title: PC and GC B cells, mM-only prime, GEX

description:
Library name: 4_EXP_2_ex
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: GC B cells + Plasma cells


title: HH23, H3K9ac IP, 1W-treated, 10min, replicate 1

status: Public on Apr 02 2026

type: SRA

city: Washington

first: Reddick

middle: R

last: Walker

state: DC

address: 800 22nd St NW SEH 8960

department: MITM

country: USA

institute: The George Washington University

description: Library name: HH23_H3K9ac_1W_10min_rep1

library_source: genomic

data_processing:
Adaptors were trimmed using Cutadapt.
Sequences were aligned to hg38 using (mapq 30, very-sensitive-loca, soft-clipped-unmapped-tlen, dovetail, no-mixed,  no-discordant, I 10, X 1000)
Peaks were called against IgG control files using MACS2 (q-value: 0.05, BAMPE, nomodel, keep-dup, broad)
Assembly: hg38
Supplementary files format and content: bigwig format
Library strategy: CUT&Run

molecule: genomic DNA

organism: Homo sapiens

source_name: HH23 - Hey CRISPR-modified (R175H)

growth_protocol: DMEM, 10% FBS, 1% P/S

extract_protocol:
H3K9ac-targeted CUT&RUN-sequencing was performed according the the Cell Signaling Technologies CUT&RUN kit.
Libraries were prepared using the NEBNext Ultra II DNA library preparation kit.

treatment_protocol: 0.15mg/mL Prussian blue nanoparticles are introduced into 0.5mL suspension of cells with a final concentration of 10e6/mL. Suspensions treated with near infrared (808nm) light for 10 minutes at 1W laser intensity.

tag: cell line

value: HH23 - Hey CRISPR-modified (R175H)

tag: treatment

value: 1W photothermal therapy

tag: batch


title: GC B cell, mM-only prime RBD pos, HTO

city: New York

first: Gabriela

middle: S

last: Silva Santos

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description:
Library name: 3_EXP_2_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

library_source: transcriptomic

data_processing:
Single-cell BCR libraries were mapped to the Cell Ranger VDJ GRCm38 reference using Cell Ranger vdj v.8.1.0 (10x genomics). Contigs containing less than 50 reads and more than one heavy or light chain were removed. scRNA-seq and Hashtag-oligos unique molecular identifier quantification were performed with Cell Ranger counts v.8.0.1 using the Cell Ranger GEX reference mm10, and analyzed in R with Seurat v.5.1.0. Cells were demultiplexed with MULTISeqDemux, and those classified as doublets or with mitochondrial content greater than 10 % and feature count less than 1,000 or greater than 6,500 were excluded. Cell cycle genes were regressed out. Sample batches were then merged, scaled and normalized with SCTransform.
Assembly: GRCm38
Supplementary files format and content: CellRanger output files: RNA_barcodes.tsv.gz, RNA_features.tsv.gz, RNA_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: airr_rearrangement.tsv
Supplementary files format and content: CellRanger output files:  HTO_barcodes.tsv.gz, HTO_features.tsv.gz, HTO_matrix.mtx.gz
Library strategy: CITE-Seq

molecule: polyA RNA

organism: Mus musculus

source_name: Lymph node

extract_protocol:
Popliteal (draining) lymph nodes were isolated from the immunized mice and dissociated using a pestel. The resulting cell suspensions were incubated in FcBlock, followed by antibody incubation and hashtagged using the TotalSeqC antibodies (Biolegend). They were then sorted using the BD FACS Symphony S6 in tubes containing buffer before being charged on the Chromium.
RNA-seq libraries were prepared using the Chromium Single Cell 5' v.2 Reagent Kit (10x Genomics) according to the manufacturer's protocol. Libraries were then loaded on the Illumina NovaSeq for GEX (gene expression), VDJ (BCR) and HTO (hashtags) libraries at the Rockefeller University Genomics Resource Center.

treatment_protocol: Mice were immunised using 5µg of RBD, Spike, or different HIV CD4bs derived antigens in both footpad of the given mice with 33% alhydrogel (Invivogen). When indicated, boosts were perfomed using the same protocol.

tag: tissue

value: Lymph node

tag: cell type

value: GC B cells + CD8 T

tag: genotype

value: mM-only

value: D14 RBD prime


title: Hey, IgG IP, PBO control, 10min, replicate 2

description: Library name: Hey_IgG_PBO_10min_rep2

source_name: Hey

value: Hey

value: PBO control


title: Hey, H3K9ac IP, 1W-treated, 10min, replicate 1

description: Library name: Hey_H3K9ac_1W_10min_rep1


title: Hey, H3K9ac IP, PBO control, 10min, replicate 2

description: Library name: Hey_H3K9ac_PBO_10min_rep2


title: MB27_S11_L002

city: Durham

first: Amanda

middle: D

last: Barreto

address: 1427 Fitzpatrick Center

institute: Duke University

description:
Library name: Sample 27
raw data file

data_processing:
RNA-seq reads were trimmed using Trim Galore v 0.6.4 and mapped to the human genome (GRCh38) with STAR (Spliced Transcripts Alignment to a Reference) 76 (v 2.6.1d, with parameters --twopassMode Basic and supplying the Ensembl GRCh38 annotation). Mapped reads were filtered by MAPQ (Mapping quality) (no smaller than 30) (Supplementary table 3) and counted using featureCounts 77 (v 1.6.4, with parameters -s 2). Bioconductor package DESeq2 78 (v 1.26.0) was used to analyze differential gene expression (Supplementary Table 4) . TPM (transcripts per million) values were quantified using Salmon 79 (v 0.14.1) and summarized using tximport 80 (v 1.14.2). To account for multiple testing, we applied the False Discovery Rate (FDR) correction, with an adjusted p-value threshold of < 0.05 to identify statistically significant differentially expressed genes.
Assembly: GRCh38
Supplementary files format and content: excel worksheet files with DESeq2.Salmon.diff for each disease model compared to control

molecule: total RNA

source_name: kidney

extract_protocol:
RNA isolation was performed using a NucleoSpin RNA extraction kit (Takara Bio, 740955.25, CA, USA). Three samples of RNA per treatment condition were collected in three independent experiments.
RNA integrity was assessed using an Agilent 2100 Bioanalyzer. All samples used for sequencing had an RNA Integrity Number (RIN) of 8.0 or higher, ensuring high-quality RNA suitable for high-resolution transcriptomic analyses (Supplementary Table 5). RNA-seq libraries were sequenced on an Illumina NovaSeq 6000 platform using three lanes of SP flow cells with 51 base pair paired-end (PE) reads. This setup provided high-throughput sequencing with robust data output per sample.

value: kidney

value: human induced pluripotent stem cell

value: WT

value: LPS

value: Round 2


title: A2780, IgG IP, PBO control, 10min, replicate 1

description: Library name: A2780_IgG_PBO_10min_rep1


title: GC B cell, mM-only prime RBD neg, BCR

description:
Library name: 2_EXP_2_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Single-cell BCR libraries were mapped to the Cell Ranger VDJ GRCm38 reference using Cell Ranger vdj v.8.1.0 (10x genomics). Contigs containing less than 50 reads and more than one heavy or light chain were removed. scRNA-seq and Hashtag-oligos unique molecular identifier quantification were performed with Cell Ranger counts v.8.0.1 using the Cell Ranger GEX reference mm10, and analyzed in R with Seurat v.5.1.0. Cells were demultiplexed with MULTISeqDemux, and those classified as doublets or with mitochondrial content greater than 10 % and feature count less than 1,000 or greater than 6,500 were excluded. Cell cycle genes were regressed out. Sample batches were then merged, scaled and normalized with SCTransform.
Assembly: GRCm38
Supplementary files format and content: CellRanger output files: RNA_barcodes.tsv.gz, RNA_features.tsv.gz, RNA_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: airr_rearrangement.tsv
Supplementary files format and content: CellRanger output files:  HTO_barcodes.tsv.gz, HTO_features.tsv.gz, HTO_matrix.mtx.gz
Library strategy: BCR-Seq

value: GC B cells + TFH


title: MB28_S12_L001

description:
Library name: Sample 26
raw data file

value: DMSO


title: A2780, IgG IP, 1W-treated, 10min, replicate 1

description: Library name: A2780_IgG_1W_10min_rep1


title: GC B cell, mM-only prime RBD neg, HTO

description:
Library name: 2_EXP_2_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag


title: GC B cell, mM-only prime RBD neg, GEX

description:
Library name: 2_EXP_2_ex
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

library_source: transcriptomic single cell

data_processing:
Single-cell BCR libraries were mapped to the Cell Ranger VDJ GRCm38 reference using Cell Ranger vdj v.8.1.0 (10x genomics). Contigs containing less than 50 reads and more than one heavy or light chain were removed. scRNA-seq and Hashtag-oligos unique molecular identifier quantification were performed with Cell Ranger counts v.8.0.1 using the Cell Ranger GEX reference mm10, and analyzed in R with Seurat v.5.1.0. Cells were demultiplexed with MULTISeqDemux, and those classified as doublets or with mitochondrial content greater than 10 % and feature count less than 1,000 or greater than 6,500 were excluded. Cell cycle genes were regressed out. Sample batches were then merged, scaled and normalized with SCTransform.
Assembly: GRCm38
Supplementary files format and content: CellRanger output files: RNA_barcodes.tsv.gz, RNA_features.tsv.gz, RNA_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: airr_rearrangement.tsv
Supplementary files format and content: CellRanger output files:  HTO_barcodes.tsv.gz, HTO_features.tsv.gz, HTO_matrix.mtx.gz


title: A2780, H3K9ac IP, 1W-treated, 10min, replicate 2

description: Library name: A2780_H3K9ac_1W_10min_rep2


title: MB28_S12_L002

description:
Library name: Sample 25
raw data file


title: CD38+ B cell, mM-only prime, BCR

description:
Library name: 1_EXP_2_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: CD38+ B cells


title: A2780, IgG IP, PBO control, 10min, replicate 2

description: Library name: A2780_IgG_PBO_10min_rep2


title: A2780, IgG IP, 1W-treated, 10min, replicate 2

description: Library name: A2780_IgG_1W_10min_rep2


title: A2780, H3K9ac IP, 1W-treated, 10min, replicate 1

description: Library name: A2780_H3K9ac_1W_10min_rep1


title: A2780, H3K9ac IP, PBO control, 10min, replicate 1

description: Library name: A2780_H3K9ac_PBO_10min_rep1


title: MB29_S13_L001

description:
Library name: Sample 24
raw data file

value: HG


title: A2780, H3K9ac IP, PBO control, 10min, replicate 2

description: Library name: A2780_H3K9ac_PBO_10min_rep2


title: CD38+ B cell, mM-only prime, HTO

description:
Library name: 1_EXP_2_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag


title: MB29_S13_L002

description:
Library name: Sample 23
raw data file


title: INT407 cells infected with C. jejuni

city: PULLMAN

first: Eric

middle: Aaron

last: Shelden

state: WA

address: 1770 NE Stadium Way

department: School of Molecular Biosciences

institute: Washington State University

description:
Library name: Sample 2
10x Genomics

data_processing:
Reads were aligned to the human referecence genome using services of the Illumina corporation.
Matrix files were imported into Seurat using R and differentially expressed genes identififed using the FindMarkers function.
Assembly: human hg38
Supplementary files format and content: tab separated values files and matrix files

growth_protocol: C. jejuni were incubated with INT 407 cells for 20 hours

extract_protocol:
Samples were processed as outlined in Sample Preparation Demonstrated Protocol, as instructed (10xgenomics.com).
cDNA libraries were prepared using the 10xGenomics NextGEM 3'RNA v3.1 workflow according to the manufacturer's protocol.

treatment_protocol: Cells were treated with 20 µM of lovastatin and 9 µM of RO-3306 for 20-24 hours for cell cycle synchronization. Following incubation, the cells were rinsed with a tissue culture medium and infected with C. jejuni.

