

first: Byungjin

last: Hwang

address: 50-1, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University

description:
Library name: 3-2_VDJ
vdj contig for all samples included

library_source: other

data_processing:
Each set of replicate raw data was processed using CellRanger v7.1.0 multi, producing separate outputs.
Sample demultiplexing
Genes and cells were filtered by QC criteria (total count, n_gene per cells, mitochondrial contnts)
Doublets removed
Assembly: GRCh38
Supplementary files format and content: The GEX h5ad file contains all sample demultiplexed information and filtered cells.
Supplementary files format and content: The VDJ contig file contains all VDJ contig information and filtered cell indice.

molecule: other

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using a Histopaque gradient. Single cells were then encapsulated in GEMs using the 10X Controller.
Libraries were generated using 10X Chromium VDJ & 5’ library and Gel Bead according to the user guide. To produce hashtag antibody libraries, TSC additive primer were spiked in at the step of cDNA amplification small size-selected amplified cDNA sample were used as template.

value: Blood

value: PBMC

value: Mixed (non-rejection, acute rejection)


title: TP53alt4_D

description: Sample from Aviano

value: Primary CLL cells


title: THP-1, T2-rabbit-IgG

description: Library name: 49-T2-rabbit-IgG


title: THP-1, MLL3-FULL-1+DOX

description: Library name: 46


title: TP53alt4_C

description: Sample from Aviano

value: Condition C


title: THP-1, MLL3-FULL-2+DOX

description: Library name: 47


title: TP53alt5_A

description: Sample from Aviano


title: PBMC_3-1, GEX

description:
Library name: 3-1_GEX
count matrix for all samples included

library_source: transcriptomic single cell


title: PBMC_3-1, VDJ

description:
Library name: 3-1_VDJ
vdj contig for all samples included


title: THP-1, MLL3-T3-3+DOX

description: Library name: 42


title: PBMC_3-2, GEX

description:
Library name: 3-2_GEX
count matrix for all samples included


title: THP-1, MLL3-T6-2+DOX

description: Library name: 44


title: PBMC, Pre-AR10, Batch3

description: Library name: Pre-AR10

data_processing:
Reads were first trimmed using Trimmomatic and then aligned to the genomic reference using STAR2. Counting was performed with HTSeq-count.
Assembly: GRCh38
Supplementary files format and content: Filtered VCF file containing reference genotypes used for Souporcell analysis.

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using a Histopaque gradient, and RNA was purified from the cells using TRIzol reagent.
TruSeq Stranded mRNA Library Prep Kit, Library Protocol TruSeq Stranded mRNA Reference Guide # 1000000040498 v00


title: THP-1, MLL3-T6-1+DOX

description: Library name: 43


title: TP53alt3_D

description: Sample from Aviano


title: TP53alt4_A

description: Sample from Aviano


title: THP-1, MLL3-T3-1+DOX

description: Library name: 40


title: TP53alt4_B

description: Sample from Aviano


title: TP53alt3_C

description: Sample from Aviano


title: THP-1, MLL3-T2-3+DOX

description: Library name: 39


title: THP-1, MLL3-FULL-3

description: Library name: 36


title: THP-1, MLL3-T6-3+DOX

description: Library name: 45


title: THP-1, MLL3-T2-1+DOX

description: Library name: 37


title: THP-1, MLL3-FULL-3+DOX

description: Library name: 48


title: THP-1, MLL3-FULL-2

description: Library name: 35


title: PBMC, Pre-AR7, Batch3

description: Library name: Pre-AR7


title: PBMC, Pre-AR8, Batch3

description: Library name: Pre-AR8


title: THP-1, MLL3-T6-3

description: Library name: 33


title: TP53alt3_B

description: Sample from Aviano


title: TP53alt3_A

description: Sample from Aviano


title: THP-1, MLL3-FULL-1

description: Library name: 34


title: THP-1, MLL3-T3-2+DOX

description: Library name: 41


title: PBMC, Pre-NR10, Batch3

description: Library name: Pre-NR10


title: PBMC, Pre-NR9, Batch3

description: Library name: Pre-NR9


title: THP-1, MLL3-T6-1

description: Library name: 31


title: THP-1, MLL3-T6-2

description: Library name: 32


title: PBMC, Pre-AR9, Batch3

description: Library name: Pre-AR9


title: TP53alt2_D

description: Sample from Aviano


title: THP-1, MLL3-T3-3

description: Library name: 30


title: TP53alt2_C

description: Sample from Aviano


title: THP-1, MLL3-T2-3

description: Library name: 27


title: PBMC, Pre-NR8, Batch3

description: Library name: Pre-NR8


title: THP-1, MLL3-T3-2

description: Library name: 29


title: MEC-1 cell line- Scrambled Gapmer treatment (Exp CYTOR) - rep1

value: Control LINC00152 silencing


title: OCUG-1 Sorafenib 1.25 uM biological replicate 2

description:
Library name: OCUG1_Sora1.25uM_Rep2
Bulk RNA-seq of OCUG-1 gallbladder cancer cells after sorafenib 1.25 uM for 72 h, biological replicate 2.


title: PBMC, Pre-NR7, Batch3

description: Library name: Pre-NR7


title: THP-1, MLL3-T2-2+DOX

description: Library name: 38


title: M55 line with Dox-inducible CCNA2 transgene, Dox_1000ng/mL, P12, Rep2

description:
Library name: A10
Donor age 55, Passage 12


title: TC-71_CIAP1_DOX, 1 biologial Rep, 96h

description: Gene expression data


title: THP-1, MLL3-T3-1

description: Library name: 28


title: TC-71_CIAP1_noDOX, 1 biologial Rep, 96h

description: Gene expression data


title: M55 line with Dox-inducible CCNB1 transgene, Dox_1000ng/mL, P12, Rep1

description:
Library name: A11
Donor age 55, Passage 12


title: THP-1, MLL3-T2-2

description: Library name: 26


title: TP53alt2_B

description: Sample from Aviano


title: SK-N-MC_CIAP1_DOX, 1 biologial Rep, 96h

description: Gene expression data


title: PBMC, Post-AR6, Batch2

data_processing:
Reads were first trimmed using Trimmomatic and then aligned to the genomic reference using STAR2. Counting was performed with HTSeq-count.
Assembly: GRCh38
Supplementary files format and content: The comma-separated text file contains the raw counts for all samples from each batch.


title: THP-1, H3K4me1-FULL-3+DOX

description: Library name: 24-H3K4me1-FULL-3+DOX


title: THP-1, MLL3-T2-1

description: Library name: 25


title: THP-1, H3K4me1-FULL-2+DOX

description: Library name: 23-H3K4me1-FULL-2+DOX


title: PBMC, Post-AR5, Batch2


title: TP53alt1_D

description: Sample from Aviano


title: TP53alt2_A

description: Sample from Aviano


title: PBMC, Post-AR4, Batch2


title: THP-1, H3K4me1-T6-3+DOX

description: Library name: 21-H3K4me1-T6-3+DOX


title: THP-1, H3K4me1-FULL-1+DOX

description: Library name: 22-H3K4me1-FULL-1+DOX


title: HuCCT1 Sorafenib 1.25 uM biological replicate 3

description:
Library name: HuCCT1_Sora1.25uM_Rep3
Bulk RNA-seq of HuCCT1 intrahepatic cholangiocarcinoma cells after sorafenib 1.25 uM for 72 h, biological replicate 3.


title: THP-1, H3K4me1-T6-1+DOX

description: Library name: 19-H3K4me1-T6-1+DOX


title: THP-1, H3K4me1-T6-2+DOX

description: Library name: 20-H3K4me1-T6-2+DOX


title: HuCCT1 Sorafenib 1.25 uM biological replicate 2

description:
Library name: HuCCT1_Sora1.25uM_Rep2
Bulk RNA-seq of HuCCT1 intrahepatic cholangiocarcinoma cells after sorafenib 1.25 uM for 72 h, biological replicate 2.


title: PBMC, Post-AR3, Batch2


title: TP53alt1_C

description: Sample from Aviano


title: TP53alt1_B

description: Sample from Aviano


title: THP-1, H3K4me1-T2-2+DOX

description: Library name: 14-H3K4me1-T2-2+DOX


title: THP-1, H3K4me1-T3-2+DOX

description: Library name: 17-H3K4me1-T3-2+DOX


title: PBMC, Post-AR1, Batch1


title: PBMC, Post-AR2, Batch1


title: THP-1, H3K4me1-T3-1+DOX

description: Library name: 16-H3K4me1-T3-1+DOX


title: THP-1, H3K4me1-FULL-3

description: Library name: 12-H3K4me1-FULL-3


title: TP53alt1_A

description: Sample from Aviano


title: WT_AVI6_D

description: Sample from Aviano


title: THP-1, H3K4me1-T2-3+DOX

description: Library name: 15-H3K4me1-T2-3+DOX


title: THP-1, H3K4me1-FULL-1

description: Library name: 10-H3K4me1-FULL-1


title: THP-1, H3K4me1-T3-3+DOX

description: Library name: 18-H3K4me1-T3-3+DOX


title: TP53alt6_B

description: Sample from Aviano


title: WT_AVI6_B

description: Sample from Aviano


title: THP-1, H3K4me1-FULL-2

description: Library name: 11-H3K4me1-FULL-2


title: THP-1, H3K4me1-T3-3

description: Library name: 6-H3K4me1-T3-3


title: PBMC, Post-NR4, Batch2


title: THP-1, H3K4me1-T3-2

description: Library name: 5-H3K4me1-T3-2


title: THP-1, H3K4me1-T2-1+DOX

description: Library name: 13-H3K4me1-T2-1+DOX


title: THP-1, H3K4me1-T6-3

description: Library name: 9-H3K4me1-T6-3


title: WT_AVI6_A

description: Sample from Aviano


title: PBMC, Post-NR2, Batch1


title: PBMC_2-2, VDJ

description: vdj contig for all samples included

data_processing:
Each set of replicate raw data was processed using CellRanger v7.1.0 multi, producing separate outputs.
Sample demultiplexing
Genes and cells were filtered by QC criteria (total count, n_gene per cells, mitochondrial contnts)
Doublets removed
Assembly: GRCh38
Supplementary files format and content: The GEX h5ad file contains all sample demultiplexed information and filtered cells.
Supplementary files format and content: The VDJ h5ad file contains all VDJ contig information and filtered cell indice.


