title: CD122 low 3

city: Montreal

first: Helene

last: Decaluwe

state: QC

address: 3175 Chem. de la Côte-Sainte-Catherine

country: Canada

institute: CHU Sainte Justine

description:
Library name: Sample 6
Day 21 post-infection

data_processing:
Reads were trimmed using Cutadapt.
The raw gene count matrices were generated using HTSeq (v0.6.1p1) in non-stranded mode.
Raw counts were filtered to remove low-expressed transcripts.
Assembly: RNA-seq FASTQ files were aligned and mapped to the mouse genome (GENCODE M6/Ensembl v81 GRCm38) using the STAR aligner (v2.4.2) with 2-pass mapping mode and a re-generated genome index.
Supplementary files format and content: counts

source_name: Spleen

growth_protocol: CD45.1+ C57BL/6 recipient mice were housed under specific pathogen-free conditions at the CHU Sainte-Justine Research Center. Congenically distinct P14 TCR-transgenic CD8+ T cells specific for the LCMV gp33-41 epitope were used for adoptive co-transfer experiments.

extract_protocol:
Total RNA was extracted from FACS-sorted CD8+ Tetramer+ CD11a+ IL2Rβhi and IL2Rβlo T cells using a TRIzol-based protocol. Cells were sorted directly into TRIzol, lysed for 5 min at room temperature, followed by chloroform phase separation, isopropanol precipitation, ethanol washing, air drying, and resuspension of RNA in RNase-free water.
RNA libraries were prepared using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to the manufacturer's instructions. Poly(A)+ RNA was enriched prior to library preparation.

treatment_protocol: Recipient mice received an adoptive co-transfer of 5,000 P14 IL2Rβ+/+ CD8+ T cells and 5,000 P14 IL2Rβ-/- CD8+ T cells one day before intravenous infection with 2 × 10^6 PFU of LCMV Clone 13. At day 21 post-infection, splenic virus-specific CD8+ Tetramer+ CD11a+ T cells were sorted according to IL2Rβ/CD122 surface expression into IL2Rβhi and IL2Rβlo populations for RNA sequencing.

value: Spleen

tag: cell type

value: CD8 T cells

value: C57BL/6J CD45.2+ P14+ TCR transgenic specific for the gp33-41 epitope of the LCMV virus

value: Infected mice with LCMV-cl 13


title: Cd_ABA2

status: Public on Jul 15 2026

type: SRA

city: Hong Kong

first: Shumin

last: LIANG

address: 224 Waterloo Road, Kowloon Tong, HK

department: Biology

country: China

institute: Hong Kong Baptist University

description: Library name: Cd_A2

library_source: transcriptomic

data_processing:
After sequencing, raw read were subjected to quality control and trimmed by using fastqc (v0.11.8) to get high-quality reads.
High-quality reads were mapped to the Arabidopsis genome (TAIR10) using hisat2 (v2.2.1).
Calculated the read counts of each gene with FeatureCounts (included in Subread v2.0.8 software) to generate the count matrix for expression analysis.
Assembly: TAIR10(Assembly: GCA_000001735.1)
Supplementary files format and content: format:txt; content:raw counts for each sample

molecule: total RNA

organism: Arabidopsis thaliana

source_name: 5-day-old seedlings

growth_protocol: To grow seedlings on solid media, surface-sterilized seeds were placed on half-strength Murashige and Skoog (MS) Basal Salts (M524, Sigma-Aldrich) containing 1% (w/v) sucrose (15503-022, Invitrogen) and 1% agar (A1296, Sigma-Aldrich), with a pH of 5.8 adjusted by 1 M KOH.The plates with seeds were stratified in the dark at 4 ºC for three days and then placed in a growth chamber (Percival Scientific) at 22 ºC with 60% humidity and a light intensity of 125 mol m-2 sec-1 under a 16-h light/8-h dark photoperiod for 5 days.

extract_protocol:
Total RNA were extracted using TRIzol reagent (15596026, ThermoFisher) following the manufacturer's instruction.
The mRNA libraries (poly A enrichment) were prepared by Novogene Incorporation (Beijing, China) using reagents for Illumina.

treatment_protocol: The 5-day-old seedlings in plates were then transferred to MS liquid medium with or without 50 μM ABA (962169,Sigma-Aldrich) for 3 hours, and then sampling with liquid nitrogen.

tag: tissue

value: 5-day-old seedlings

tag: genotype

tag: treatment

value: ABA


title: KMS-11-1uM-Day14-Rep1

city: San Diego

first: Bo

last: Hu

address: 10300 Campus Point Dr

country: USA

institute: Bristol Myers Squibb

description: Library name: KMS-11-1uM-Day14-Rep1-RNAseq

data_processing:
Adapter sequences and low-quality bases were removed from paired-end RNA-seq FASTQ files using cutadapt
Trimmed paired-end reads were aligned using STAR v2.6.0c to the GRCh38 reference genome with ERCC spike-in sequences, using gene annotation from Ensembl release 91
STAR was run to generate coordinate-sorted genomic BAM files, as well as transcriptome alignments and gene-level counts
Duplicate reads were marked using Picard MarkDuplicates. Duplicate reads were flagged in the BAM file but not removed
Gene-level read counts were generated from aligned reads using featureCounts with GENCODE gene annotation
Assembly: hg38
Supplementary files format and content: TSV of gene counts

molecule: polyA RNA

organism: Homo sapiens

source_name: Bone marrow

growth_protocol: Cell lines were maintained in standard mammalian aseptic cell culture conditions at 37 °C and 5% CO2. All cell lines used in this study were cultured in RPMI 1640 supplemented with 10% heat-inactivated Fetal Bovine Serum (Gibco) and 10U/ml penicillin, 10ug/mL streptamycin

extract_protocol:
Purified total RNA from 2 million cells was sent to Azenta for Poly(A) RNA library preparation, with ERCC spike-in, using the Illumina Stranded mRNA Preparation protocol. Total RNA yield and quality was assessed using Qubit™ RNA HS Assay Kit (Q32855, ThermoFisher) and TapeStation High Sensitivity RNA ScreenTape (5067-5579, Agilent)
NGS libraries were pooled in equal quantity and sequenced at the Azenta NextGen DNA sequencing core using the NovaSeq 6000 (Illumina) to produce 20 million paired-end reads (50x50 bases) per each RNA-Seq library

treatment_protocol: Drug treatments or DMSO vehicle were administered to exponentially growing cells in fresh media at indicated concentrations. Cells were washed and diluted in fresh media containing compounds every 3-4 days over which the number of doublings were calculated from cell counts measured using Vi-CELL XR (Beckmann Coulter, CA).

value: Bone marrow

tag: cell line

value: Multiple myeloma

tag: time point


title: Cd_ABA1

description: Library name: Cd_A1


title: P120_G93AKO_2

city: Minato-ku

first: Yuta

last: Morisaki

state: Tokyo

address: 1-5-30, Shibakoen

department: Faculty of Pharmacy

country: Japan

institute: Keio University

description: Library name: P120_G93AKO_2

data_processing:
Raw sequencing data were processed using Trim Galore (version 0.6.7) for quality control and adapter trimming. Transcript abundance was quantified using Salmon (version 1.9.0) against the mouse reference transcriptome (GRCm39). Count matrices were generated using tximport in R (version 4.2.1).
Assembly: GRCm39
Supplementary files format and content: Raw count data

organism: Mus musculus

source_name: microglia

extract_protocol:
RNA extraction from FACS-sorted cells using SMART-seq mRNA HT LP Kit
Using the SMART-seq mRNA HT LP Kit (Takara Bio), prepare a cDNA library from each sample.

value: microglia


title: UC-34

city: Boston

first: Minyi

last: Lee

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University Chobanian & Avedisian School of Medicine

description: Library name: UC-34

data_processing:
Demultiplexing and creation of FASTQ files were automatically performed using the Illumina BaseSpace platform with default parameters.
Reads were aligned to the Genome Reference Consortium human build 38 (GRCh38) using STAR v2.6.0c.
Both gene and transcript level counts were calculated using RSEM v1.3.1 with annotation from Ensembl build 107.
Genes were filtered for analysis based on counts per million (CPM) reads mapped across all samples. Genes with CPM counts greater than 1 in more than 10% of the total number of patients were used in subsequent analyses. CPM was calculated using the calcNormFactors and cpm functions from the edgeR package (version 4.4.1).
Assembly: hg38
Supplementary files format and content: counts.tsv: tab-separated values (TSV) file containing 5737 x 120 matrix of "expected_count" values computed by RSEM

source_name: Nasal brushing

extract_protocol:
Total RNA was isolated from nasal brushings using the miRNeasy Mini Kit (Qiagen, Valencia, CA).
Libraries were generated using the Illumina TruSeq RNA Exome kit.