value: epithelial


title: MB31_S15_L001

description:
Library name: Sample 20
raw data file

value: HG cytokines


title: CD38+ B cell, WT prime, BCR

description:
Library name: 5_CTRL_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: Lymph node

value: wildtype, C57BL/6J


title: CD38+ B cell, mM-only prime, GEX

description:
Library name: 1_EXP_2_ex
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: mM-only


title: MB30_S14_L001

description:
Library name: Sample 22
raw data file

value: NG


title: MB31_S15_L002

description:
Library name: Sample 19
raw data file


title: Uninfected INT407 cells

description:
Library name: Sample 1
10x Genomics


title: WT_Liver_5

city: Chicago

first: Navdeep

middle: S.

last: Chandel

state: IL

address: 303 E. Superior Street

department: Department of Medicine & Biochemistry and Molecular Genetics

institute: Northwestern University

description: Library name: WT_31Li

data_processing:
Data were processed using nf-core/rnaseq v3.12.0 of the nf-core collection of workflows. The pipeline was executed using Nextflow v23.10.1 and singularity v3.8.1 with the public nu_genomics configuration. Transcriptome alignment and gene-level count assignment were performed using the STAR/Salmon method with the GRCm38/mm10 genome as the reference.
Assembly: GRCm38
Supplementary files format and content: Raw counts from Salmon quant
Supplementary files format and content: Sample metadata

source_name: Liver

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured in 2i media consisting of 0.5X Neurobasal media (Gibco, catalog no. 21103049), 0.5X DMEM/F12 (Gibco, catalog no. 11320033), 0.5X N-2 Supplement (Gibco, catalog no. 17502048), 0.5X B-27 Supplement (Gibco, catalog no. 17504-044), 0.05% Bovine Albumin Fraction V (Gibco, catalog no. 15260037), 1X Antibiotic-Antimycotic solution (Gibco, catalog no. 15240062),  2.5 µg mL-1 Plasmocin Prophylactic (InvivoGen, catalog no. ant-mpp), 1 μM PD0325901 (Reprocell, catalog no. 04-0006-02), 3 μM CHIR99021 (Reprocell, catalog no. 04-0004-02), 2 mM Glutamine (Gibco, catalog no. 25030081), 150 μM 1-Thioglycerol (Sigma-Aldrich, catalog no. M6145), 1000 U/mL Leukemia Inhibitory Factor (LIF) (Sigma-Aldrich, catalog no. ESG1106), 1 mM methyl pyruvate (Sigma-Aldrich, catalog no. 371173), and 400 µM uridine (Sigma-Aldrich, catalog no. U3003). Cells were incubated at 37 °C, 5% CO2, and 95% humidity.

extract_protocol:
RNA was isolated with the AllPrep DNA/RNA Micro Kit (Qiagen, catalog no. 80284) according to the manufacturer’s protocol. The quantity and quality of the extracted RNA were assessed using TapeStation 4200 (Agilent).
mRNA libraries were prepared using NEBNext Ultra Kit with polyA selection (New England BioLabs, catalog nos. E7530 and E7490).

treatment_protocol: Mouse embryonic stem cells (mESCs) were treated with vehicle or 500 nM myxothiazol for 16 hours.

value: Liver

value: Wild-Type


title: INT407 cells infected with C. jejuni lacking CiaC

description:
Library name: Sample 3
10x Genomics


title: PC and GC B cells, WT prime BCR

description:
Library name: 8_CTRL_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: GC B cells + Plasma cells + TFH +/- CD8 T

value: D14 RBD prime


title: WT_Liver_1

description: Library name: WT_15Li


title: Pre-Treatment Biopsy 1 sample, rep1 [Li55535-A1_S1]

city: Calgary

first: Sorana

last: Morrissy

state: Alberta

address: 3330 Hospital Dr NW

department: Department of Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

description:
Library name: Pre-Treatment Biopsy_S1
FFPE Spatial Transcriptomics Sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline. They were alligned to a modified GRCh38 that included the GCAR1 construct. Barcode/UMI counting was performed using Space Ranger's default settings.
Gene expression data was factorized using consensus non-negative matrix factorization (cNMF) to generate program a usage matrix and gene-score matrix.
Assembly: GRCh38-2024-A
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.png: image of tissue and spots
Supplementary files format and content: scale_factors_json.json: scalefactors in jason formal
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: Gene expression count matrix in Matrix Marker file format
Library strategy: Spatial Transcriptomics

source_name: ASPS lung needle biopsy

extract_protocol:
FFPE tissue were cut into 10um section using a microtome.
Spatial Transcriptome sequencing libraries were prepared with 10x Genomics Visium HD Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction.

value: ASPS lung needle biopsy

value: Pre-Treatment Biopsy


title: Primary Sample, rep1

description: FFPE Spatial Transcriptomics Sequencing

source_name: ASPS thigh primary tumor

extract_protocol:
FFPE tissue were cut into 10um section using a microtome.
Sptial Transcriptome sequencing libraries were prepared with 10x Genomics Visium HD Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction.

value: ASPS thigh primary tumor


title: Post-Treatment Biopsy 2 sample, rep1 [Li55536-D1_S2]

description:
Library name: Post-Treatment Biopsy_S2
FFPE Spatial Transcriptomics Sequencing

value: Post-Treatment Biopsy


title: PC and GC B cells, WT prime, HTO

description:
Library name: 8_CTRL_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag


title: CD38+ B cell, WT prime, HTO

description:
Library name: 5_CTRL_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag


title: WT_Liver_4

description: Library name: WT_30Li


title: Biopsy Sample, rep1

description: FFPE Spatial Transcriptomics Sequencing


title: Biopsy Sample, rep2

description: FFPE Spatial Transcriptomics Sequencing


title: MB32_S16_L002

description:
Library name: Sample 17
raw data file

value: kidney

value: human induced pluripotent stem cell

value: WT

value: UNT

value: Round 2


title: L2HGDH_OE_Liver_3

description: Library name: Hom_17Li

value: L2HGDH-Overexpressing (homozygous)


title: WT_Liver_3

description: Library name: WT_22Li


title: AO16_S20_L001

description:
Library name: Sample 16
raw data file

value: DMSO

value: Round 1


title: MB32_S16_L001

description:
Library name: Sample 18
raw data file


title: PC and GC B cells, WT prime, GEX

description:
Library name: 8_CTRL_ex
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: Lymph node

value: wildtype, C57BL/6J


title: L2HGDH_OE_Liver_5

description: Library name: Hom_25Li

value: Liver


title: WT_Liver_2

description: Library name: WT_21Li

value: Wild-Type


title: MB30_S14_L002

description:
Library name: Sample 21
raw data file

value: NG


title: AO16_S20_L002

description:
Library name: Sample 15
raw data file


title: L2HGDH_OE_Liver_2

description: Library name: Hom_16Li


title: AO14_S19_L002

description:
Library name: Sample 14
raw data file


title: CD38+ B cell, WT prime, GEX

description:
Library name: 5_CTRL_ex
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: CD38+ B cells

value: D14 RBD prime


title: AO14_S19_L001

description:
Library name: Sample 13
raw data file


title: WT_Kidney_4

description: Library name: WT_30K

source_name: Kidney

value: Kidney


title: L2HGDH_OE_Liver_4

description: Library name: Hom_24Li


title: PC + GC B cells, M-only prime, BCR

description:
Library name: 4_EXP_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: GC B cells + Plasma cells + TFH +/- CD8 T

value: M-only


title: PC + GC B cells, M-only prime, HTO

description:
Library name: 4_EXP_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag


title: WT_Kidney_3

description: Library name: WT_22K


title: L2HGDH_OE_Liver_1

description: Library name: Hom_14Li


title: WT_Kidney_2

description: Library name: WT_21K


title: L2HGDH_OE_Kidney_5

description: Library name: Hom_25K


title: WT_Kidney_5

description: Library name: WT_31K


title: WT_Kidney_1

description: Library name: WT_15K


title: AO17_S21_L002

description:
Library name: Sample 11
raw data file

value: kidney

value: human induced pluripotent stem cell

value: LPS


title: PC + GC B cells, M-only prime, GEX

description:
Library name: 4_EXP_ex
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AO3_S17_L001

description:
Library name: Sample 10
raw data file

value: WT

value: HG


title: AO3_S17_L002

description:
Library name: Sample 9
raw data file


title: AO17_S21_L001

description:
Library name: Sample 12
raw data file


title: GC B cell, M-only prime RBD pos, BCR

description:
Library name: 3_EXP_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: GC B cells


title: Input_L2HGDH_Myxo_rep1_H3K27me3.mm10.Rx

first: Ali

last: Shilatifard

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: Library name: S07

data_processing:
Raw files were demultiplexed using bcl2fastq v2.19 with adatpter removal.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
The mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, normalized using internal spike-in (dm6) and reformatted in the bigWig file format.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: mESC

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured in 2i media consisting of 0.5X Neurobasal media, 0.5X DMEM/F12, 0.5X N-2 Supplement , 0.5X B-27 Supplement, 0.05% Bovine Albumin Fraction V, 1X Antibiotic-Antimycotic solution,  2.5 µg ml-1 Plasmocin Prophylactic, 1 μM PD03259010, 3 μM CHIR99021 , 2 mM Glutamine, 150 μM 1-Thioglycerol, 1000 U/mL Leukemia Inhibitory Factor (LIF), 1 mM methyl-pyruvate, and 400 µM uridine. DMSO, EtOH, piericidin A, 3-nitropropionic acid (3-NPA) , atpenin A5, antimycin A, myxothiazol, Na-Azide, L-ascorbic acid, N,N,N',N'-tetramethyl-1,4-phenylenediamine (TMPD), and the MDH2 inhibitor were used to treat cells in different experiments.

extract_protocol:
AS described in Lee TI, Johnstone SE & Young RA (Nat Proc 2006, 1:729-748). Fixation was performed using 1% paraformaldehyde (PFA). For H3K27me3 ChIP-Seq, chromatin sonication was performed using 20% duty cycle, 140 peak intensity power, and 200 cycles per burst for 10 min. Successively, the pulldown of chromatin was carried out overnight at 4 °C using the specific antibodies. Drosophila spike-in chromatin and antibody were added as internal normalization control following manufacturer’s instructions (ActiveMotif, catalog no. 53083, 61686). Reverse cross-linking was performed at 65 °C overnight while shaking at 1,200 rpm. Immunoprecipitated DNA was extracted using the ChIP-DNA purification kit (Zymo Research, catalog no. D5205) following the manufacturer’s instructions.
Libraries were made using the KAPA HTP Biosystems Library Prep kit (Roche, KK8234) using Perkin Elmer Unique Dual Index Barcodes for NextSeq 2000.

treatment_protocol: mESC cells were treated with 500 nM myxothiazol (16 hours, unless mentioned otherwise), and incubated at 37 °C, 5% CO2, and 95% humidity.