title: THP-1, FULL+DOX-MOUSE-IGG

description: Library name: FULL+DOX


title: THP-1, H3K4me1-T3-1

description: Library name: 4-H3K4me1-T3-1


title: THP-1, H3K4me1-T2-3

description: Library name: 3-H3K4me1-T2-3


title: WT_AVI6_C

description: Sample from Aviano


title: THP-1, H3K4me1-T6-1

description: Library name: 7-H3K4me1-T6-1


title: WT_AVI4_D

description: Sample from Aviano


title: THP-1, H3K4me1-T2-2

description: Library name: 2-H3K4me1-T2-2


title: THP-1, H3K4me1-T2-1

description: Library name: 1-H3K4me1-T2-1


title: WT_AVI4_C

description: Sample from Aviano


title: PBMC_2-1, VDJ

description: vdj contig for all samples included


title: THP-1, FULL-MOUSE-IGG

description: Library name: FULL


title: WT_AVI5_A

description: Sample from Aviano


title: THP-1, T6+DOX-MOUSE-IGG

description: Library name: T6+DOX


title: WT_AVI4_B

description: Sample from Aviano


title: THP-1, T2-MOUSE-IGG

description: Library name: T2


title: PBMC_2-1, GEX

description: count matrix for all samples included


title: THP-1, T2+DOX-MOUSE-IGG

description: Library name: T2+DOX


title: WT_AVI5_B

description: Sample from Aviano


title: PBMC_1-2, VDJ

description: vdj contig for all samples included


title: THP-1, FLAG-FULL-2+DOX-REP2

description: Library name: FLAG-FULL-2+DOX


title: PBMC_2-2, GEX

description: count matrix for all samples included


title: PBMC_1-1, VDJ

description: vdj contig for all samples included


title: WT_AVI3_D

description: Sample from Aviano


title: THP-1, FLAG-FULL-1+DOX-REP1

description: Library name: FLAG-FULL-1+DOX


title: THP-1, FLAG-T6-1+DOX-REP1

description: Library name: FLAG-T6-1+DOX


title: WT_AVI3_B

description: Sample from Aviano


title: PBMC_1-2, HTO

molecule: protein


title: PBMC_1-1, HTO


title: THP-1, FLAG-T6-2+DOX-REP2

description: Library name: FLAG-T6-2+DOX


title: WT_AVI3_A

description: Sample from Aviano


title: THP-1, FLAG-T3-2+DOX-REP2

description: Library name: FLAG-T3-2+DOX


title: PBMC_1-2, GEX

description: count matrix for all samples included


title: WT_AVI2_D

description: Sample from Aviano


title: THP-1, FLAG-T2-2+DOX-REP2

description: Library name: FLAG-T2-2+DOX


title: THP-1, FLAG-T3-1+DOX-REP1

description: Library name: FLAG-T3-1+DOX


title: THP-1, FLAG-T2-3+DOX-REP3

description: Library name: FLAG-T2-3+DOX


title: THP-1, FLAG-FULL-REP3

description: Library name: FLAG-FULL-3


title: THP-1, FLAG-T2-1+DOX-REP1

description: Library name: FLAG-T2-1+DOX


title: THP-1, FLAG-FULL-REP2

description: Library name: FLAG-FULL-2


title: K975 3

city: Tokyo

first: Tetsuya

last: Saito

state: Tokyo

address: 1-5-45 Yushima Bunkyo-ku

department: Rheumatology

country: Japan

institute: Institute of Science Tokyo

description: Library name: SAMPLE 6

data_processing:
Raw reads were processed with SOAPnuke v1.5.6.
Clean reads were aligned to the GRCh38.p12 human reference genome using HISAT2 v2.2.1.
For gene-set realignment, Bowtie2 v2.4.5 was employed, and transcript abundance was estimated in transcripts per million (TPM) using RSEM v1.3.1.
Assembly: GRCh38.p12 human reference genome
Supplementary files format and content: xlsx files include average counts for all samples

source_name: Rheumatoid arthritis synovial fibroblasts

growth_protocol: DMEM with 10% FCS and P/S (passages < 5) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNAs were extracted with Qiagen Rneasy mini kit
RNA libraries were prepared using the BGI Optimal Dual-mode mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: RASFs (n=3) were  treated with Veh or K975 (0.5 microM) for 24 hours


title: WT_AVI2_B

description: Sample from Aviano


title: K975 2

description: Library name: SAMPLE 5

value: Rheumatoid arthritis synovial fibroblasts


title: WT_AVI2_C

description: Sample from Aviano


title: THP-1, FLAG-FULL-REP1

description: Library name: FLAG-FULL-1


title: NEPC_rep1

status: Public on Aug 16 2026

city: New York

first: Teng

last: Han

state: New York

address: 417 E 68th St

institute: MSKCC

description: Library name: NEPC_rep1

data_processing:
Raw FASTQ files were aligned to the mouse reference genome (mm10). Peaks were called, and normalized signal tracks (bigWig) were generated for visualization.
Assembly: mus musculus mm10
Supplementary files format and content: Bigwig

source_name: prostate organoid

extract_protocol:
Organoids were dissociated to obtain intact nuclei for bulk ATAC library preparation using standard protocols appropriate for each assay.
Sequencing libraries were prepared according to the manufacturer's recommended protocols for ATAC-seq.

value: prostate organoid


title: THP-1, FLAG-T6-REP3

description: Library name: FLAG-T6-3


title: Allograft, tacrolimus+anti-Gr-1 antibody (Day 0 to Day 15), Day15

city: Changsha

first: Limin

last: Xie

state: Hunan

address: No.139，Renmin Road Central Changsha, Hunan, China

institute: The second xiangya hospital of central south university

description:
Library name: Sample5
SeekOne DD
One sample from murine corneal tissue 15 days post-transplantation.

data_processing:
Raw sequencing data were processed through consensus assessment of sequence and variation (CASAVA) for base calling and conversion into Sequenced Reads, which were then stored in the FASTQ format. Sequencing adapters and low-quality fragments were trimmed before alignment to the reference genome using STAR software. Subsequently, gene expression levels were quantified using the FeatureCounts software, resulting in the generation of a preliminary cell-gene expression matrix. To obtain clean data, cells with low RNA expression in the matrix were filtered out using the EmptyDrops software. The count data were then imported into the Seurat R package for quality control analysis of each sample. Cells with fewer than 500 detected genes or a proportion of mitochondrial genes exceeding 10% were excluded, and genes expressed in fewer than five cells were removed. Doublets were identified and removed using the DoubletFinder package, where the Bayesian corrected Mahalanobis distance (BCMVN) was calculated for each sample to determine the optimal “pK_value,” with the “pN_value” set to 0.25. Each sample underwent these filtering procedures individually to prepare for subsequent analyses.
Assembly: mm10
Supplementary files format and content: matrix files

source_name: Mouse Cornea

extract_protocol:
Corneas (n=4-6) were isolated and each cornea was placed in 1 ml of 0.25% trypsin. Samples were incubated at 37°C for 1 hour, with mixing every 10 minutes. After incubation, 200 μl FBS was added to the wells of a 24-well plate. The corneas were then mechanically dissociated using a 2.5 ml syringe. The resulting suspension was filtered through a 40 μm cell strainer into a flow cytometry tube. The well plate and strainer were washed with 4 ml of 2% FBS-1640 medium. The cell suspension was centrifuged at 1300 RPM for 5 minutes, and the supernatant was discarded.
Each cornea was processed independently using the SeekOne® Digital Droplet System (SeekOne® DD) to complete the workflow from labeling single-cell nucleic acids to constructing the transcriptome library.  The entire procedure followed the manufacturer’s instructions for the SeekOne Digital Droplet Single-Cell 3′ library preparation kit (SeekGene), resulting in the generation of a single-cell transcriptome library suitable for high-throughput sequencing.  All libraries underwent quality testing using the Agilent 4200 TapeStation.  Qualified libraries exhibited a primary peak fragment size between 350 and 750 bp, with no small fragments, and a library concentration of at least 1 ng/μl, as measured by the Qubit 4.0.  Subsequently, the libraries were sequenced on an Illumina NovaSeq 6000 System with paired-end 150 bp read length, aiming for an approximate coverage of 50,000 raw reads per cell.

value: Mouse Cornea

value: Corneal stromal cells, corneal endothelial cells, fibroblasts, vascular endothelial cells, vascular smooth muscle cells, T cells, monocyte and dendritic cells

value: C57BL/6 and BALB/c

tag: age

value: 8-10 weeks

value: tacrolimus++anti-Gr-1 antibody

value: Wild type


title: THP-1, FLAG-T6-REP2

description: Library name: FLAG-T6-2


title: WT_AVI2_A

description: Sample from Aviano

value: Condition A


title: THP-1, FLAG-T6-REP1

description: Library name: FLAG-T6-1

value: AML cell


title: WT_AVI1_D

description: Sample from Aviano

value: Condition D


title: NEPC_YAP1

description: Library name: NEPC_YAP1

data_processing:
Raw FASTQ files were aligned to the mouse reference genome (mm10). Peaks were identified, and normalized signal tracks (bigWig) were generated for downstream analyses.
Assembly: mus musculus mm10
Supplementary files format and content: Bigwig
Library strategy: CUT&Run

extract_protocol:
Organoids were dissociated to obtain intact nuclei for CUT and RUN library preparation using standard protocols appropriate for each assay.
Sequencing libraries were prepared according to the manufacturer's recommended protocols for CUT and RUN.