value: Nasal brushing

tag: subject id

tag: median tin

tag: cancer status

value: Benign

tag: age

tag: gender

value: male

tag: smoking status

value: FORMER

tag: sequencing batch


title: KMS-11-100nM-Day7-Rep2

description: Library name: KMS-11-100nM-Day7-Rep2-RNAseq


title: d1_ABA-3

description: Library name: d1_A3


title: P120_G93AKO_1

description: Library name: P120_G93AKO_1


title: UC-31

description: Library name: UC-31

value: Cancer

value: NEVER


title: KMS-11-100nM-Day7-Rep1

description: Library name: KMS-11-100nM-Day7-Rep1-RNAseq


title: P140_G93A_3

description: Library name: P140_G93A_3


title: d1_ABA-2

description: Library name: d1_A2


title: UC-20

description: Library name: UC-20

value: Metastatic

value: female


title: P140_G93A_2

description: Library name: P140_G93A_2


title: d1_ABA-1

description: Library name: d1_A1


title: KMS-11-100nM-Day14-Rep2

description: Library name: KMS-11-100nM-Day14-Rep2-RNAseq


title: UC-2

description: Library name: UC-2


title: KMS-11-100nM-Day14-Rep1

description: Library name: KMS-11-100nM-Day14-Rep1-RNAseq


title: WT_ABA-3

description: Library name: WT_A3


title: Synovial mesenchymal stem cell

city: Bunkyo-ku

first: Kentaro

last: Endo

address: 1-5-45 Yushima

institute: Institute of Science Tokyo

description: Library name: SyMSC

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using Cell Ranger (version 6.1.2, 10x Genomics) with the cellranger count pipeline.
Assembly: hg38
Supplementary files format and content: h5 file generated from Cellranger Count output

source_name: Synovial mesenchymal stem cell

extract_protocol:
Frozen SyMSCs and AdMSCs at P0 were thawed rapidly in a 37°C water bath.
Single-cell libraries were prepared using the Chromium Next GEM Single Cell 3′ Gene Expression platform (10x Genomics, Pleasanton, CA). Briefly, single cells were encapsulated into gel bead-in-emulsions using the Chromium Controller, and barcoded cDNA was generated and amplified by PCR. Amplified cDNA was enzymatically fragmented, size-selected using SPRIselect beads (Beckman Coulter, Brea, CA), and subjected to end repair, A-tailing, adaptor ligation, and index PCR. Libraries were constructed using the Chromium Next GEM Single Cell 3′ Kit v3.1 Dual Index Kit TT Set A.

value: Synovial mesenchymal stem cell


title: P140_G93A_1

description: Library name: P140_G93A_1


title: P120_G93A_3

description: Library name: P120_G93A_3


title: UC-17

description: Library name: UC-17


title: UC-16

description: Library name: UC-16


title: WT_ABA-2

description: Library name: WT_A2


title: WT_ABA-1

description: Library name: WT_A1


title: Adipose mesenchymal stem cell

description: Library name: AdMSC

source_name: Adipose mesenchymal stem cell

value: Adipose mesenchymal stem cell


title: P120_G93A_2

description: Library name: P120_G93A_2


title: scRNA-seq of human T cells vaccinated with UniCVac

city: Shanghai

first: wang

last: wanting

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

description: Library name: scRNA_Human_UniCVac

data_processing:
Raw sequencing data (FASTQ files) were processed, aligned to the mm10 mouse (or hg38 homo sapiens) reference genome, and quantified using the official 10x Genomics Cell Ranger pipeline.
Assembly: mm10; hg38
Supplementary files format and content: MTX and TSV files containing raw UMI counts per cell

source_name: T cell

extract_protocol:
Freshly excised tumors were mechanically minced and enzymatically digested using a tumor dissociation kit containing Collagenase IV and DNase I at 37°C. The digested cell suspensions were passed through a 70um cell strainer. Red blood cells were lysed, and dead cells were removed to ensure high cell viability (>80%) prior to sequencing.
Single-cell suspensions were loaded onto the 10x Genomics Chromium Controller to generate single-cell gel beads-in-emulsion (GEMs). Single-cell RNA-seq libraries were constructed using the Chromium Single Cell 3' Reagent Kits (10x Genomics) according to the manufacturer's official protocol.

value: T cell


title: UC-11

description: Library name: UC-11


title: scRNA-seq of human T cells vaccinated with BAPC

description: Library name: scRNA_Human_BAPC


title: Mixed, barcode-transduced primary bulk human T cells, ex vivo day 7, donor 2, barcode library

city: Denver

first: Kole

middle: R

last: DeGolier

state: Colorado

address: 1400 Jackson St

department: Immunology and Genomic Medicine

institute: National Jewish Health

description:
Library name: 2025.KRD040bc
10X Genomics with custom retroviral barcoding

library_source: genomic

data_processing:
scATAC-seq files were demultiplexed using cellranger-atac mkfastq
Demultiplexed data was processed using the cellranger-atac pipeline.
Peaks were called and .bam files were generated using the ArchR pipeline (https://www.archrproject.com/bookdown/index.html).
Assembly: GRCmm10, GRChg38
Supplementary files format and content: .bam files containing peaksets called on single murine data experiment (2025.KRD012) or compiled human data experiments (KRD024, KRD029, KRD039, KRD040).

molecule: genomic DNA

source_name: Bone Marrow

growth_protocol:
In Vitro, Murine Cells: Mouse CAR T cells were cultured in cRPMI as described above. CD8+ T cells were isolated from 10-16 week old C57BL/6 mouse splenocytes using the MojoSort Mouse CD8 T Cell Isolation Kit (BioLegend, Cat No. 480035). On day 0, T cells were activated with 1µg/mL anti-CD3 and 1µg/mL anti-CD28 overnight. Cells were transduced on day 1 by centrifugation at 2000xg for 90 minutes at 37°C with fresh gammaretrovirus and 10ug/mL polybrene, followed by removal of retrovirus and polybrene after the spin and replacement with fresh media containing the specified amount of IL-2, either 10IU/mL or 100IU/mL (National Cancer Institute). Transduction was repeated on the following day (day 2), and then cells were removed from anti-CD3/anti-CD28 stimulation and plated at 1x106 cells/mL in fresh media containing IL-2. On day 3 and 4, cells were replated at 1x106 cells/mL in fresh media containing IL-2. For the “swap” condition, IL-2 concentration was changed from 100IU/mL to 10IU/mL. Cells were FACS sorted (Lymphocytes > Singlets > Live > CD8+ > mThy1.1+) and captured for scATAC-seq on day 5, 16 hours after the IL-2 “swap” (or media replacement for the “high” and “low” IL-2 conditions).
In Vitro, Human Cells: CD3+ human T cells were cultured in Human T Cell Expansion Media (hTCEM), consisting of AIM-V (Gibco, Cat No 12055-091) supplemented with 5% FBS and 10mM HEPES (Gibco, 15630-080). On day 0, T cells were thawed and activated with Dynabeads Human T cell Expander CD3/CD28 (Gibco, Cat No. 11141D) at a 3:1 bead:cell ratio at 1x106 cells/mL, in hTCEM supplemented with 40IU/mL IL-2 and cultured for 48 hours. On day 2, T cells were counted and transduced at 2x106 cells per well in a 6 well plate, with 10µg/mL Protamine Sulfate (Millipore-Sigma, Cat No. P4020-1G), spinning at 1000xg for 2.5 hours at 32°C. On day 3, T cells were transduced again with fresh virus. On day 4, beads were removed, and cells were plated in fresh hTCEM supplemented with 100IU/mL IL-2 at 0.5x106 cells/mL. On day 6, cells were replated at 0.5x106 cells/mL with fresh hTCEM and 100IU/mL IL-2, and a small aliquot was taken to check transduction efficiency. On day 8, cells were counted with a small aliquot taken for FACS sorting (Lymphocytes > Singlets > Live > CD4+ or CD8+ > mThy1.1+) and scATAC-seq capture (‘Pretransfer’ timepoint), with the rest cryopreserved in Freeze Media as described above.