value: mESC

value: mouse embryonic stem cells

value: myxothiazol 500nM

tag: antibody


title: GC B cell, M-only prime RBD pos, GEX

description:
Library name: 3_EXP_ex
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: Lymph node


title: Input_EV_Myxo_rep2_H3K27me3.mm10.Rx

description: Library name: S06

value: EV


title: GC B cell, M-only prime RBD pos, HTO

description:
Library name: 3_EXP_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag


title: L2HGDH_OE_Kidney_4

description: Library name: Hom_24K

value: L2HGDH-Overexpressing (homozygous)


title: Input_EV_Myxo_rep1_H3K27me3.mm10.Rx

description: Library name: S05


title: MB34_S25_L001

description:
Library name: Sample 6
raw data file

value: ADR

value: Round 1


title: L2HGDH_OE_Kidney_1

description: Library name: Hom_14K

value: Kidney


title: L2HGDH_OE_Kidney_2

description: Library name: Hom_16K


title: CD38+ B cell, M-only prime, HTO

description:
Library name: 1_EXP_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

value: CD38+ B cells

value: D14 RBD prime


title: L2HGDH_OE_Kidney_3

description: Library name: Hom_17K


title: AO4_S18_L002

description:
Library name: Sample 7
raw data file

value: kidney

value: NG


title: Input_L2HGDH_Myxo_rep2_H3K27me3.mm10.Rx

description: Library name: S08


title: GC B cell, M-only prime RBD neg, GEX

description:
Library name: 2_EXP_ex
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: M-only


title: GC B cell, M-only prime RBD neg, HTO

description:
Library name: 2_EXP_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag


title: AO4_S18_L001

description:
Library name: Sample 8
raw data file

value: human induced pluripotent stem cell

value: WT


title: CutRun_Pol2_L2HGDHoe_Kidney_rep3

first: Yuki

last: Aoi

address: 303 E Superior St. SQBRC 7-300

department: Biochemistry & Molecular Genetics

description:
Library name: CutRun-SAMPLE_20
CutRun_Pol2_L2HGDHoe_Kidney_merged.bw

data_processing:
Adapter removal and quality trimming were carried out using cutadapt 4.2. The paired end reads were aligned to the concatenated genome assembly (mm10+sacCer3) by bowtie 2.5.4 with local alignment mode and very-sensitive option. Read mates that dovetailed were allowed. To study H3K9me3 and Pol II occupancies at repetitive sequences, the multimappers were included in downstream analysis as described previously (https://doi.org/10.1038/s41556-024-01547-z), by keeping the aligned reads with MAPQ ≥ 1. The duplicated reads were discarded by picard 2.21.4.  Pairwise correlation was assessed by deepTools 3.5.6. Samples with Pearson coefficient > 0.8 within the same condition and target were kept. The reads generated from different mice (H3K9me3 WT, n = 5; H3K9me3 L2HGDHoe, n = 5; Pol II WT, n = 5; H3K9me3 L2HGDHoe, n = 4) were merged to obtain sufficient coverage at repetitive sequences. The occupancy was normalized by the spike-in reads.
Assembly: mm10
Supplementary files format and content: Bigwig files containing genome coverage data
Library strategy: CUT&Run

extract_protocol:
Mouse kidneys were minced in ice-cold nuclei EZ lysis buffer (Sigma, #NUC101) with scissors and homogenized with 10 (pestle A) and 5 (pestle B) strokes of 2-ml Dounce tissue grinders (DWK, #8853000002).  The homogenized samples were filtered by 100-µm and 30-µm strainers (Miltenyi, #130110917, #130110915). Nuclei were centrifuged at 300 g for 5 min at 4°C and resuspended in CUT&RUN wash buffer. Reagents in CUT&RUN Assay Kit (CST, #86652) were used throughout the assays. 500k nuclei were bound to Concanavalin A beads and incubated at 4°C overnight with antibodies (H3K9me3: abcam, #ab176916; RPB1-S2P/S5P: CST, #13546; IgG: CST, #66362). Note that RPB1-S2P/S5P antibody recognizes the Pol II C-terminal domain phosphorylated at both serine 2 and serine 5 and is used to target elongating Pol II. Following the incubation with pAG-MNase at 4°C for 1 h, DNA was digested in the presence of calcium chloride at 4°C for 1 h. STOP buffer containing yeast spike-in DNA was added to stop the digestion. The targeted DNA was eluted from nuclei at 37°C for 10 min and purified by DNA Clean & Concentrator (Zymo, #D5205).
Libraries were prepared using KAPA HyperPrep Kit (Roche) with minor modifications. End repair and A-tailing reactions were carried out at 20°C for 30min, followed by inactivation at 50°C for 30 min. 100 fmol UDI barcodes (Revvity, NOVA-514150) was used for adapter ligation. The ligated DNA was cleaned up by x1.2 volume of AMPure XP beads (Beckman Coulter, #A63881). Following PCR amplification, the libraries were cleaned up three times by x1.2 volume of AMPure XP beads. The pooled libraries were sequenced by NextSeq 2000 (Illumina) to obtain 2x 51 bp paired end reads.


title: AO8_S22_L002

description:
Library name: Sample 3
raw data file

value: CytoD


title: GC B cell, M-only prime RBD neg, BCR

description:
Library name: 2_EXP_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: GC B cells


title: CD38+ B cell, M-only prime, GEX

description:
Library name: 1_EXP_ex
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: L2HGDH_Myxo_rep1_K27me3.mm10.Rx

description: Library name: S03

value: mESC

value: mouse embryonic stem cells

value: H3K27me3 (CST, catalog no. 9733S)


title: L2HGDH_Myxo_rep2_K27me3.mm10.Rx

description: Library name: S04

value: myxothiazol 500nM


title: CutRun_Pol2_L2HGDHoe_Kidney_rep4

description:
Library name: CutRun-SAMPLE_21
CutRun_Pol2_L2HGDHoe_Kidney_merged.bw


title: CutRun_Pol2_L2HGDHoe_Kidney_rep1

description:
Library name: CutRun-SAMPLE_18
CutRun_Pol2_L2HGDHoe_Kidney_merged.bw


title: CutRun_Pol2_WT_Kidney_rep5

description:
Library name: CutRun-SAMPLE_17
CutRun_Pol2_WT_Kidney_merged.bw


title: AO8_S22_L001

description:
Library name: Sample 4
raw data file


title: AO9_S23_L001

description:
Library name: Sample 2
raw data file

value: HG cytokines


title: CD38+ B cell, M-only prime, BCR

description:
Library name: 1_EXP_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: Lymph node


title: EV_Myxo_rep2_H3K27me3.mm10.Rx

description: Library name: S02

value: EV


title: CutRun_Pol2_WT_Kidney_rep4

description:
Library name: CutRun-SAMPLE_16
CutRun_Pol2_WT_Kidney_merged.bw

value: Kidney


title: MB34_S25_L002

description:
Library name: Sample 5
raw data file

value: ADR

value: Round 1


title: scRNA_GSC1NC

city: Shenyang

first: Sun

middle: Xiang

last: Hao

state: Liaoning

address: puhe road 77th

country: China

institute: CMU

description: Library name: GSC1NC

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation weremade using the Cell Ranger software v2.1.1(https://support.10xgenomics.com/single-cell-gene.expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
The isolated human glioma stem cells (GSCs) were resuspended in digestion buffer (HBSS with Mg²⁺/Ca²⁺ supplemented with 2 mg/ml collagenase type Ⅰ and 40 U/ml DNase Ⅰ) and incubated at 37℃ for 30 minutes.The cells were centrifuged, washed, and resuspended in PBS, then stained with a Viability Dye. After another wash, the cells were resuspended in FACS buffer (HBSS without Mg²⁺/Ca²⁺, 2% v/v Fetal Calf Serum (FCS), 5 mM EDTA).Using normal human brain glial cells as the negative control, viable human glioma stem cells were sorted by FACS Jazz flow cytometer (Becton Dickinson) according to the presence or absence of mCherry signal.The sorted human glioma stem cells were washed with HBSS without Mg²⁺/Ca²⁺ and then resuspended in HBSS supplemented with 0.04% (w/v) Bovine Serum Albumin (BSA) for subsequent experiments.
Single-cell suspension was added to the 10xChromium chip according to theinstructions for the 10xGenomics Chromium Single-Cell 3' kit (V3.1), with the expectation ofcapturing 8,000 cells. cDNA amplification and library construction were performedaccording to standard protocols. Libraries were sequenced by LC-Bio Technology (Hangzhou.hina) on an Illumina NovaSeg 6000 sequencing system (double-end sequencing, 150 bp) ata minimum depth of 20,000 reads per cell.

value: brain


title: CutRun_Pol2_L2HGDHoe_Kidney_rep2

description:
Library name: CutRun-SAMPLE_19
CutRun_Pol2_L2HGDHoe_Kidney_merged.bw


title: scRNA_GSC1ShPDLIM4

description: Library name: GSC1ShPDLIM4


title: EV_Myxo_rep1_H3K27me3.mm10.Rx

description: Library name: S01


title: CutRun_Pol2_WT_Kidney_rep3

description:
Library name: CutRun-SAMPLE_15
CutRun_Pol2_WT_Kidney_merged.bw


title: AO9_S23_L002

description:
Library name: Sample 1
raw data file

value: kidney


title: CutRun_Pol2_WT_Kidney_rep2

description:
Library name: CutRun-SAMPLE_14
CutRun_Pol2_WT_Kidney_merged.bw


title: HFD_ONX4

city: Wuhan

first: Ye

last: zhou

address: 1037 Luoyu Road, Hongshan District, Wuhan, Hubei, 430074, P.R. China

institute: Huazhong University of Science and Technology Tongji Medical College

description: Library name: Sample 6

data_processing:
Raw sequencing reads were quality-checked using FastQC (v0.11.5). Adapter trimming and quality filtering were performed using Cutadapt (v1.11) with the following parameters: -a R1_adapter -A R2_adapter -m 20 --max-n 0.05 -q 20. Clean reads were aligned to the reference genome using HISAT2 (v2.0.1-beta). Gene-level read counts were generated using featureCounts (v1.6.0) and normalized as FPKM values. Differential expression analysis was performed using edgeR, with significance thresholds set at FDR < 0.05 and |log2FC| > 1.
Assembly: Mus musculus reference genome (GRCm38/mm10).
Supplementary files format and content: FPKM values for each Sample

extract_protocol:
Total RNA was extracted from liver tissues using a TRIzol-based method according to the manufacturer’s instructions. RNA concentration and integrity were assessed prior to library preparation.
RNA-seq libraries were prepared following standard Illumina library preparation protocols. Briefly, mRNA was enriched, fragmented, reverse-transcribed into cDNA, ligated with sequencing adapters, PCR amplified, and subjected to quality control prior to sequencing.

value: Liver

tag: strain

tag: Sex

value: male

value: HFD‑fed + ONX‑0914 (10 mg/kg, s.c., every other day, 6 weeks)


title: HFD_ONX3

description: Library name: Sample 5


title: CutRun_Pol2_WT_Kidney_rep1

description:
Library name: CutRun-SAMPLE_13
CutRun_Pol2_WT_Kidney_merged.bw

value: WT


title: CutRun_H3K9me3_L2HGDHoe_Kidney_rep5

description:
Library name: CutRun-SAMPLE_10
CutRun_H3K9me3_L2HGDHoe_Kidney_merged.bw


title: HFD_ONX1

description: Library name: Sample 4


title: CutRun_IgG_WT_Kidney_rep1

description:
Library name: CutRun-SAMPLE_11
CutRun_IgG_WT_Kidney_merged.bw

value: IgG


title: CutRun_H3K9me3_L2HGDHoe_Kidney_rep4

description:
Library name: CutRun-SAMPLE_09
CutRun_H3K9me3_L2HGDHoe_Kidney_merged.bw


title: U138, siAATF, rep1

city: Rome

first: Stefano

last: Di Giovenale

address: Via Elio Chianesi,  53

country: Italy

institute: IRCCS National Cancer Institute Regina Elena

description: Library name: RNA_U138_siAATF_rep1

data_processing:
Samples were aligned to the reference genome hg19 using STAR, and transcript quantification was performed with RSEM, employing the nf-core/rnaseq pipeline (v. 3.12.0) with Nextflow (v. 24.10.4.5934) with default parameters.
Assembly: hg19
Supplementary files format and content: Processed data are composed of tsv files obtained by RSEM quantificatio.