title: THP-1, FLAG-T3-REP2

description: Library name: FLAG-T3-2


title: Veh 2

description: Library name: SAMPLE 2

value: Veh


title: THP-1, FLAG-T3-REP3

description: Library name: FLAG-T3-3


title: Veh 3

description: Library name: SAMPLE 3


title: THP-1, FLAG-T3-REP1

description: Library name: FLAG-T3-1


title: Veh 1

description: Library name: SAMPLE 1


title: WT_AVI1_B

description: Sample from Aviano

value: Condition B


title: WT_AVI1_A

description: Sample from Aviano


title: THP-1, FLAG-T2-REP3

description: Library name: FLAG-T2-3


title: 4mix_3

description: Library name: SAMPLE 6

treatment_protocol: RASFs (n=3) were treated with Veh or 4mix for 24 hours


title: ASH2L-FULL+DOX-REP3

description: Library name: 24

data_processing:
Subsequent analysis followed established computational pipelines detailed in the CUT&Tag Data Processing and Analysis Protocol (Zheng et al., 2020; Protocol.io). Differential peaks analysis was performed using Diff Bind (v3.10.1) with statistically significant peaks identified at p < 0.05.
Assembly: GRCh38/hg38
Supplementary files format and content: 1-ASH2L-T2-rep1_CPM.bw
Supplementary files format and content: 2-ASH2L-T2-rep2_CPM.bw
Supplementary files format and content: 3-ASH2L-T2-rep3_CPM.bw
Supplementary files format and content: 4-ASH2L-T3-rep1_CPM.bw
Supplementary files format and content: 5-ASH2L-T3-rep2_CPM.bw
Supplementary files format and content: 6-ASH2L-T3-rep3_CPM.bw
Supplementary files format and content: 7-ASH2L-T6-rep1_CPM.bw
Supplementary files format and content: 8-ASH2L-T6-rep2_CPM.bw
Supplementary files format and content: 9-ASH2L-T6-rep3_CPM.bw
Supplementary files format and content: 10-ASH2L-full-rep1_CPM.bw
Supplementary files format and content: 11-ASH2L-FULL-REP2_CPM.bw
Supplementary files format and content: 12-ASH2L-FULL-REP3_CPM.bw
Supplementary files format and content: 13-ASH2L-T2+dox-rep1_CPM.bw
Supplementary files format and content: 14-ASH2L-T2+dox-rep2_CPM.bw
Supplementary files format and content: 15-ASH2L-T2+dox-rep3_CPM.bw
Supplementary files format and content: 16-ASH2L-T3+DOX-rep1_CPM.bw
Supplementary files format and content: 17-ASH2L-T3+DOX-rep2_CPM.bw
Supplementary files format and content: 18-ASH2L-T3+DOX-rep3_CPM.bw
Supplementary files format and content: 19-ASH2L-T6+DOX-rep1_CPM.bw
Supplementary files format and content: 20-ASH2L-T6+DOX-rep2_CPM.bw
Supplementary files format and content: 21-ASH2L-T6+DOX-rep3_CPM.bw
Supplementary files format and content: 22-ASH2L-FULL+DOX-rep1_CPM.bw
Supplementary files format and content: 23-ASH2L-FULL+DOX-REP2_CPM.bw
Supplementary files format and content: 24-ASH2L-FULL+DOX-REP3_CPM.bw
Library strategy: CUT&Tag


title: ASH2L-FULL+DOX-REP2

description: Library name: 23


title: 4mix_2

description: Library name: SAMPLE 5


title: K975 1

description: Library name: SAMPLE 4


title: TRI12_3_D

description: Sample from Barcelona


title: PBMC, Post-NR5, Batch2

value: Blood

value: PBMC


title: TRI12_3_C

description: Sample from Barcelona

value: Primary CLL cells

value: Condition C


title: 4mix_1

description: Library name: SAMPLE 4

value: Rheumatoid arthritis synovial fibroblasts


title: ASH2L-FULL+DOX-REP1

description: Library name: 22


title: PBMC, Post-NR3, Batch2


title: ASH2L-T6+DOX-REP2

description: Library name: 20


title: THP-1, H3K4me1-T6-2

description: Library name: 8-H3K4me1-T6-2


title: TRI12_3_B

description: Sample from Barcelona


title: ASH2L-T3+DOX-REP3

description: Library name: 18


title: WT_AVI1_C

description: Sample from Aviano


title: ASH2L-T6+DOX-REP3

description: Library name: 21


title: Veh_2

description: Library name: SAMPLE 2


title: TRI12_3_A

description: Sample from Barcelona


title: PBMC, Post-NR1, Batch1


title: ASH2L-T3+DOX-REP1

description: Library name: 16


title: WT_AVI5_D

description: Sample from Aviano


title: WT_AVI5_C

description: Sample from Aviano


title: ASH2L-T6+DOX-REP1

description: Library name: 19


title: Veh_3

description: Library name: SAMPLE 3


title: THP-1, FLAG-T2-REP2

description: Library name: FLAG-T2-2


title: Veh_1

description: Library name: SAMPLE 1


title: ASH2L-T2+DOX-REP3

description: Library name: 15


title: ASH2L-T3+DOX-REP2

description: Library name: 17


title: THP-1, FLAG-T2-REP1

description: Library name: FLAG-T2-1


title: ASH2L-T2+DOX-REP2

description: Library name: 14


title: THP-1, T3-MOUSE-IGG

description: Library name: T3


title: THP-1, T6-MOUSE-IGG

description: Library name: T6


title: siTEAD4_3

description: Library name: SAMPLE 6


title: THP-1, T3+DOX-MOUSE-IGG

description: Library name: T3+DOX


title: siTEAD4_2

description: Library name: SAMPLE 5


title: ASH2L-FULL-REP1

description: Library name: 10


title: ASH2L-FULL-REP2

description: Library name: 11


title: ASH2L-T6-REP3

description: Library name: 9


title: TRI12_2_B

description: Sample from Barcelona


title: ASH2L-T6-REP2

description: Library name: 8


title: ASH2L-T6-REP1

description: Library name: 7


title: siCtrl_3

description: Library name: SAMPLE 3


title: ASH2L-T3-REP3

description: Library name: 6


title: ASH2L-T3-REP1

description: Library name: 4


title: ASH2L-T2-REP1

description: Library name: 1


title: ASH2L-FULL-REP3

description: Library name: 12


title: ASH2L-T2+DOX-REP1

description: Library name: 13


title: TRI12_2_D

description: Sample from Barcelona


title: ASH2L-T3-REP2

description: Library name: 5


title: Hypergravity treated rep1

city: Dharwad

first: Ravikumar

last: Hosamani

state: Karnataka

address: Krishinagar

department: Biotechnology

country: India

institute: UAS-Dharwad

description: Treated

data_processing:
The raw reads were trimmed to remove adapters and checked for quality with a minimum Phred score set to 30 for filtering using Fastp (v.0.20) (Chen et al., 2018)
De Novo assembly was performed using Trinity with 5X average depth and 70% coverage.
Quantification using RSEM was done
Supplementary_files_format_and_content: excel file includes FPKM values

organism: Triticum aestivum

source_name: Roots

growth_protocol: The hypergravity treated wheat seeds and control seeds were sown in greenhouse condition using PVC pipes (width 6 inches, 3 feet height) with CRD design

extract_protocol:
Total RNA from the root tissues of 45-day-old wheat plants was extracted using Quick-RNA Plant Miniprep Plus kit (ZYMO Research).
The paired-end RNA sequencing libraries were prepared using Illumina TruSeq Stranded mRNA sample prep kit

treatment_protocol: Wheat seeds were treated with hypergravity at 10g for 12 hrs and sown in greenhouse condition

value: Root

value: 45 days old


title: siTEAD4_1

description: Library name: SAMPLE 4


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep2

description:
Library name: S421
Donor age 79, Passage 11

value: Fibroblast

value: Dox_1000ng/mL, 5d-ON/2d-OFF


title: ASH2L-T2-REP2

description: Library name: 2


title: TRI12_2_C

description: Sample from Barcelona

data_processing: The data was analyzed with Transcriptome Expression Console Software (TAC v4.0.2) using (log2)  SST-RMA algorithm normalization.


title: siCtrl_1

description: Library name: SAMPLE 1


title: TRI12_1_B

description: Sample from Barcelona


title: TRI12_2_A

description: Sample from Barcelona


title: TRI12_1_D

description: Sample from Barcelona


title: WT_BCN6_C

description: Sample from Barcelona


title: M68 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep2

description:
Library name: S417
Donor age 68, Passage 11

data_processing:
To minimize variability arising from differences in sequencing depth, FASTQ files for all libraries (except LIB058979, LIB092645, and LIB083102) were downsampled to 20 million reads using Seqtk-1.3.
Raw RNA-seq reads were aligned to the GRCh38/GRCm39 reference genome using STAR v2.5.2b and checked for quality control using FastQC v0.11.5
Alignment files were indexed using SAMtools v1.3.154 and gene-level counts were obtained using featureCounts from the Subread v2.0.1 package
Assembly: GRCh38, GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample


title: TRI12_1_C

description: Sample from Barcelona


title: WT_BCN6_D

description: Sample from Barcelona


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep1

description:
Library name: S420
Donor age 79, Passage 11


title: Control rep2

description: Untreated


title: TRI12_1_A

description: Sample from Barcelona


title: Hypergravity treated rep2

description: Treated


title: Liver from systemic AAV8-SRSF1, Dox_200mg/kg, Mouse#16

type: genomic

description: Age at death 959 days

hyb_protocol: DNA was bisulfite-converted using the Zymo EZ DNA Methylation Kit (Zymo Research), fragmented, and hybridized using standard Illumina protocol

