title: Aged caloric restriction, tumor-infiltrating CD8+ T cells, biological replicate 3

city: Kumamoto City

first: Yuichi

last: Oike

state: Kumamoto

address: 1-1-1 Honko, Chuo-Ku

department: Department of Molecular Genetics

country: Japan

institute: Kumamoto University

description:
Library name: AG_CR_3
Column name in gene_counts.xlsx: DK25028_09

data_processing:
Raw sequencing reads were trimmed using Trim Galore.
Trimmed reads were aligned to the mouse reference genome (GRCm38/mm10) using STAR.
Gene-level read counts were generated using featureCounts.
Assembly: GRCm38 (mm10)
Supplementary files format and content: gene_counts.xlsx contains gene-level raw read counts generated using featureCounts. Rows correspond to genes and columns correspond to individual RNA-seq samples.
Supplementary files format and content: Columns DK25028_01–DK25028_09 correspond to the individual RNA-seq samples listed in the SAMPLES section.

source_name: tumor

growth_protocol: Male C57BL/6N mice were purchased from CLEA (Japan) and maintained under specific pathogen-free conditions on a standard diet (CE-2, CLEA) with a 12 h light/12 h dark cycle at 22 ± 2°C and 40–80% relative humidity. Young mice were maintained under ad libitum feeding. Aged mice were maintained under either ad libitum feeding or long-term caloric restriction.

extract_protocol:
Tumor tissues were minced into 2–3 mm3 pieces and digested with 1 mg/mL collagenase D and 0.5 mg/mL dispase for 30 min at 37°C. Cell suspensions were filtered through a 100-μm cell strainer, treated with red blood cell lysis buffer, and tumor-infiltrating CD8+ T cells were isolated using CD8a MicroBeads (Miltenyi Biotec). Total RNA was extracted from isolated CD8+ T cells.
RNA quality was assessed using the Agilent 2100 Bioanalyzer and Agilent RNA6000 Pico Kit. Libraries were prepared using the QuantSeq 3′ mRNA-Seq V2 Library Prep Kit (FWD) with UDI (Lexogen) and sequenced on an Illumina NextSeq 500 platform to generate 75 bp single-end reads.

treatment_protocol: C57BL/6N male mice were randomly assigned to ad libitum (AL) or caloric restriction (CR) groups. CR mice received 70% of the average food intake of AL mice. Young (5-month-old) AL, aged (20-month-old) AL, and aged (20-month-old) CR mice were subcutaneously injected with 5 × 10^5 MC38 colorectal adenocarcinoma cells. Tumors were collected 21 days after transplantation.

value: tumor

value: tumor-infiltrating CD8+ T cells

value: aged

value: caloric restriction


title: CD4 T cell donor 3 edit replicate 6

status: Public on Jul 26 2026

type: SRA

city: Oxford

first: Joseph

last: Hamley

address: John Radcliffe Hospital/Headley Way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
Library name: cd4_don3_edit_6
Raw junction counts & normalized bigwig per capture point

library_source: genomic

data_processing:
The raw fastq file is processed to reconstruct a single read from the paired end sequencing. This is then mapped to the 800bp sequence surrounding the capture oligonucleotide using the non-stringent aligner BLAT. This allows the reads to be cut into ‘slices’ depending on whether they align to the sequence around the capture site. This strategy allows ligation junctions in the read to be determined with base pair accuracy. The resulting fastq file is aligned to the genome using bowtie.
The resulting fastq file is aligned to the genome using bowtie.
Assembly: hg38
Supplementary files format and content: BigWig of data from multiple viewpoints
Library strategy: Capture-C

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

growth_protocol: Jurkat cells, clone E6-1 (ATCC TIB-152) were culture in ATCC modified RPMI (Gibco A1049101) with 10% foetal bovine serum (Sigma) at 370C with 5% CO2, Isolated CD4+ cells were cultured at 1x106 cells per ml in Immunocult-XF T cell expansion medium (Stemcell 10981) supplemented with 10ng/ml human IL-2 (Invitrogen X). For edited T cell MCC samples, T cells were nucleofected post activation and allowed to cycle for 3 days before collection.

extract_protocol:
Qiagen DNeasy blood and tissue kit
7-10 µg of each 3C library was sonicated to a mean fragment size of 200 bp using a Covaris S220 Focussed Ultrasonicator (1-3 cycles of 60s: duty cycle 10%; intensity 5; cycles per burst 200). The library size was assessed using an Agilent TapeStation (DNA 1000) and an Ampure XP (Beckman Coulter) bead clean-up was performed once the sample had been adequately sonicated. To maximise library complexity three aliquots, each containing 2 µg sonicated 3C library, were processed in parallel for each sample to add sequencing adaptors. NEB Ultra II reagents were used following the standard protocol with the following modifications: first, additional adapter was added into the ligation reactions (7.5 µl rather than 2.5 µl); no size selection was performed (Ampure XP bead clean ups were always performed with a sample:bead ratio of 1:1.8) and the final PCR to add indices was amplified in triplicate from each aliquot using the Herculase II PCR kit (Agilent) to maximise DNA yield. All parallel library preparations and PCR reactions were pooled for each reaction. CHIP libraries were prepared and analyzed as previously reported in Hanssen LLP. et al., 2017.

treatment_protocol: 25ul/ml of Immunocult Human CD3/CD28/CD2 T cell activator for 60 hours before collection.

tag: tissue

value: Blood

tag: cell type

value: CD4 T cell

tag: genotype

value: CRISPR Edited

tag: treatment

value: Activated


title: CD4 T cell donor 3 edit replicate 5

description:
Library name: cd4_don3_edit_5
Raw junction counts & normalized bigwig per capture point


title: Aged caloric restriction, tumor-infiltrating CD8+ T cells, biological replicate 2

description:
Library name: AG_CR_2
Column name in gene_counts.xlsx: DK25028_08

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

value: WT

tag: age


title: H3K4me3_CT_mESC_Gabpa_12h_dTAG_rep2

city: Beijing

first: Hang

last: Yang

state: Beijing

address: No.1 West Beichen Road,Chaoyang District

country: China

institute: CAS

description: Library name: H3K4me3_CT_mESC_Gabpa_12h_dTAG_rep2

data_processing:
For RNA-seq, raw reads were trimmed with Trim Galore v0.6.7, followed by mapping to the mm39 genome using STAR v2.7.11a. Gene expression levels were calculated by RSEM v1.3.1, and differential expression analysis was performed using the DESeq2 R package v1.44.0.  For SLAM-seq, BCL files containing raw sequencing data were converted to FASTQ format. Adapters were trimmed from raw reads using Cutadapt v3.5 through Trim Galore v0.6.7. SLAM-seq analyses were performed using the SLAMdunk pipeline v0.4.3, which includes mapping, read filtering, SNP variant calling, conversion counts and rate calculation. The significantly differentially expressed genes were called using DESeq2 v1.44.0 with size factors estimated on corresponding total mRNA reads for global normalization. For ATAC-seq and CUT&Tag, the raw reads were first trimmed of the adaptors with Trim Galore v0.6.7 and then aligned to the mm39 genomes using Bowtie2 v2.4.4 with the following parameters: --no-unal --no-mixed --no-discordant. Low mapping quality reads, unmapped reads and duplicated reads were removed using Picard v2.21.4 and SAMtools v1.13. For the INTS11 CUT&Tag, the mapped reads were further filtered to retain only proper paired reads with fragment length between 48 and 158 bp. For the histone modification CUT&Tag, the mapped reads were further filtered to retain only proper paired reads with fragment length at least 178 bp. Read coverages over the genome were estimated by bamCoverage from deepTools v3.5.1 with the following parameters: --binSize 20 --minMappingQuality 30 --scaleFactor 1 --normalizeUsing RPKM.
Assembly: mm39
Supplementary files format and content: tab-delimited txt files contain gene-level reads counts for each sample; bigWig files contain ATAC-seq and CUT&Tag signals.
Library strategy: CUT&Tag

source_name: cell line

growth_protocol: The B6 mESCs were maintained in DMEM supplemented with 15% foetal bovine serum (FBS), 100 U/mL penicillin-streptomycin, 2 mM L-Glutamine, 1 mM sodium pyruvate, 0.084 mM 2-mercaptoethanol, 1x MEM NEAA, 1,000 IU/mL LIF, 0.5 μM PD0325901, and 3 μM CHIR99021 at 37ºC with 5% CO2.

extract_protocol:
For RNA-seq, RNA was isolated with TRIzol. For SLAM-seq, the 4sU-labeled RNA was isolated using a 1:1 volume of RNA XP magnetic beads. After 10 mins incubation at room temperature, the beads were washed twice with 200 μL 80% freshly prepared ethanol on the magnetic stand and the dried beads pellets were resuspended in 7 μL RNase-free water. For ATAC-seq and CUT&Tag, DNA was purified using the SPRI beads.
For RNA-seq, libraries were prepared according to the Fast RNA-seq Lib Prep Kit V2 with 0.2 μg RNA following the manufacturer's protocols. For SLAM-seq, alkylated RNA was used for 3'-end polyA RNA sequencing library preparation with Smart-seq2 according to the manufacturer's protocol. For ATAC-seq, mESCs cells were digested with adapter-loaded Tn5 in the tagmentation buffer (33 mM Tris-Acetate, 66 mM K-Acetate, 10 mM Mg-Acetate,16% DMF, 0.02% Digitonin) for 30 mins at 37 °C, and the reaction was stopped by stop buffer (100 mM Tris pH 8.0, 100 mM NaCl, 0.4% SDS and 40 μg/mL Proteinase K) and incubated overnight at 55 °C. 25% Tween-20 was added to quench SDS. Sequencing libraries were prepared with NEBNext High-Fidelity 2x PCR Master Mix. The PCR product was purified using a 1:1.6 volume ratio of SPRI beads. For CUT&Tag, libraries were performed using the Hyperactive Universal CUT&Tag Assay Kit following the manufacturer's protocols.

treatment_protocol: Cells were treated with 500 nM dTAG-13 for 1, 2, 4 and12 hours, and the corresponding control cells were treated with DMSO. Nascent RNA was labeled with 500 μM 4-thiouridine for SLAM-seq.

value: cell line

tag: cell line

value: mESCs

value: GabpadTAG/dTAG

value: treated with dTAG13 for 12 hours


title: Aged caloric restriction, tumor-infiltrating CD8+ T cells, biological replicate 1

description:
Library name: AG_CR_1
Column name in gene_counts.xlsx: DK25028_07


title: CD4 T cell donor 3 edit replicate 4

description:
Library name: cd4_don3_edit_4
Raw junction counts & normalized bigwig per capture point


title: H3K4me3_CT_mESC_Gabpa_12h_dTAG_rep1

description: Library name: H3K4me3_CT_mESC_Gabpa_12h_dTAG_rep1


title: Aged ad libitum, tumor-infiltrating CD8+ T cells, biological replicate 3

description:
Library name: AG_AL_3
Column name in gene_counts.xlsx: DK25028_06

value: ad libitum feeding


title: Aged ad libitum, tumor-infiltrating CD8+ T cells, biological replicate 2

description:
Library name: AG_AL_2
Column name in gene_counts.xlsx: DK25028_05


title: Aged ad libitum, tumor-infiltrating CD8+ T cells, biological replicate 1

description:
Library name: AG_AL_1
Column name in gene_counts.xlsx: DK25028_04


title: H3K4me3_CT_mESC_Gabpa_12h_DMSO_rep2

description: Library name: H3K4me3_CT_mESC_Gabpa_12h_DMSO_rep2

value: treated with DMSO for 12 hours


title: Young ad libitum, tumor-infiltrating CD8+ T cells, biological replicate 3

description:
Library name: YA_AL_3
Column name in gene_counts.xlsx: DK25028_03

value: young


title: H3K4me3_CT_mESC_Gabpa_12h_DMSO_rep1

description: Library name: H3K4me3_CT_mESC_Gabpa_12h_DMSO_rep1


title: CD4 T cell donor 3 edit replicate 2

description:
Library name: cd4_don3_edit_2
Raw junction counts & normalized bigwig per capture point


title: Young ad libitum, tumor-infiltrating CD8+ T cells, biological replicate 2

description:
Library name: YA_AL_2
Column name in gene_counts.xlsx: DK25028_02


title: CD4 T cell donor 3 edit replicate 1

description:
Library name: cd4_don3_edit_1
Raw junction counts & normalized bigwig per capture point


title: H3K4me3_CT_mESC_Gabpa_1h_dTAG_rep2

description: Library name: H3K4me3_CT_mESC_Gabpa_1h_dTAG_rep2

value: treated with dTAG13 for 1 hour


title: Young ad libitum, tumor-infiltrating CD8+ T cells, biological replicate 1

description:
Library name: YA_AL_1
Column name in gene_counts.xlsx: DK25028_01

value: tumor


title: HEK293 Minocycline polysome profiling Heavy polysome fraction replicate 3

city: San Diego

first: Khalyd

last: Clay

state: CA

address: 10550 N. Torry Pines. Rd.