extract_protocol:
After sorting, cells were pooled, washed once in cold PBS and then lysed in Lysis Buffer (Nuclease-Free H2O with 10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween20, and 0.01% Digitonin) for the following times: 5 mins (cell lines), 3 mins (in vitro primary cells), 3 mins 45 seconds (ex vivo primary cells). Cells were then resuspended in 1X Nuclei Buffer and analyzed for nuclei count and lysis efficiency via 0.4% Trypan Blue staining on the Countess 3 (ThermoFisher), with >95% lysis efficiency typical. Cells were then diluted to ≤2.4x106 cells/mL for capture of ~8000 nuclei in a single 10X capture well, following manufacturer protocols for Chromium Next GEM Single Cell ATAC Reagent Kits v2 (10X Genomics, User Guide CG000496). Two modifications were required to this protocol for barcode enrichment, as described previously19: first, 1.32µL of 50µM spike-in barcode enrichment oligo was added to the GEM reaction master mix (step 2.1a in 10X protocol); second, the PCR following GEM generation was increased from 12 to 15 cycles (step 2.5a in 10X protocol). Libraries were prepared per manufacturer specifications and analyzed using the TapeStation (Agilent) and Qubit Fluorometer (ThermoFisher).
Final scATAC and barcode libraries were pooled to 10nM concentration for sequencing. Final concentrations for individual libraries in the pool were calculated to achieve a target sequencing depth of 40,000 reads/nuclei (scATAC library) and 1,000 reads/nuclei (barcode library).

treatment_protocol: In Vivo, Human Cells: NOD-Scid-Gamma (‘NSG’, NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ; Strain #: 005557, Jackson Laboratories) were obtained commercially and then bred in-house. For xenograft studies, between 4 and 9 male or female NSG mice (up to 20 weeks of age, same gender in a single experiment) received 1x106 NALM6-CD22Lo leukemia on day -3, followed by 1x106 CAR+ cells (pooled equally from all six CAR conditions) on day 0. Leukemia burden was monitored before CAR injection (day -1), on day 4, and on day 7 before marrow harvest, using the Xenogen In Vivo Imaging System (IVIS) Spectrum (Caliper Life Sciences) after intraperitoneal injection with D-Luciferin Potassium Salt (Revvity, Cat No. 122799A-5). Total flux (photons/s) was measured for each mouse using Living Image software (Revvity, v4.8.2). On day 7, bone marrow was harvested, filtered through a 70µm strainer, and red blood cells were lysed using ACK Lysing Buffer. Cells were then filtered again, and human cells were enriched using MojoSort Mouse CD45 Nanobead (BioLegend, Cat No. 480028) depletion of mouse bone marrow. Cells were stained and FACS sorted (Lymphocytes > Singlets > Live > CD45+/GFP- > CD4+ or CD8+ > mThy1.1+) for scATAC-seq capture (‘ex vivo’ timepoint). Xenograft animal studies were conducted at University of Colorado Anschutz Medical Campus in accordance with an animal protocol approved by the Institutional Animal Care and Use Committee (IACUC, Protocol 751).

value: Bone Marrow

value: CD4 and CD8 T cells

value: Harvest bone marrow T cells at day 7 after response to NALM6-CD22Lo leukemia


title: LAG-3-High_G93A_microglia_5

description: Library name: LAG-3-High_G93A_microglia_5


title: P120_G93A_1

description: Library name: P120_G93A_1


title: r1_Mock3

description: Library name: r1_M3

value: 5-day-old seedlings

value: Mock


title: r1_Mock2

description: Library name: r1_M2


title: Mixed, barcode-transduced primary bulk human T cells, ex vivo day 7, donor 2, scATAC library

description:
Library name: 2025.KRD040
10X Genomics with custom retroviral barcoding
Human_CD22-CAR_allPeaks.raw.bed

library_source: genomic single cell


title: bulk RNA-seq of human HA-TCR-T cells vaccinated with UniCVac rep_3

description: Library name: F11_vac_3

data_processing:
Raw sequencing data in FASTQ format were processed using fastp to remove adapters and low-quality reads. The clean paired-end reads were aligned to the reference genome using HISAT2 (version 2.2.1). The read numbers mapped to each gene were quantified using featureCounts (version 2.0.6), and FPKM values were calculated to estimate gene expression levels. Differential expression analysis between groups was performed using the DESeq2 R package (version 1.42.0). The significance threshold was set at padj <= 0.05 and |log2(foldchange)| >= 1.
Assembly: hg38
Supplementary files format and content: tab-delimited text files containing raw read counts per gene

extract_protocol:
After in vitro stimulation, primary T cells were collected and washed. Total RNA was extracted using TRIzol reagent according to the manufacturer's protocol. The RNA quality and concentration were assessed before library preparation.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. The sequencing library was constructed through end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Library quality was checked with Qubit, real-time PCR, and a bioanalyzer.

value: HA-TCR-T cells

value: vaccinated with UniCVac


title: DSP-1001660014603-Y-F07

city: Dallas

first: Chengsong

last: Zhu

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

description: Library name: Sample 116

library_source: other

data_processing:
/opt/illumina/Isas/1.37.0/bcl2fastq2/bin/bcl2fastq  --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls --auto-set-to-zero-barcode-mismatches --find-adapters-with-sliding-window --adapter-stringency 0.9 --mask-short-adapter-reads 35 --minimum-trimmed-read-length 35 -R  /data/scratch/workspace/RunFolder --sample-sheet "/data/scratch/workspace/RunFolder/SampleSheet.csv" -o "/data/scratch/workspace/RunFolder/Analysis/Temp_01.01-GenerateFASTQ.FastqGeneration"
raw sequencing data  were processed using Illumina basespace pipeline to generate fastq files
Run Nanostring GeoMx NGS pipeline ( version 3.1.1.6)  to generate DCC files
Upload DCC files to GeoMx DSP platform and create the study
Perfom standand QC using default parameters setting recommended by the manufacture
Q3 normalization was carried out to generate Q3 normalization datasets  which are for the all downstream analysis
Assembly: GRCh38
Supplementary files format and content: raw_dcc.tar:  raw read counts in DCC of tar
Supplementary files format and content: Protein_Q3_normalized_expression_matrix.txt  :  normalization gene expression matrix by Q3 normalization recommended by manufacture which are used for all the downstream analysis in txt format

molecule: protein

source_name: Lupus 2

extract_protocol:
FFPE tissues were parafilm embedded, 5 µM sections were cut with cryostat
Spatial transcritpome sequencing libraries were prepared with Nanostring GeoMx DSP NGS library preparation kit according to manufacturer's instruction

value: Lupus 2

tag: panel (wta_+ipa)

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein

value: IA

tag: scan name

tag: roi

tag: segment


title: r1_Mock1

description: Library name: r1_M1


title: ThB1M;fly whole body;Thor[2];Lsp2[B14];monosome-Seq;rep1

city: changsha

first: cai

last: zixin

email: 964530737@qq.com, cangjie@hnu.edu.cn

state: 湖南Hunan

address: yuelu district tianma road

institute: Hunan university

description:
Library name: ThB1M
Monosome-seq

data_processing:
We first performed quality control and adapter trimming on the raw sequencing reads using fastp (v0.23.2). Reads were then mapped to species-specific rRNA using Bowtie2 (v2.3.4.1) to remove ribosomal RNA contaminants. Clean reads were aligned to the Drosophila melanogaster (BDGP6.46) reference genome (ensembl.org/Drosophila_melanogaster/Info/Index) by STAR (v2.2.1). Uniquely mapped reads were summarized to Drosophila_melanogaster.BDGP6.46.110.chr.gtf annotated genes using featureCounts (v1.6.0). The resulting raw gene expression matrix was then imported into the R (v4.2.0) environment for further processing and analysis.
Assembly: BDGP6.46
Supplementary files format and content: csv file includes raw counts for each Sample

organism: Drosophila melanogaster

source_name: whole body

extract_protocol:
Whole female flies were ground in liquid nitrogen. A portion of the powdered tissue was reserved for total RNA extraction, while the remaining material was lysed and subjected to 10–45% sucrose density gradient centrifugation. Monosome and polysome fractions were collected after gradient fractionation. Total RNA and RNA from the monosome and polysome fractions were separately isolated using TRIzol reagent (Invitrogen, #15596026).
Poly(A)+ RNA was enriched from 2 μg of total RNA, monosome-bound RNA, or polysome-bound RNA using VAHTS mRNA Capture Beads (Vazyme, #N401). The enriched RNA was fragmented and subjected to end repair, adaptor ligation, and PCR amplification using the VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme, #NR604). Following library quality control and quantification, the libraries were sequenced on an Illumina NovaSeq 6000 platform to generate 150-bp paired-end reads.