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

data_processing:
For EPIC v1 experiments (S1-S8), data was exported using Illumina GenomeStudio without normalization or background subtraction. For the other experiments (S9-S30), raw intensity data were processed and normalized using the minfi v1.48.0 R package.
Average Beta

label: Cy3, Cy5

source_name: Liver

label_protocol: Standard Illumina protocol

growth_protocol: NHDFs were maintained in low-glucose DMEM supplemented with 15% fetal bovine serum (FBS) and 1% Pen-strep (P/S) in humidified atmosphere with 5% CO2 and 5% O2, at 37C.

extract_protocol: Genomic DNA was extracted from endpoint frozen liver or human cell pellet using the Quick-DNA HMW MagBead Kit (Zymo Research, Irvine, CA, USA).

treatment_protocol: Transgene was induced using doxycycline at the specified concentration for the specified amount of time. Similarly, rapamycin was added to the media at the 100nM for the specified amount of time. Mice were fed Dox chow at the specified concentration

value: Liver

value: Dox_200mg/kg, 1wk-ON/1wk-OFF


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep2

description:
Library name: S419
Donor age 79, Passage 11


title: M68 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep1

description:
Library name: S416
Donor age 68, Passage 11


title: ASH2L-T2-REP3

description: Library name: 3


title: siCtrl_2

description: Library name: SAMPLE 2


title: WT_BCN5_D

description: Sample from Barcelona


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep1

description:
Library name: S418
Donor age 79, Passage 11


title: Control rep1

description: Untreated


title: M68 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep1

description:
Library name: S414
Donor age 68, Passage 11


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 3d-ON, Rep4

description:
Library name: S409
Donor age 79, Passage 11

value: Dox_1000ng/mL, 3d-ON


title: WT_BCN5_C

description: Sample from Barcelona


title: Liver from systemic AAV8-SRSF1, Dox_200mg/kg, Mouse#15

description: Age at death 872 days


title: M68 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep2

description:
Library name: S415
Donor age 68, Passage 11


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 3d-ON, Rep3

description:
Library name: S408
Donor age 79, Passage 11


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep2

description:
Library name: S411
Donor age 55, Passage 11


title: Liver from systemic AAV8-SRSF1, Dox_200mg/kg, Mouse#1

description: Age at death 901 days


title: WT_BCN5_A

description: Sample from Barcelona

value: Condition A


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep2

description:
Library name: S413
Donor age 55, Passage 11


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep1

description:
Library name: S412
Donor age 55, Passage 11


title: WT_BCN6_A

description: Sample from Barcelona


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep1

description:
Library name: S410
Donor age 55, Passage 11


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, 3d-ON, Rep3

description:
Library name: S404
Donor age 79, Passage 11


title: Liver from systemic AAV8-SRSF1, Dox_200mg/kg, Mouse#19

description: Age at death 818 days


title: WT_BCN6_B

description: Sample from Barcelona


title: WT_BCN4_D

description: Sample from Barcelona


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, 3d-ON, Rep2

description:
Library name: S403
Donor age 79, Passage 11


title: Liver from systemic AAV8-GFP, Dox_200mg/kg, Mouse#8

description: Age at death 865 days

value: GFP


title: M68 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 3d-ON, Rep2

description:
Library name: S399
Donor age 68, Passage 11


title: Liver from systemic AAV8-SRSF1, Dox_200mg/kg, Mouse#3

description: Age at death 778 days


title: Liver from systemic AAV8-GFP, Dox_200mg/kg, Mouse#17

description: Age at death 721 days


title: WT_BCN5_B

description: Sample from Barcelona


title: Liver from systemic AAV8-GFP, Dox_200mg/kg, Mouse#9

description: Age at death 806 days


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, 3d-ON, Rep4

description:
Library name: S405
Donor age 79, Passage 11


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 3d-ON, Rep1

description:
Library name: S406
Donor age 79, Passage 11


title: M68 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 3d-ON, Rep4

description:
Library name: S401
Donor age 68, Passage 11


title: M68 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 3d-ON, Rep1

description:
Library name: S398
Donor age 68, Passage 11


title: Liver from systemic AAV8-GFP, Dox_200mg/kg, Mouse#7

description: Age at death 778 days


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 3d-ON, Rep2

description:
Library name: S407
Donor age 79, Passage 11


title: M68 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 3d-ON, Rep3

description:
Library name: S400
Donor age 68, Passage 11


title: WT_BCN4_A

description: Sample from Barcelona


title: M68 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, 3d-ON, Rep4

description:
Library name: S397
Donor age 68, Passage 11


title: WT_BCN4_C

description: Sample from Barcelona


title: M68 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, 3d-ON, Rep3

description:
Library name: S396
Donor age 68, Passage 11


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep2

description: Donor age 79, Passage 11


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, 3d-ON, Rep1

description:
Library name: S402
Donor age 79, Passage 11


title: M68 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, 3d-ON, Rep2

description:
Library name: S395
Donor age 68, Passage 11


title: M55 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P11, 3d-ON, Rep3

description:
Library name: S392
Donor age 55, Passage 11

value: OSKM


title: WT_BCN3_D

description: Sample from Barcelona

value: Condition D


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep1

description: Donor age 79, Passage 11


title: WT_BCN3_C

description: Sample from Barcelona


title: M55 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P11, 3d-ON, Rep2

description:
Library name: S391
Donor age 55, Passage 11


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 3d-ON, Rep4

description:
Library name: S389
Donor age 55, Passage 11


title: WT_BCN4_B

description: Sample from Barcelona

value: Condition B


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 3d-ON, Rep3

description:
Library name: S388
Donor age 55, Passage 11


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep1

description: Donor age 79, Passage 11


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 3d-ON, Rep2

description:
Library name: S387
Donor age 55, Passage 11


title: M68 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, 3d-ON, Rep1

description:
Library name: S394
Donor age 68, Passage 11


title: WT_BCN3_B

description: Sample from Barcelona


title: M55 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P11, 3d-ON, Rep4

description:
Library name: S393
Donor age 55, Passage 11


title: M68 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep2

description: Donor age 68, Passage 11


title: Liver from systemic AAV8-GFP, Dox_200mg/kg, Mouse#5

description: Age at death 785 days


title: M55 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P11, 3d-ON, Rep1

description:
Library name: S390
Donor age 55, Passage 11


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep2

description: Donor age 79, Passage 11


title: HCT116,shCHTOP3

city: xi’an

first: mingchao

last: mu

state: Shannxi

address: No. 277 Yanta West Road, Yanta District, Xi'an City, Shaanxi Province

institute: xi'an jiaotong university

description: Library name: Sample6

data_processing:
RNA-seq data were processed through a standard workflow including quality control, read alignment, expression quantification, differential expression analysis, and functional enrichment. Additional analyses such as alternative splicing, variant calling, WGCNA, GSEA, and PPI network construction were performed as needed.
Assembly: Homo sapiens: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text file includes FPKM

source_name: HCT116 cell line

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco, Grand Island, NY) supplemented with 10% fetal bovine serum (FBS; Gibco, Grand Island, NY).

extract_protocol:
Total RNA was extracted from the samples and assessed for concentration and purity using a NanoDrop 2000 spectrophotometer. RNA integrity was examined by agarose gel electrophoresis, and RNA quality numbers (RQN) were determined using the Agilent 5300 system.
RNA-seq libraries were prepared following standard protocols. Briefly, total RNA was extracted and assessed for purity and integrity using a NanoDrop 2000, agarose gel electrophoresis, and an Agilent 5300 system. Poly(A)+ mRNA was enriched using Oligo(dT) magnetic beads. The purified mRNA was then fragmented and used as a template to synthesize first- and second-strand cDNA. After end repair and A-tailing, sequencing adapters were ligated to the cDNA fragments. Adapter-ligated products were purified, size-selected, and amplified by PCR to generate the final libraries.

value: HCT116 cell line

value: Colorectal cancer cell

value: shCHTOP


title: 630∆erm ∆Cdi1_6-CD1980.2 a plasmid expressing Cdi1_6-CD1980.2_rep4

city: Gif-sur-Yvette

first: Johann

last: PELTIER

address: avenue de la Terrasse

country: France

institute: I2BC, CNRS

description: Library name: p_CD1980.2_rep4

data_processing:
Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence using AlienTrimmer. Only sequence with a minimum length of 30 were considered. Sequenced were mapped to Clostridiaceae difficile 630 whole genome sequence complemented by the known ncRNA using bowtie v2 HtSeqCount was used for counting genes with default parameters Statistical analyses were performed using R version 3 and Bioconductor packages. The whole dataset was first normalized using the normalization function of DESeq2 and with default parameters. The statistical test function of DESeq2 was then applied.
Assembly: Peptoclostridium difficile 630 (NC_009089.1) complemented by the known ncRNA (PMID: 23675309)
Supplementary files format and content: Genome annotation (Gene ID), Raw Counts and Normalized Counts, Normalized Counts, Statistics (FC, pvalue, Significant)

organism: Clostridioides difficile

growth_protocol: Strains were grown anaerobically in TY at 37°C for 7 H

extract_protocol:
Total RNA was extracted using phenol, Trizol reagent and chloroform/isoamylalcohol.
RNA libraries were prepared for sequencing using standard Illumina protocols; Truseq stranded RNA seq kit

treatment_protocol: growth with 250 ng/ml anhydrotetracycline

value: bacteria

value: 250 ng/ml anhydrotetracycline


title: WT_BCN3_A

description: Sample from Barcelona

extract_protocol: miRNAeasy kit (Qiagen)

value: Primary CLL cells


title: HCT116,shCHTOP1

description: Library name: Sample4


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 3d-ON, Rep1

description:
Library name: S386
Donor age 55, Passage 11

extract_protocol:
Cells were lysed using the Monarch DNA/RNA Protection Reagent (NEB T2011) and stored at -80°C until RNA extraction. Total RNA was extrqacted using the Monarch Total RNA Miniprep kit (NEB T2010). Mouse tissues were processed by Novogene.
Libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina using the polyA mRNA workflow according to manufacturer's instructions. LIB058979 was genereated using the Tecan MagicPrepRevelo mRNA-seq kit acoording to manufacturare's instructions. LIB083102 was generated by Novogene using a directional mRNA library preparation method.