country: USA

institute: Scripps Research

description:
Library name: M_P3
HEK293 polysome profiling minocycline heavy-polysome fraction replicate 3. Processed matrix HEK293_polysome_control_fraction_MRL_matrix.tsv covers control fraction percentages, fraction-enrichment classes, polyEN, and MRL; recompute_HEK293_polysome_MRL.R recomputes MRL from the matrix.

data_processing:
Single-end reads were processed as polysome-fraction RNA-seq libraries. Aligned reads were counted with featureCounts against ERCC92_merged_CRCh38.99.gtf using exon features and gene_id attributes; libraries were treated as single-end and unstranded. ERCC spike-in behavior was used as a normalization QC layer.
Remote GEO upload subfolder: PolysomeProfiling
The raw FASTQ upload includes all 18 polysome-fraction libraries.
The primary processed file is HEK293_polysome_control_fraction_MRL_matrix.tsv; it contains gene-level control monosome, light-polysome, and heavy-polysome fraction values, percent-of-total distributions, fraction-enrichment bins, polyEN, and deposited MRL_Ctr values.
The supplementary R script recompute_HEK293_polysome_MRL.R recomputes MRL from the deposited matrix using MRL = (1*A + 2.5*F + 6*P)/(A + F + P), averaged across the three control replicates.
Assembly: GRCh38
Supplementary files format and content: HEK293_polysome_control_fraction_MRL_matrix.tsv: tab-delimited quantitative gene-level control fraction and MRL matrix. Rows are genes; columns include Ensembl gene IDs, symbols, fraction-normalized counts, percent distributions, fraction-enrichment classifications, polyEN, and MRL_Ctr.
Supplementary files format and content: recompute_HEK293_polysome_MRL.R: lightweight base-R reviewer script that reads HEK293_polysome_control_fraction_MRL_matrix.tsv and writes recomputed replicate-level and mean control MRL values.

source_name: HEK293 (ATCC CRL-1573)

growth_protocol: HEK293 cells were grown in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin under standard mammalian cell-culture conditions.

extract_protocol:
Cytoplasmic lysates were separated by sucrose-gradient polysome profiling into monosome, light-polysome, and heavy-polysome fractions. ERCC spike-ins were added after fractionation and before RNA extraction from each fraction.
RNA from each polysome fraction was converted into Illumina sequencing libraries and sequenced as single-end 75 nt reads on an Illumina NextSeq 500 instrument.

treatment_protocol: Cells were treated for 12 h with DMSO vehicle control or 100 uM minocycline before polysome profiling.

value: HEK293 (ATCC CRL-1573)

value: Minocycline; compound:minocycline; dose:100 uM; duration:12 h

tag: batch


title: Eye-skin, filaggrin-deficient (ft/ft), rep 1

status: Public on Jul 27 2026

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

description: Library name: 291-XX-6

data_processing:
The CellRanger Pipeline (10X Genomics) was used to align reads and generate count matrices.”
Assembly: GRCm38
Supplementary files format and content: count matrix

source_name: skin

growth_protocol: ft/ftMyD88 /-  mice were generated as an in-house cross between a spontaneous loss-of-function point mutation in filaggrin (ft/ft) and MyD88 deficient (MyD88-/-) mice on a BALB/c background. All mouse strains were bred and maintained under the same specific pathogen-free conditions.

extract_protocol:
Protocol Overview: gentleMACS Octo Dissociator for Isolation of Cells from FFPE [https://cdn.10xgenomics.com/image/upload/v1721078231/support-documents/CG000632_DemonstratedProtocol_SamplePrep_from__FFPETissueSections_RevD.pdf]
Tissue Sections;  https://cdn.10xgenomics.com/image/upload/v1722287750/support-documents/CG000527_Chromium_FixedRNAProfiling_MultiplexedSamples_UserGuide_Rev_F.pdf

value: skin

value: skin cells

value: filaggrin-deficient


title: SPT_303_C4_E_R3

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description:
Library name: Sample 82
raw cell lysate and Illumina NextSeq 2081

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.23.2
Alignment was performed using STAR v2.7.10b
Gene counts were performed with qCount in the QuasR R package v1.38.0
Normalization was performed with DESeq2 v1.38.0
Assembly: Biospyder Human Whole Transcriptome Gene Set
Supplementary files format and content: 260722_count_table_GEO.tsv is a genes by samples count matrix of raw counts from the TempO-Seq data alignments.

source_name: liver tumor associated with chronic hepatitis C

growth_protocol: Cryopreserved differentiated HepaRG cells (Biopredic International, Saint-Grégoire, France) were cultivated according to the manufacturer’s protocol. Differentiated HepaRG cells were thawed and seeded into collagen-coated wells at a density of approximately 0.072 x 10e6 viable cells per well (i.e. 100 μL of the cell suspension per well) in 96-well plates, using HepaRG Thawing/Plating/General Purpose Medium 670 (ADD670C, Biopredic International, Saint-Grégoire, France). After 24h, the media were changed to HepaRG Maintenance Medium 620 (ADD620C, Biopredic International, Saint-Grégoire, France) for cell maintenance. Cells were incubated for 7 days at 37C, 5% CO2 and saturating humidity.

extract_protocol:
Cell lysates were used directly for TempO-Seq library building.
TempO-Seq® gene expression analysis was conducted on exposed and control HepaRG cell lysates. Libraries were prepared in a 96-well plate format using the TempO-Seq® Human Whole Transcriptome Panel reagent kit (BioSpyder Technologies, Carlsbad, CA, USA), following the manufacturer’s protocol. Human Brain Total RNA and qPCR Human Reference Total RNA (Takara Bio, CA, USA) were included as positive assay controls and a no-lysate control (1X TempO-Seq® R Lysis Buffer only) was included as a negative assay control (two replicates per control). In brief, 2 µl cell lysates were hybridized with the targeted detector oligo (DO) probe mix in 1X TempO-Seq® R Lysis Buffer for 10 min at 70C followed by a temperature gradient with a ramp rate of 0.5C/min to 45C over a 50 min period, followed by a nuclease digestion at 37C for 90 min to remove excess, unbound, or incorrectly bound DOs enzymatically. Ligation of the DO pairs bound to adjacent target sequences was then completed with a 60 min incubation at 37C, immediately followed with a 15 min enzyme denaturation at 80C to generate a pool of amplification templates. All amplification templates (i.e., 10 µl of ligated DOs) were transferred to its corresponding well of the 96-well PCR Pre-Mix and Primers plate. Amplification proceeded with a CFX96 Real-Time PCR Detection System (Bio-Rad, Mississauga, ON, Canada) to attach a unique sequence tag and the sequencing adaptors to each sample using the following PCR program settings: 37C for 10 min, 95C for 2 min; 6 cycles of 95C for 30 sec, 54C for 30 sec, 72C for 120 sec; 16 cycles of 95C for 30 sec; 72C for 2 min; 72C for 1 min. The TempO-Seq® libraries were pooled (5 µl of all 96 samples) and purified using the Macherey-Nagel NucleoSpin® Gel and PCR Clean-Up kit (Clontech Laboratories Inc., Bethlehem, PA, USA), according to the manufacturer’s instructions for PCR cleanup with three modifications outlined in the TempO-Seq® Assay User Guide. The pooled, purified TempO-Seq® libraries were sequenced using a NextSeq® 2000 High Output flow cell (v2 kit, 75 cycles) on an Illumina NextSeq® 2000 Sequencing platform (Illumina, San Diego, CA, USA).

treatment_protocol: At day 7, cells were exposed in triplicate to 5 concentrations of test chemical and refreshed with test chemical in HepaRG Induction Medium 640 (ADD640C, Biopredic International, Saint-Grégoire, France) daily for 72 hours (i.e., 3-day repeat exposures; 0 h, 24 h, 48 h). Cells were exposed to trichostatin A ( 0.018811, 0.056433, 0.1693, 0.5079, 1.5237 µM), panobinostat (0.001468, 0.004403, 0.01321, 0.03963, 0.084 µM), valproic acid (0.100478, 0.301433, 0.9043, 2.7129, 3.038 µM), mocetinostat (0.177222, 0.531667, 1.595, 2.5, 3.9 µM), apicidin (0.041722, 0.125167, 0.3755, 0.5, 0.86 µM), tacedinaline (1.143333, 3.43, 10.29, 30.87, 44 µM), scriptaid  (4.94, 14.82, 44.46, 60, 94.5 µM), vorinostat (0.404778, 1.214333, 3.643, 10.929, 23.5 µM). After 72 h exposure, cells were used to generate cell lysates for gene expression analysis (n = 3 per treatment group per assay for TempO-Seq®).

value: HepaRG

value: liver progenitor cells

tag: chemical shortname

value: SPT

tag: chemical longname

value: scriptaid

tag: dose

tag: well

tag: dose group

tag: plate

value: E

tag: index

value: TCAGTACAT

value: GACGCGTTA

tag: group

tag: replicate

tag: chemical type

value: test

tag: cas-nr

tag: batch nr_heparg


title: GBM43 intracranial xenografts, vehicle control, sample 1

city: San Francsico

first: Sixuan

last: Pan

state: California

institute: UCSF

description:
Library name: ctrl-1
PIP-seq

library_source: transcriptomic single cell

data_processing:
Perturb dataset: Cell Ranger (v6.1.2) was used to align reads to mm10, count UMIs, and assign sgRNAs, while deMULTIplex2 was used to demultiplex MULTI-seq sample hashes. Seurat SCTransform v2 normalization and QC filtering retained only cells with correct dual-sgRNA capture and adequate knockdown. Differential expression was performed with DElegate (DESeq2 pseudoreplicates), followed by fgsea-based pathway analysis. Perturbation signatures were visualized using LDA and UMAP, and interaction modeling between gene perturbations and drug treatment was performed using Theil-Sen regression and random forest-based feature importance.  Xeno dataset: FASTQs were processed with PIPseeker for alignment to a combined human–mouse reference, droplet calling, and UMI matrix generation. Human tumor cells were identified by >85% human read mapping. Subsequent analyses were performed in Seurat using QC filtering, SCTransform v2 normalization, and Scanorama integration. Cell states were assigned with Neftel et al. signatures, and differential gene expression and GSEA were performed to characterize drug-specific transcriptional programs.
Assembly: Perturb dataset: mm10  Xeno dataset: GRCh38
Supplementary files format and content: Feature Barcode Market Exchange Matrices

molecule: polyA RNA

source_name: brain

extract_protocol:
Perturb datasest: SB28 glioma cells expressing dCas9-KRAB were transduced with a dual-sgRNA CRISPRi library, FACS-sorted, treated with MEK inhibitor, SHP2 inhibitor, or vehicle for five days, then collected by trypsinization. Single-cell suspensions were labeled using MULTI-seq lipid barcodes through sequential incubation with anchor, barcode, and co-anchor oligos, washed in BSA-PBS, pooled, and loaded onto the 10x Chromium Controller for droplet partitioning.  Xeno dataset: Tumors from GBM43 intracranial xenografts were surgically harvested after in vivo drug treatment, mechanically minced, and enzymatically dissociated using the Papain Dissociation System to generate a single-cell suspension. The dissociated cells were filtered through a 70-µm strainer, centrifuged, washed in PBS, and prepared on ice for downstream PIPseq single-cell RNA-sequencing.
Perturb dataset: Dual-sgRNA constructs were cloned with direct-capture tags and used to generate the CRISPRi perturbation pool. Single-cell 3′ transcriptome and sgRNA-capture libraries were constructed using the 10x Genomics Chromium Next GEM Single Cell 3′ v3.1 kit with Feature Barcoding. MULTI-seq barcode libraries were amplified separately from cDNA supernatant after the SPRI cleanup step. All libraries were sequenced on an Illumina NovaSeq X.  Xeno dataset: Single-cell suspensions were processed using the Fluent BioSciences PIPseq T20 3′ Single Cell RNA Kit (v3.0), following the manufacturer’s workflow for barcoding, reverse transcription, amplification, and library preparation. Completed libraries were sequenced on an Illumina NovaSeq X to generate paired-end FASTQ files for downstream processing.