extract_protocol:
Total RNA was extracted using Qiazol (Qiagen, IT), purified from DNA contamination through a DNase I (Qiagen, IT) digestion step and further enriched by Qiagen RNeasy columns specific for gene expression profiling (Qiagen, IT). Quantity and integrity of the extracted RNA were assessed using a NanoDrop Spectrophotometer (NanoDrop Technologies, DE) and a TapeStation System (Agilent), respectively.
RNA libraries for sequencing were generated in triplicate using the same amount of RNA for each sample according to the Illumina Stranded Total RNA Prep kit, with an initial ribosomal depletion step using Ribo-Zero Plus (Illumina, CA). The libraries were quantified by qPCR and sequenced in paired-end mode (2x100 bp) with NovaSeq 6000 System (Illumina, CA). For each sample generated by the Illumina platform, a pre-process step for quality control was performed to assess sequence data quality and to discard low-quality reads


title: CutRun_IgG_WT_Kidney_rep2

description:
Library name: CutRun-SAMPLE_12
CutRun_IgG_WT_Kidney_merged.bw


title: CutRun_H3K9me3_L2HGDHoe_Kidney_rep3

description:
Library name: CutRun-SAMPLE_08
CutRun_H3K9me3_L2HGDHoe_Kidney_merged.bw


title: U138, siAATF, rep3

description: Library name: RNA_U138_siAATF_rep3


title: U138, siAATF, rep2

description: Library name: RNA_U138_siAATF_rep2


title: U138, siControl, rep3

description: Library name: RNA_U138_siControl_rep3


title: HFD2

description: Library name: Sample 2

value: HFD‑fed + vehicle


title: CutRun_H3K9me3_L2HGDHoe_Kidney_rep2

description:
Library name: CutRun-SAMPLE_07
CutRun_H3K9me3_L2HGDHoe_Kidney_merged.bw


title: CutRun_H3K9me3_WT_Kidney_rep3

description:
Library name: CutRun-SAMPLE_03
CutRun_H3K9me3_WT_Kidney_merged.bw


title: CutRun_H3K9me3_WT_Kidney_rep5

description:
Library name: CutRun-SAMPLE_05
CutRun_H3K9me3_WT_Kidney_merged.bw


title: HFD1

description: Library name: Sample 1


title: U138, siControl, rep2

description: Library name: RNA_U138_siControl_rep2


title: CutRun_H3K9me3_WT_Kidney_rep2

description:
Library name: CutRun-SAMPLE_02
CutRun_H3K9me3_WT_Kidney_merged.bw


title: CutRun_H3K9me3_WT_Kidney_rep4

description:
Library name: CutRun-SAMPLE_04
CutRun_H3K9me3_WT_Kidney_merged.bw


title: CutRun_H3K9me3_L2HGDHoe_Kidney_rep1

description:
Library name: CutRun-SAMPLE_06
CutRun_H3K9me3_L2HGDHoe_Kidney_merged.bw


title: U251, antiNRF1, siAATF, ChIP-seq, rep1

description: Library name: ChIP_U251_antiNRF1_siAATF_rep1

data_processing:
Samples were aligned to hg19 with Bowtie2 and peaks were called with MACS2 available in the nf-core/atac-seq pipeline (v2.0) with Nextflow (v. 24.10.4.5934), using default parameters.
Assembly: hg19
Supplementary files format and content: bigwig and broadpeaks files

extract_protocol:
ChIP-sequencing (ChIP-seq) experiment was performed following the ChIPmentation protocol in duplicate using a specific NRF-1 Antibody (Diagenode, C15200013).
The final libraries were controlled on TapeStation system (Agilent) and sequenced on a NovaSeq 6000 System (Illumina, CA) using 2 x 100 cycles in paired-end mode.

value: siAATF

value: NRF-1 Antibody (Diagenode, C15200013)


title: HFD4

description: Library name: Sample 3


title: CutRun_H3K9me3_WT_Kidney_rep1

description:
Library name: CutRun-SAMPLE_01
CutRun_H3K9me3_WT_Kidney_merged.bw


title: Xenograft Sample, rep1

description: FFPE Spatial Transcriptomics Sequencing

source_name: Intramuscular tumor of a PDX-derived ASPS cell line


title: iCLIP2, E14, Sam68, day10, rep4

city: Barcelona

first: Elias

last: Bechara

address: Dr Aiguader 88

country: Spain

institute: CRG

description:
Library name: iCLIP2_Sam68_day10_rep4
iCLIP2

data_processing:
Processing pipeline racoon_clip (v2.0.11): experiment_type: "iCLIP2" quality_filter_barcodes: True adapter_cycles: 1 adapter_trimming: True morePureclipParameters: "-iv 'chr1;chr2;chr3;'"; The racoon_clip pipeline performed the following steps.
Quality control: FastQC (v0.12.1), MultiQC (v.1.31)
Quality filter: reads are  filtered for a Phred score >= 10 inside the UMI and barcode positions (1-15)
Adapter and 5'UMI trimming: Flexbar (v3.5.0) with non-default parameters: flexbar --zip-output GZ --adapters AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG  --adapter-trim-end RIGHT --adapter-error-rate 0.1 --adapter-min-overlap 1 --adapter-cycles 1 --min-read-length 15
3'UMI trimming: Flexbar (v3.5.0) with non-default parameters: flexbar --zip-output GZ -y 3 --min-read-length 15
Mapping: STAR (v2.7.11a) with non-default parameters: STAR --sjdbGTFfile gencode.vM14.annotation.gtf --sjdbOverhang 135 --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --outSAMattributes All --outReadsUnmapped Fastx --outSJfilterReads Unique --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate (output: SAMPLE.mapped.bam)
Duplicate removal: UMI-tools (v1.1.6) with non-default parameters: umi_tools dedup -I SAMPLE.bam -S SAMPLE.duprm.bam --extract-umi-method read_id --method unique
Convert bed file format using BEDTools (v2.31.1) bedtools bamtobed. (output: SAMPLE.bed)
Remove reads directly mapped at chromosome ends (their upstream/crosslink position does not exist): awk 'BEGIN{{OFS="\t"}} FNR==NR{{chr_len[$1]=$2; next}} !(($6=="+" && $2==0) || ($6=="-" && $3==chr_len[$1]))' GRCh38.p14.genome.fa.fai SAMPLE.bed > SAMPLE.bed.tmp && mv SAMPLE.bed.tmp SAMPLE.bed
Shifting one base upstream; BEDTools (v2.31.1): bedtools shift -m 1 -p -1 -i stdin -g GRCh38.p14.genome.fa.fai | sort -k1,1 -k2,2n -k3,3n > SAMPLE.shifted1bp.bed
BED to bedGraph considering only 5' end positions;  BEDTools (v2.31.1): bedtools genomecov -bg -strand + -5 -i SAMPLE.shifted1bp.bed -g GRCh38.p14.genome.fa.fai > SAMPLE.duprm.plus.bedgraph | LC_COLLATE=C sort -k1,1 -k2,2n -k3,3n; bedtools genomecov -bg -strand - -5 -i SAMPLE.shifted1bp.bed -g GRCh38.p14.genome.fa.fai | LC_COLLATE=C sort -k1,1 -k2,2n -k3,3n > SAMPLE.duprm.minus.bedgraph
bedGraph to bigWig using bedGraphToBigWig of the UCSC tool suite (v472)
Merge of bam files from replicates; samtools (v1.22.1)
Peakcalling on merged replicates; PureCLIP (v1.3.1) -iv 'chr1;chr2;chr3;'
Definition of binding sites; BindingSiteFinder (Bioconductor R package, v2.6.0) BSFind function: non-default parameters bsSize = 5, cutoff.geneWiseFilter = 0, repro.nReps = 3, repro.cutoff = 0.05, overlaps.geneAssignment = “remove”, overlaps.TranscriptRegions = “hierarchy”, overlaps.rule.TranscriptRegions = transcript_region_hierarcy, transcript_region_hierarcy = c(“UTR5”, "INTRON", "CDS", “UTR3”)
Assembly: GRCm38.p5 (Gencode release M14)
Supplementary files format and content: bigWig files containing the genomic coordinates and duplicate removed counts of uniquely mapped crosslinks for each replicate separated by strand.
Supplementary files format and content: bed files containing the defined reproducible binding sites (removed crosslinking background) per day (0, 3, 10)
Library strategy: iCLIP

source_name: mESC, eb

growth_protocol: All cell lines used in this study were grown at 37°C, 5% CO2 and tested for mycoplasma contamination. E14 mouse embryonic stem cells (mESCs) were obtained from the Tissue Engineering Unit of the Center for Genomic Regulation (Supplementary Table S1). For maintenance culture cell were seeded onto plates pre-coated with 0,1% gelatin (ES-006-B, Millipore) under feeder-free conditions at a density of 1,5X104 cells/cm2 in knock-out DMEM supplemented with 15% embryonic stem cells qualified FBS (16141079, Gibco), 1% Penicillin/Streptomycin (15140122, Gibco), 1% L-Glutamine (25030081, Gibco), 1% Sodium Pyruvate (11360070, Gibco), 1% non-essential amino acids (NEAA) (11140068, Gibco), 50mM β-mercaptoethanol (31350010, Invitrogen), Leukemia Inhibitory Factor (LIF) (ESG-1106, Millipore) and the 2i inhibitors GSKi (CHIR-99021, Tocris) and MEKi (PD0325901, Tocris). For differentiation culture, the medium was supplemented with 10% FBS. For normal maintenance, cells were passed any other day by dissociating them with the ACCUTASE® cell detachment solution (SCR005, Millipore). To set up the embryoid body (EB) assay, E14 mESCs suspended in KO-DMEM supplemented with 10% serum at a density of 5x104 cells/ml were seeded in hanging drops of 20 μl onto the surface of a 150 mm culture plate filled with PBS to avoid evaporation of the drops. After three days, the hanging drops containing the EBs were flushed and seeded on a low attachment plate. For the generation of EBs collected at day 10 (d10) of differentiation, E14 mESCs were directly plated into Corning spheroid microplates (Corning) at a density of 5 × 10⁴ cells/ml. Medium was replenished during differentiation, and EBs were collected at d10 for downstream experiments. In order to derive cardiomyocytes, at day three (d3) the cells were seeded on a gelatin pre-coated 96 multi-well plate and cultured for a maximum of 8 more days.

extract_protocol:
Crosslinked cells were lysed in 50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% Igepal CA-630, 0.1% SDS, and 0.5% sodium deoxycholate, supplemented with protease inhibitors, and sonicated using a Bioraptor Pico (Diagenode; 3 cycles, 30 sec ON/OFF). Subsequently, RNA was digested with RNase I (1:200 dilution, AM2295, Thermo Fisher Scientific) to generate RNA fragments of 50–200 nt
SAM68 protein immunoprecipitation was performed using a SAM68-specific antibody (SAM68 Polyclonal Antibody; PA5-96507; Thermo Fisher Scientific) conjugated to Dynabeads Protein G beads (10004D, Thermo Fisher Scientific) for 1 h at 4°C. Protein–RNA complexes were visualized using 3'-end pCp-IR750 RNA labeling of 10% of the beads, while the remaining 90% underwent the first adapter ligation with the pre-adenylated L3-App oligo (Supplementary Table 2S). After SDS-PAGE and transfer to a nitrocellulose membrane, RNA–protein complexes were isolated from the membrane, treated with proteinase K (Merck), and RNA was extracted using the RNA Clean and Concentrator-5 kit (Zymo, R1016). cDNA was generated by reverse transcription using SuperScript III (18080085, Thermo Fisher Scientific); reverse transcription terminates at the crosslinked site, generating truncated cDNAs. A second adapter, containing a unique molecular identifier (UMI) and an experimental barcode, was ligated to the 3′ OH of the cDNAs. MyONE beads were used to purify the cDNA, and the library was subsequently subjected to two rounds of PCR amplification (6 and 15 cycles, respectively) and size-selected using ProNex chemistry (NG2001, Promega). Library quality was assessed using a TapeStation system with the High Sensitivity D1000 Kit.

treatment_protocol: mESCs were collected at d0 or allowed to differentiate in EBs as previously described (above) and collected at d3 and d10 of differentiation. Cells were irradiated with UVC light at 254nm using a CL-1000 UV crosslinker (Bio-Link 254, Vilber) at a dose of 150 mJ/cm² to induce covalent protein–RNA crosslinking. For the d3 and d10 time points, EBs were dissociated into single cells using TrypLE™ Express Enzyme (1X), no phenol red (Thermo Fisher Scientific), prior to crosslinking to ensure uniform UV exposure.