title: M68 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep1

description: Donor age 68, Passage 11


title: 630∆erm ∆Cdi1_6-CD1980.2 a plasmid expressing Cdi1_6-CD1980.2_rep3

description: Library name: p_CD1980.2_rep3


title: WT_BCN2_D

description: Sample from Barcelona


title: HCT116,NC2

description: Library name: Sample2

value: shCtrl


title: M68 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep2

description: Donor age 68, Passage 11

value: Fibroblast


title: HCT116,NC1

description: Library name: Sample1


title: 630∆erm ∆Cdi1_6-CD1980.2 a plasmid expressing Cdi1_6-CD1980.2_rep1

description: Library name: p_CD1980.2_rep1


title: 630∆erm ∆Cdi1_6-CD1980.2 a plasmid expressing Cdi1_6-CD1980.2_rep2

description: Library name: p_CD1980.2_rep2


title: THP-1 cells overexpression-NRBP2-3

description: Library name: OE-NRBP2-3

data_processing:
Raw reads underwent quality control and adapter trimming using Fastp (v0.23.4) Clean reads were aligned to reference genomes (mm10 for murine samples; hg38 for human samples) via STAR (v2.7.10b) with ENCODE-standard parameters .Properly paired, uniquely mapped reads were selected using Samtools (v1.16)  and read counts were generated with HTSeq (v2.0.2).
Assembly: NCBI,FPKM（expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced）
Supplementary files format and content: count.xlx

growth_protocol: cell lines were cultured in RPMI1640 with 10% FBS

extract_protocol:
AFTMag Quick Viral DNA/RNA Extraction Kit (RK30153)
Illumina RNA library preparation TruSeq PE kit

value: AML cell

value: overexpression NRBP2


title: HCT116,shCHTOP2

description: Library name: Sample5


title: M68 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep1

description: Donor age 68, Passage 11

value: Dox_1000ng/mL, 5d-ON/2d-OFF


title: WT_BCN2_C

description: Sample from Barcelona

value: Condition C


title: HCT116,NC3

description: Library name: Sample3


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep2

description: Donor age 55, Passage 11


title: THP-1 cells overexpression-NRBP2-2

description: Library name: OE-NRBP2-2


title: THP-1 cells overexpression-NRBP2-1

description: Library name: OE-NRBP2-1


title: crwn1;4 pnet2_b,leaves,3 week,rep2

city: beijing

first: xiao

last: liu

address: yiheyuan road 5, Haidian

institute: peking university

data_processing:
Clean mRNA-seq reads were aligned to the Arabidopsis thaliana reference genome (TARI10) using HISAT2 (v2.0.4) with default parameters.
Assembly: TAIR 10
Supplementary files format and content: tab-delimited excel files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: leaves

extract_protocol:
Total RNA was extracted from about 50 mg samples of 4-week-old leaves using RNAprep pure Plant Kit (Genesee Scientific, Catalog #11– 330).
mRNA-Seq(Strand-Specific) libraries were prepared for sequencing using standard Illumina protocols

value: leaves

value: 3 week

value: CRWN 1 CRWN4 knock out CRISPR PNET2_B

value: NO


title: 630∆erm ∆Cdi1_6-CD1980.2 carrying an empty plasmid_rep2

description: Library name: p_empty_rep2

value: Cdi1_6-CD1980.2 deletion


title: M92 WT line, Rapa_100ng/mL, 72h

description: Donor age 92, Passage 5

value: WT


title: crwn1;4 pnet2_b,leaves,3 week,rep3


title: 630∆erm ∆Cdi1_6-CD1980.2 carrying an empty plasmid_rep4

description: Library name: p_empty_rep4


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep2

description: Donor age 55, Passage 11


title: 630∆erm ∆Cdi1_6-CD1980.2 carrying an empty plasmid_rep1

description: Library name: p_empty_rep1


title: 630∆erm ∆Cdi1_6-CD1980.2 carrying an empty plasmid_rep3

description: Library name: p_empty_rep3


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep1

description: Donor age 55, Passage 11


title: crwn1;4 pnet2_a,leaves,3 week,rep3

value: CRWN 1 CRWN4 knock out CRISPR PNET2_A


title: THP-1 cells control-NRBP2-1

description: Library name: CT-NRBP2-1

value: control


title: THP-1 cells control-NRBP2-3

description: Library name: CT-NRBP2-3


title: THP-1 cells control-NRBP2-2

description: Library name: CT-NRBP2-2


title: crwn1;4 pnet2_a,leaves,3 week,rep2


title: crwn1;4 pnet2_b,leaves,3 week,rep1


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P11, 5d-ON/2d-OFF, Rep1

description: Donor age 55, Passage 11


title: crwn1;4 pnet2_a,leaves,3 week,rep1


title: THP-1 cells overexpression-KLF4-2

description: Library name: OE-KLF4-2

value: overexpression KLF4


title: 630∆erm Ptet-dccA_rep2

description: Library name: dccA_rep2

value: bacteria

value: Ptet insertion upstream dccA

value: 250 ng/ml anhydrotetracycline


title: 630∆erm Ptet-dccA_rep1

description: Library name: dccA_rep1


title: M73 WT line, Rapa_100ng/mL, 72h

description: Donor age 73, Passage 16

value: Fibroblast


title: M55 WT line, Rapa_100ng/mL, 72h

description: Donor age 55, Passage 5


title: M36 WT line, Rapa_100ng/mL, 72h

description: Donor age 36, Passage 5


title: 630∆erm Ptet-dccA_rep4

description: Library name: dccA_rep4


title: 630∆erm Ptet-dccA_rep3

description: Library name: dccA_rep3


title: crwn1;4,leaves,3 week,rep3

value: CRWN 1 CRWN4 knock out


title: THP-1 cells overexpression-KLF4-1

description: Library name: OE-KLF4-1

value: AML cell


title: THP-1 cells overexpression-KLF4-3

description: Library name: OE-KLF4-3


title: THP-1 cells control-KLF4-2

description: Library name: CT-KLF4-2


title: crwn1;4,leaves,3 week,rep2


title: M73 WT line, No Rapa

description: Donor age 73, Passage 16

value: NT


title: THP-1 cells control-KLF4-3

description: Library name: CT-KLF4-3


title: M92 WT line, No Rapa

description: Donor age 92, Passage 5


title: 630∆erm WT_rep4

description: Library name: WT_rep4


title: M55 WT line, No Rapa

description: Donor age 55, Passage 5


title: crwn1;4,leaves,3 week,rep1


title: Huh7 cells, DMSO

city: Tianjin

first: 佳仪

last: 吴

address: No.94 Weijin Road

institute: Nankai University

description:
Library name: Samole1
Column name in raw counts.txt:H3

data_processing:
After library preparation and pooling of different samples, the samples were subjected for NGS platform by Berry Genomics Co., Ltd
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

growth_protocol: Huh7 cells were maintained in DMEM suppleented with 10% fetal bovine serum and antibiotics inhumidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was qualified and quantified as follows: (1) RNA purity and concentration were then examined using NanoDrop 2000; (2) RNA integrity and quantity were measured using the Agilent 2100/4200 system.
mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library

treatment_protocol: After cell attachment, replace medium with DMSO (control) or HD-containing medium, then harvest cells at 48h post-treatment.

value: Hepatocellular carcinoma cells

value: DMSO


title: Huh7 cells, HD

description:
Library name: Sample2
Column name in raw counts.txt:H4

value: Homochlorcyclizine Dihydrochloride


title: M36 WT line, No Rapa

description: Donor age 36, Passage 5


title: whole fish, PBI-derived

status: Public on Aug 14 2026

city: Shenzhen

first: Zilong

last: WEN

country: Hong Kong

institute: Southern University of Science and Technology

description:
Library name: Sample 7
10x Genomics

data_processing:
FASTQ raw data were pre-processed  following Cell Ranger 7.1.0 pipeline.
Assembly: Gene reference genome: Ensembl Danio rerio GRCz11 release 109.
Supplementary files format and content: Processed data files are provided as Cell Ranger filtered feature-barcode matrices, including matrix.mtx.gz (gene-cell expression matrix), features.tsv.gz (gene annotations), and barcodes.tsv.gz (cell barcodes).

organism: Danio rerio

source_name: whole fish

extract_protocol:
Tissues were dissected from adult zebrafish, with scales and intestines collected separately. Samples were transferred to 0.25% Trypsin-EDTA and homogenized by repeated passage through a needle and syringe. Enzymatic digestion was then performed at 32°C for 20 minutes (intestine) or 30 minutes (epidermis). For juvenile fish, whole animals at one-month-old age were directly homogenized and digested in trypsin for 20 minutes using the same method. Adult leukocyte samples were obtained by pooling cells from three individual fish. For juvenile leukocyte isolation, 15 fish at 1 mpf were pooled and homogenized. To obtain HPC-derived leukocytes, 120 fish that underwent heat-shock editing were collected at 2 week-post-fertilization. The digestion reaction was quenched by supplementing the solution with CaCl₂ to a final concentration of 10 mM and fetal bovine serum to 10% (v/v). The dissociated cell preparations were washed twice with ice-cold PBS containing 1% bovine serum albumin, then filtered through a 35-μm cell strainer to obtain single-cell suspensions. Cell viability was examined using 4′,6-diamidino-2-phenylindole at 1 μg/mL. Finally, eGFP-positive cells were purified via fluorescence-activated cell sorting on a BD FACS Fusion instrument.
Single-cell RNA sequencing libraries were prepared using the 10× Genomics Chromium Next GEM Single Cell 3' Reagent Kit v3.1 according to the manufacturer's protocol.