treatment_protocol: Vehicle (DMSO), selumetinib (MEK inhibitor), or RMC-4550 (SHP2 inhibitor)

tag: tissue

value: brain

tag: cell type

value: glioblastoma

tag: genotype

value: Vehicle (DMSO)


title: Eye-skin, filaggrin-deficient (ft/ft), rep 3

description: Library name: 291-XX-8

tag: cell line


title: HEK293 Minocycline polysome profiling Heavy polysome fraction replicate 1

description:
Library name: M_P1
HEK293 polysome profiling minocycline heavy-polysome fraction replicate 1. Processed matrix HEK293_polysome_control_fraction_MRL_matrix.tsv covers control fraction percentages, fraction-enrichment classes, polyEN, and MRL; recompute_HEK293_polysome_MRL.R recomputes MRL from the matrix.

tag: treatment

tag: batch


title: SPT_330_C4_E_R2

description:
Library name: Sample 81
raw cell lysate and Illumina NextSeq 2080

value: liver tumor associated with chronic hepatitis C

tag: chemical shortname

tag: chemical longname

value: TAAGGTAGC

value: AATTCGGAA


title: H3K4me3_CT_mESC_Gabpa_1h_dTAG_rep1

description: Library name: H3K4me3_CT_mESC_Gabpa_1h_dTAG_rep1

value: cell line

value: mESCs

value: GabpadTAG/dTAG

value: treated with dTAG13 for 1 hour


title: CD4 T cell donor 3 promoter replicate 5

description:
Library name: cd4_don3_promoter_5
Raw junction counts & normalized bigwig per capture point

value: Blood

value: CD4 T cell

value: WT

value: Activated


title: H3K4me3_CT_mESC_Gabpa_1h_DMSO_rep2

description: Library name: H3K4me3_CT_mESC_Gabpa_1h_DMSO_rep2

value: treated with DMSO for 1 hour


title: HEK293 Minocycline polysome profiling Monosome fraction replicate 1

description:
Library name: M_M1
HEK293 polysome profiling minocycline monosome fraction replicate 1. Processed matrix HEK293_polysome_control_fraction_MRL_matrix.tsv covers control fraction percentages, fraction-enrichment classes, polyEN, and MRL; recompute_HEK293_polysome_MRL.R recomputes MRL from the matrix.

value: HEK293 (ATCC CRL-1573)

value: Minocycline; compound:minocycline; dose:100 uM; duration:12 h


title: H3K4me3_CT_mESC_Gabpa_1h_DMSO_rep1

description: Library name: H3K4me3_CT_mESC_Gabpa_1h_DMSO_rep1


title: HEK293 Minocycline polysome profiling Light polysome fraction replicate 1

description:
Library name: M_F1
HEK293 polysome profiling minocycline light-polysome fraction replicate 1. Processed matrix HEK293_polysome_control_fraction_MRL_matrix.tsv covers control fraction percentages, fraction-enrichment classes, polyEN, and MRL; recompute_HEK293_polysome_MRL.R recomputes MRL from the matrix.


title: CD4 T cell donor 3 promoter replicate 3

description:
Library name: cd4_don3_promoter_3
Raw junction counts & normalized bigwig per capture point


title: CD4 T cell donor 3 promoter replicate 4

description:
Library name: cd4_don3_promoter_4
Raw junction counts & normalized bigwig per capture point


title: HEK293 Minocycline polysome profiling Light polysome fraction replicate 3

description:
Library name: M_F3
HEK293 polysome profiling minocycline light-polysome fraction replicate 3. Processed matrix HEK293_polysome_control_fraction_MRL_matrix.tsv covers control fraction percentages, fraction-enrichment classes, polyEN, and MRL; recompute_HEK293_polysome_MRL.R recomputes MRL from the matrix.


title: HEK293 Minocycline polysome profiling Light polysome fraction replicate 2

description:
Library name: M_F2
HEK293 polysome profiling minocycline light-polysome fraction replicate 2. Processed matrix HEK293_polysome_control_fraction_MRL_matrix.tsv covers control fraction percentages, fraction-enrichment classes, polyEN, and MRL; recompute_HEK293_polysome_MRL.R recomputes MRL from the matrix.


title: HEK293 Control polysome profiling Heavy polysome fraction replicate 3

description:
Library name: C_P3
HEK293 polysome profiling vehicle control heavy-polysome fraction replicate 3. Processed matrix HEK293_polysome_control_fraction_MRL_matrix.tsv covers control fraction percentages, fraction-enrichment classes, polyEN, and MRL; recompute_HEK293_polysome_MRL.R recomputes MRL from the matrix.

value: Control; compound:DMSO vehicle; dose:vehicle; duration:12 h


title: CD4 T cell donor 3 promoter replicate 2

description:
Library name: cd4_don3_promoter_2
Raw junction counts & normalized bigwig per capture point


title: HEK293 Control polysome profiling Heavy polysome fraction replicate 2

description:
Library name: C_P2
HEK293 polysome profiling vehicle control heavy-polysome fraction replicate 2. Processed matrix HEK293_polysome_control_fraction_MRL_matrix.tsv covers control fraction percentages, fraction-enrichment classes, polyEN, and MRL; recompute_HEK293_polysome_MRL.R recomputes MRL from the matrix.


title: CD4 T cell donor 3 promoter replicate 1

description:
Library name: cd4_don3_promoter_1
Raw junction counts & normalized bigwig per capture point


title: HEK293 Control polysome profiling Heavy polysome fraction replicate 1

description:
Library name: C_P1
HEK293 polysome profiling vehicle control heavy-polysome fraction replicate 1. Processed matrix HEK293_polysome_control_fraction_MRL_matrix.tsv covers control fraction percentages, fraction-enrichment classes, polyEN, and MRL; recompute_HEK293_polysome_MRL.R recomputes MRL from the matrix.


title: HEK293 Control polysome profiling Monosome fraction replicate 3

description:
Library name: C_M3
HEK293 polysome profiling vehicle control monosome fraction replicate 3. Processed matrix HEK293_polysome_control_fraction_MRL_matrix.tsv covers control fraction percentages, fraction-enrichment classes, polyEN, and MRL; recompute_HEK293_polysome_MRL.R recomputes MRL from the matrix.


title: HEK293 Control polysome profiling Monosome fraction replicate 2

description:
Library name: C_M2
HEK293 polysome profiling vehicle control monosome fraction replicate 2. Processed matrix HEK293_polysome_control_fraction_MRL_matrix.tsv covers control fraction percentages, fraction-enrichment classes, polyEN, and MRL; recompute_HEK293_polysome_MRL.R recomputes MRL from the matrix.


title: CD4 T cell donor 3 rs4409785 replicate 6

description:
Library name: cd4_don3_rs4409785_6
Raw junction counts & normalized bigwig per capture point


title: HEK293 Control polysome profiling Monosome fraction replicate 1

description:
Library name: C_M1
HEK293 polysome profiling vehicle control monosome fraction replicate 1. Processed matrix HEK293_polysome_control_fraction_MRL_matrix.tsv covers control fraction percentages, fraction-enrichment classes, polyEN, and MRL; recompute_HEK293_polysome_MRL.R recomputes MRL from the matrix.


title: INTS11_CT_mESC_Gabpa_12h_DMSO_rep1

description: Library name: INTS11_CT_mESC_Gabpa_12h_DMSO_rep1

value: treated with DMSO for 12 hours


title: HEK293 Control polysome profiling Light polysome fraction replicate 3

description:
Library name: C_F3
HEK293 polysome profiling vehicle control light-polysome fraction replicate 3. Processed matrix HEK293_polysome_control_fraction_MRL_matrix.tsv covers control fraction percentages, fraction-enrichment classes, polyEN, and MRL; recompute_HEK293_polysome_MRL.R recomputes MRL from the matrix.


title: HEK293 Control polysome profiling Light polysome fraction replicate 2

description:
Library name: C_F2
HEK293 polysome profiling vehicle control light-polysome fraction replicate 2. Processed matrix HEK293_polysome_control_fraction_MRL_matrix.tsv covers control fraction percentages, fraction-enrichment classes, polyEN, and MRL; recompute_HEK293_polysome_MRL.R recomputes MRL from the matrix.


title: HEK293 Control polysome profiling Light polysome fraction replicate 1

description:
Library name: C_F1
HEK293 polysome profiling vehicle control light-polysome fraction replicate 1. Processed matrix HEK293_polysome_control_fraction_MRL_matrix.tsv covers control fraction percentages, fraction-enrichment classes, polyEN, and MRL; recompute_HEK293_polysome_MRL.R recomputes MRL from the matrix.


title: CD4 T cell donor 3 rs4409785 replicate 4

description:
Library name: cd4_don3_rs4409785_4
Raw junction counts & normalized bigwig per capture point


title: Mouse HSPC Sesn3 replictate 2

description:
Library name: mouse_sesn3_rep2
Nucleotide percentage table around gRNA

data_processing:
Reads were trimmed with Trimgalore, before reconstruction with FLASH. Editing efficiencies were esitmated using the CRSIPRESSO2 package using  base-editor mode and allele=specific editing flags for CD4 T cells edit and default flags for mouse HSPC edit experiemnts.
Assembly: hg38, mm39
Supplementary files format and content: Text file of the nucleotide percentages around the gRNA for editing efficiency calculation.

growth_protocol: Isolated CD4+ cells were cultured at 1x106 cells per ml in Immunocult-XF T cell expansion medium (Stemcell 10981) supplemented with 10ng/ml human IL-2 (Invitrogen).  For mouse HSPCs,  C57/BL6 mice (Charles River) were culled and bone-marrow cells were isolated from tibia, femur and pelvis, before staining with APC-c Kit antibody. Enrichment was achieved with anti-APC magnetic beads and LS columns (Miltenyi Biotec). cKit+ cells were cultured in a serum-albumin-free polyvinyl alcohol (PVA) based system using a media composed of F12 medium, 1% ITSX, 10mM HEPES, 1% P/S/G, 100 ng ml−1 mouse TPO, 10 ng ml−1 mouse SCF and 0.1%  PVA (P8136, 363081). Cells were cultured in CellBIND 24-well plates (Corning) at a Density of 1 x 106 cells per ml.

extract_protocol:
Qiagen DNAeasy kit
NEB Next Ultra II

treatment_protocol: For T cells 25ul/ml of Immunocult Human CD3/CD28/CD2 T cell activator for 60 hours before collection.

value: HSPC

value: CRISPR-Edited


title: INTS11_CT_mESC_Gabpa_1h_dTAG_rep1

description: Library name: INTS11_CT_mESC_Gabpa_1h_dTAG_rep1


title: Mouse HSPC Sesn3 replictate 1

description:
Library name: mouse_sesn3_rep1
Nucleotide percentage table around gRNA


title: Mouse HSPC Rosa26 replictate 1

description:
Library name: mouse_rosa26_rep1
Nucleotide percentage table around gRNA


title: INTS11_CT_mESC_Gabpa_1h_DMSO_rep2

description: Library name: INTS11_CT_mESC_Gabpa_1h_DMSO_rep2


title: Organoid D, Matrigel

city: Bozeman

first: Michelle

last: Cherne

state: Mt

address: 2155 Analysis Drive

department: Microbiology and Cell Biology

institute: Montana State University

description:
Library name: Matrigel-D
GEM-X 3’ Reagent kit v4

data_processing:
Organoids A and B: FASTQ files from Illumina sequencing were processed with CellRanger v7.1.0 with manufacturer's default parameters Organoids C and D: FASTQ files from Illumina sequencing were processed with CellRanger v9.0.1 with manufacturer's default parameters
Assembly: GRCh38
Supplementary files format and content: Tab separated value and matrix files

source_name: Stomach

extract_protocol:
Organoids were disassociated into single cells using trypsinization or cold enzyme protease digestion. Trypsinization: organoid pellets were washed in 1 mL of ice-cold PBS per well, then centrifuged at 200 g for five minutes. HGO pellets were then treated with 350 µL of 0.25% trypsin EDTA for ten minutes at 37°C. Next the trypsin was diluted with 600 µL of cold DMEM, then the pipetted 100 times, to further disassociate the HGOs. The organoid cells were then washed with 5 mL of ice cold DMEM, then centrifuged for 7 minutes at 300 g. The organoid cells were then washed two additional times with ice cold DMEM, to remove any remaining Matrigel or hgECM. Ccold protease digestion: HGOs were washed with 1 mL of ice-cold PBS per well, then incubated for one hour on a shaker at 4°C in 2 mL of ice-cold PBS with 4 mg/mL native Bacillus licheniformis protease, 10 µg/mL DNase, and 5 mM CaCl2. The cell mixture was vortexed for 30 seconds every 20 minutes. After digestion, the cell mixture was filtered through a 60 µm filter, then washed twice with 5 mL of ice-cold DMEM and centrifuged at 300 g for 10 minutes. After disassociation, the total cell concentration and viability were determined using a hemocytometer and trypan blue staining.
Organoids A and B: Library preparation followed 10X Genomics protocols for Next GEM 3' kit V3.1 with no modifications. Organoids A and B: Library preparation followed 10X Genomics protocols for GEM-X 3' kit V4 with no modifications. Briefly, dissociated organoids were encapsulated by partitioning oil with reverse transcription master mix and gel beads containing barcode sequences using either the Chromium Controller (organoids A and B) or Chromium X (organoids C and D) machine from 10X Genomics. Poly-A RNA was ligated to the 10X barcodes and reverse transcribed. Barcoded cDNA was then amplified, fragmented, size-selected, and prepared for Illumina paired-end sequencing.