value: whole body

tag: time

value: 15 day

tag: batch

value: ThB*M


title: PT22_Tamoxifen_24_day_Rep2

city: Ann Arbor

first: Jeffrey

middle: A

last: Beamish

state: MI

address: 1500 E. Medical Center Drive, SPC 5364

department: Department of Internal Medicine, Division of Nephrology

institute: University of Michigan

description: Library name: PT22_Tamoxifen_24_day_Rep2

data_processing:
ATAC-seq libraries were sequenced on an Illumina HiSeq 2500 (125-nucleotide read length, paired end), trimmed, and aligned to the GRCm38/mm10 mouse using Bowtie2.
Assembly: GRCm38
Supplementary files format and content: bigWig files

source_name: Kidney

growth_protocol: Modified PT-22 cells were cultured in DMEM supplemented with 3% fetal bovine serum and penicillin/streptomycin.

extract_protocol:
Samples were washed with PBS and nuclei were prepared using the NE-PER Nuclear and Cytoplasmic Extraction Reagents Kit (Invitrogen).
Nuclei were resuspended in 50 μl of 1× TD buffer, then incubated with 2–2.5 μl Tn5 enzyme for 30 min at 37 ⁰C (DNA Library Preparation Kit, Nextera). Samples were immediately purified by Qiagen minElute column and PCR-amplified with the NEBNext High-Fidelity 2X PCR Master Mix (NEB). qPCR was used to determine the optimal PCR cycles to prevent over-amplification. The amplified library was further purified by Qiagen minElute column and SPRI beads (Beckman Coulter).

treatment_protocol: Cells were treated with 1 uM 4-hydroxytamoxifen 2 d to deplete PAX8 or with vehicle. Samples were collected at 0, 3, 24 d.

tag: tissue

value: Kidney

tag: cell type

value: Proximal tubule

tag: genotype

value: 4-hydroxytamoxifen (1 uM)

tag: replicate


title: DSP-1001660014603-Y-F03

description: Library name: Sample 112

source_name: Lupus 1

value: Lupus 1

tag: treatment

value: PF

value: DESMIN


title: bulk RNA-seq of human HA-TCR-T cells vaccinated with UniCVac rep_2

description: Library name: F11_vac_2

tag: cell line

value: T cell


title: ThB2R;fly whole body;Thor[2];Lsp2[B14];RNA-Seq;rep2

description:
Library name: ThB2R
RNA-seq

value: ThB*R


title: LAG-3-High_G93A_microglia_4

description: Library name: LAG-3-High_G93A_microglia_4

value: microglia


title: LAG-3-High_G93A_microglia_3

description: Library name: LAG-3-High_G93A_microglia_3


title: LAG-3-High_G93A_microglia_2

description: Library name: LAG-3-High_G93A_microglia_2


title: bulk RNA-seq of human HA-TCR-T cells vaccinated with UniCVac rep_1

description: Library name: F11_vac_1

value: HA-TCR-T cells


title: Mixed, barcode-transduced primary bulk human T cells, ex vivo day 7, donor 1, barcode library

description:
Library name: 2025.KRD039bc
10X Genomics with custom retroviral barcoding

value: Bone Marrow

value: CD4 and CD8 T cells

value: Harvest bone marrow T cells at day 7 after response to NALM6-CD22Lo leukemia


title: Nd_Mock2

description: Library name: Nd_M2

value: 5-day-old seedlings

value: Mock


title: Mixed, barcode-transduced primary bulk human T cells, in vitro, donor 2, barcode library

description:
Library name: 2025.KRD029bc
10X Genomics with custom retroviral barcoding

source_name: PBMC-derived T cells

value: PBMC-derived T cells

value: Barcoded CAR transduction


title: LAG-3-High_G93A_microglia_1

description: Library name: LAG-3-High_G93A_microglia_1


title: Mixed, barcode-transduced primary bulk human T cells, in vitro, donor 2, scATAC library

description:
Library name: 2025.KRD029
10X Genomics with custom retroviral barcoding
Human_CD22-CAR_allPeaks.raw.bed


title: bulk RNA-seq of human HA-TCR-T cells vaccinated with BAPC rep_2

description: Library name: F11_R_2

value: vaccinated with BAPC


title: LAG-3-Low_G93A_microglia_5

description: Library name: LAG-3-Low_G93A_microglia_5


title: Cd_Mock3

description: Library name: Cd_M3


title: bulk RNA-seq of human HA-TCR-T cells vaccinated with BAPC rep_1

description: Library name: F11_R_1


title: LAG-3-Low_G93A_microglia_4

description: Library name: LAG-3-Low_G93A_microglia_4


title: Mixed, barcode-transduced primary bulk human T cells, in vitro, donor 1, barcode library

description:
Library name: 2025.KRD024bc
10X Genomics with custom retroviral barcoding


title: bulk RNA-seq of human HA-TCR-T cells vaccinated with control rep_3

description: Library name: F11_nc_3

value: vaccinated with control


title: Cd_Mock2

description: Library name: Cd_M2


title: Cd_Mock1

description: Library name: Cd_M1


title: bulk RNA-seq of human HA-TCR-T cells vaccinated with control rep_2

description: Library name: F11_nc_2


title: Mixed, barcode-transduced primary bulk human T cells, in vitro, donor 1, scATAC library

description:
Library name: 2025.KRD024
10X Genomics with custom retroviral barcoding
Human_CD22-CAR_allPeaks.raw.bed


title: LAG-3-Low_G93A_microglia_2

description: Library name: LAG-3-Low_G93A_microglia_2


title: d1_Mock-3

description: Library name: d1_M3


title: bulk RNA-seq of human HA-TCR-T cells vaccinated with control rep_1

description: Library name: F11_nc_1


title: LAG-3-Low_G93A_microglia_1

description: Library name: LAG-3-Low_G93A_microglia_1


title: bulk RNA-seq of human E7-TCR-T cells vaccinated with UniCVac rep_3

description: Library name: E7_vac_3

value: E7-TCR-T cells

value: vaccinated with UniCVac


title: WT_microglia_4

description: Library name: WT_microglia_4


title: d1_Mock-1

description: Library name: d1_M1


title: KMS34_NSD2LDD_Dup1_Day10

description: Library name: KMS34_NSD2LDD_Dup1_Day10_ATACseq

data_processing:
Paired-end FASTQ files were adapter trimmed and quality filtered using fastp with automatic detection of paired-end adapters
Trimmed reads were aligned to the human reference genome hg38 using bwa-mem2 in paired-end mode.
Aligned reads were collated by read name using samtools collate to prepare the BAM file for duplicate marking.
PCR/optical duplicate reads were marked using Picard MarkDuplicates.
Duplicate-marked BAM files were coordinate sorted using samtools sort and indexed using samtools index.
Reads were filtered using samtools view to retain only properly paired, uniquely mapped primary alignments with mapping quality ≥ 30, while excluding unmapped reads, secondary alignments, duplicate reads, and supplementary alignments. Only reads mapping to included reference chromosomes were retained
Peaks were called from the filtered paired-end BAM files using MACS3 callpeak with BAMPE input format, human genome size (hs), and q-value cutoff 0.01
Genome-wide coverage tracks were generated from filtered BAM files using deepTools bamCoverage, with read centering, blacklist exclusion, and CPM normalization, producing bigWig files
Assembly: hg38
Supplementary files format and content: narrrowPeak
Supplementary files format and content: bigWig