value: mESC, eb

value: day 10


title: iCLIP2, E14, Sam68, day10, rep5

description:
Library name: iCLIP2_Sam68_day10_rep5
iCLIP2


title: U138, siControl, rep1

description: Library name: RNA_U138_siControl_rep1


title: PROseq_Myxo_L2hgdh_Rep3

data_processing:
Raw files were demultiplexed using bcl2fastq v2.19 with adatpter removal.
Low-quality bases were removed from 3’ end using cutadapt, with min. length 30b. UMI was extracted using UMI-tools 1.1.5
PE reads were aligned to a concatenated genome (mm10 + dm6) using Bowtie 2.4.5 with --very--sensitive option. reads with MAPQ ≥ 20 were retained
After the strand of R1 reads were swapped, a single base incorporated during nuclear run-on assays was removed from the 3’ end. Coverage of the 3’ end of the resulting R1 reads was calculated using bedtools genomecov and converted to bw.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: PRO-seq

molecule: nuclear RNA

extract_protocol:
performed according to the qPRO-seq protocol (Judd, J. et al. https://doi.org/10.1101/2020.05.18.102277). Briefly, 2.5 million mESC nuclei and 1% spike-in fly S2 nuclei were used for nuclear run-on assay with biotin-11-UTP/CTP/ATP/CTP, 40 µM each (Revvity). REV3 adaptor was ligated to 3’ end of fragmented nuclear RNA using T4 RNA ligase 1 (NEB). 5’ hydroxyl repair with PNK (NEB), decapping with RppH (NEB), and REV5 ligation to 5’ end of RNA were performed on Dynabeads MyOne Streptavidin C1 beads (ThermoFisher).
cDNA was generated using SuperScript III (ThermoFisher). Libraries were amplified using Phusion Hot Start II (ThermoFisher) with 15 PCR cycles and sequenced on NextSeq 2000 (Illumina)

value: mESC

value: mouse embryonic stem cells

value: myxothiazol 500nM


title: PROseq_Myxo_EV_Rep2

value: EV


title: U251, antiNRF1, siControl, ChIP-seq, rep1

description: Library name: ChIP_U251_antiNRF1_siControl_rep1

value: siControl


title: hPSC-CMs(WTC-11), Day30 cultured in HPLM/B27, bio rep 3

city: Madison

first: Xiaotian

last: Zhang

state: WI

address: 1415 Engineering Hall

department: Chemical and Biological Engineering

institute: University of Wisconsin-Madison

description:
Library name: Mtb-HB-3
Column name in TPM all samples. csv:Mtb-HB-3

data_processing:
STAR version 2.5.3a
Trimmed sequence reads were aligned to the Homo sapiens hg38 genome with decoy sequences using STAR version 2.5.3a
Gene-level transcript abundances were calculated using featureCounts v2.0.3
TPM values are next calculated in R v4.1.3
Assembly: hg38
Supplementary files format and content: csv files include TPM values for each sample

source_name: Cardiomyocytes

growth_protocol: Day 16 hPSC-CMs differentiated by GiWi protocol were cultured in different media conditions with media change every 3 days until Day 30 in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from Trizol-collected samples by tri-phasic extraction followed by purification and concentration with Zymo Direct-zol MiniPrep Plus columns (Zymo – R2072) per kit instructions (including on-column DNAse treatment)
Sequencing libraries were constructed from 500 ng of total RNA per sample using the Takara SMARTer Stranded Total RNA Kit – HI Mammalian

treatment_protocol: Day 16 hPSC-CMs were cultured in standard RPMI/B27, 5mM glucose RPMI/B27, and HPLM/B27 for 2 weeks until Day30.

value: Cardiomyocytes

value: Day30 HPLM/B27


title: PROseq_Myxo_EV_Rep1


title: iCLIP2, E14, Sam68, day10, rep2

description:
Library name: iCLIP2_Sam68_day10_rep2
iCLIP2


title: PROseq_Myxo_L2hgdh_Rep1


title: Input_L2HGDH_Myxo_K9me3

extract_protocol:
AS described in Lee TI, Johnstone SE & Young RA (Nat Proc 2006, 1:729-748). Fixation was performed using 1% paraformaldehyde (PFA). For H3K9me3 ChIP-Seq, chromatin sonication was performed using 20% duty cycle, 140 peak intensity power, and 200 cycles per burst for 10 min. Successively, the pulldown of chromatin was carried out overnight at 4 °C using the specific antibodies: H3K9me3 (CST, catalog no. 13969). Drosophila spike-in chromatin and antibody were added as internal normalization control following manufacturer’s instructions (ActiveMotif, catalog no. 53083, 61686). Reverse cross-linking was performed at 65 °C overnight while shaking at 1,200 rpm. Immunoprecipitated DNA was extracted using the ChIP-DNA purification kit (Zymo Research, catalog no. D5205) following the manufacturer’s instructions.
Libraries were made using the KAPA HTP Biosystems Library Prep kit (Roche, KK8234) using Perkin Elmer Unique Dual Index Barcodes for NextSeq 2000.


title: iCLIP2, E14, Sam68, day10, rep1

description:
Library name: iCLIP2_Sam68_day10_rep1
iCLIP2


title: iCLIP2, E14, Sam68, day10, rep3

description:
Library name: iCLIP2_Sam68_day10_rep3
iCLIP2


title: Input_EV_Myxo_K9me3


title: hPSC-CMs(WTC-11), Day30 cultured in HPLM/B27, bio rep 4

description:
Library name: Mtb-HB-4
Column name in TPM all samples. csv:Mtb-HB-4


title: PROseq_Myxo_L2hgdh_Rep2


title: hPSC-CMs(WTC-11), Day30 cultured in HPLM/B27, bio rep 2

description:
Library name: Mtb-HB-2
Column name in TPM all samples. csv:Mtb-HB-2


title: EV_Myxo_rep2_k9me3

value: H3K9me3 (CST, catalog no. 13969)


title: iCLIP2, E14, Sam68, day3, rep4

description:
Library name: iCLIP2_Sam68_day3_rep4
iCLIP2

value: day 3


title: L2HGDH_Myxo_rep2_K9me3


title: hPSC-CMs(WTC-11), Day30 cultured in HPLM/B27, bio rep 1

description:
Library name: Mtb-HB-1
Column name in TPM all samples. csv:Mtb-HB-1


title: L2HGDH_Myxo_rep1_K9me3


title: EV_Myxo_rep1_k9me3


title: hPSC-CMs(WTC-11), Day30 cultured in low-glucose (5mM) RPMI/B27, bio rep 4

description:
Library name: Mtb-RB-4
Column name in TPM all samples. csv:Mtb-RB-4

value: Day30 5mM glucose RPMI/B27


title: iCLIP2, E14, Sam68, day3, rep3

description:
Library name: iCLIP2_Sam68_day3_rep3
iCLIP2


title: iCLIP2, E14, Sam68, day3, rep5

description:
Library name: iCLIP2_Sam68_day3_rep5
iCLIP2


title: plasmid, PE150, Sample_ID HI

city: Stanford

first: Haiqing

last: Xu

state: CA

address: 327 Campus Drive

department: Biology

institute: Stanford University

description: Library name: mCherry-SIIN-Cre-BCsgPOOL

library_source: other

data_processing:
Paired-end reads were processed with regular expressions to identify the gRNA and clonal barcodes. When identifying guide sequences, we strictly required a perfect match with the designed sequences.
For the same gRNA, when we encountered low-frequency clonal barcodes within a 1-hamming distance of high-frequency clonal barcodes, we attributed them to sequencing or PCR errors. These low-frequency barcodes were merged with barcodes of higher frequencies
After extracting barcode and gRNA information, we converted the read counts associated with clonal tumors into absolute neoplastic cell numbers. This conversion was accomplished by normalizing the reads of the clonal tumor to the number of reads of the "spike-in" benchmark cell lines added to each sample prior to lung lysis and DNA extraction
Assembly: GRCm39
Supplementary files format and content: Immunoediting_tumor.txt: This file contains processed Tuba-seq data for tumor sample. It includes information on mouse genotype, sex, ID, vector type.sample weight, tumor growth duration, tumor gRNA, tumor clonal barcodes, and tumor size.
Supplementary files format and content: Plasmid_summary.txt: This file contains processed plasmid library information for all three vector type. It includes read count read each gRNA.

molecule: other

organism: Escherichia coli

source_name: plasmid

extract_protocol:
Lung lobes were harvested from mice and weighed. Then, each lung was placed into 10mL of digestion buffer containing 100 mM NaCl, 20 mM Tris, 10 mM EDTA, 0.5% SDS, and 100uL of 20mg/mL Proteinase K as previously described. 5x10^5 cells from each of the three benchmark cell lines was added to each sample. Tissue was cut into small pieces and incubated at 55ºC overnight. Once tissue was digested the next day, DNA was extracted from 5mL of each digested sample by phenol-chloroform extraction.
Q5 Hot Start High-Fidelity 2x Master Mix (New England Biolabs, M0494X) was used to amply the barcode-gRNA region. 32ug of gDNA was used as template, split over 8 reactions with a final volume of 100uL each

value: plasmid


title: plasmid, PE150, Sample_ID NI

description: Library name: UbC-Cre-BCsgPOOL


title: hPSC-CMs(WTC-11), Day30 cultured in low-glucose (5mM) RPMI/B27, bio rep 3

description:
Library name: Mtb-RB-3
Column name in TPM all samples. csv:Mtb-RB-3

value: WT


title: hPSC-CMs(WTC-11), Day30 cultured in low-glucose (5mM) RPMI/B27, bio rep 2

description:
Library name: Mtb-RB-2
Column name in TPM all samples. csv:Mtb-RB-2


title: brain, RNAi, DMAP1, r6

city: Philadelphia

first: Dong

last: Li

state: PA

address: 3615 Civic Center BLVD

institute: Children's Hospital of Philadelphia

description: Library name: Samples 9

data_processing:
aligned onto the BDGP6 fly reference genome
features were counted by featureCounts
DESeq2 was then used to detected differentially expressed genes
Assembly: BDGP6 fly reference genome
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Drosophila melanogaster

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen)
RNA libararies were prepared using Illumina TruSeq Library Prep Kit folloiwing manufacturer's protocols

value: brain

value: DMAP1 RNAi


title: brain, RNAi, DMAP1, r5

description: Library name: Samples 8


title: plasmid, PE150, Sample_ID MI

description: Library name: UbC-mCherry-Cre-BCsgPOOL


title: brain, RNAi, DMAP1, r3

description: Library name: Samples 6


title: iCLIP2, E14, Sam68, day3, rep1

description:
Library name: iCLIP2_Sam68_day3_rep1
iCLIP2


title: iCLIP2, E14, Sam68, day3, rep2

description:
Library name: iCLIP2_Sam68_day3_rep2
iCLIP2


title: WT_Met32-MNase R2

city: Montreal

first: Adnane

last: Sellam

address: 5000, rue Bélanger

institute: Universite de Montreal

description:
Library name: WT_Met32-MNase R2
Met32_treat_pileup.bw

data_processing:
*library strategy: Chromatin endogenous cleavage (ChEC)-seq
Sequencing reads were filtered with fastp version 0.23.2
Sequences were trimmed to remove adapters using TRIMMOMATIC with options “TRAILING:30”. Filtered reads were mapped to the reference genome sequence of strain SC5314 with STAR version 2.7.9a
For RNA-seq, the number of reads mapping on each of the genes was calculated by featurecount version 2.0.1. Differential gene expression was calculated with DESeq2 version 1.26.0.
For the CheC-seq experiment, reads were mapped to the C. albicans genome (Candida_albicans_SC5314 assembly 22) using Bowtie2 with “-q --phred33 --no-unal” options. Peaks were determined using MACS2 algorithm with options “-BAM -nomodel-extsize 200-keep-dup all.”.
Assembly: Reference genome of the C. albicans SC5314 strain assembly 22 were used (http://www.candidagenome.org).
Supplementary files format and content: RNA-seq processed data files contain the raw counts for each sequencing experiment.
Supplementary files format and content: ChEC-seq peak bw files

organism: Candida albicans

growth_protocol: For RNA-seq experiment, C. albicans overnight cultures grown in MDM medium were diluted to an OD600 of 0.1 in 250 ml of fresh MDM medium and grown at 30°C under agitation (200 rpm) to logarithmic phase (OD600 = 0.6). For the ChEC-seq experiment, overnight cultures of C. albicans MNase-tagged and free MNase strains (control strain) were diluted to a starting OD600 of 0.1 in 50 ml MDM medium and grown at 30°C to an OD600 of 0.8.

extract_protocol:
Total RNA was extracted using an RNAeasy purification kit (Qiagen) and glass bead lysis in a Biospec Mini 24 bead-beater. For ChEC-seq, DNA was purified using the MasterPure Yeast DNA Purification Kit (Epicentre) following the manufacturer’s instructions and resuspended in 50µl of 10 mM Tris-HCl buffer (pH 8.0)
The NEBNext UltraTM II RNA Library Prep Kit for Illumina was used to construct the RNA-seq library. For the ChEC-seq, sequencing libraries were prepared using the KAPA HyperPrep Kits.

treatment_protocol: For RNA-seq experiment, cultures first washed thrice with sterile water and transferred to different media including: SLD, SLD supplemented with different sulfur sources: 50µM mixture of Methionine/Cysteine (Met/Cys), 50µM ammonium sulfate ((NH4)2SO4), 50µM taurine and 80µM GSH, and incubated at 30°C for 1 hour. For the ChEC-seq experiment, exponentially cells were pelleted and washed twice with PBS buffer and grown for an additional hour in SLD medium.