value: whole fish

value: leukocytes

value: wild type


title: WT,leaves,3 week,rep2

value: leaves

value: 3 week

value: WT

value: NO


title: WT,leaves,3 week,rep1


title: intestine, rag1 mutant

description:
Library name: Sample 4
10x Genomics

source_name: intestine

value: intestine

value: rag1 mutant


title: WT,leaves,3 week,rep3


title: whole fish, rag1 mutant

description:
Library name: Sample 2
10x Genomics


title: THP-1 cells control-KLF4-1

description: Library name: CT-KLF4-1

value: control


title: scale, rag1 mutant

description:
Library name: Sample 6
10x Genomics

source_name: scale

value: scale


title: TimeLapse, THP1 Macrophages, 10 uM STM2457 & Hypoxia(1% O2) 24hr, 500 uM S4U for 2hr, replicate 1

city: Boulder

first: Edward

last: Courvan

address: 3415 Colorado Ave

institute: University of Colorado

description: Library name: TL_STMandHypox_S4U_1

data_processing:
fastq files were processed with fastq2EZbakR to obtain cB files
Assembly: GRCh38.p14, Gencode release 49
Supplementary files format and content: TL_cB.csv contains mutation count data for input into bakR or EZbakR
Supplementary files format and content: TL_raw_counts.csv contains raw count data for mature transcripts in each sample
Library strategy: TimeLapse-seq

source_name: THP1 Macrophage

growth_protocol: THP1 monocytes were grown in RPMI supplemented with 10% fetal bovine serum. THP1 macrophages were differentiated by 48 hr of 50 ng/mL PMA treatment followed by 48 hr rest after removing PMA

extract_protocol:
RNA was extracted in Trizol and isolated via isopropanol precipitation. Samples were treated with TURBO DNase, processed via TimeLapse-seq chemistry and then purified with RNA Clean XP beads.
Libraries were prepared from 10 ng total RNA with the Watchmaker Genomics RNA-seq kit with polaris ribosomal RNA depletion kit.

treatment_protocol: THP1 macrophages were treated with either 0.1% DMSO or 10 uM STM2457 in DMSO in either normoxia (17% sea level O2) or hypoxia (1% sea level O2). Treatment was carried out for 24 hours, where in the last two hours, media was supplemented with 500 uM S4U to enable TimeLapse chemistry in S4U fed samples.

value: THP1 Macrophage

value: PMA differentiated myeloid leukemia

tag: treatment -_stm2457

tag: treatment -_oxygen

tag: treatment -_s4u

value: 500 uM S4U, 2 hr


title: 630∆erm WT_rep1

description: Library name: WT_rep1

value: bacteria

value: 250 ng/ml anhydrotetracycline


title: 630∆erm WT_rep2

description: Library name: WT_rep2


title: TimeLapse, THP1 Macrophages, Hypoxia(1% O2) 24hr, 500 uM S4U for 2hr, replicate 2

description: Library name: TL_Hypox_S4U_2

value: DMSO


title: TimeLapse, THP1 Macrophages, 10 uM STM2457 & Hypoxia(1% O2) 24hr, unfed, replicate 1

description: Library name: TL_STMandHypox_unfed_1

value: unfed


title: TimeLapse, THP1 Macrophages, 10 uM STM2457 24hr, 500 uM S4U for 2hr, replicate 3

description: Library name: TL_STM_S4U_3


title: TimeLapse, THP1 Macrophages, Untreated, unfed, replicate 1

description: Library name: TL_CTL_unfed_1

value: 17% O2, DMSO


title: TimeLapse, THP1 Macrophages, 10 uM STM2457 & Hypoxia(1% O2) 24hr, 500 uM S4U for 2hr, replicate 3

description: Library name: TL_STMandHypox_S4U_3


title: TimeLapse, THP1 Macrophages, Hypoxia(1% O2) 24hr, unfed, replicate 1

description: Library name: TL_Hypox_unfed_1


title: TimeLapse, THP1 Macrophages, 10 uM STM2457 24hr, 500 uM S4U for 2hr, replicate 1

description: Library name: TL_STM_S4U_1


title: intestine, wild type

description:
Library name: Sample 3
10x Genomics

value: leukocytes

value: wild type


title: TimeLapse, THP1 Macrophages, 10 uM STM2457 & Hypoxia(1% O2) 24hr, 500 uM S4U for 2hr, replicate 2

description: Library name: TL_STMandHypox_S4U_2


title: TimeLapse, THP1 Macrophages, 10 uM STM2457 24hr, unfed, replicate 1

description: Library name: TL_STM_unfed_1


title: TimeLapse, THP1 Macrophages, Hypoxia(1% O2) 24hr, 500 uM S4U for 2hr, replicate 1

description: Library name: TL_Hypox_S4U_1


title: 630∆erm WT_rep3

description: Library name: WT_rep3


title: TimeLapse, THP1 Macrophages, Hypoxia(1% O2) 24hr, 500 uM S4U for 2hr, replicate 3

description: Library name: TL_Hypox_S4U_3


title: RNA-seq of NEE technical replicate 1

city: Singapore

first: Andy

last: Tay

address: 4 Engineering Drive 3

department: Biomedical Engineering

country: Singapore

institute: National University of Singapore

description:
Library name: NEE_Rep1
A549 technical replicate RNA sample 1 prepared with NEE and sequenced

data_processing:
Raw paired-end reads were quality-checked using FastQC, and adapter sequences and low-quality bases were removed using Trimmomatic. Cleaned reads were aligned to the human reference genome (GRCh38) using HISAT2, and gene-level counts were generated with featureCounts based on GENCODE v44 annotations.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw counts for each sample

extract_protocol:
For timepoint samples, total RNA was extracted using the E.Z.N.A.® Total RNA Kit I (Omega Biotek). For NEE-derived RNA samples, RNA was extracted using the NEE protocol and purified with the E.Z.N.A.® MicroElute® RNA Clean Up Kit (Omega Biotek).
Timepoint RNA-seq libraries and NEE-derived RNA libraries were prepared according to the Smart-Seq2 protocol, following the manufacturer’s instructions.

value: A549 monolayer

value: Technical replicate


title: TimeLapse, THP1 Macrophages, Untreated, 500 uM S4U for 2hr, replicate 3

description: Library name: TL_CTL_S4U_3

value: WT


title: 33_P1_Ctrl_NGFR_neg_Organoid

city: Stockholm

first: Maria

last: Genander

address: Tomtebodavägen 16

department: Department of Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

description:
Library name: 33_P1_Ctrl_NGFR_neg
Column name in raw_counts_All_Samples.txt : 33_P1_Ctrl_NGFR_neg

data_processing:
Bulk Prime-seq libraries were processed following the Deng Lab Prime-seq Analysis Pipeline (GitHub: https://github.com/paulojannig/Prime-seq_analysis).
Assembly: GRCh38
Supplementary files format and content: text file includes raw counts for each sample

source_name: Esophageal Organoid

growth_protocol: Human esophageal organoids were expanded according to (Eenjes et al.,2026).

extract_protocol:
Fresh tissue as well as corresponding organoids from 5 different donors were used to isolate 10.000 NGFR-negative and 10.000 NGFR-positive cells. Cell populations were lysed in TRI Reagent (ZymoResearch, #R2050) and stored at -80°C until RNA isolation.
Libraries for bulk RNA-sequencing were prepared according to the prime-seq protocol as previously described (Janjic et al., 2022).

value: Esophageal Organoid

value: Epithelial

value: Control

value: Organoid d7


title: whole fish, wild type

description:
Library name: Sample 1
10x Genomics

value: whole fish


title: RNA-seq of NEE technical replicate 3

description:
Library name: NEE_Rep3
A549 technical replicate RNA sample 3 prepared with NEE and sequenced


title: TimeLapse, THP1 Macrophages, Untreated, 500 uM S4U for 2hr, replicate 1

description: Library name: TL_CTL_S4U_1

value: THP1 Macrophage

value: PMA differentiated myeloid leukemia


title: 31_P1_IL1A_NGFR_neg_Organoid

description:
Library name: 31_P1_IL1A_NGFR_neg
Column name in raw_counts_All_Samples.txt : 31_P1_IL1A_NGFR_neg


title: RNA-seq of NEE technical replicate 2

description:
Library name: NEE_Rep2
A549 technical replicate RNA sample 2 prepared with NEE and sequenced


title: TimeLapse, THP1 Macrophages, Untreated, 500 uM S4U for 2hr, replicate 2

description: Library name: TL_CTL_S4U_2

value: 500 uM S4U, 2 hr


title: RNA-seq of Sph 24h Rep2

description:
Library name: Sph_24h_Rep2
RNA-seq of A549 spheroids, 24h after NEE, Rep2

value: A549 spheroids

value: 24h after NEE


title: 33_P1_IL1A_NGFR_pos_Organoid

description:
Library name: 33_P1_IL1A_NGFR_pos
Column name in raw_counts_All_Samples.txt : 33_P1_IL1A_NGFR_pos


title: TimeLapse, THP1 Macrophages, 10 uM STM2457 24hr, 500 uM S4U for 2hr, replicate 2

description: Library name: TL_STM_S4U_2


title: 33_P0_NGFR_pos_Epithelium

description:
Library name: 33_P0_NGFR_pos
Column name in raw_counts_All_Samples.txt : 33_P0_NGFR_pos

source_name: Esophageal epithelium

value: Esophageal epithelium

value: From tissue


title: 30_P1_IL1A_NGFR_pos_Organoid

description:
Library name: 30_P1_IL1A_NGFR_pos
Column name in raw_counts_All_Samples.txt : 30_P1_IL1A_NGFR_pos