extract_protocol:
200K cells were used to perform ATAC-Seq. The cells were washed twice with 200 μL of cold PBS and spun at 600 g for 3 mins at 4 °C. Cells were then incubated with 100 μL of transposition reaction mix (50 μL 2x TD buffer, 5 μL Tn5 transposase, 44 μL Nuclease free H2O, 1 μL 10% Tween-20, 1 μL 1% Digitonin) (20034198, Illumina) and incubated on a thermomixer at 37°C for 30 mins at 750 rpm. Samples were then purified using the MinElute PCR Purification kit (28004, Qiagen) and stored at -20°C.
The Nextera Index kit (FC-121-1011, Ilumina) was used for library preparation following manufactures instructions. 50 µl of reaction mix (10 μL of transposed DNA, 9.7 μL H2O, 2.5 μL Nextera i7 primer, 2.5 μL Nextera i5 primer, 0.3 μL 100x SYBR Green, and 25 μL NEBNext High-Fidelity 2x PCR master mix) was added to each sample and 5 μL was removed to perform qPCR to determine CtD (72 °C for 5mins, 98 °C for 30 secs, (98 °C for 10 sec, 63 °C for 30 sec, 72 °C for 1 min). The samples were purified using Ampure XP beads (A63881, Beckman Coulter) eluted in 20 μL TE buffer and quantified using Qubit™ DNA HS Assay Kit (Q33230, ThermoFisher) and TapeStation High Sensitivity DNA ScreenTape (5067-5584, Agilent) prior to sequencing.

value: Bone marrow

value: Multiple myeloma

tag: time point


title: KMS34_NSD2LDD_Dup1_Day4

description: Library name: KMS34_NSD2LDD_Dup1_Day4_ATACseq


title: WT_microglia_3

description: Library name: WT_microglia_3


title: bulk RNA-seq of human E7-TCR-T cells vaccinated with UniCVac rep_1

description: Library name: E7_vac_1

value: T cell


title: WT_Mock-3

description: Library name: WT_M3


title: bulk RNA-seq of human E7-TCR-T cells vaccinated with BAPC rep_3

description: Library name: E7_R_4


title: WT_microglia_2

description: Library name: WT_microglia_2


title: WT_microglia_1

description: Library name: WT_microglia_1


title: KMS34_Dup1_Day0

description: Library name: KMS34_Dup1_Day0_ATACseq


title: bulk RNA-seq of human E7-TCR-T cells vaccinated with BAPC rep_2

description: Library name: E7_R_3


title: KMS34_DMSO_Dup2_Day4

description: Library name: KMS34_DMSO_Dup2_Day4_ATACseq

value: DMSO


title: E14 TKO AEBP2 short rescue RNA Day4 rep2

city: Seoul

first: Yingying

last: Li

state: Seoul

address: 103 Daehak-ro

department: Department of Biomedical Sciences

country: South Korea

institute: Seoul National University

description: Library name: E14_TKO_AEBP2_Short_rescue_Day4_RNA_rep2

data_processing:
CUTnTag: Adaptor sequences were trimmed using Cutadapt, and the filtered reads were aligned to the mouse reference genome (mm10) with Bowtie2 using default parameters. Duplicate reads were identified and removed with Samtools markdup. Reads that failed to align to the mouse genome were subsequently mapped to the Drosophila genome (dm6), and the number of Drosophila-mapped reads was used to calculate the spike-in normalization factor.  ChIP-seq: and Libraries were prepared with NEB DNA library prep kit (NEB, E7645L) following the manufacturer’s protocol. Libraries were validated using the Tapestation HS D5000 screen tape.  RNA-seq: Adapter sequences were trimmed using Trimmomatic and reads were aligned to the hg38 reference genome using HISAT2. Transcript assembly was performed with StringTie for downstream analysis. Differential gene expression analysis was carried out using DESeq2 with p-value < 0.05 and log2 |fold change| > 1.
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x antibiotics/antimycotics, 1x MEM non-Essential Amino Acids, 10mM 2-Mercaptoethanol, Leukemia inhibitory Factor, 1mM MEK1/2 inhibitor (PD0325901), 3mM GSK3 inhibitor (CHIR99021). Cells were cultured at 37°C at 5% CO2.

extract_protocol:
CUTnTag: CUT&Tag was carried out following the Epicypher protocol.  ChIP-seq: 3 x 106 cells were harvested and fixed sequentially with 2mM disuccinimidyl glutarate (DSG; Thermo Fisher, 20593) for 35 minutes followed by 1% formaldehyde for 10 minutes at room temperature. Crosslinking was quenched with 0.125M glycine, and nuclei were isolated in NE buffer and extracted nuclei were then resuspended 1% SDS lysis buffer (50mM Tris-HCl pH 8, 10mM EDTA pH 8, 1% SDS) and sonicated by Covaris S220 sonicator (Power 175 W, Duty 10%, 200 cycles per burst) for 430 seconds to generate DNA fragments of approximately 200bp. Sheared chromatin was diluted in ChIP dilution buffer (16.7 mM Tris-HCl, pH 8.0, 0.01% SDS, 1.1% Triton X-100, 16.7 mM NaCl, 1.2 mM EDTA) and clarified by centrifugation at 13,000 rpm for 15 minutes at 4 °C. Chromatin was incubated overnight at 4 °C with Dynabeads protein A pre-bound to 2.4mg target antibody. 1 µg of Drosophila chromatin (Active Motif, #53083) and 0.1 µg of anti-Drosophila H2A.X antibody (Active Motif, #61686) were added per reaction to perform spike-in normalization. The next day, Dynabeads were washed three times with buffer A (140mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, 10mM Tris-HCl pH 8), twice with buffer B (300mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 1% Triton X-100, 0.2% SDS, 0.1% sodium deoxycholate, 10mM Tris-HCl pH 8) and once with buffer C (250 mM LiCl, 10mM Tris-HCl pH 8, 1mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate). RNA was removed by treatment with RNAse A at 37 °C for 30 minutes and crosslinks were reversed overnight at 65 °C in the presence of Proteinase K and SDS treatment. Eluted DNAs were size selected using SPRIselect beads (Beckman B23319).  RNA-seq: cells were resuspended in 1 ml of Trizol (ThermoFisher, 15596026) and incubated for 5 minutes at room temperature. Then, 0.2 ml of Chloroform (Sigma, C2432) was added and the solution was vortexed vigorously. The mixture was centrifuged at 13,000 rpm for 15 minutes at 4°C, and the upper phase was transferred to a fresh tube. RNA was precipitated using isopropanol (Duksan, 857) and washed with ice-cold 70% ethanol (Sigma, E7023). The precipitated RNA was dissolved in DEPC-treated water (Invitrogen, AM9915G).
CUTnTag: The eluted DNA was amplified using 2x PCR master mix (Epicypher, 15-1018) with i5 and barcoded i7 primers. Subsequently, library DNA was purified with SPRIselect beads (Beckman B23319) ).  ChIP-seq: and Libraries were prepared with NEB DNA library prep kit (NEB, E7645L) following the manufacturer’s protocol. Libraries were validated using the Tapestation HS D5000 screen tape.  RNA-seq: Library preparation was performed using TruSeq Stranded Total RNA Ribo-Zero H/M/R Gold kit (Illumina, RS-122-2301).

value: Mouse embryonic stem cell

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- ; AEBP2-short rescue


title: ISO-seq PARN CKO rep2

city: Beijing

first: NAIJING

last: HU

address: No.11 Xizhimen South Street, Xicheng District

institute: Peking University People's Hospital

description:
Library name: Sample 4
PromethION 48

data_processing:
To assess the read quality, raw reads were base called using Dorado software (version 0.9.1) and adapter sequences were trimmed by Dorado as well. Low quality reads (Q-value < 7) and short-length reads (<50 bp) were filtered by Nanofilt (version 2.7.1). The remaining clean reads were corrected using the Fclmr2 (version 0.1.2) with our short-length RNA-Seq data .
Clean reads from each library were aligned to the genome of mm10 using Minimap2 (version 2.17-r941). The alignment ratio of clean reads to the reference genes was calculated using Samtools (version 1.10). To obtain the gene and isoform count matrix using salmon software (version: 1.9.0). Differential gene expression analysis was performed using the DESeq2 R-package.
Assembly: mm10
Supplementary files format and content: Genome-wide ISO-seq signal in bigwig format

growth_protocol: The primary B cells were cultured in RPMI1640 medium supplemented with 10% FBS and 100U of Penicillin-Streptomycin in 5% CO2 incubator at 37℃.