treatment_protocol: Primary human gastric tissue was decellularized, cleaned of residual DNA, and freeze-dried. Freeze-dried material was homogenized and digested with porcine pepsin. Following digestion, the material was neutralized on ice. This final product was the human gastric extracellular matric (hgECM). Organoids were suspended in either 100% Matrigel or 75% hgECM/25% Matrigel. Cultured for four to six days before extraction from matrix.

value: Stomach

value: Organoid

value: Mucosal (pit, neck, stem)

tag: passage number

tag: donor sex

value: F

value: Matrigel

tag: organoid dissociation_method

value: Cold protease digest

tag: library preparation_kit

value: scRNA-seq


title: CD4 T cell donor 3 rs4409785 replicate 3

description:
Library name: cd4_don3_rs4409785_3
Raw junction counts & normalized bigwig per capture point

value: Blood

value: CD4 T cell


title: Organoid D, 75% hgECM

description:
Library name: hgECM-D
GEM-X 3’ Reagent kit v4

value: human gastric ECM + 25% Matrigel


title: MDS_AZA_064

city: Miami

first: Qin

state: FL

address: 1501 NW 10th Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami Miller School of Medicine

data_processing:
The quality of the resulting reads was assessed using FastQC (v0.11.8) and multiQC (1.11). Then all reads were processed using Trim Galore (version 0.6.2) to trim to paired end 50 basepairs and remove adapters.
The resulting reads were aligned to the hg19 Gencode v19 reference genome using the STAR aligner (version 2.7.6a) with specific parameters: outFilterType=BySJout, outFilterMultimapNmax=20, alignSJoverhangMin=8, alignSJDBoverhangMin=1, outFilterMismatchNmax=999, alignIntronMin=20, alignIntronMax=1000000, alignMatesGapMax=1000000, and alignEndsType=EndToEnd.
Gene expression was quantified using featureCounts (v2.0.1), which was run in paired-end mode with the hg19 gencode annotation file (excluding entries for ribosomal RNA).
Differential expression analysis was performed using DESeq2 (v1.32.0) with a multifactor design that accounted for both the donor's condition and any batch effects. Genes with an absolute fold change of at least 1.5 and a p-value adjusted for multiple comparisons of less than or equal to 0.05 were considered significant.
Assembly: hg19
Supplementary files format and content: featureCounts  files

source_name: Bone marrow

extract_protocol:
RNA extracted from the CD34+ fraction was employed for RNA-seq. To guarantee RNA quality, Tapestation was utilized prior to library preparation. The RNA was treated with Illumina Ribo-Zero
For library preparation, we used the Nugen Ovation Solo RNA-seq ultra-low input kit, following the manufacturer's instructions. Subsequently, the prepared libraries were sequenced on an Illumina NextSeq platform. These libraries were paired-end and they were strand-specific.

value: Bone marrow

tag: individual

value: MDS patient

tag: age

tag: Sex

value: Female

tag: responder

value: Responder


title: CD4 T cell donor 3 rs4409785 replicate 2

description:
Library name: cd4_don3_rs4409785_2
Raw junction counts & normalized bigwig per capture point

value: WT

value: Activated


title: HEC-1A, THC 20uM, 72h, ATAC-seq, Biol rep 3

city: L'Hospitalet de Llobregat

first: David

last: Llobet

state: Barcelona

address: Gran Via de L'Hospitalet 199-203

department: Gynecologic cancer

country: Spain

institute: Bellvitge Biomedical Research Institute (IDIBELL)

description: Library name: 72_3

data_processing:
RNA-seq TPM generated with Salmon and Tximport; ATAC-seq Raw FASTQ files were trimmed with Trim Galore, quality assessed with FastQC. Reads aligned to GRCh38 using Bowtie2. Mitochondrial reads removed, properly paired reads retained with samtools. Library complexity estimated with ATACseqQC, datasets normalized by subsampling. PCR duplicates removed with Picard MarkDuplicates. Reads converted to BEDPE format, fragment coordinates adjusted for Tn5 bias (+4/-5 bp). Broad peaks called with MACS3 (FDR < 0.05, no control input).; Cut&run reads were processed with nf-core/cutandrun pipeline (v3.2.2) using Nextflow (v24.10.5). Aligned to GRCh38 human reference genome. GRCh38 unified blacklist regions excluded. Peaks called using MACS2 (v2.2.7.1) against IgG controls. narrowPeak files generated for each biological replicate.
Assembly: GRCh38
Supplementary files format and content: RNA-seq: Tab-delimited text file includes TPM values for each sample. ATAC-seq: broadPeak per sample. Cut&run narrowPeak except for NEG sample

source_name: endometrial adenocarcinoma

extract_protocol:
RNA-seq: Total RNA was purified using the RNeasy Mini Kit (QIAgen, 74104) following manufacturer's instructions. ATAC-seq: 50x10^3 HEC-1A cells per condition were pelleted (500xg, 4°C, 5min), washed with PBS, and lysed in buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal CA-630) for 20min at 4°C. Nuclei were isolated by centrifugation and resuspended in 2x transposition reaction mix (Diagenode, C01070012) for 1h at 37°C. DNA was purified with cleanup buffer containing 5% SDS and Proteinase K, followed by 2x SPRI bead cleanup and elution in 10mM Tris-HCl pH 8. Cut&run: 10x10^4 HEC-1A cells per condition were isolated with concanavalin A magnetic beads, permeabilized with digitonin, and incubated with anti-H3K4me3 antibody or IgG control. Cut&Run was performed using pAG-MNase digestion following manufacturer's protocol (Cell Signaling Technology, 86652).
RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA library prep kit according to manufacturer's protocol; ATAC-seq Genomic libraries were prepared using Buenrostro et al. 2013 primers with PCR program: 72°C 5min, 98°C 30sec, 9 cycles of (98°C 10sec, 63°C 30sec, 72°C 1min). Libraries purified with SPRI beads, eluted in 21μL 10mM Tris-HCl pH 8.0. DNA quantified using Qubit dsDNA BR assay kit (ThermoFisher Scientific, Q32850).;  Cut&run DNA libraries were purified and prepared with standard end repair/adapter ligation, and sequenced on NextSeq550 (150bp paired-end)

value: endometrial adenocarcinoma

value: endometrial adenocarcinoma epithelial cells


title: CD4 T cell donor 3 rs4409785 replicate 1

description:
Library name: cd4_don3_rs4409785_1
Raw junction counts & normalized bigwig per capture point


title: Organoid C, Matrigel

description:
Library name: Matrigel-C
GEM-X 3’ Reagent kit v4

value: Stomach

value: Organoid


title: Organoid C, 75% hgECM

description:
Library name: hgECM-C
GEM-X 3’ Reagent kit v4

value: Mucosal (pit, neck, stem)

value: F


title: ATAC_mESC_Gabpa_12h_dTAG_rep2

description: Library name: ATAC_mESC_Gabpa_12h_dTAG_rep2

data_processing:
For RNA-seq, raw reads were trimmed with Trim Galore v0.6.7, followed by mapping to the mm39 genome using STAR v2.7.11a. Gene expression levels were calculated by RSEM v1.3.1, and differential expression analysis was performed using the DESeq2 R package v1.44.0.  For SLAM-seq, BCL files containing raw sequencing data were converted to FASTQ format. Adapters were trimmed from raw reads using Cutadapt v3.5 through Trim Galore v0.6.7. SLAM-seq analyses were performed using the SLAMdunk pipeline v0.4.3, which includes mapping, read filtering, SNP variant calling, conversion counts and rate calculation. The significantly differentially expressed genes were called using DESeq2 v1.44.0 with size factors estimated on corresponding total mRNA reads for global normalization. For ATAC-seq and CUT&Tag, the raw reads were first trimmed of the adaptors with Trim Galore v0.6.7 and then aligned to the mm39 genomes using Bowtie2 v2.4.4 with the following parameters: --no-unal --no-mixed --no-discordant. Low mapping quality reads, unmapped reads and duplicated reads were removed using Picard v2.21.4 and SAMtools v1.13. For the INTS11 CUT&Tag, the mapped reads were further filtered to retain only proper paired reads with fragment length between 48 and 158 bp. For the histone modification CUT&Tag, the mapped reads were further filtered to retain only proper paired reads with fragment length at least 178 bp. Read coverages over the genome were estimated by bamCoverage from deepTools v3.5.1 with the following parameters: --binSize 20 --minMappingQuality 30 --scaleFactor 1 --normalizeUsing RPKM.
Assembly: mm39
Supplementary files format and content: tab-delimited txt files contain gene-level reads counts for each sample; bigWig files contain ATAC-seq and CUT&Tag signals.

value: cell line

value: mESCs

value: GabpadTAG/dTAG

value: treated with dTAG13 for 12 hours


title: CD4 T cell donor 3 replicate 6

description:
Library name: cd4_don3_6
Raw junction counts & normalized bigwig per capture point

value: Blood

value: CD4 T cell


title: Organoid B, Matrigel

description:
Library name: Matrigel-B
Next GEM 3’ Reagent Kit v3.1

value: M

value: Matrigel

value: Cold protease digest

value: scRNA-seq


title: Organoid B, 75% hgECM

description:
Library name: hgECM-B
Next GEM 3’ Reagent Kit v3.1

value: human gastric ECM + 25% Matrigel


title: Atherosclerosis1

city: Stockholm

first: Cenk

last: Gurdap

address: SciLifeLab, Tomtebodavägen 23

country: Sweden

institute: Karolinska Institute

description:
Library name: Sample 5
10x genomics

data_processing:
cellranger-9.0.1
Assembly: GRCh38
Supplementary files format and content: H5

source_name: PBMCs

extract_protocol:
PBMC samples (four atherosclerosis and four sex- and age-matched healthy controls: A. Healthy) were processed for scRNA-seq using the 10x Genomics Chromium Single Cell 3' v4 platform, following the manufacturer’s protocol. Briefly, after thawing and washing, cells were resuspended in PBS containing 0.04% BSA, counted, and assessed for viability.
Cell suspensions were loaded into the Chromium Controller to generate Gel Bead-In-Emulsions, followed by reverse transcription, cDNA amplification, and library construction using the Single Cell 3' v4 Reagent Kit. Final libraries were quality-checked using an Agilent Bioanalyzer and quantified by qPCR. Sequencing was performed on an Illumina NovaSeq X Plus system (NovaSeq X Series Control Software v1.2.2.48004) using a 151 nt (Read 1) – 10 nt (Index 1) – 10 nt (Index 2) – 151 nt (Read 2) configuration on a ‘25B’ mode flow cell.

value: PBMCs

value: Atherosclerosis


title: ATAC_mESC_Gabpa_12h_dTAG_rep1

description: Library name: ATAC_mESC_Gabpa_12h_dTAG_rep1


title: Organoid A, Matrigel

description:
Library name: Matrigel-A
Next GEM 3’ Reagent Kit v3.1

value: Stomach

value: Trypsinization


title: CD4 T cell donor 3 replicate 5

description:
Library name: cd4_don3_5
Raw junction counts & normalized bigwig per capture point

value: WT

value: Activated


title: Organoid A, 75% hgECM

description:
Library name: hgECM-A
Next GEM 3’ Reagent Kit v3.1

value: Organoid

value: Mucosal (pit, neck, stem)

value: F


title: ATAC_mESC_Gabpa_12h_DMSO_rep2

description: Library name: ATAC_mESC_Gabpa_12h_DMSO_rep2

value: cell line

value: mESCs

value: GabpadTAG/dTAG

value: treated with DMSO for 12 hours


title: CD4 T cell donor 3 replicate 4

description:
Library name: cd4_don3_4
Raw junction counts & normalized bigwig per capture point

value: Blood

value: CD4 T cell


title: ERL6

city: Nanjing

first: Zhang

last: Sasa

address: Tongjiaxiang 24

institute: China Pharmaceutical University

description:
Library name: Sample37
Column name in raw counts: sortedbam/ERL6.bam

data_processing:
After quality control, libraries were sequenced on the DNBSEQ platform.
Clean reads were aligned to the rat reference genome (mRatBN7.2) using STAR
and transcript abundance was quantified with RSEM
Gene-level read counts were generated using featureCounts
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text fileincludes raw counts for each Samples
Supplementary files format and content: csv files includes TPM values for each Samples

organism: Rattus norvegicus

source_name: liver

growth_protocol: On day 28, rats were euthanized, and liver tissues were excised, weighed, and processed

extract_protocol:
Total RNA was extracted  by RNAprep Pure Plant Plus KIT.
Transcriptome libraries were constructed using the Hieff NGS® Ultima Dual-mode RNA Library Prep Kit (premixed version; Yeasen) according to the manufacturer’s protocol.