title: 30_P1_IL1A_NGFR_neg_Organoid

description:
Library name: 30_P1_IL1A_NGFR_neg
Column name in raw_counts_All_Samples.txt : 30_P1_IL1A_NGFR_neg


title: 30_P1_Ctrl_NGFR_pos_Organoid

description:
Library name: 30_P1_Ctrl_NGFR_pos
Column name in raw_counts_All_Samples.txt : 30_P1_Ctrl_NGFR_pos


title: 33_P0_NGFR_neg_Epithelium

description:
Library name: 33_P0_NGFR_neg
Column name in raw_counts_All_Samples.txt : 33_P0_NGFR_neg


title: 30_P1_Ctrl_NGFR_neg_Organoid

description:
Library name: 30_P1_Ctrl_NGFR_neg
Column name in raw_counts_All_Samples.txt : 30_P1_Ctrl_NGFR_neg


title: 33_P1_Ctrl_NGFR_pos_Organoid

description:
Library name: 33_P1_Ctrl_NGFR_pos
Column name in raw_counts_All_Samples.txt : 33_P1_Ctrl_NGFR_pos


title: scale, wild type

description:
Library name: Sample 5
10x Genomics

value: scale

value: leukocytes


title: 31_P1_IL1A_NGFR_pos_Organoid

description:
Library name: 31_P1_IL1A_NGFR_pos
Column name in raw_counts_All_Samples.txt : 31_P1_IL1A_NGFR_pos


title: 30_P0_NGFR_pos_Epithelium

description:
Library name: 30_P0_NGFR_pos
Column name in raw_counts_All_Samples.txt : 30_P0_NGFR_pos


title: M55 line with Dox-inducible DDX3X transgene, Dox_1000ng/mL, P12, Rep1

city: Boston

first: Alex

last: Plesa

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

description:
Library name: A35
Donor age 55, Passage 12

value: Fibroblast

value: Dox_1000ng/mL, 3days


title: 31_P1_Ctrl_NGFR_neg_Organoid

description:
Library name: 31_P1_Ctrl_NGFR_neg
Column name in raw_counts_All_Samples.txt : 31_P1_Ctrl_NGFR_neg_


title: M41 WT line (isogenic with S34)

description:
Library name: S33
Donor age 41, Passage 5

value: WT

value: NT


title: 30_P0_NGFR_neg_Epithelium

description:
Library name: 30_P0_NGFR_neg
Column name in raw_counts_All_Samples.txt : 30_P0_NGFR_neg

value: Epithelial


title: 31_P0_NGFR_pos_Epithelium

description:
Library name: 31_P0_NGFR_pos
Column name in raw_counts_All_Samples.txt : 31_P0_NGFR_pos


title: 31_P1_Ctrl_NGFR_pos_Organoid

description:
Library name: 31_P1_Ctrl_NGFR_pos
Column name in raw_counts_All_Samples.txt : 31_P1_Ctrl_NGFR_pos

value: Esophageal Organoid

value: Control


title: 27_P1_Ctrl_NGFR_pos_Organoid

description:
Library name: 27_P1_Ctrl_NGFR_pos
Column name in raw_counts_All_Samples.txt : 27_P1_Ctrl_NGFR_pos

value: Organoid d7


title: 27_P1_Ctrl_NGFR_neg_Organoid

description:
Library name: 27_P1_Ctrl_NGFR_neg
Column name in raw_counts_All_Samples.txt : 27_P1_Ctrl_NGFR_neg


title: 31_P0_NGFR_neg_Epithelium

description:
Library name: 31_P0_NGFR_neg
Column name in raw_counts_All_Samples.txt : 31_P0_NGFR_neg


title: 27_P0_NGFR_pos_Epithelium

description:
Library name: 27_P0_NGFR_pos
Column name in raw_counts_All_Samples.txt : 27_P0_NGFR_pos


title: 33_P1_IL1A_NGFR_neg_Organoid

description:
Library name: 33_P1_IL1A_NGFR_neg
Column name in raw_counts_All_Samples.txt : 33_P1_IL1A_NGFR_neg


title: 27_P0_NGFR_neg_Epithelium

description:
Library name: 27_P0_NGFR_neg
Column name in raw_counts_All_Samples.txt : 27_P0_NGFR_neg


title: 26_P1_IL1A_NGFR_pos_Organoid

description:
Library name: 26_P1_IL1A_NGFR_pos
Column name in raw_counts_All_Samples.txt : 26_P1_IL1A_NGFR_pos


title: 27_P1_IL1A_NGFR_pos_Organoid

description:
Library name: 27_P1_IL1A_NGFR_pos
Column name in raw_counts_All_Samples.txt : 27_P1_IL1A_NGFR_pos


title: 26_P0_NGFR_pos_Epithelium

description:
Library name: 26_P0_NGFR_pos
Column name in raw_counts_All_Samples.txt : 26_P0_NGFR_pos


title: 26_P1_Ctrl_NGFR_neg_Organoid

description:
Library name: 26_P1_Ctrl_NGFR_neg
Column name in raw_counts_All_Samples.txt : 26_P1_Ctrl_NGFR_neg


title: 26_P0_NGFR_neg_Epithelium

description:
Library name: 26_P0_NGFR_neg
Column name in raw_counts_All_Samples.txt : 26_P0_NGFR_neg


title: RNA-seq of Sph 24h Rep1

description:
Library name: Sph_24h_Rep1
RNA-seq of A549 spheroids, 24h after NEE, Rep1


title: RNA-seq of Sph RightAway Rep2

description:
Library name: Sph_RightAway_Rep2
RNA-seq of A549 spheroids, Right away after NEE, Rep2

value: Right away after NEE


title: 26_P1_Ctrl_NGFR_pos_Organoid

description:
Library name: 26_P1_Ctrl_NGFR_pos
Column name in raw_counts_All_Samples.txt : 26_P1_Ctrl_NGFR_pos


title: MEC-1 cell line- Scrambled Gapmer treatment (Exp RP11-161H23.5) - rep3

city: Barcelona

first: Lluís

last: Hernández

address: Rossello 153

institute: IDIBAPS

source_name: MEC-1 cell line after Scrambled Gapmer treatment by 4 days

value: Control RP11-161H23.5 silencing


title: RNA-seq of Mono 2h Rep2

description:
Library name: Mono_2h_Rep2
RNA-seq of A549 monolayer, 2h after NEE, Rep2

value: A549 monolayer

value: 2h after NEE


title: 27_P1_IL1A_NGFR_neg_Organoid

description:
Library name: 27_P1_IL1A_NGFR_neg
Column name in raw_counts_All_Samples.txt : 27_P1_IL1A_NGFR_neg


title: RNA-seq of Mono 2h Rep1

description:
Library name: Mono_2h_Rep1
RNA-seq of A549 monolayer, 2h after NEE, Rep1


title: 26_P1_IL1A_NGFR_neg_Organoid

description:
Library name: 26_P1_IL1A_NGFR_neg
Column name in raw_counts_All_Samples.txt : 26_P1_IL1A_NGFR_neg


title: RNA-seq of Mono RightAway Rep2

description:
Library name: Mono_RightAway_Rep2
RNA-seq of A549 monolayer, Right away after NEE, Rep2


title: RNA-seq of Mono Before Rep1

description:
Library name: Mono_Before_Rep1
RNA-seq of A549 monolayer, Before NEE, Rep1

value: Before NEE


title: RNA-seq of Sph Before Rep1

description:
Library name: Sph_Before_Rep1
RNA-seq of A549 spheroids, Before NEE, Rep1

value: A549 spheroids


title: RNA-seq of Sph 2h Rep1

description:
Library name: Sph_2h_Rep1
RNA-seq of A549 spheroids, 2h after NEE, Rep1


title: RNA-seq of Sph Before Rep2

description:
Library name: Sph_Before_Rep2
RNA-seq of A549 spheroids, Before NEE, Rep2


title: MJM5029 replicate 1

city: Madison

first: Mark

middle: J

last: Mandel

state: WI

address: 1550 Linden Drive

department: Medical Microbiology and Immunology

institute: University of Wisconsin-Madison

description: Library name: Sample9

data_processing:
Read demultiplexing, read trimming, and run analytics were performed using DRAGEN v4.2.7, an on-board analysis software on the NextSeq2000.
Processed with fastp V0.23.4
Fastp-processed sequence files were aligned to the V. fischeri ES114 reference genome ENSEMBL_GCA_000011805 (MJM3381 and MJM5250) or to ENSEMBL_GCA_000011805-reform (MJM5028 and MJM5029) using bwa-mem V0.7.18. For both genomes, information for the 10 currently known sRNAs (VF_2577 csrB2, VF_2578 ryhB, VF_2579 spf, VF_2593 csrB1, VF_2597 qrr1, VF_2599 ffs, VF_2639 ssrA, VF_2651 ssrS, VF_2654 rnpB, VF_A1194 psrN) was manually appended.
Reads were assigned to gene features using htseq-count V0.6.1
Assembly: ENSEMBL_GCA_000011805
Supplementary files format and content: csv file with raw read counts for the sample

organism: Aliivibrio fischeri

source_name: Vibrio fischeri ES114

growth_protocol: Vibrio fischeri cells were streaked onto LBS and grown overnight at 25 ˚C. Single colonies of each strain were inoculated into 3 mL LBS and grown for 16 hrs at 28 ˚C with shaking. Overnight cultures were diluted 1/100 into 20 mL fresh LBS and grown at 28 ˚C with shaking until OD600 ~1.8

extract_protocol:
1 mL samples of each strain were taken and centrifuged at 10,000 x g, for 1 min. Supernatants were discarded and each pellet was resuspended in 600 uL TriReagent (Zymo Research), and total RNA was purified using a Direct-Zol kit (Zymo Research).
RNA samples were prepared for sequencing using the Illumina Stranded Total RNA Prep Ligation Kit with Ribo-Zero Plus Microbiome (#20072063) with Illumina Unique Dual Indexes.