extract_protocol:
The spleen was isolated from 8-week old mice and disrupted in PBS  containing 2% fetal bovine serum. Remove aggregates and debris by passing cell suspension through a 70 μm mesh nylon strainer. The untouched and highly purified B cells were isolated from mouse splenocytes by immunomagnetic negative selection following the manufacture’s protocol for EasyStepTM mouse B cell isolate kit (Stem cell, Catalog # 19754).
ISO-seq was performed by Guangzhou Epibiotek Co., Ltd. The library is obtained by connecting sequencing adapter to the amplified cDNAs. The concentrations were loaded onto the R10.4.1 sequencing chip and perform sequencing on the PromethION sequencer (Oxford Nanopore Technologies, Oxford, UK) for 48 h.

treatment_protocol: Primary B cells were activated by LPS (5ug/ml, Sigma, Catalog #L3024) for 3 days.

value: Spleen

tag: strain

value: B cells

value: PARN knockout

value: LPS treatement


title: bulk RNA-seq of human E7-TCR-T cells vaccinated with BAPC rep_1

description: Library name: E7_R_2


title: KMS34_DMSO_Dup2_Day10

description: Library name: KMS34_DMSO_Dup2_Day10_ATACseq


title: E14 TKO AEBP2 short rescue RNA Day4 rep1

description: Library name: E14_TKO_AEBP2_Short_rescue_Day4_RNA_rep1


title: ISO-seq PARN CKO rep1

description:
Library name: Sample 3
PromethION 48


title: E14 TKO AEBP2 long rescue RNA Day4 rep2

description: Library name: E14_TKO_AEBP2_Long_rescue_Day4_RNA_rep2

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- ; AEBP2-long rescue


title: ISO-seq PARN Ctrl rep2

description:
Library name: Sample 2
PromethION 48

value: WT


title: bulk RNA-seq of human E7-TCR-T cells vaccinated with control rep_2

description: Library name: E7_nc_2


title: KMS34_DMSO_Dup1_Day10

description: Library name: KMS34_DMSO_Dup1_Day10_ATACseq


title: E14 TKO AEBP2 long rescue RNA Day4 rep1

description: Library name: E14_TKO_AEBP2_Long_rescue_Day4_RNA_rep1


title: ISO-seq PARN Ctrl rep1

description:
Library name: Sample 1
PromethION 48


title: bulk RNA-seq of human E7-TCR-T cells vaccinated with control rep_1

description: Library name: E7_nc_1


title: E14 TKO RNA Day04 rep2

description: Library name: E14_TKO_Day4_RNA_rep2

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- (triple knockout)


title: KMS11_TKO_Dup2_Day0

description: Library name: KMS11_TKO_Dup2_Day0_ATACseq

value: TKO


title: BMC06481-001 Healthy

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

description:
Library name: BMC06481-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software (version 3.1.0; Released July 24, 2019), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each Well.
To identify cells originating from each sample, we utilized software tools for HTO quantification and sample demultiplexing to generate separate HDF5-formatted files for each originating sample (as described in Swanson, et al. (2021); DOI: 10.1186/s12859-022-04620-2). This process also removes Cell Barcodes that contain HTOs from multiple samples (doublets or multiplets) or with no detectable sample label (no hash).
After demultiplexing, data from individual samples assembled across all hashed wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
For analysis, high quality cells were selected based on the following cutoffs: <10% mitochondria reads, number of genes detected between 200 and 5000, RNA UMIs/cells between 1500 and 750000. After QC filtering, all remaining cells were clustered using a Scanpy (v1.9.6) workflow that consisted of normalization using scanpy.pp.normalize_total with the parameter target_sum = 1e4; log transformation using scanpy.pp.log1p; highly variable gene detection using scanpy.pp.highly_variable_genes; scaling of highly variable gene data using sc.pp.scale; Dimensionality reduction using scanpy.tl.pca with the parameter svd_solver = 'arpack'.
Supplementary files format and content: Ensembl GRCh38-3.0.0
Supplementary files format and content: h5 files, gene expression matrix
Library strategy: CITE-seq

extract_protocol:
BMMCs were removed from liquid nitrogen and rapidly thawed in a 37°C water bath. Cells were diluted dropwise into 40 mL AIM V media (Thermo Fisher Scientific) pre-warmed to 37°C. Cells were pelleted at 400 x g for 5–10 min at 4–10°C, resuspended in 5 mL cold AIM V media, and counted using a Cellometer Spectrum or Cellaca automatic cell counter.  Individual samples are hashtagged with unique oligo barcodes and stained with an antibody dependent tag (ADT) panel and pooled. Pools are stained with a viability dye (FSV510) and sorted for live cells using BD Aria Cell Sorter. Live cells are then collected and diluted to appropriate concentrations for 3' CITEseq.
scRNAseq libraries were generated using a modified 10x genomics chromium 3′ single cell gene expression assay with Cell Hashing. Sample libraries were constructed across different batches, with the addition of a common healthy donor leukopak sample in each library as batch control. Libraries were sequenced on the Illumina Novaseq platform. Hashed 10x Genomics scRNA-seq data processing was carried out using BarWare (BMC Bioinformatics 2022, doi: 10.1186/s12859-022-04620-2) to generate sample-specific output files.

value: Bone Marrow

value: BMMC

tag: subject id

tag: Sex

value: Male

tag: race

value: Caucasian

tag: days since_first_visit

tag: visit

value: Healthy

tag: batch id

tag: sample bridging_control

value: FALSE


title: KMS11_TKO_Dup1_Day0

description: Library name: KMS11_TKO_Dup1_Day0_ATACseq

value: Bone marrow

value: Multiple myeloma


title: E14 TKO RNA Day04 rep1

description: Library name: E14_TKO_Day4_RNA_rep1

value: Mouse embryonic stem cell


title: NCOR2 18h Exp2 - Rep 2

city: San Francisco

first: Valerie

last: Weaver

state: CA

address: 513 Parnassus Avenue, HSE 560, Box 0456

department: Department of Surgery and Center for Bioengineering and Tissue Regeneration

institute: Johns Hopkins Univeristy

description:
Library name: NCOR2_18h.exp2.NCOR2.2_24_S228_L008.markdup.q30
Draw data to be made available on SRA

data_processing:
Reads were trimmed for adapters and low-quality bases (Phred <20).
Trimmed reads were aligned to mm39 using bowtie2 (MAPQ ≥30 retained).
Duplicate-marked BAM files were generated; proper paired reads used for analysis.
Peaks were called using MACS3 (FDR ≤1%) with IgG background subtraction.
Peak counts were generated; differential analysis performed using DESeq2 (adjusted p <0.05).
Assembly: Mouse genome build mm39.
Supplementary files format and content: Processed files include deduplicated BAM files, bigWig coverage tracks, and peak count matrices.
Supplementary files format and content: Peak files (BED/narrowPeak) and differential peak analysis results with adjusted p-values and log fold changes.
Library strategy: CUT&Tag

growth_protocol: 4T07 cells (NCOR2 knockdown or EGFP control) were plated (20,000 cells/well) and grown 24–48 h before CUT&Tag.

extract_protocol:
CUT&Tag performed in situ on adherent unfixed cells using NCOR2 antibody and pA-Tn5 tagmentation.
Tagmented DNA was PCR-amplified with indexed primers, pooled, purified, and sequenced (51 bp paired-end, NovaSeq X).

treatment_protocol: Cells were treated with IFNγ (6 hr timepoint) or vehicle control.