treatment_protocol: intragastric doses of EF, PF, and RD extracts were administered at 2.5 g/kg, 2.5 g/kg, and 200 mg/kg, respectively.

value: liver

value: hepatocyte

value: Sprague-Dawley

value: Intraperitoneal injection of LPS,Gavage EF+ RD


title: ERL8

description:
Library name: Sample38
Column name in raw counts: sortedbam/ERL8.bam


title: Healthy2

description:
Library name: Sample 2
10x genomics

value: PBMCs

value: Healthy


title: CD4 T cell donor 3 edit replicate 3

description:
Library name: cd4_don3_edit_3
Raw junction counts & normalized bigwig per capture point

value: CRISPR Edited


title: ATAC_mESC_Gabpa_12h_DMSO_rep1

description: Library name: ATAC_mESC_Gabpa_12h_DMSO_rep1


title: ERL4

description:
Library name: Sample36
Column name in raw counts: sortedbam/ERL4.bam


title: CD4 T cell donor 3 replicate 3

description:
Library name: cd4_don3_3
Raw junction counts & normalized bigwig per capture point

value: WT

value: Activated


title: ERL2

description:
Library name: Sample35
Column name in raw counts: sortedbam/ERL2.bam


title: ERL1

description:
Library name: Sample34
Column name in raw counts: sortedbam/ERL1.bam


title: ATAC_mESC_Gabpa_1h_dTAG_rep2

description: Library name: ATAC_mESC_Gabpa_1h_dTAG_rep2

value: treated with dTAG13 for 1 hour


title: CD4 T cell donor 3 replicate 2

description:
Library name: cd4_don3_2
Raw junction counts & normalized bigwig per capture point


title: EPL6

description:
Library name: Sample33
Column name in raw counts: sortedbam/EPL6.bam

value: Intraperitoneal injection of LPS,Gavage EF+ PF


title: Single cell multiome, BM-MSCs, In vitro,rep1,ATAC

city: Lund

first: Paul

last: Bourgine

state: Skane

address: Sölvegatan 17

institute: Lund University

description: Library name: D008_IV_ATAC

library_source: genomic single cell

data_processing:
Demultiplexing and reference genome mapping using cellranger-ATC V2.1. reference genome Human GRCh38 (GENCODE v32/Ensembl98)
Supplementary files format and content: Human GRCh38 (GENCODE v32/Ensembl98)
Supplementary files format and content: data.RDS : RDS file matrix with celltypes and annotations

extract_protocol:
Tissues selected for multiomics sequencing were explanted from the mice and digested in Nattokinase (MedChemExpress #HY-P2373) as described 23.
Following isolation, cells were assessed for viability and lysed for nuclei isolation according to the 10X Genomics Demonstrated Protocol CG000365-Rev C. Library construction and sequencing were performed by the Centre for Translational Genomics (CTG Lund) using a 10X Multiome kit. Sequencing was performed on the NovaSeq X Series platform. Reference mapping and feature counting were performed  CellRanger-ARC.
10X genomics single nuclei multiome libraries

value: Bone marrow

value: primary BM-MSCs

value: MSCs

value: wt

value: In vitro


title: EPL4

description:
Library name: Sample32
Column name in raw counts: sortedbam/EPL4.bam


title: ATAC_mESC_Gabpa_1h_dTAG_rep1

description: Library name: ATAC_mESC_Gabpa_1h_dTAG_rep1

value: cell line

value: mESCs

value: GabpadTAG/dTAG


title: HEK293 Minocycline polysome profiling Heavy polysome fraction replicate 2

description:
Library name: M_P2
HEK293 polysome profiling minocycline heavy-polysome fraction replicate 2. Processed matrix HEK293_polysome_control_fraction_MRL_matrix.tsv covers control fraction percentages, fraction-enrichment classes, polyEN, and MRL; recompute_HEK293_polysome_MRL.R recomputes MRL from the matrix.

value: HEK293 (ATCC CRL-1573)

value: Minocycline; compound:minocycline; dose:100 uM; duration:12 h


title: CD4 T cell donor 3 promoter replicate 6

description:
Library name: cd4_don3_promoter_6
Raw junction counts & normalized bigwig per capture point

value: Blood

value: CD4 T cell


title: EPL3

description:
Library name: Sample31
Column name in raw counts: sortedbam/EPL3.bam

value: liver

value: hepatocyte

value: Sprague-Dawley


title: ATAC_mESC_Gabpa_1h_DMSO_rep2

description: Library name: ATAC_mESC_Gabpa_1h_DMSO_rep2

value: treated with DMSO for 1 hour


title: CD4 T cell donor 3 replicate 1

description:
Library name: cd4_don3_1
Raw junction counts & normalized bigwig per capture point

value: WT

value: Activated


title: HEK293 Minocycline polysome profiling Monosome fraction replicate 2

description:
Library name: M_M2
HEK293 polysome profiling minocycline monosome fraction replicate 2. Processed matrix HEK293_polysome_control_fraction_MRL_matrix.tsv covers control fraction percentages, fraction-enrichment classes, polyEN, and MRL; recompute_HEK293_polysome_MRL.R recomputes MRL from the matrix.


title: HEK293 Minocycline polysome profiling Monosome fraction replicate 3

description:
Library name: M_M3
HEK293 polysome profiling minocycline monosome fraction replicate 3. Processed matrix HEK293_polysome_control_fraction_MRL_matrix.tsv covers control fraction percentages, fraction-enrichment classes, polyEN, and MRL; recompute_HEK293_polysome_MRL.R recomputes MRL from the matrix.


title: Single cell multiome, BM-MSCs, OSS, rep2,GEX

description: Library name: D009_O_GEX

value: Bone marrow

value: primary BM-MSCs

value: Ossigel


title: CD4 T cell donor 2 replicate 6

description:
Library name: cd4_don2_6
Raw junction counts & normalized bigwig per capture point


title: EL7

description:
Library name: Sample29
Column name in raw counts: sortedbam/EL7.bam

value: Intraperitoneal injection of LPS,Gavage EF


title: CD4 T cell donor 2 replicate 5

description:
Library name: cd4_don2_5
Raw junction counts & normalized bigwig per capture point


title: EL6

description:
Library name: Sample28
Column name in raw counts: sortedbam/EL6.bam


title: ATAC_mESC_Gabpa_1h_DMSO_rep1

description: Library name: ATAC_mESC_Gabpa_1h_DMSO_rep1

value: cell line


title: EL5

description:
Library name: Sample27
Column name in raw counts: sortedbam/EL5.bam


title: SLAM_mESC_Gabpa_12h_dTAG_rep2

description: Library name: SLAM_mESC_Gabpa_12h_dTAG_rep2

value: mESCs

value: treated with dTAG13 for 12 hours


title: HEC-1A, THC 20uM, 24h, ATAC-seq, Biol rep 1

description: Library name: 24_1

value: endometrial adenocarcinoma

value: endometrial adenocarcinoma epithelial cells


title: EL4

description:
Library name: Sample26
Column name in raw counts: sortedbam/EL4.bam


title: INTS11_CT_mESC_Gabpa_12h_dTAG_rep2

description: Library name: INTS11_CT_mESC_Gabpa_12h_dTAG_rep2

value: GabpadTAG/dTAG


title: EL3

description:
Library name: Sample25
Column name in raw counts: sortedbam/EL3.bam


title: EPL1

description:
Library name: Sample30
Column name in raw counts: sortedbam/EPL1.bam

value: Intraperitoneal injection of LPS,Gavage EF+ PF


title: 57, AD, CD154

city: Doha

first: Asmma

last: Doudin

address: Al Gharrafa Street, Ar Rayyan

department: Research

country: Qatar

institute: Sidra Medicine

description: Library name: 200901421

data_processing:
Raw sequencing data were demultiplexed using bcl2fastq v2.20 to generate FASTQ files for each sample. Downstream processing of RNA-seq data was carried out using the bcbio-nextgen v1.2.0 pipeline.Reads were aligned to the reference genome using STAR v2.6.1d, and gene-level quantification was performed using featureCounts v2.0.0.
Assembly: GRCh38
Supplementary files format and content: CPM_ComBat_seq_geo.csv
Supplementary files format and content: a gene expression matrix that contains normalized CPM (Counts Per Million) values — after batch correction using ComBat-seq.

growth_protocol: Cells revived in RPMI 1640 GlutaMAX medium  and 10% human serum

extract_protocol:
Cells were sorted based on the surface staining of CD154+CD137- for TconCM+ cells and CD137+CD154- for TregCM+ cells and RNA was extracted using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing based on manufacturer's instructions.
Isolated RNA was used to create double-stranded cDNA fragments using SMARTer® Pico PCR cDNA Synthesis Kit (Takara) according to the manufacturer’s protocol. SeqAmp DNA Polymerase (Takara) was used to amplify purified first-strand cDNA into RNA-seq libraries based on the manufacturer’s instructions. Nextera XT Index Kit v2 (Illumina, USA) was used for library indexing.

treatment_protocol: Cells stimulated in RPMI 1640 GlutaMAX medium and 10% human serum, for 6 hours (5% CO2, 37oC) with 100μg CM,  1 μg/ml CD40 and 1μg/ml CD28 functional grade antibodies.

tag: sample group

value: AD


title: CD4 T cell donor 2 replicate 3

description:
Library name: cd4_don2_3
Raw junction counts & normalized bigwig per capture point

tag: tissue

value: Blood

value: CD4 T cell


title: L4

description:
Library name: Sample23
Column name in raw counts: sortedbam/L4.bam

value: liver

tag: cell type

value: hepatocyte

value: Sprague-Dawley

value: Intraperitoneal injection of LPS


title: SLAM_mESC_Gabpa_12h_dTAG_rep1

description: Library name: SLAM_mESC_Gabpa_12h_dTAG_rep1

tag: genotype


title: SLAM_mESC_Gabpa_12h_DMSO_rep2

description: Library name: SLAM_mESC_Gabpa_12h_DMSO_rep2

tag: cell line

value: treated with DMSO for 12 hours


title: CD4 T cell donor 2 replicate 2

description:
Library name: cd4_don2_2
Raw junction counts & normalized bigwig per capture point

value: WT

tag: treatment

value: Activated


title: L5

description:
Library name: Sample24
Column name in raw counts: sortedbam/L5.bam

tag: batch


title: L3

description:
Library name: Sample22
Column name in raw counts: sortedbam/L3.bam


title: INTS11_CT_mESC_Gabpa_12h_DMSO_rep2

description: Library name: INTS11_CT_mESC_Gabpa_12h_DMSO_rep2

value: cell line


title: SLAM_mESC_Gabpa_12h_DMSO_rep1

description: Library name: SLAM_mESC_Gabpa_12h_DMSO_rep1

value: mESCs


title: INTS11_CT_mESC_Gabpa_12h_dTAG_rep1

description: Library name: INTS11_CT_mESC_Gabpa_12h_dTAG_rep1

value: treated with dTAG13 for 12 hours


title: CD4 T cell donor 2 replicate 4

description:
Library name: cd4_don2_4
Raw junction counts & normalized bigwig per capture point


title: L2

description:
Library name: Sample21
Column name in raw counts: sortedbam/L2.bam


title: L1

description:
Library name: Sample20
Column name in raw counts: sortedbam/L1.bam


title: CD4 T cell donor 2 replicate 1

description:
Library name: cd4_don2_1
Raw junction counts & normalized bigwig per capture point


title: CD4 T cell donor 3 rs4409785 replicate 5

description:
Library name: cd4_don3_rs4409785_5
Raw junction counts & normalized bigwig per capture point