value: Yeast cells

value: SN148- MET32/MET32::Mnase

value: 1h in SLD medium


title: hPSC-CMs(WTC-11), Day30 cultured in standard RPMI/B27, bio rep 4

description:
Library name: Mtb-CTRL-4
Column name in TPM all samples. csv:Mtb-CTRL-4

value: Day30 Standard RPMI/B27


title: iCLIP2, E14, Sam68, day0, rep5

description:
Library name: iCLIP2_Sam68_day0_rep5
iCLIP2

value: mESC

value: day 0


title: iCLIP2, E14, Sam68, day0, rep4

description:
Library name: iCLIP2_Sam68_day0_rep4
iCLIP2


title: hPSC-CMs(WTC-11), Day30 cultured in low-glucose (5mM) RPMI/B27, bio rep 1

description:
Library name: Mtb-RB-1
Column name in TPM all samples. csv:Mtb-RB-1


title: brain, RNAi, DMAP1, r4

description: Library name: Samples 7


title: WT_Met32-MNase R1

description:
Library name: WT_Met32-MNase R1
Met32_treat_pileup.bw


title: hPSC-CMs(WTC-11), Day30 cultured in standard RPMI/B27, bio rep 2

description:
Library name: Mtb-CTRL-2
Column name in TPM all samples. csv:Mtb-CTRL-2


title: hPSC-CMs(WTC-11), Day30 cultured in standard RPMI/B27, bio rep 3

description:
Library name: Mtb-CTRL-3
Column name in TPM all samples. csv: Mtb-CTRL-3


title: mESC_L2HGDH_Myxothiazol_rep4

description: Library name: mESC_L2HGDH_Myxothiazol_rep4

data_processing:
Indexed samples were demultiplexed to fastq files with bcl-convert v3.10.5.
Reads were  trimmed of 10 base pairs from the 5’ end with TrimGalore! v0.4.3 to remove primer and adapter sequences.
Sequence alignment to the GRCm38/mm10 reference genome and methylation extraction ignoring one base at the 3′ end (after reviewing the M-bias plots) were performed with Bismark v0.16.3.
Assembly: GRCm38
Supplementary files format and content: Bismark tab-delimited "coverage" files for cytosines in CpG context with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

source_name: Mouse Embryonic Stem Cells

extract_protocol:
DNA was isolated with the AllPrep DNA/RNA Micro Kit (Qiagen, catalog no. 80284) according to the manufacturer’s protocol.
Libraries for Illumina-based sequencing were prepared with the Pico Methyl-Seq Library Prep Kit (Zymo Research).

treatment_protocol: Mouse embryonic stem cells (mESCs) were treated with 500 nM myxothiazol for 16 hours.

value: Mouse Embryonic Stem Cells

value: Wild-Type

value: Myxothiazol

tag: transfection


title: brain, RNAi, DMAP1, r2

description: Library name: Samples 5


title: WT_Mnase-free R2

description:
Library name: WT_Mnase-free R2
control.bw


title: hPSC-CMs(WTC-11), Day30 cultured in standard RPMI/B27, bio rep 1

description:
Library name: Mtb-CTRL-1
Column name in TPM all samples. csv: Mtb-CTRL-1

value: Cardiomyocytes


title: brain, RNAi, DMAP1, r1

description: Library name: Samples 4


title: WT_Mnase-free R1

description:
Library name: WT_Mnase-free R1
control.bw


title: iCLIP2, E14, Sam68, day0, rep3

description:
Library name: iCLIP2_Sam68_day0_rep3
iCLIP2


title: iCLIP2, E14, Sam68, day0, rep2

description:
Library name: iCLIP2_Sam68_day0_rep2
iCLIP2


title: iCLIP2, E14, Sam68, day0, rep1

description:
Library name: iCLIP2_Sam68_day0_rep1
iCLIP2


title: mESC_L2HGDH_Myxothiazol_rep3

description: Library name: mESC_L2HGDH_Myxothiazol_rep3


title: met32 (gsh)_SLD+Glutathione_R1

description:
Library name: met32 (gsh)_SLD+Glutathione_R1
raw count_met32_GSH.txt

data_processing:
Sequencing reads were filtered with fastp version 0.23.2
Sequences were trimmed to remove adapters using TRIMMOMATIC with options “TRAILING:30”. Filtered reads were mapped to the reference genome sequence of strain SC5314 with STAR version 2.7.9a
For RNA-seq, the number of reads mapping on each of the genes was calculated by featurecount version 2.0.1. Differential gene expression was calculated with DESeq2 version 1.26.0.
For the CheC-seq experiment, reads were mapped to the C. albicans genome (Candida_albicans_SC5314 assembly 22) using Bowtie2 with “-q --phred33 --no-unal” options. Peaks were determined using MACS2 algorithm with options “-BAM -nomodel-extsize 200-keep-dup all.”.
Assembly: Reference genome of the C. albicans SC5314 strain assembly 22 were used (http://www.candidagenome.org).
Supplementary files format and content: RNA-seq processed data files contain the raw counts for each sequencing experiment.
Supplementary files format and content: ChEC-seq peak bw files

value: 1h in SLD medium + glutathione


title: MC38-Leiden

city: Pittsburgh

first: Warren

last: Shlomchik

address: 5051 Centre Ave

institute: University of Pittsburgh

description:
Library name: MC38L
Whole Genome Sequencing

data_processing:
Alignment to GRCm38 with BWA
GATK MarkDuplicates
GATK Mutect 2 (exonic regions only)
GATK FilterMutectCalls
Ensembl Variant Effect Predictor
Assembly: GRCm38
Supplementary files format and content: Variant Call File containing exonic region variants

source_name: Colon

growth_protocol: MC38 cells were cultured in RPMI medium supplemented with 10% fetal bovine serum, 1mM sodium pyruvate, non-essential amino acids, 2mM L-glutamine, 10mM HEPES and 50mM beta-mercaptoethanol.

extract_protocol:
Total DNA was extracted from cells using Qiagen DNEasy tissue kits
Illumina Nextera DNA prep

value: Colon

value: Epithelial cancer cell line


title: mESC_EV_Myxothiazol_rep4

description: Library name: mESC_EV_Myxothiazol_rep4

value: EV


title: met32 (gsh)_SLD_R2

description:
Library name: met32 (gsh)_SLD_R2
raw count_met32_GSH.txt


title: WT2

city: Saint Louis

first: Shitong

last: Wu

state: MO

address: 660 S Euclid Avenue

institute: Washington University in St. Louis

description:
Library name: sample.wt2
column name in all.gene_counts.tsv

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom Python demultiplexing program with a maximum of one mismatch in the indexing read.
RNAseq reads were then aligned to the Ensembl release 76 primary assembly with Spliced Transcripts Alignment to a Reference version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5. Aligned gene counts were processed using the DESeq2 package with R (version 4.1) 5.
Assembly: mm39
Supplementary files format and content: Tab-separated values (TSV) file containing raw gene-level read counts. Each row corresponds to an Ensembl gene identifier with associated annotation (Entrez ID, gene symbol, biotype, description, etc.). Columns correspond to individual biological samples, and cell values represent the number of uniquely aligned reads assigned to each gene (as generated by Subread:featureCounts).

source_name: Small Intestine Lamina Propria

growth_protocol: ILC3s were sort-purified from small intestine lamina propria of WT and Lingo4-/- mice.

extract_protocol:
Small intestine or colon was harvested from mice, cleaned of Payer’s patches and/or luminal content and opened lengthwise. The tissue was incubated in Hank’s balanced salt solution (HBSS) with HEPES, 10% bovine calf serum (BCS) and 5 mM EDTA for 20 minutes on the rotator, followed by vigorous vortexing, and another round of incubation in HBSS, and vortexing. For LP cells extraction, the tissue was further digested in 10% RPMI medium containing 1mg/mL collagenase IV (MilliporeSigma) for 40 min with vigorous shaking at 37C. LP leukocytes were purified by density gradient centrifugation using a 40% and 70% Percoll (Cytiva) gradient.
Total RNA was extracted using RNeasy Mini Kits (Qiagen) per manufacturer’s instructions. Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.  Library preparation was performed using SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer’s protocol.  Samples were indexed, pooled, and sequenced on an Illumina NovaSeq 6000.

value: Small Intestine Lamina Propria

value: primary cells

value: WT


title: hPSC-CMs(WTC-11), Day16 differentiation baseline cultured in standard RPMI/B27, bio rep 1

description:
Library name: Mtb-d0-1
Column name in TPM all samples. csv: Mtb-d0-1

value: Day16 Standard RPMI/B27


title: met32 (gsh)_SLD+Glutathione_R2

description:
Library name: met32 (gsh)_SLD+Glutathione_R2
raw count_met32_GSH.txt

value: Yeast cells


title: hPSC-CMs(WTC-11), Day16 differentiation baseline cultured in standard RPMI/B27, bio rep 4

description:
Library name: Mtb-d0-4
Column name in TPM all samples. csv: Mtb-d0-4


title: met32 (gsh)_SLD_R1

description:
Library name: met32 (gsh)_SLD_R1
raw count_met32_GSH.txt

value: 1h in SLD medium


title: mESC_L2HGDH_Myxothiazol_rep1

description: Library name: mESC_L2HGDH_Myxothiazol_rep1


title: WT1

description:
Library name: sample.wt1
column name in all.gene_counts.tsv


title: hPSC-CMs(WTC-11), Day16 differentiation baseline cultured in standard RPMI/B27, bio rep 3

description:
Library name: Mtb-d0-3
Column name in TPM all samples. csv: Mtb-d0-3


title: WT3

description:
Library name: sample.wt3
column name in all.gene_counts.tsv


title: mESC_EV_Myxothiazol_rep3

description: Library name: mESC_EV_Myxothiazol_rep3


title: mESC_L2HGDH_Myxothiazol_rep2

description: Library name: mESC_L2HGDH_Myxothiazol_rep2


title: WT (SN250-gsh)_SLD_R2

description:
Library name: WT (SN250-gsh)_SLD_R2
raw count_met32_GSH.txt


title: mESC_EV_Myxothiazol_rep1

description: Library name: mESC_EV_Myxothiazol_rep1


title: mESC_EV_Myxothiazol_rep2

description: Library name: mESC_EV_Myxothiazol_rep2


title: KO1

description:
Library name: sample.ko1
column name in all.gene_counts.tsv


title: RNA-Seq, CUX1 Overexpression, Replicate 2

first: Ryan

middle: Patrick

last: Calhoun

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

description:
Library name: CUX1_OE2
CUX1_OE2

data_processing:
The raw paired-end Fastq files were trimmed using the tool TrimGalore (version 0.6.5) with default parameters and paired option enabled.
The trimmed files were then aligned to the GRCh38 (version 104) genome using kallisto (version 0.46.1) with the default parameters of the kallisto quant command for paired-end data.
Kallisto output files were read into R (version 4.3.0) and differentially expressed genes were generated by EdgeR (version 4.0.2)
Assembly: hg38
Supplementary files format and content: Raw counts in a comma-separated file for GFP and CUX1 OE samples
Supplementary files format and content: Raw counts in a comma-separated file for CTRL and CUX1 KO samples

source_name: adipose

extract_protocol:
Tissue RNA was harvested using RNeasy according to the manufacturer’s protocol.
Extracted cellular total RNA samples were sequenced by NovaSeq 6000 PE150 (Novogene)

value: adipose

value: primary adipocyte

value: CUX1 Overexpression

value: differention cocktail


title: WT (SN250-gsh)_SLD+Glutathione_R1

description:
Library name: WT (SN250-gsh)_SLD+Glutathione_R1
raw count_met32_GSH.txt


title: RNA-Seq, CUX1 Overexpression, Replicate 3

description:
Library name: CUX1_OE3
CUX1_OE3


title: RNA-Seq, CUX1 Overexpression, Replicate 1

description:
Library name: CUX1_OE1
CUX1_OE1


title: Myxothiazol_L2hgdh_4

description: Library name: NC_21_139

data_processing:
Data were processed using nf-core/rnaseq v3.12.0 of the nf-core collection of workflows. The pipeline was executed using Nextflow v23.10.1 and singularity v3.8.1 with the public nu_genomics configuration. Transcriptome alignment and gene-level count assignment were performed using the STAR/Salmon method with the GRCm38/mm10 genome as the reference.
Assembly: GRCm38
Supplementary files format and content: Raw counts from Salmon quant
Supplementary files format and content: Sample metadata

extract_protocol:
RNA was isolated with the AllPrep DNA/RNA Micro Kit (Qiagen, catalog no. 80284) according to the manufacturer’s protocol. The quantity and quality of the extracted RNA were assessed using TapeStation 4200 (Agilent).
mRNA libraries were prepared using NEBNext Ultra Kit with polyA selection (New England BioLabs, catalog nos. E7530 and E7490).