value: Malignant neoplasms of the mouse mammary gland

value: NCOR2 Knockdown


title: BMC06482-001 Healthy

description:
Library name: BMC06482-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: KMS11_NSD2LDD_Dup2_Day4

description: Library name: KMS11_NSD2LDD_Dup2_Day4_ATACseq


title: E14 WT RNA Day4 rep2

description: Library name: E14_WT_Day4_RNA_rep2

value: Wild type


title: BMC06853-001 Healthy

description:
Library name: BMC06853-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Female

value: Other


title: E14 WT RNA Day4 rep1

description: Library name: E14_WT_Day4_RNA_rep1


title: NCOR2 06h Exp1 - Rep 2

description:
Library name: NCOR2_06h.exp1.NCOR2.1_11_S219_L008.markdup.q30
Draw data to be made available on SRA


title: BMC06479-001 Healthy

description:
Library name: BMC06479-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: KMS11_NSD2LDD_Dup1_Day4

description: Library name: KMS11_NSD2LDD_Dup1_Day4_ATACseq


title: NCOR2 06h Exp1 - Rep 1

description:
Library name: NCOR2_06h.exp1.NCOR2.1_10_S218_L008.markdup.q30
Draw data to be made available on SRA


title: KMS11_NSD2LDD_Dup1_Day10

description: Library name: KMS11_NSD2LDD_Dup1_Day10_ATACseq


title: E14 TKO AEBP2 short rescue RNA Day0 rep1

description: Library name: E14_TKO_AEBP2_Short_rescue_Day0_RNA_rep1

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- ; AEBP2-short rescue


title: NCOR2 00h Exp2 - Rep 2

description:
Library name: NCOR2_00h.exp2.NCOR2.2_11_S223_L008.markdup.q30
Draw data to be made available on SRA


title: BMC06478-001 Healthy

description:
Library name: BMC06478-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture


title: KMS11_Dup2_Day0

description: Library name: KMS11_Dup2_Day0_ATACseq


title: PMs, WT2, VSV 4h

first: Xingguang

last: Liu

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

description: Library name: WT2

data_processing:
We first apply Stringtie (version: 1.3.0) to count the number of Fragments for each gene after Hisat2 alignment.
Then the TMM (trimmed mean of M values) method was used to standardize the expression levels across various samples.
We then use Perl script to calculate the FPKM (Fragments Per Kilobase of transcript per Million mapped fragments) value for each gene.
Apply edgeR for differential gene analysis, obtain p-value, and perform multiple hypothesis testing correction. By controlling the FDR (False Discovery Rate) to determine the threshold of p-value, the corrected p-value is q-value. At the same time, we calculate the differential expression multiple, which is Fold change
Genes that exhibit a fold change in expression level larger than 2.0 and a q-value less than 0.05 are referred to as differentially expressed genes (DEGs).
Assembly: mm10
Supplementary files format and content: matrix table with raw gene counts for every gene and every sample

source_name: macrophages

growth_protocol: PMs were generated from mice in DMEM medium with 10% FBS.

extract_protocol:
Total RNA was extracted using MJzol animal RNA Extraction Kit (MagBeads) (Cat#T102096) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Library construction was perfromed following the steps of mRNA isolation, fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, end repair, adding A at the 3 'end, connecting connectors, enrichment, using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme), AHTS® mRNA Capure Beads (Human/Mouse/Rat) (Vazyme), VAHTS DNA Clean Beads (Vazyme), Qubit™ dsDNA HS Assay Kit (Invitrogen) and Agilent High Sensitivity DNA Kit (Aligent).

treatment_protocol: WT and Rbm25 deficient PMs were infected with vesicular stomatitis virus for 4 hours

value: macrophages

value: PMs

value: Mouse peritoneal macrophages

value: WT

value: VSV for 4 hours


title: NCOR2 00h Exp2 - Rep 1

description:
Library name: NCOR2_00h.exp2.NCOR2.2_10_S222_L008.markdup.q30
Draw data to be made available on SRA


title: BMC06475-001 Healthy

description:
Library name: BMC06475-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Bone Marrow

value: BMMC

value: Asian


title: E14 TKO AEBP2 long rescue RNA Day0 rep1

description: Library name: E14_TKO_AEBP2_Long_rescue_Day0_RNA_rep1

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- ; AEBP2-long rescue


title: KMS11_Dup1_Day0

description: Library name: KMS11_Dup1_Day0_ATACseq

value: Bone marrow

value: Multiple myeloma


title: NCOR2 00h Exp1 - Rep 2

description:
Library name: NCOR2_00h.exp1.NCOR2.1_7_S215_L008.markdup.q30
Draw data to be made available on SRA

value: Malignant neoplasms of the mouse mammary gland


title: BMC06476-001 Healthy

description:
Library name: BMC06476-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Hispanic or Latino origin

value: Healthy

value: FALSE


title: KMS11_DMSO_Dup2_Day4

description: Library name: KMS11_DMSO_Dup2_Day4_ATACseq

value: DMSO


title: E14 TKO RNA Day0 rep2

description: Library name: E14_TKO_Day0_RNA_rep2

value: Mouse embryonic stem cell

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- (triple knockout)


title: KMS11_DMSO_Dup2_Day10

description: Library name: KMS11_DMSO_Dup2_Day10_ATACseq


title: BMC06477-001 Healthy

description:
Library name: BMC06477-001
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Female

value: Caucasian


title: EGFP 18h Exp2 - Rep 2

description:
Library name: EGFP_18h.exp2.NCOR2.2_20_S226_L008.markdup.q30
Draw data to be made available on SRA

value: EGFP Knockdown


title: KMS11_DMSO_Dup1_Day4

description: Library name: KMS11_DMSO_Dup1_Day4_ATACseq


title: E14 TKO AEBP2 long rescue RNA Day0 rep2

description: Library name: E14_TKO_AEBP2_Long_rescue_Day0_RNA_rep2


title: EGFP 18h Exp2 - Rep 1

description:
Library name: EGFP_18h.exp2.NCOR2.2_19_S225_L008.markdup.q30
Draw data to be made available on SRA


title: snMultiome(snRNA-seq) of human mid-fetal dlPFC sample H429DFCm

city: New Haven

first: Saejeong

last: Park

state: Connecticut

address: 100 College St

institute: Yale University

description:
Library name: H429DFCm_GEX
snMultiome(snRNA-seq) of human mid-fetal dlPFC samples

data_processing:
Single-nucleus multiomic data were processed using Cell Ranger ARC (v2.0.1, 10x Genomics) with default parameters. Reads were aligned to the reference genome, and gene expression matrices and chromatin accessibility fragment files were generated. CUT&Tag sequencing reads were processed using standard pipelines, including read alignment to the reference genome and identification of enriched regions. Bulk RNA-seq data were processed using standard pipelines, including read alignment to the reference genome and quantification of gene expression levels to generate gene-level count matrices.
Assembly: Human: hg38 Mouse: mm10
Supplementary files format and content: Tab-delimited text files containing gene expression count matrices for each sample. For single-nucleus multiomic data, processed files include gene expression matrices and chromatin accessibility fragment files. For CUT&Tag data, processed files include BigWig files, peak files, and signal tracks representing enriched genomic regions. For bulk RNA-seq, processed files include gene-level count matrices for each sample as well as differential gene expression analysis results.

source_name: dlPFC

extract_protocol:
For human samples, nuclei were isolated from mid-fetal dorsolateral prefrontal cortex (dlPFC) tissue using a Dounce homogenization-based protocol in ice-cold lysis buffer, followed by filtration and iodixanol gradient centrifugation. The resulting nuclear pellets were resuspended in nuclei buffer supplemented with RNase inhibitor and DTT. For mouse samples, nuclei were isolated from medial prefrontal cortex (mPFC) and motor cortex (MC) tissues at postnatal day 1 (P1) using a similar homogenization-based protocol followed by filtration and centrifugation. For CUT&Tag experiments, nuclei were isolated from fresh frozen human cortical tissue using a commercial nuclei isolation kit according to the manufacturer’s instructions. For bulk RNA-seq, total RNA was extracted from dissociated mouse mPFC cells following enzymatic digestion and cell dissociation.
Single-nucleus multiomic libraries for gene expression (snRNA-seq) and chromatin accessibility (snATAC-seq) were prepared using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit according to the manufacturer’s instructions. CUT&Tag libraries were prepared using a Hyperactive Universal CUT&Tag Assay Kit (Vazyme) following standard protocols. Briefly, isolated nuclei were incubated with primary antibodies targeting transcription factors (RARA, RARB, RXRG, MEIS2) or histone modifications (H3K27ac, H3K4me3), followed by secondary antibody incubation, Tn5 transposase binding, tagmentation, and PCR amplification. Bulk RNA-seq libraries were prepared from mouse mPFC cells using the VAHTS Universal V10 RNA-seq Library Prep Kit (Vazyme) according to the manufacturer’s protocol.