title: ER3

description:
Library name: Sample18
Column name in raw counts: sortedbam/ER3.bam

value: Gavage EF+ RD


title: ER4

description:
Library name: Sample19
Column name in raw counts: sortedbam/ER4.bam


title: INTS11_CT_mESC_Gabpa_1h_DMSO_rep1

description: Library name: INTS11_CT_mESC_Gabpa_1h_DMSO_rep1

value: treated with DMSO for 1 hour


title: SLAM_mESC_Gabpa_4h_dTAG_rep2

description: Library name: SLAM_mESC_Gabpa_4h_dTAG_rep2

value: GabpadTAG/dTAG

value: treated with dTAG13 for 4 hours


title: CD4 T cell donor 1 replicate 6

description:
Library name: cd4_don1_6
Raw junction counts & normalized bigwig per capture point


title: ER1

description:
Library name: Sample16
Column name in raw counts: sortedbam/ER1.bam


title: ER2

description:
Library name: Sample17
Column name in raw counts: sortedbam/ER2.bam


title: INTS11_CT_mESC_Gabpa_1h_dTAG_rep2

description: Library name: INTS11_CT_mESC_Gabpa_1h_dTAG_rep2

value: treated with dTAG13 for 1 hour


title: SLAM_mESC_Gabpa_4h_dTAG_rep1

description: Library name: SLAM_mESC_Gabpa_4h_dTAG_rep1


title: EP6

description:
Library name: Sample15
Column name in raw counts: sortedbam/EP6.bam

value: Gavage EF+ PF


title: SLAM_mESC_Gabpa_2h_dTAG_rep2

description: Library name: SLAM_mESC_Gabpa_2h_dTAG_rep2

value: treated with dTAG13 for 2 hours


title: CD4 T cell donor 1 replicate 4

description:
Library name: cd4_don1_4
Raw junction counts & normalized bigwig per capture point

value: Blood

value: CD4 T cell


title: SLAM_mESC_Gabpa_2h_dTAG_rep1

description: Library name: SLAM_mESC_Gabpa_2h_dTAG_rep1


title: EP5

description:
Library name: Sample14
Column name in raw counts: sortedbam/EP5.bam

value: liver

value: hepatocyte

value: Sprague-Dawley


title: EP2

description:
Library name: Sample12
Column name in raw counts: sortedbam/EP2.bam


title: CD4 T cell donor 1 replicate 3

description:
Library name: cd4_don1_3
Raw junction counts & normalized bigwig per capture point

value: WT


title: EP1

description:
Library name: Sample11
Column name in raw counts: sortedbam/EP1.bam


title: CD4 T cell donor 1 replicate 2

description:
Library name: cd4_don1_2
Raw junction counts & normalized bigwig per capture point

value: Activated


title: SLAM_mESC_Gabpa_2-4h_DMSO_rep2

description: Library name: SLAM_mESC_Gabpa_2-4h_DMSO_rep2

value: cell line

value: treated with DMSO for 2 hours


title: SLAM_mESC_Gabpa_2-4h_DMSO_rep1

description: Library name: SLAM_mESC_Gabpa_2-4h_DMSO_rep1

value: mESCs


title: EP3

description:
Library name: Sample13
Column name in raw counts: sortedbam/EP3.bam


title: E2

description:
Library name: Sample7
Column name in raw counts: sortedbam/E2.bam

value: Gavage EF


title: E5

description:
Library name: Sample10
Column name in raw counts: sortedbam/E5.bam


title: SLAM_mESC_Gabpa_1h_dTAG_rep2

description: Library name: SLAM_mESC_Gabpa_1h_dTAG_rep2


title: E1

description:
Library name: Sample6
Column name in raw counts: sortedbam/E1.bam


title: jurkat replicate 6

description:
Library name: jurkat_6
Raw junction counts & normalized bigwig per capture point

value: Jurkat


title: C7

description:
Library name: Sample5
Column name in raw counts: sortedbam/C7.bam

value: control


title: jurkat replicate 5

description:
Library name: jurkat_5
Raw junction counts & normalized bigwig per capture point


title: C6

description:
Library name: Sample4
Column name in raw counts: sortedbam/C6.bam


title: C5

description:
Library name: Sample3
Column name in raw counts: sortedbam/C5.bam


title: C3

description:
Library name: Sample1
Column name in raw counts: sortedbam/C3.bam


title: SLAM_mESC_Gabpa_1h_DMSO_rep1

description: Library name: SLAM_mESC_Gabpa_1h_DMSO_rep1

value: GabpadTAG/dTAG

value: treated with DMSO for 1 hour


title: jurkat replicate 4

description:
Library name: jurkat_4
Raw junction counts & normalized bigwig per capture point


title: H4R3me2s_2

city: Shanghai

first: Yaodi

last: Shao

address: 2699 West Gaoke Road

institute: Shanghai First Maternity and Infant Hospital

description: Library name: H4R3me2s_2

data_processing:
Raw FASTQ files in Rawdata folder were subjected to adapter removal and quality filtering via fastp, with output clean reads deposited in Cleandata folder. Clean reads were aligned to GRCh38(hg38) using Bowtie2, PCR duplicates were removed by Picard, and final aligned files were saved in the bam folder. Peak calling was performed with SEACR for H4R3me2s binding sites.
Assembly: Human GRCh38 (hg38)
Supplementary files format and content: bigwig
Library strategy: CUT&Run

source_name: ovarian cancer cells

extract_protocol:
CUT&RUN assay for H4R3me2s was performed in human ovarian cancer cells. Cells were immobilized on ConA magnetic beads, permeabilized with digitonin buffer, and incubated with H4R3me2s-specific primary antibody overnight at 4°C. After washing, protein A-MNase was applied for targeted chromatin cleavage. CaCl₂-induced MNase digestion was performed on ice and terminated with EDTA/EGTA stop buffer. Soluble chromatin fragments were eluted, purified, and subjected to Illumina sequencing library preparation.
Purified CUT&RUN DNA fragments were end-repaired, A-tailed, and ligated to Illumina sequencing adapters. Adapter-ligated DNA was PCR-amplified with indexed primers, followed by size purification to enrich fragments between 150–500 bp. Final libraries were quality-checked by Qubit quantification and agarose gel electrophoresis. Validated libraries were sequenced on the Illumina platform with paired-end 150 bp reads.

value: ovarian cancer cells


title: RNA_mESC_Gabpb1_b2_12h_dTAG_rep2

description: Library name: RNA_mESC_Gabpb1_b2_12h_dTAG_rep2

value: treated with dTAG13 for 12 hours


title: IgG_2

description: Library name: IgG_2


title: A100_1

city: Guangzhou

first: Yang

last: Ziqi

address: Jinsui Road

institute: Zhongshan opythalmic center

description: Library name: Sample16

data_processing:
Raw sequencing reads were processed to remove adaptor sequences and low-quality reads.Clean reads were aligned to the human reference genome using HISAT2 (v2.0.5).Gene expression levels were quantified as fragments per kilobase per million mapped reads (FPKM) using featureCounts.Differential gene expression analysis was performed using DESeq2 with adjusted P < 0.05 considered statistically significant.Gene Ontology (GO) and pathway enrichment analyses were conducted using clusterProfiler R package.
Assembly: hg38
Supplementary files format and content: csv files include FPKM values for each Sample

growth_protocol: HMC3 cells were cultured in MEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. RNA quality and integrity were assessed by agarose gel electrophoresis and an Agilent 2100 Bioanalyzer system.
RNA sequencing libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s protocol. Briefly, mRNA was enriched using poly-T oligo-attached magnetic beads, fragmented, and reverse-transcribed to synthesize first- and second-strand cDNA. After end repair, adaptor ligation, and PCR amplification, libraries with insert sizes of approximately 250–300 bp were generated and sequenced on an Illumina NovaSeq platform to obtain paired-end 150-bp reads.

treatment_protocol: HMC3 cells were treated with oxidized low-density lipoprotein (oxLDL) at concentrations of 0, 1, 2.5, 10, 50, or 100 μg/mL for 24 hours.

value: microglial cell line

value: wild type

value: oxLDL 100 μg/ml, 24h


title: NOA3

city: hangzhou

first: Huimei

last: Zheng

address: yuhangtang roda866

institute: ZheJiang Univerisity

description:
Library name: NOA-3
Column name in raw_counts.txt: NOA_3

data_processing:
The quality of fastq files was assessed using FASTQC (v 0.11.9)
Reads were trimmed using Fastp (v 0.21.0)
Trimmed reads were mapped to human GRCh38 reference genome using STAR (v 2.7.9a). Raw read counts were generated using RSEM (v 1.3.3).
Read counts were used as input and normalized using built-in algorithms in DESeq2.
Differential expression in RNA-Seq was analyzed using the R DESeq2 package.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: xls files include FPKM values for each Sample

source_name: seminiferous tubules

extract_protocol:
RNA was harvested using R6834 Total RNA Kit I (OMEGA). 1.3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: seminiferous tubules

value: spermatogenic cells

value: SPDYA variant


title: A50_3

description: Library name: Sample15

value: oxLDL 50 μg/ml, 24h


title: RNA_mESC_Gabpb1_12h_dTAG_rep2

description: Library name: RNA_mESC_Gabpb1_12h_dTAG_rep2

value: cell line


title: NOA1

description:
Library name: NOA-1
Column name in raw_counts.txt: NOA_1


title: RNA_mESC_Gabpb1_12h_dTAG_rep1

description: Library name: RNA_mESC_Gabpb1_12h_dTAG_rep1


title: A10_1

description: Library name: Sample10

value: oxLDL 10 μg/ml, 24h


title: A2.5_3

description: Library name: Sample9

value: oxLDL 2.5 μg/ml, 24h


title: RNA_mESC_Gabpb1_12h_DMSO_rep2

description: Library name: RNA_mESC_Gabpb1_12h_DMSO_rep2

value: mESCs

value: treated with DMSO for 12 hours


title: OA2

description:
Library name: OA-2
Column name in raw_counts.txt: OA_2

value: WT


title: A2.5_1

description: Library name: Sample7


title: A2.5_2

description: Library name: Sample8


title: A1_2

description: Library name: Sample5

value: oxLDL 1 μg/ml, 24h


title: CD4 T cell donor 1 replicate 5

description:
Library name: cd4_don1_5
Raw junction counts & normalized bigwig per capture point

data_processing:
The raw fastq file is processed to reconstruct a single read from the paired end sequencing. This is then mapped to the 800bp sequence surrounding the capture oligonucleotide using the non-stringent aligner BLAT. This allows the reads to be cut into ‘slices’ depending on whether they align to the sequence around the capture site. This strategy allows ligation junctions in the read to be determined with base pair accuracy. The resulting fastq file is aligned to the genome using bowtie.
The resulting fastq file is aligned to the genome using bowtie.
Assembly: hg38
Supplementary files format and content: BigWig of data from multiple viewpoints
Library strategy: Capture-C

extract_protocol:
Qiagen DNeasy blood and tissue kit
7-10 µg of each 3C library was sonicated to a mean fragment size of 200 bp using a Covaris S220 Focussed Ultrasonicator (1-3 cycles of 60s: duty cycle 10%; intensity 5; cycles per burst 200). The library size was assessed using an Agilent TapeStation (DNA 1000) and an Ampure XP (Beckman Coulter) bead clean-up was performed once the sample had been adequately sonicated. To maximise library complexity three aliquots, each containing 2 µg sonicated 3C library, were processed in parallel for each sample to add sequencing adaptors. NEB Ultra II reagents were used following the standard protocol with the following modifications: first, additional adapter was added into the ligation reactions (7.5 µl rather than 2.5 µl); no size selection was performed (Ampure XP bead clean ups were always performed with a sample:bead ratio of 1:1.8) and the final PCR to add indices was amplified in triplicate from each aliquot using the Herculase II PCR kit (Agilent) to maximise DNA yield. All parallel library preparations and PCR reactions were pooled for each reaction. CHIP libraries were prepared and analyzed as previously reported in Hanssen LLP. et al., 2017.