value: Mouse Embryonic Stem Cells

value: Wild-Type


title: WT4

description:
Library name: sample.wt4
column name in all.gene_counts.tsv


title: KO2

description:
Library name: sample.ko2
column name in all.gene_counts.tsv


title: hPSC-CMs(WTC-11), Day16 differentiation baseline cultured in standard RPMI/B27, bio rep 2

description:
Library name: Mtb-d0-2
Column name in TPM all samples. csv: Mtb-d0-2

value: Cardiomyocytes


title: RNA-Seq, GFP Overexpression, Replicate 3

description:
Library name: GFP3
GFP3

value: GFP Overexpression


title: WT (SN250-gsh)_SLD+Glutathione_R2

description:
Library name: WT (SN250-gsh)_SLD+Glutathione_R2
raw count_met32_GSH.txt

value: 1h in SLD medium + glutathione


title: RNA-Seq, GFP Overexpression, Replicate 2

description:
Library name: GFP2
GFP2


title: met32_SLD+taurine_R2

description:
Library name: met32_SLD+taurine_R2
raw count_met32_Taurine.txt

value: 1h in SLD+taurine medium


title: WT (SN250-gsh)_SLD_R1

description:
Library name: WT (SN250-gsh)_SLD_R1
raw count_met32_GSH.txt


title: HIF-1α overexpression

city: Chengdu

first: Xiaoli

last: Mu

address: No. 37 Guoxue Lane

institute: West China Hospital of Sichuan University

description:
Library name: B16F10Q
Column name in counts_anno.txt: B16F10Q

data_processing:
After using Cutadapt to filter out invalid sequences from the original data to obtain valid data (Clean Data), Hisat2 was used for reference genome alignment. Based on the Hisat2 alignment results, StringTie was used to quantify the genes in each sample.
Assembly: GRCm38.p6 (mm10)
Supplementary files format and content: gene_counts.txt.gz

growth_protocol: Perform standard digestion on normally passaged tumor cell line B16F10. After centrifugation, discard the cell supernatant. Resuspend the cell pellet in an appropriate volume of serum-free DMEM/F12 medium (Hyclone, USA) and count the cells. Transfer the cell suspension to a pre-filled culture dish containing 5-6 mL of serum-free basal medium (without exogenous growth factors), and gently mix using a figure-eight motion. Place the dish in a horizontal CO₂-tolerant shaker and incubate at 37°C, 5% CO₂ at 60-80 rpm. Monitor cell culture status daily, replacing or supplementing medium as needed based on cell density and growth, and adjust shaker speed accordingly to optimize conditions. All procedures must be performed under aseptic conditions with detailed documentation of culture parameters. After 7–10 days of shaking culture, assess tumor spheroid maturity using an inverted microscope. Select spheroids meeting experimental requirements based on size, morphology, and other criteria for subsequent studies.

extract_protocol:
RNA from the total sample was isolated and purified using TRIzol (thermofisher) according to the manufacturer's operating protocol. The quantity and purity of the total RNA were then quality controlled using a NanoDrop ND-1000, and RNA integrity was detected using a Bioanalyzer 2100; concentration >50 ng/μL, RIN value >7.0, and total RNA >1 μg met the requirements for downstream experiments.
Poly(A)+ mRNA was enriched from total RNA using oligo(dT) magnetic beads and fragmented at high temperature in the presence of divalent cations. The fragmented RNA was reverse transcribed into first-strand cDNA, followed by second-strand synthesis using DNA polymerase I and RNase H. During second-strand synthesis, dUTP was incorporated to generate strand-specific libraries. The double-stranded cDNA was end-repaired, A-tailed, and ligated to sequencing adapters. After size selection and purification, the second strand was digested using UDG, and the library was amplified by PCR. The final libraries (~300 bp insert size) were sequenced on the Illumina NovaSeq 6000 platform with paired-end 150 bp reads.

treatment_protocol: no

value: mouse skin melanoma

value: overexpression

value: NO


title: KO3

description:
Library name: sample.ko3
column name in all.gene_counts.tsv

value: Small Intestine Lamina Propria

value: primary cells


title: RNA-Seq, GFP Overexpression, Replicate 1

description:
Library name: GFP1
GFP1


title: Myxothiazol_L2hgdh_3

description: Library name: NC_21_138

value: Myxothiazol


title: KO4

description:
Library name: sample.ko4
column name in all.gene_counts.tsv


title: Myxothiazol_L2hgdh_1

description: Library name: NC_21_136


title: Myxothiazol_L2hgdh_2

description: Library name: NC_21_137


title: Untreated_L2hgdh_4

description: Library name: NC_21_135

value: Untreated


title: met32_SLD+taurine_R1

description:
Library name: met32_SLD+taurine_R1
raw count_met32_Taurine.txt

value: Yeast cells


title: shControl

description:
Library name: B5
Column name in counts_anno.txt: B5

value: WT


title: WT (SN250)_SLD+taurine_R1

description:
Library name: WT (SN250)_SLD+taurine_R1
raw count_met32_Taurine.txt


title: RNA-Seq, CUX1 Knockout, Replicate 3

description:
Library name: CUX1_KO3
CUX1_KO3

value: adipose

value: primary adipocyte

value: CUX1 Knockout


title: RNA-Seq, CUX1 Knockout, Replicate 2

description:
Library name: CUX1_KO2
CUX1_KO2

value: differention cocktail


title: Untreated_L2hgdh_3

description: Library name: NC_21_134

value: Mouse Embryonic Stem Cells

value: Wild-Type


title: HIF-1α knockdown

description:
Library name: B16F10
Column name in counts_anno.txt: B16F10

value: knockdown


title: WT_SLD+ammonium sulfate_R2

description:
Library name: WT_SLD+ammonium sulfate_R2
raw count_WT_Sulf starvation.txt

value: 1h in SLD medium + ammonium sulfate


title: WT (SN250)_SLD+taurine_R2

description:
Library name: WT (SN250)_SLD+taurine_R2
raw count_met32_Taurine.txt

value: 1h in SLD+taurine medium


title: dynamic suspension culture

description:
Library name: B4
Column name in counts_anno.txt: B4

value: mouse skin melanoma


title: RNA-Seq, Control, Replicate 3

description:
Library name: CTRL3
CTRL3

value: Wild Type


title: Untreated_L2hgdh_2

description: Library name: NC_21_133


title: WT_SLD+ammonium sulfate_R1

description:
Library name: WT_SLD+ammonium sulfate_R1
raw count_WT_Sulf starvation.txt


title: RNA-Seq, CUX1 Knockout, Replicate 1

description:
Library name: CUX1_KO1
CUX1_KO1


title: Pressure4

city: Kunming

first: Shuyun

last: Yang

address: Dianmian Street Num374

department: Department of Dermatology

institute: The Second Affiliated Hospital of Kunming Medical University

description: Library name: RIGHT_C4

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Ensembl release-112
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

source_name: ear

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: ear

value: Pressure


title: Untreated_L2hgdh_1

first: Navdeep

last: Chandel

address: 303 E. Superior Street

description: Library name: NC_21_132


title: Pressure3

description: Library name: RIGHT_C3


title: conventional three-dimensional culture

description:
Library name: B3
Column name in counts_anno.txt: B3

value: NO


title: Myxothiazol_EV_4

description: Library name: NC_21_127

value: Myxothiazol

value: EV


title: Myxothiazol_EV_3

description: Library name: NC_21_126


title: RNA-Seq, Control, Replicate 2

description:
Library name: CTRL2
CTRL2


title: D42, VDJ

first: Sorana

last: Morrissy

address: 3330 Hospital Dr NW

description:
Library name: scTCR_longPB__D42
VDJ (5' mRNA library)

data_processing:
GEX and VDJ(TCR) libraries were demultiplexed using cellranger mkfastq.
Demultiplexed data was processed using the cellranger multi pipeline using the Human-GCAR1 customized reference.
Assembly: customized reference (GRCh38/hg38 + GCAR1 construct sequences)
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: TCR-Seq

source_name: peripheral blood

extract_protocol:
Patient’s PBMCs samples were thawed and washed with warm DMEM + 10% FBS followed by automated cell count. Cells were resuspended in 1X PBS + 1% BSA on a range of 100-2,000 cells/μl. The number of cells loaded on the 10X Genomics Single Cell Chromium Controller was adjusted according to differences in samples concentrations aiming to achieve the highest targeted cell recovery number.
After the generation of the single cell gel beads (GEMs), captured cells were lysed and barcoded full-length cDNA from poly-adenylated mRNA was produced and amplified. An additional amplification was performed with primers specific to TCR constant regions prior to TCR library construction. GEX and TCR libraries were prepared according to the manufacturer’s protocols (10x Genomics Chromium Next GEM Single Cell V(D)J + 5′ Gene Expression).

value: peripheral blood

value: T cell

tag: library type

value: VDJ

tag: vdj

value: scTCR-seq D42


title: WT_SLD+Taurine_R2

description:
Library name: WT_SLD+Taurine_R2
raw count_WT_Sulf starvation.txt

value: Yeast cells

value: WT


title: Myxothiazol_EV_2

description: Library name: NC_21_125

value: Mouse Embryonic Stem Cells

value: Wild-Type


title: WT_SLD+Met/Cys_R2

description:
Library name: WT_SLD+Met/Cys_R2
raw count_WT_Sulf starvation.txt

value: 1h in SLD medium +equimolar mixture of methionine and cycteine


title: WT_SLD+Taurine_R1

description:
Library name: WT_SLD+Taurine_R1
raw count_WT_Sulf starvation.txt

value: 1h in SLD+taurine medium


title: RNA-Seq, Control, Replicate 1

description:
Library name: CTRL1
CTRL1

value: adipose

value: primary adipocyte

value: differention cocktail


title: Myxothiazol_EV_1

description: Library name: NC_21_124


title: WT_SLD+Met/Cys_R1

description:
Library name: WT_SLD+Met/Cys_R1
raw count_WT_Sulf starvation.txt


title: Pressure1

description: Library name: RIGHT_C1

value: ear

value: Pressure


title: D22, VDJ

description:
Library name: scTCR_longPB__D22
VDJ (5' mRNA library)

value: scTCR-seq D22


title: WT_SLD_R2

description:
Library name: WT_SLD_R2
raw count_WT_Sulf starvation.txt

value: 1h in SLD medium


title: Untreated_EV_4

description: Library name: NC_21_123

value: Untreated

value: EV


title: Pressure2

description: Library name: RIGHT_C2


title: Untreated_EV_2

description: Library name: NC_21_121


title: JIA9

type: RNA

city: Aurora

first: Kentaro

last: Yomogida

state: Colorado

address: 1775 Aurora Ct

department: Pediatrics

institute: University of Colorado

hyb_protocol: The Xenium Prime RNA probe set (10x Genomics) was hybridized overnight, ligated, and amplified using rolling circle amplification (10x Genomics protocol CG000760). All incubations are performed using reagents provided by 10x Genomics on a VeritiPro Thermocycler (Applied Biosystems). Autofluorescence was quenched and morphology stains were added, including nuclear, cytoplasmic, and membrane stains for improved cell segmentation (10x Genomics)

scan_protocol: Slides were then loaded onto the Xenium instrument for whole slide tissue overview scanning and region selection. Regions containing tissue were selected and the onboard cyclic decoding and imaging was initiated over a 72-120-hour period.

data_processing: Data was processed on the instrument after image acquisition, performing probe deconvolution, cell segmentation

label: Xenium probe set

source_name: synovium

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: FFPE tissue sections were dried in an oven, deparaffinized through a xylene gradient, and 6 de-crosslinked according to the manufacturer’s instructions (10x Genomics protocol CG000578 7 and CG000580).