value: Vibrio fischeri ES114

value: rscs* rtmR deletion attTn7::rtmR-3xFLAG-erm

value: Liquid culture


title: RNA-seq of Mono 24h Rep2

description:
Library name: Mono_24h_Rep2
RNA-seq of A549 monolayer, 24h after NEE, Rep2

value: 24h after NEE


title: RNA-seq of Mono 24h Rep1

description:
Library name: Mono_24h_Rep1
RNA-seq of A549 monolayer, 24h after NEE, Rep1


title: MJM5250 repcliate 1

description: Library name: Sample13

value: WT rtmR deletion attTn7::erm


title: RNA-seq of Sph 2h Rep2

description:
Library name: Sph_2h_Rep2
RNA-seq of A549 spheroids, 2h after NEE, Rep2


title: RNA-seq of Mono RightAway Rep1

description:
Library name: Mono_RightAway_Rep1
RNA-seq of A549 monolayer, Right away after NEE, Rep1


title: RNA-seq of Mono Before Rep2

description:
Library name: Mono_Before_Rep2
RNA-seq of A549 monolayer, Before NEE, Rep2


title: MJM5029 replicate 4

description: Library name: Sample12


title: RNA-seq of Sph RightAway Rep1

description:
Library name: Sph_RightAway_Rep1
RNA-seq of A549 spheroids, Right away after NEE, Rep1


title: MJM5250 repcliate 2

description: Library name: Sample14


title: MJM5029 replicate 2

description: Library name: Sample10


title: MJM5029 replicate 3

description: Library name: Sample11


title: MJM3381 replicate 1

description: Library name: Sample1

value: WT attTn7::erm


title: MJM5250 repcliate 4

description: Library name: Sample16


title: MJM5250 repcliate 3

description: Library name: Sample15


title: MJM5028 replicate 2

description: Library name: Sample6

value: rscs* rtmR deletion attTn7::erm


title: MJM5028 replicate 3

description: Library name: Sample7


title: snRNA-seq, visceral adipose tissue, 10x channel AD6 (donors Ob_01, Ob_02, Ob_03)

city: Seongnam city

first: SungHee

last: Choi

address: Dolmaro 172, Bundang dist

department: Internal Medicine, Division of Endocrinology and Metabolism

institute: Seoul National University Bundang Hospital

description:
Library name: AD6
Single-nucleus RNA-seq of visceral adipose tissue, 10x Genomics channel AD6, pool of nuclei from donors Ob_01, Ob_02, Ob_03, combined in equal proportions before loading. Metabolic group: obesity. No cell-labelling reagent was used; donor identity was assigned after sequencing by Souporcell genotype clustering from natural genetic variation, matched to donor-specific whole-exome sequencing. Sequenced across 4 lanes; all lane-level FASTQ files belong to this one library. This channel is the initial load of this donor pool and gave a low nuclei yield; the same pool was re-processed as channel AD8.
VAT_snRNA_matrix.mtx.gz
VAT_snRNA_barcodes.tsv.gz
VAT_snRNA_features.tsv.gz
VAT_snRNA_metadata.tsv

data_processing:
snRNA-seq: Raw reads were aligned to the human reference genome GRCh38 and gene-by-cell count matrices generated with CellRanger v7.0.1 using default parameters (11 channels, 21 donors).
snRNA-seq: Ambient RNA and empty droplets were removed with the remove-background function of CellBender v0.3.2. Per-cell QC metrics were computed with perCellQCMetrics (scuttle v1.4.0); nuclei with <2.5 log10 UMIs or >10% mitochondrial reads were excluded. Doublets were flagged with scDblFinder v1.8.0.
snRNA-seq: Donor identity in pooled channels was assigned with Souporcell v2.5, with the expected number of genotype clusters set to the number of pooled donors. Souporcell clusters were matched to donors by genotype concordance against donor-specific whole-exome sequencing (BWA-MEM2 v2.2.1 alignment, GATK v4.4.0.0 variant calling, exonic SNPs with QD >= 10, concordance computed with vcfR v1.14.0).
Bulk RNA-seq: Nextera adapter sequences and low-quality reads were removed with Trimmomatic v0.39. Reads were aligned to GRCh38 with HISAT2 v2.2.1, PCR and optical duplicates were removed with Picard v2.18.29, and reads were counted against the GRCh38 GTF annotation with HTSeq v0.11.2.
Assembly: GRCh38
Supplementary files format and content: VAT_Bulk_FPKM.txt: Tab-delimited text file containing the FPKM expression matrix for the 20 whole-tissue visceral adipose bulk RNA-seq samples (rows, 13,791 protein-coding genes identified by HGNC symbol; columns, samples labelled Lean_01-08, Ob_01-05 and DM_01-07). Values are FPKM computed from HTSeq gene counts.
Supplementary files format and content: VAT_Exvivo_mAb_Treated_RCM.csv: Comma-delimited text file containing the raw gene-level read count matrix for the 8 ex vivo explant libraries (rows, 61,541 genes identified by Ensembl gene ID; columns, 4 donors x 2 treatments, labelled AT_GS_01-04 with Naive or mAb suffix). Counts were generated with HTSeq v0.11.2 against the GRCh38 GTF annotation.
Supplementary files format and content: VAT_Exvivo_mAb_Treated_fpkm_combat.csv: Comma-delimited text file containing the batch-corrected FPKM expression matrix for the same 8 ex vivo explant libraries (rows, 19,424 protein-coding genes identified by HGNC symbol; columns as above). FPKM values were corrected for inter-donor variation with ComBat (sva package), treating each donor as a batch, and were used for the paired differential expression analysis reported in the manuscript.
Supplementary files format and content: Per-channel snRNA-seq matrices (AD1_barcodes.tsv.gz, AD1_features.tsv.gz, AD1_matrix.mtx.gz and the equivalent files for AD2-AD11): Gene-by-nucleus count matrix in 10x Genomics Market Exchange (MEX) format, provided as one set of three files per snRNA-seq channel. Matrices are the filtered_feature_bc_matrix output of CellRanger v7.0.1, before ambient-RNA removal and downstream filtering. Rows correspond to genes listed in the features file; columns correspond to nuclei listed in the barcodes file.
Supplementary files format and content: VAT_snRNA_matrix.mtx.gz, VAT_snRNA_barcodes.tsv.gz, VAT_snRNA_features.tsv.gz: Gene-by-nucleus count matrix in 10x Genomics Market Exchange (MEX) format, integrated across all 11 snRNA-seq channels after CellBender ambient-RNA removal, quality filtering, doublet removal and Souporcell donor demultiplexing. This is the matrix used for the analyses reported in the manuscript. Readable in R with Seurat::ReadMtx() or in Python with scanpy.read_10x_mtx().
Supplementary files format and content: VAT_snRNA_metadata.tsv: Tab-delimited per-nucleus metadata table for the integrated matrix, containing the 10x channel of origin, donor assignment, metabolic group, quality-control metrics, and the cell-type and subtype annotations reported in the manuscript. Row order matches the barcode order in VAT_snRNA_barcodes.tsv.gz.

molecule: nuclear RNA

source_name: visceral adipose tissue

growth_protocol: Visceral adipose tissue was collected fresh at surgery and either snap-frozen in liquid nitrogen and stored at -80C, or processed immediately. For the ex vivo explant subset, tissue was minced and maintained in DMEM/F-12 supplemented with 10% FBS and 1% penicillin-streptomycin at 37C in 5% CO2, with medium replenished every 2 days.

extract_protocol:
snRNA-seq: Snap-frozen visceral adipose tissue was thawed in DMEM with 10% FBS at 37C for 10 min and washed twice in PBS, then minced into 2-4 mm pieces. Nuclei were released in TST buffer (10 mM Tris-HCl pH 8.0, 0.25% SDS, 1 mM EDTA, 150 mM NaCl, 1x protease inhibitor cocktail) for 20 min on ice with gentle shaking. The lysate was passed through 100 um, 70 um and 10 um strainers in sequence and pelleted at 500 x g for 5 min at 4C. Nuclei were resuspended in 10x Genomics Nuclei Buffer (PN-1000268) and counted on a hemocytometer. For multiplexed channels, nuclei from 2-3 donors of the same metabolic condition were pooled in equal proportions (approximately 10,000 nuclei per donor).  Bulk RNA-seq: Total RNA was extracted from whole visceral adipose tissue, or from ex vivo explant cultures, using TRIzol Reagent (15596018, Ambion) according to the manufacturer's protocol. RNA concentration and purity were assessed on a NanoDrop ND-1000 spectrophotometer.
snRNA-seq: Libraries were prepared with the Chromium Single Cell 3' Gene Expression Kit v3.1 (10x Genomics) following the manufacturer's instructions. For pooled channels, nuclei from 2-3 donors were combined in equal proportions before loading; no cell-labelling reagent was used, and donor identity was recovered computationally from natural genetic variation after sequencing. Libraries were sequenced on an Illumina NovaSeq 6000 by Genome Insight Inc. (Republic of Korea).  Bulk RNA-seq: Libraries were prepared with the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Plus (Illumina); ribosomal RNA was depleted to enrich for mRNA and non-coding RNA. Libraries were sequenced paired-end on an Illumina NovaSeq 6000.

treatment_protocol: Not applicable for the primary tissue samples. For the ex vivo explant subset, human visceral adipose tissue explants were treated for 5 days with an anti-THBS1 monoclonal antibody (clone A6-1, GTX21823, GeneTex; 1:100) or left untreated as the paired control from the same donor; treatment medium was replenished every 2 days.

value: visceral adipose tissue

value: nucleus


title: MJM5028 replicate 4

description: Library name: Sample8