value: Blood

value: CD4 T cell

value: Activated


title: E4

description:
Library name: Sample9
Column name in raw counts: sortedbam/E4.bam

value: liver

value: hepatocyte

value: Sprague-Dawley

value: Gavage EF


title: E3

description:
Library name: Sample8
Column name in raw counts: sortedbam/E3.bam


title: CD4 T cell donor 1 replicate 1

description:
Library name: cd4_don1_1
Raw junction counts & normalized bigwig per capture point


title: SLAM_mESC_Gabpa_1h_dTAG_rep1

description: Library name: SLAM_mESC_Gabpa_1h_dTAG_rep1

extract_protocol:
For RNA-seq, RNA was isolated with TRIzol. For SLAM-seq, the 4sU-labeled RNA was isolated using a 1:1 volume of RNA XP magnetic beads. After 10 mins incubation at room temperature, the beads were washed twice with 200 μL 80% freshly prepared ethanol on the magnetic stand and the dried beads pellets were resuspended in 7 μL RNase-free water. For ATAC-seq and CUT&Tag, DNA was purified using the SPRI beads.
For RNA-seq, libraries were prepared according to the Fast RNA-seq Lib Prep Kit V2 with 0.2 μg RNA following the manufacturer's protocols. For SLAM-seq, alkylated RNA was used for 3'-end polyA RNA sequencing library preparation with Smart-seq2 according to the manufacturer's protocol. For ATAC-seq, mESCs cells were digested with adapter-loaded Tn5 in the tagmentation buffer (33 mM Tris-Acetate, 66 mM K-Acetate, 10 mM Mg-Acetate,16% DMF, 0.02% Digitonin) for 30 mins at 37 °C, and the reaction was stopped by stop buffer (100 mM Tris pH 8.0, 100 mM NaCl, 0.4% SDS and 40 μg/mL Proteinase K) and incubated overnight at 55 °C. 25% Tween-20 was added to quench SDS. Sequencing libraries were prepared with NEBNext High-Fidelity 2x PCR Master Mix. The PCR product was purified using a 1:1.6 volume ratio of SPRI beads. For CUT&Tag, libraries were performed using the Hyperactive Universal CUT&Tag Assay Kit following the manufacturer's protocols.

value: GabpadTAG/dTAG

value: treated with dTAG13 for 1 hour


title: B09D

first: Jun Hee

last: Lee

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

description: Library name: B09D

data_processing:
Seq-Scope array-construction, or 1st-Seq, FASTQ files were processed using the NovaScope pipeline to generate a lookup table containing array-region indices, quality-filtered spatial barcode sequences, and their corresponding XY coordinates. The complete Seq-Scope experimental and computational procedures are described in Kim, Y., Cheng, W., Cho, C.S. et al. Seq-Scope: repurposing Illumina sequencing flow cells for high-resolution spatial transcriptomics. Nature Protocols 20, 643-689 (2025). https://doi.org/10.1038/s41596-024-01065-0. The NovaScope processing pipeline is available at https://seqscope.github.io/NovaScope. Because GEO/SRA processing does not preserve the barcode-coordinate relationship required for Seq-Scope analysis, the 1st-Seq data and associated coordinate information were deposited separately in Deep Blue Data: https://doi.org/10.7302/p25z-mk61.
Spatial transcriptomic, or 2nd-Seq, FASTQ reads were matched to the 1st-Seq lookup table. Reads were assigned to array regions, mapped to validated HDMI spatial barcodes, filtered to retain valid barcode sequences, and assigned spatial XY coordinates. GEO/SRA deposition includes only the 2nd-Seq sequencing data. The same 2nd-Seq data are also available through Deep Blue Data together with the 1st-Seq barcode-coordinate information required for complete spatial reconstruction: https://doi.org/10.7302/p25z-mk61.
Spatially indexed reads were aligned to the Mus musculus mm10 reference genome using STAR. Aligned reads were summarized to generate spatial digital gene expression matrices containing gene-level transcript counts and spatial coordinates.
H&E images were registered to the spatial digital gene expression coordinate system using historef version 0.1.3 and fiducial marks visible in both datasets. DAPI/WGA images were subsequently aligned to the registered H&E images using the Georeferencer function in QGIS version 3.22.9.
WGA-stained myofiber membranes were segmented using a custom-trained Cellpose model, with manual correction when necessary. Segmentation masks were exported as NumPy arrays, and transcripts within each segmented myofiber were aggregated into single-myofiber spatial digital gene expression matrices. For non-myocyte analysis, transcripts were aggregated into non-overlapping 24 μm hexagonal spatial bins. Low-quality myofibers with fewer than 200 detected features were removed. Normalization, integration, dimensionality reduction, clustering, and annotation were performed in Seurat using SCTransform, PCA, UMAP, FindNeighbors, and FindClusters.
Assembly: Mus musculus genome assembly mm10, also known as GRCm38.
Supplementary files format and content: Spatial digital gene expression matrices containing gene-level transcript counts associated with Seq-Scope spatial barcodes and XY coordinates for each tissue section.
Library strategy: Spatial Transcriptomics

source_name: Muscle (SOL + EDL)

growth_protocol: Tsc1F/F and Ckm-Cre mice on a C57BL/6J background were obtained from The Jackson Laboratory, and Depdc5F/F mice were obtained from the European Mouse Mutant Archive. Tsc1F/F Depdc5F/F mice were generated by interbreeding and subsequently crossed with Ckm-Cre mice to produce skeletal muscle-specific Tsc1/Depdc5 knockout mice. Male control and knockout littermates were maintained under protocols approved by the University of Michigan Institutional Animal Care and Use Committee and analyzed at 10 weeks of age.

extract_protocol:
Frozen muscle blocks were cryosectioned at 10 μm thickness and placed directly onto Seq-Scope arrays. Sections were fixed with 4% formaldehyde, imaged after DAPI/WGA and H&E staining, and permeabilized with collagenase I followed by pepsin. Released tissue RNA was captured in situ by spatially barcoded oligo-dT probes on the array and reverse-transcribed overnight at 42°C. Tissue was subsequently removed with SDS, EDTA, and Proteinase K, leaving spatially indexed cDNA on the array surface.
Second-strand synthesis was performed directly on the Seq-Scope array using a TruSeq Read2-conjugated random primer, dNTPs, and Klenow Fragment. Libraries were released from the array by two sequential 0.1 N NaOH elutions, neutralized with potassium acetate, and purified using AMPure XP beads. Libraries were amplified by two rounds of PCR using KAPA HiFi HotStart ReadyMix. The first PCR used TruSeq forward and reverse primers, and the second PCR introduced TruSeq indexing primers. Final libraries were size-selected with AMPure XP beads, assessed using an Agilent 2100 Bioanalyzer, and sequenced using paired-end 100-cycle sequencing.

treatment_protocol: No pharmacological treatment was administered. Constitutive skeletal muscle mTORC1 hyperactivation was induced genetically through Ckm-Cre-mediated deletion of Tsc1 and Depdc5. Tsc1F/F Depdc5F/F littermates lacking Ckm-Cre were used as controls. Immediately after dissection, EDL and SOL muscles were embedded in O.C.T. compound and snap-frozen in liquid nitrogen-cooled 2-methylbutane.

value: Muscle (SOL + EDL)

value: mixed

value: Ckm-Cre Tsc1F/F Depdc5 F/F


title: jurkat replicate 2

first: Joseph

institute: University of Oxford

description:
Library name: jurkat_2
Raw junction counts & normalized bigwig per capture point

value: Jurkat


title: C4

description:
Library name: Sample2
Column name in raw counts: sortedbam/C4.bam

value: control


title: SLAM_mESC_Gabpa_1h_DMSO_rep2

first: Hang

institute: CAS

description: Library name: SLAM_mESC_Gabpa_1h_DMSO_rep2

value: cell line

value: mESCs

value: treated with DMSO for 1 hour


title: H4R3me2s_1

description: Library name: H4R3me2s_1

value: ovarian cancer cells


title: jurkat replicate 1

description:
Library name: jurkat_1
Raw junction counts & normalized bigwig per capture point

value: Blood

value: WT


title: A100_3

description: Library name: Sample18

value: microglial cell line

value: wild type

value: oxLDL 100 μg/ml, 24h


title: RNA_mESC_Gabpa_12h_dTAG_rep1

description: Library name: RNA_mESC_Gabpa_12h_dTAG_rep1

value: treated with dTAG13 for 12 hours


title: RNA_mESC_Gabpb1_b2_12h_DMSO_rep2

description: Library name: RNA_mESC_Gabpb1_b2_12h_DMSO_rep2

value: treated with DMSO for 12 hours


title: A100_2

description: Library name: Sample17


title: RNA_mESC_Gabpb1_b2_12h_dTAG_rep1

description: Library name: RNA_mESC_Gabpb1_b2_12h_dTAG_rep1


title: IgG_1

description: Library name: IgG_1


title: wildtype timecourse 4 hours post fertilization rep2

city: Farmington

first: Jean-Denis

last: Beaudoin

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: UConn Health Center

description:
Library name: WT_4hpf_Rep2
Referred to as WT_4hpf_Rep3 in analysis.The raw data are available in the European Nucleotide Archive database.
SDataset5_WT_perread_processed_pa_filtered.csv
SDataset8_MZT_ZF_MZT_Decay_Cov25_RawData_ReplicableSites.tsv
SDataset9_per_read_WT_allsamples.csv

data_processing:
Master of Pores pipeline version 2 (MOP2):The mop_preprocess module was used to basecall the raw signal with Guppy v6.0.6 (Oxford Nanopore Technologies) using the m6A-aware basecalling model rna_r9.4.1_70bps_m6A_hac.cfg (m6Abasecaller).
The DeePlexiCon algorithm was used to demultiplex multiplexed reads.
ModPhred used to encode the modification probabilities and map reads to the GRCz11 genome with minimap2 2.17-r941 using the parameters “-ax map-ont -k13”.
Per-read gene and isoform annotation using the samtools flag “-F 3488”, with Isoquant v3.3.0 using parameters “--complete_genedb --data_type nanopore” and the zebrafish Ensembl annotation version 110. Poly(A) tail length estimation was performed using the mop_tail module of MoP2 with tailfindr v1.3.
m6AB_PerRead pipeline generated replicable m6A sites and per_read tables. For isoform-level and read-level analysis, reads were required to map uniquely to a single isoform that had at least 25 reads per replicate. Reads lacking a tailfindr poly(A) tail estimate (NaN values) were removed (pa_filtered files).
Assembly: GRCz11
Supplementary files format and content: SDataset5,6,7... .csv file of per_read tables produced by the m6AB_PerRead pipeline (m6Abasecaller_per_read_analysis) that has been filtered for isoform-level and read-level analysis. This includes isoform/gene assignment, m6A modification number and location, read length, poly(A) tail length, and relevant timepoint/treatment for each read.
Supplementary files format and content: SDataset8.. .tsv file of replicable m6A sites with information on their chromosome position, coverage, and modification frequency.
Supplementary files format and content: SDataset9,10,11... .csv file of pre_read tables produced by the m6AB_PerRead pipeline that includes m6A modification number and location, chromosomal alignment information, poly(A) tail length, isoform/gene assignment information, and sample for each read.

organism: Danio rerio

source_name: embryos

growth_protocol: Embryos were maintained at 28 °C

extract_protocol:
RNA from frozen embryos was extracted using TRIzol (Invitrogen).  Poly(A)+ mRNAs were isolated with oligo d(T)25 magnetic beads (New England BioLabs) according to the manufacturer’s protocol and eluted in 30 µL of water.
RNA libraries were prepared using the direct RNA sequencing kit (SQK-RNA002), following ONT protocol version DRS_9080_v2_revI_14Aug2019 with half reactions of 250 ng of poly(A)+ RNA for each library up to the RNA Adapter (RMX) ligation step, with the following adaptations. Samples were ligated to pre-annealed custom RT adaptors (IDT) containing barcodes. For non-barcoded runs, the commercial RT adapter included in the SQK-RNA002 kit was used instead. Reverse transcription was then performed. Ligated products were purified using 1.8X Agencourt RNAClean XP beads (Fisher Scientific, NC0068576).For the final ligation, 50 ng of reverse-transcribed RNA from each reaction was pooled, and ligated with the RMX adapter. For non-barcoded runs, 200 ng of reverse-transcribed RNA was used for ligation with the RMX adapter. The ligated RNA:DNA hybrid was purified using 1X Agencourt RNAClean XP beads. Samples were run on a R9.4.1 flowcell on a MinION or PromethION device.

treatment_protocol: All injections into zebrafish embryos were performed on dechorionated one-cell stage embryos with 1 nL volumes. To inhibit RNA Polymerase II, embryos were injected with 0.2 ng of α-amanitin (Sigma-Aldrich, A2263) resuspended in nuclease-free water. To inhibit miR-430 activity, embryos were injected with 10 µM of tiny locked nucleic acid (tinyLNA), complementary to the seed region of miR-430 (5′-TAGCACTT-3′ (Exiqon)).