value: synovium

tag: tissue preservation method

value: FFPE

tag: subject status

value: patients with juvenile idiopathic arthritis


title: Acne_Pressure2

description: Library name: LEFT_C2


title: D15, VDJ

description:
Library name: scTCR_longPB__D15
VDJ (5' mRNA library)

value: peripheral blood

value: T cell

value: VDJ

value: scTCR-seq D15


title: Acne_Pressure4

description: Library name: LEFT_C4


title: D28, VDJ

description:
Library name: scTCR_longPB__D28
VDJ (5' mRNA library)

value: scTCR-seq D28


title: JIA8


title: Untreated_EV_1

institute: Northwestern University

description: Library name: NC_21_120

value: Mouse Embryonic Stem Cells

value: Wild-Type


title: GCAR1_Product, VDJ

institute: University of Calgary

description:
Library name: scTCR_longPB__GCAR1_Product
VDJ (5' mRNA library)

value: GCAR1 product

value: scTCR-seq GCAR1_Product


title: Acne_Pressure1

description: Library name: LEFT_C1

value: ear


title: D08, VDJ

description:
Library name: scTCR_longPB__D08
VDJ (5' mRNA library)

value: scTCR-seq D08


title: mmKidney_2H-GLIS2-IP

city: Research Triangle Park

first: Anton

middle: M

last: Jetten

state: NC

address: 111 TW Alexander Drive

department: DIR

institute: NIEHS, NIH

data_processing:
Raw sequenced reads were filtered to remove any with mean base quality score < 20.
Adapters were removed by Cutadapt v1.12 (-a AGATCGGAAGAG -O 5 -q 0), then reads were filtered to retain only those with length at least 30nt.
Filtered and trimmed reads were mapped via Bowtie v1.2 with parameter "-m 1".
Duplicate mapped reads were removed via MarkDuplicates.jar (Picard tools v1.110) with flag "REMOVE_DUPLICATES=TRUE".
Peak calls were made by HOMER (v4.10.3) with parameters “-style factor -F 10 -L 8 -fdr 1e-10” then re-sized to 300bp centered on the called peak midpoints.  Peaks overlapping blacklist regions were filtered out.
For visualization purposes, uniquely-mapped non-duplicate reads were extended to the 200bp estimated fragment size via BEDTools v2.29.2 "slop -s -r 125 -l 0", converted to bedGraph via BEDTools v2.29.2 "genomecov -bg", scaled to 10 million fragments per sample, then converted to bigWig format via UCSC utility bedGraphToBigWig.
Read counts (extended to 200bp fragments) at peaks were collected via BEDTools v2.92.2 "coverage -counts".
Assembly: mm10
Supplementary files format and content: fragment counts at called peaks (tab-delimited text)
Supplementary files format and content: normalized depth tracks (bigWig)

source_name: kidney

growth_protocol: ChIP was performed with renal epithelial cells from Glis2-HA mice.

extract_protocol:
Immunoprecipitated chromatin was washed and ChIPed-DNA was eluted, reverse cross-linked, and DNA fragments purified using PCR purification kit form Qiagen.
NEXTflex DNA-Seq kit from PerkinElmer was used.

value: kidney

value: primary renal epithelial cell

value: HA antibody


title: Untreated_EV_3

description: Library name: NC_21_122

value: Untreated

value: EV


title: WT_SLD_R1

description:
Library name: WT_SLD_R1
raw count_WT_Sulf starvation.txt

value: Yeast cells

value: WT

value: 1h in SLD medium


title: Acne_Pressure3

description: Library name: LEFT_C3


title: JIA7

value: synovium

value: FFPE

value: patients with juvenile idiopathic arthritis


title: Acne4

description: Library name: LEFT_B4

value: Acne


title: Enriched_Apheresis, VDJ

description:
Library name: scTCR_longPB__Enriched_Apheresis
VDJ (5' mRNA library)

value: peripheral blood

value: T cell

value: apheresis product

value: VDJ

value: scTCR-seq Enriched_Apheresis


title: JIA5


title: JIA6


title: Acne3

description: Library name: LEFT_B3

value: ear


title: mmKidney_2H-GLIS2-input

value: kidney

value: primary renal epithelial cell


title: D42, GEX

description:
Library name: scRNA_longPB__D42
GEX (5' mRNA library)

data_processing:
GEX and VDJ(TCR) libraries were demultiplexed using cellranger mkfastq.
Demultiplexed data was processed using the cellranger multi pipeline using the Human-GCAR1 customized reference.
Assembly: customized reference (GRCh38/hg38 + GCAR1 construct sequences)
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

value: Peripheral blood mononuclear cell (PBMC)

value: GEX

tag: gex

value: scRNA-seq D42


title: High IRES,Cap MEP Replicate 3

city: Boston

first: Lai Ping

last: Wong

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital

description:
Mouse 1447
RNASeq_count.txt

data_processing:
RNASeq sequencing reads were mapped to reference genome mm10 with ENSEMBL annotation using STAR version 2.5.4a
RNASeq read counts for individual genes were produced using the unstranded count feature in HTSeq 0.9.1
Raw sequencing  data of CRISPRi are pre-processed by using MAGeCK to obtain the read counts for each sgRNA
Assembly: mm10
Supplementary files format and content: genes based raw counts of RNA-sequencing reads
Supplementary files format and content: CRISPRi raw sequencing  data are pre-processed by using MAGeCK to obtain the read counts for each sgRNA

source_name: Bone marrow

extract_protocol:
For RNA-Seq, full-length cDNA was prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing  (Takara Bio USA, Inc.)
For CRISPRi, genomic DNA was isolated using NucleoSpin Blood Maxi kit (Macherey-Nagel, 740950).
RNA-Seq libraries prepared using the Nextera XT DNA library preparation kit (Illumina)
CRISPRi sgRNA target regions were PCR amplified  with Illumina adaptors and indexes using Ultra II Q5 (NEB Biolabs, M0544X) and products were purified  with DNA Clean & Concentrator-100 (Zymo Research, D4030). sgRNA target regions (260-280bp) were further enriched by gel extraction (Qiagen, 28704) after running agarose gel
Smart-seq v4

value: Bone marrow

value: MEP

value: Translator


title: JIA4

value: synovium

value: FFPE


title: High IRES,Cap MEP Replicate 2

description:
Mouse 1446
RNASeq_count.txt


title: D15, GEX

description:
Library name: scRNA_longPB__D15
GEX (5' mRNA library)

value: scRNA-seq D15


title: JIA3

value: patients with juvenile idiopathic arthritis


title: Acne1

description: Library name: LEFT_B1

value: Acne


title: D28, GEX

description:
Library name: scRNA_longPB__D28
GEX (5' mRNA library)

value: peripheral blood

value: scRNA-seq D28


title: Acne2

description: Library name: LEFT_B2


title: JIA2


title: Control6

description: Library name: RIGHT_A3

value: Control


title: Control5

description: Library name: RIGHT_A2

value: ear


title: D08, GEX

description:
Library name: scRNA_longPB__D08
GEX (5' mRNA library)

value: scRNA-seq D08


title: D22, GEX

description:
Library name: scRNA_longPB__D22
GEX (5' mRNA library)

value: scRNA-seq D22


title: Control4

description: Library name: RIGHT_A1


title: High IRES,Cap MEP Replicate 1

description:
Mouse 1443
RNASeq_count.txt


title: GCAR1_Product, GEX

description:
Library name: scRNA_longPB__GCAR1_Product
GEX (5' mRNA library)

value: Peripheral blood mononuclear cell (PBMC)

value: GCAR1 product

value: scRNA-seq GCAR1_Product


title: Mid IRES,Cap MEP Replicate 3

description:
Mouse 1447
RNASeq_count.txt

value: Bone marrow


title: Mid IRES,Cap MEP Replicate 1

description:
Mouse 1443
RNASeq_count.txt

value: MEP


title: JIA1


title: Enriched_Apheresis, GEX

description:
Library name: scRNA_longPB__Enriched_Apheresis
GEX (5' mRNA library)

value: apheresis product

value: GEX

value: scRNA-seq Enriched_Apheresis


title: sci-RNA-seq3_Arabidopsis_Day9_Biological_Replicate_1_Technical_Replicate_1

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
Library name: Arabidopsis_Day9_Biological_Replicate_1_Technical_Replicate_1
sci-RNA-seq3

data_processing:
Demultiplexing, barcoded processing, and gene counting were preformed as described in https://github.com/JunyueC/sci-RNA-seq3_pipeline
Assembly: Arabidopsis TAIR10
Supplementary files format and content: Seurat object

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Plants were grown on vermiculite under well-watered conditions for 29 days, before being subject to drought stress

extract_protocol:
Frozen tissue from each time point was crushed using a bead bashing approach, and nuclei released from homogenate by resuspending in Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). The resulting suspension was passed through a 30-um filter.
Library construction was performed following the sci-RNA-seq3 workflow

value: leaf

tag: age

value: mature rosttes


title: Control2

description: Library name: LEFT_A2


title: Mid IRES,Cap MEP Replicate 2

description:
Mouse 1446
RNASeq_count.txt

value: Translator


title: Control1

description: Library name: LEFT_A1


title: Control3

description: Library name: LEFT_A3


title: Low IRES,Cap MEP Replicate 3

description:
Mouse 1447
RNASeq_count.txt


title: High IRES,Cap GMP Replicate 3

description:
Mouse 1447
RNASeq_count.txt

value: GMP


title: LZTR1-KO_ECT_6

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422
STAR version 2.7.8a was used to align the reads to the GRCh38 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in GRCh38 version 108
Assembly: GRCh38 version 108
Supplementary files format and content: Tab-delimited gene counts

source_name: Engineered conncetive tissue

extract_protocol:
Total RNA isolation using the NucleoSpin RNA kit (Macheray-Nagel)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Engineered conncetive tissue

value: iPSC-cardiac fibroblasts

value: untreated


title: Low IRES,Cap MEP Replicate 1

description:
Mouse 1443
RNASeq_count.txt


title: sci-RNA-seq3_Arabidopsis_Day5_to_Day8_Biological_Replicate_1_Technical_Replicate_1

description:
Library name: Arabidopsis_Day5_to_Day8_Biological_Replicate_1_Technical_Replicate_1
sci-RNA-seq3


title: LZTR1-KO_ECT_5


title: LZTR1-KO_ECT_4


title: Low IRES,Cap MEP Replicate 2

description:
Mouse 1446
RNASeq_count.txt


title: lymphocytes_gp_rep2

city: Freiburg

first: Thomas

last: Boehm

address: Stuebeweg 51

department: Developmental Immunology

description: Library name: 5L

data_processing:
Adapters were trimmed using cutadapt v4.9
Trimmed reads were aligned to the primary GRCm39 assembly from Ensembl using STAR 2.7.11b
Gene annotations were fetched from Ensembl (version 112)
Annotations of repeat elements were generated using RepeatMasker v4.1.5
RepeatMasker output was further processed and concatenated with the Ensembl GTF
Mapped reads were counted using featureCounts (subread 2.0.6, -p --countReadPairs -B -O -M –fraction)
Assembly: GRCm39 (primary assembly)
Supplementary files format and content: Tab-delimited text file containing raw counts for all samples

source_name: spleen

extract_protocol:
Total RNA was extracted from splenic lymphocytes (CD4+, CD8+, CD19+) of MHCI.GP+ and MHCI.GP- mice with TRI reagent (Sigma-Aldrich).
Libraries were prepared using the Illumina Stranded mRNA Prep Kit (Ligation). Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.

value: spleen

value: CD4+CD8+CD19+ lymphocytes


title: High IRES,Cap GMP Replicate 2

description:
Mouse 1446
RNASeq_count.txt


title: sci-RNA-seq3_Arabidopsis_Day0_to_Day4_Biological_Replicate_1_Technical_Replicate_1

description:
Library name: Arabidopsis_Day0_to_Day4_Biological_Replicate_1_Technical_Replicate_1
sci-RNA-seq3

source_name: Mature rosette leaves exposed to well-watered or drought conditions, Days 0 - 4 (Biological Replicate 1, Technical Replicate 1)


title: lymphocytes_gp_rep3

institute: Max Planck Institute for Immunobiology and Epigenetics

description: Library name: 6L