value: embryos


title: EU_SUP,scRNAseq

city: shanghai

first: yiqin

last: zhang

address: No. 910, Hengshan Rd

institute: International Peace Maternity and Child Health Hospital

description: 10x Genomics

data_processing:
The demultipexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1
Raw count matrices were loaded into the R (v4.1.3) package Seurat (v4.1.1). For each specimen, genes expressed in < 3 cell were discarded. Cells with < 200 or > 10,000 genes were discarded; cells with > 10% UMIs mapped to mitochondrial genes; cells with >10% UMIs mapped to erythrocyte genes were discarded. For normalization, UMI counts for all nuclei were scaled by library size (total UMI counts), multiplied by 10,000 and transformed to a log scale. Highly variable genes were identified using the function FindVariableFeatures in Seurat. The top principal components (PCs), determined by the PCElbowPlot function, were selected for dimensionality reduction, clustering with resolution = 0.9 and visualization with UMAP or t-distributed stochastic neighbour embedding (t-SNE). Marker genes for each cluster were identified with a Bimod test implemented in the FindAllMarkers function with the following criteria: adjusted P-value < 0.01 (controlled for FDR), only.pos = true, log fold change ≥ 0.25, and genes detected in < 10% of the cells within its corresponding cluster were excluded. All specimens were normalized using the sctransform method and integrated using rpca method in IntegrateData. For both integrated datasets, the top 2,000 highly variable genes and the first 30 principal components were used for cell alignment before clustering and UMAP visualization.
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab-separated  values files and matrix files

source_name: eutopic endometrium from endometriosis patients (EU)and ectopic peritoneal lesions (SUP)

extract_protocol:
Tissues were isolated by mincing the freshly obtained surgical specimens into 1-mm cubic pieces followed by enzymatic digestion using 2mg/ml collagenase II, 2mg/ml collagenase IV, and 0.1mg/ml DNase I, and were incubated on a rocker for 30 min at 37 °C. The digested tissues were then passed through a 40 µm cell strainer and washed twice with PBS prior to surface staining. Determine cell concentration using AO/PI fluorescent staining dyes.The isolated cells are then loaded directly into compatible 10x Genomics Single Cell assays.
Following cell isolation, samples were sequenced by 10x Chromium single-cell platform (10x Genomics, Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 chemistry, Rev D). In detail, Gel Beads-in-emulsion (GEMs) generation and barcoding was first performed. Then, post GEM-RT cleanup and cDNA amplification were conducted. Finally, the 3′ gene-expression library construction was performed following the manufacturer’s instructions. The library is generated and sequenced on NovaSeq6000 (Illumina).

value: Endometriosis


title: NOA2

description:
Library name: NOA-2
Column name in raw_counts.txt: NOA_2

value: seminiferous tubules

value: spermatogenic cells

value: SPDYA variant


title: B09C

description: Library name: B09C

value: Muscle (SOL + EDL)

value: mixed

value: Tsc1F/F Depdc5 F/F


title: A50_1

description: Library name: Sample13

value: oxLDL 50 μg/ml, 24h


title: RNA_mESC_Gabpb1_b2_12h_DMSO_rep1

city: Beijing

last: Yang

address: No.1 West Beichen Road,Chaoyang District

description: Library name: RNA_mESC_Gabpb1_b2_12h_DMSO_rep1

value: cell line

value: mESCs


title: A10_2

description: Library name: Sample11

value: oxLDL 10 μg/ml, 24h


title: A10_3

description: Library name: Sample12

value: microglial cell line


title: RNA_mESC_Gabpa_12h_DMSO_rep2

description: Library name: RNA_mESC_Gabpa_12h_DMSO_rep2

value: GabpadTAG/dTAG


title: B09B

description: Library name: B09B

value: Ckm-Cre Tsc1F/F Depdc5 F/F


title: NC_2

description: Library name: Sample2

value: wild type

value: oxLDL 0 μg/ml, 24h


title: EU_OMA_SUP,replicate1,scRNAseq

description: 10x Genomics

source_name: eutopic endometrium from endometriosis patients (EU), ectopic ovarian lesions (OMA) and ectopic peritoneal lesions (SUP)


title: OA3

description:
Library name: OA-3
Column name in raw_counts.txt: OA_3

value: WT


title: NC2, scRNAseq

description: 10x Genomics

source_name: Eutopic endometrium

value: Eutopic endometrium

value: Teratoma


title: RH41 cells G3_C bio rep 3

city: Washington

first: Nikola

last: Knoll

state: DC

address: 3700 O St. NW

department: Oncology

institute: Georgetown University

description: Library name: Sample 6

data_processing:
Reads were aligned to the human genome (GRCh38.p13) using HISAT2 (RRID:SCR_015530), followed by counting raw reads via featureCounts (RRID:SCR_012919) in Galaxy (GVL 4.4.0).
Assembly: human genome (GRCh38.p13)
Supplementary files format and content: tab-delimited text file and annotated excel work sheet containing raw counts for each sample

source_name: soft tissue

growth_protocol: RH41 (RRID:CVCL_2176) cells were grown in RPMI 1640 media (Gibco #11875119) supplemented with 10% FBS (Sigma #F0926) at 37°C in a high humidity 5% CO2 atmosphere incubator.

extract_protocol:
For RNA isolation, the RNeasy Plus mini kit (Qiagen #74134) was used following manufacturer’s instructions.
cDNA library preparation and RNA sequencing were performed by NovoGene using poly A enrichment and NovaSeq X Plus Series (PE150) for Illumina paired-end sequencing (150 bp reads).

treatment_protocol: RH41 cells were treated for 7 days with DMSO control or 5uM G3_C (PFP-16) PAX3::FOXO1-targeting PROTAC. Re-dosing of drug with media change after 4 days.

value: soft tissue

value: fusion-positive rhabdomyosarcoma

value: 7 days 5 uM G3_C


title: NC_1

description: Library name: Sample1


title: CD36 CKO-2

first: xialin

last: liu

institute: Zhongshan Opythalmic Center, Sun yat-sen University

description:
Library name: Sample5
CKO5OD

data_processing:
Raw sequencing reads were processed using fastp (v0.18.0) for adaptor trimming and quality control, followed by alignment to the mouse reference genome (mm10) using HISAT2 (v2.2.4).
Assembly: mm10
Supplementary files format and content: xlsx file contains the  raw counts  of gene expression for each sample.

source_name: isolated retinal cells

extract_protocol:
For smart-seq2, retinae from wildtype and CD36 cko mice were dissected and dissociated into single cell suspension. Cells were then stained at room temperature for 30 minutes with CD45-APC (559864, BD Pharmingen™) and CD11b-BV421 (101236, BioLegend) antibodies. CD11bintCD45⁺ cells were sorted using a FACSAria Fusion cell sorter (BD Biosciences) for smart-seq2.
Library quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and sequencing was performed on NovaSeq X Plus platform.

treatment_protocol: Mice were injected intravenously with 20 mg/kg of NaIO3 (Sigma-Aldrich Corp., St. Louis, MO, USA), which was dissolved in phosphate-buffered saline (PBS). The mice receiving the same volume of PBS worked as controls.Seven days later, the mice were sacrificed by carbon dioxide euthanasia and the eyes were collected for further investigation.

value: isolated retinal cells

value: CD11bintCD45+  microglia

value: CD36 CKO


title: RH41 cells G3_C bio rep 2

description: Library name: Sample 5


title: B08C

city: Ann Arbor

description: Library name: B08C

value: Muscle (SOL + EDL)

value: mixed


title: CD36 CKO-3

description:
Library name: Sample6
CKO5OS


title: B09A

description: Library name: B09A

value: Tsc1F/F Depdc5 F/F


title: B08D

description: Library name: B08D


title: RNA_mESC_Gabpa_12h_DMSO_rep1

description: Library name: RNA_mESC_Gabpa_12h_DMSO_rep1

source_name: cell line

value: cell line

value: mESCs

value: treated with DMSO for 12 hours


title: EU_OMA, scRNAseq

description: 10x Genomics

source_name: eutopic endometrium from endometriosis patients (EU) and ectopic ovarian lesions (OMA)

value: Endometriosis


title: T cells donor 3 ctcf edit replicate 2

city: Oxford

last: Hamley

address: John Radcliffe Hospital/Headley Way

description:
Library name: cd4_don3_ctcf_rep2
Nucleotide percentage table around gRNA, split for reference and alternate chromosome

data_processing:
Reads were trimmed with Trimgalore, before reconstruction with FLASH. Editing efficiencies were esitmated using the CRSIPRESSO2 package using  base-editor mode and allele=specific editing flags for CD4 T cells edit and default flags for mouse HSPC edit experiemnts.
Assembly: hg38, mm39
Supplementary files format and content: Text file of the nucleotide percentages around the gRNA for editing efficiency calculation.

source_name: Blood

extract_protocol:
Qiagen DNAeasy kit
NEB Next Ultra II

value: Blood

value: CD4 T cell

value: CRISPR-Edited

value: Activated


title: B08B

description: Library name: B08B


title: RH41 cells G3_C bio rep 1

description: Library name: Sample 4

value: soft tissue

value: WT


title: RH41 cells DMSO bio rep 3

description: Library name: Sample 3

value: fusion-positive rhabdomyosarcoma

value: 7 days DMSO


title: CD36 CKO-1

description:
Library name: Sample4
CKO2OD

value: isolated retinal cells

value: CD11bintCD45+  microglia


title: NC_3

description: Library name: Sample3

value: microglial cell line

value: wild type

value: oxLDL 0 μg/ml, 24h


title: NC1, scRNAseq

description: 10x Genomics

value: Eutopic endometrium

value: Tubal sterilization


title: B08A

description: Library name: B08A

value: Muscle (SOL + EDL)

value: mixed

value: Tsc1F/F Depdc5 F/F


title: RNA_mESC_Gabpb1_12h_DMSO_rep1

description: Library name: RNA_mESC_Gabpb1_12h_DMSO_rep1

value: cell line

value: mESCs

value: treated with DMSO for 12 hours


title: CD36 flox-3

description:
Library name: Sample3
WT3OS

value: CD36 flox


title: T cells donor 3 ctcf edit replicate 1

description:
Library name: cd4_don3_ctcf_rep1
Nucleotide percentage table around gRNA, split for reference and alternate chromosome

value: Blood

value: CD4 T cell

value: CRISPR-Edited

value: Activated


title: PBS-NaIO3_eye_ball

description:
Library name: PBS-NaIO3_eye_ball
Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the Stereo-seq Analysis Workflow (SAW, BGI Research).
Low-quality reads and invalid coordinate identity (CID) sequences were filtered with default parameters. Clean reads were aligned to the mouse reference genome (GRCm38/mm10) using STAR aligner to generate spatial gene expression matrices. The original bin1 expression matrix was aggregated into bin50 resolution for downstream analyses. Spatial coordinates were assigned to each bin based on chip layout information.
Assembly: GRCm38/mm10
Supplementary files format and content: raw barcode gene exp: An annotated list file with the information ofcoordinate, gene, MID, read counts, which isprepared to be a sampling file that performssequence saturation
Supplementary files format and content: merge. barcodeReadsCount: A mapped CID list file with read counts for eachCID, including three columns (x, y, count)
Supplementary files format and content: cellbin.gef: Cellbin feature expression matrix records the information of cells individually, including the centroid coordinate, boundary coordinates,expression of genes, and cell area
Supplementary files format and content: adjusted.cellbin.gef: Cellbin expression matrix with cell border expanding
Supplementary files format and content: tissue.gef: Feature expression matrix under the tissue coverage region. It is also a visualization GEF which includes expression counts for bin1, 5, 10, 20, 50, 100, 150, 200.
Supplementary files format and content: raw.gef: Feature expression matrix includes the whole information over a complete chip region.
Supplementary files format and content: regist.tiff: The panoramic image, having been registered with the raw expression matrix, is from staining layers in TIFF format.
Supplementary files format and content: tissue_hires_image.tiff: high-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Library strategy: Spatial Transcriptomics

source_name: eyeball

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10um frozen sections were cut with cryostat.
Indexed sequencing libraries were constructed using the Stereo-seq Library Preparation Kit following standard STOmics protocols. Final libraries were sequenced on an MGI DNBSEQ-T7 platform using paired-end sequencing

treatment_protocol: To establish the retinal degeneration model, the mice were injected intravenously with 20 mg/kg of NaIO3 (Sigma-Aldrich Corp., St. Louis, MO, USA), which was dissolved in phosphate-buffered saline (PBS). The mice receiving the same volume of PBS served as controls. All mice were sacrifaced 7 days after NaIO3 or PBS treatment, and eyes were collected for spatial transcriptomics.

value: eyeball


title: OA1

description:
Library name: OA-1
Column name in raw_counts.txt: OA_1

value: seminiferous tubules

value: spermatogenic cells

value: WT