value: dlPFC


title: KMS11_DMSO_Dup1_Day10

description: Library name: KMS11_DMSO_Dup1_Day10_ATACseq


title: E14 WT RNA Day0 rep1

description: Library name: E14_WT_Day0_RNA_rep1

value: Wild type


title: EGFP 06h Exp1 - Rep 2

description:
Library name: EGFP_06h.exp1.NCOR2.1_9_S217_L008.markdup.q30
Draw data to be made available on SRA


title: snMultiome(snATAC-seq) of human mid-fetal dlPFC sample H429DFCm

description:
Library name: H429DFCm_ATAC
snMultiome(snATAC-seq) of human mid-fetal dlPFC samples


title: E14 TKO AEBP2 short rescue ChIP AEBP2 rep2

description: Library name: E14_TKO_AEBP2_Short_rescue_ChIP_AEBP2_rep2

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- ; AEBP2-short rescue


title: EGFP 06h Exp1 - Rep 1

description:
Library name: EGFP_06h.exp1.NCOR2.1_8_S216_L008.markdup.q30
Draw data to be made available on SRA


title: snMultiome(snRNA-seq) of human mid-fetal dlPFC sample H596DFCm1

description:
Library name: H596DFCm1_GEX
snMultiome(snRNA-seq) of human mid-fetal dlPFC samples


title: A35B65L1

city: San Juan

first: Hector

last: Franco

state: Puerto Rico

address: 2nd Floor Centro Medico- Office #275

institute: University of Puerto Rico Comprehensive Cancer Center

description: Library name: Sample 41

data_processing:
Sequencing reads were quality filtered and adapter trimmed prior to alignment.
Trimmed reads were aligned to the human reference genome.
Aligned reads were filtered to remove duplicates and low-quality mappings.
Accessible chromatin regions were identified using peak calling and normalized signal tracks were generated.
Assembly: hg38
Supplementary files format and content: BigWig files represent normalized ATAC-seq signal tracks for each sample.
Supplementary files format and content: avg_BigWig files represent normalized ATAC-seq signal tracks for averaged samples

source_name: Breast

growth_protocol: Human tumor samples were obtained from surgical resections and processed according to institutional protocols. Samples were flash frozen and stored at −80 °C until chromatin accessibility profiling.

extract_protocol:
Nuclei were isolated from frozen tumor tissue and subjected to transposition using Tn5 transposase to tag accessible chromatin regions.
ATAC-seq libraries were prepared using a standard transposase-based protocol followed by PCR amplification and size selection according to the manufacturer’s instructions.

treatment_protocol: No in vitro treatment was applied. Samples represent primary and metastatic tumor tissues collected at the time of surgery.

value: Breast

value: breast tumor cells


title: BMC01671-16 Healthy

description:
Library name: BMC01671-16
H5 file contains RNA expression matrix, tsv contains ADT cell surface protein capture

value: Bone Marrow

value: BMMC

value: Male

value: TRUE


title: E14 TKO AEBP2 short rescue ChIP AEBP2 rep1

description: Library name: E14_TKO_AEBP2_Short_rescue_ChIP_AEBP2_rep1


title: E14 WT RNA Day0 rep2

description: Library name: E14_WT_Day0_RNA_rep2


title: EGFP 00h Exp2 - Rep 2

description:
Library name: EGFP_00h.exp2.NCOR2.2_9_S221_L008.markdup.q30
Draw data to be made available on SRA

value: Malignant neoplasms of the mouse mammary gland


title: bulk RNA-seq of human HA-TCR-T cells vaccinated with BAPC rep_3

description: Library name: F11_R_3

value: T cell

value: HA-TCR-T cells

value: vaccinated with BAPC


title: Mixed, barcode-transduced primary bulk human T cells, ex vivo day 7, donor 1, scATAC library

description:
Library name: 2025.KRD039
10X Genomics with custom retroviral barcoding
Human_CD22-CAR_allPeaks.raw.bed

value: CD4 and CD8 T cells

value: Harvest bone marrow T cells at day 7 after response to NALM6-CD22Lo leukemia


title: Nd_Mock3

first: Shumin

last: LIANG

address: 224 Waterloo Road, Kowloon Tong, HK

institute: Hong Kong Baptist University

description: Library name: Nd_M3

data_processing:
After sequencing, raw read were subjected to quality control and trimmed by using fastqc (v0.11.8) to get high-quality reads.
High-quality reads were mapped to the Arabidopsis genome (TAIR10) using hisat2 (v2.2.1).
Calculated the read counts of each gene with FeatureCounts (included in Subread v2.0.8 software) to generate the count matrix for expression analysis.
Assembly: TAIR10(Assembly: GCA_000001735.1)
Supplementary files format and content: format:txt; content:raw counts for each sample

extract_protocol:
Total RNA were extracted using TRIzol reagent (15596026, ThermoFisher) following the manufacturer's instruction.
The mRNA libraries (poly A enrichment) were prepared by Novogene Incorporation (Beijing, China) using reagents for Illumina.

value: 5-day-old seedlings

value: Mock


title: snMultiome(snATAC-seq) of human mid-fetal dlPFC sample H596DFCm1

description:
Library name: H596DFCm1_ATAC
snMultiome(snATAC-seq) of human mid-fetal dlPFC samples

value: dlPFC


title: Nd_Mock1

description: Library name: Nd_M1


title: A_3E0C8L

description: Library name: Sample 40


title: E14 TKO AEBP2 long rescue ChIP AEBP2 rep2

description: Library name: E14_TKO_AEBP2_Long_rescue_ChIP_AEBP2_rep2

value: Mouse embryonic stem cell

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- ; AEBP2-long rescue


title: LAG-3-Low_G93A_microglia_3

description: Library name: LAG-3-Low_G93A_microglia_3

data_processing:
Raw sequencing data were processed using Trim Galore (version 0.6.7) for quality control and adapter trimming. Transcript abundance was quantified using Salmon (version 1.9.0) against the mouse reference transcriptome (GRCm39). Count matrices were generated using tximport in R (version 4.2.1).
Assembly: GRCm39
Supplementary files format and content: Raw count data

extract_protocol:
RNA extraction from FACS-sorted cells using SMART-seq mRNA HT LP Kit
Using the SMART-seq mRNA HT LP Kit (Takara Bio), prepare a cDNA library from each sample.

value: microglia


title: KMS34_NSD2LDD_Dup2_Day

first: Bo

last: Hu

address: 10300 Campus Point Dr

institute: Bristol Myers Squibb

description: Library name: KMS34_NSD2LDD_Dup2_Day4_ATACseq

value: Bone marrow

value: Multiple myeloma


title: A_345CDL

description: Library name: Sample 39

value: Breast

value: breast tumor cells


title: KMS34_NSD2LDD_Dup2_Day10

description: Library name: KMS34_NSD2LDD_Dup2_Day10_ATACseq


title: snMultiome(snRNA-seq) of human mid-fetal dlPFC sample H431DFCm

description:
Library name: H431DFCm_GEX
snMultiome(snRNA-seq) of human mid-fetal dlPFC samples


title: E14 TKO AEBP2 long rescue ChIP AEBP2 rep1

description: Library name: E14_TKO_AEBP2_Long_rescue_ChIP_AEBP2_rep1


title: EGFP 00h Exp2 - Rep 1

description:
Library name: EGFP_00h.exp2.NCOR2.2_8_S220_L008.markdup.q30
Draw data to be made available on SRA

value: EGFP Knockdown


title: tMCAO 24h_4

city: MADISON

first: Hadjer

last: Namous

state: WI

address: 600 highland ave

department: Neurological Surgery

institute: University of Wisconsin Madison

description: Library name: AL10-244

data_processing:
Raw paired-end Hi-C FASTQ files were quality assessed using MultiQC and processed with Juicer v1.6. Reads were aligned to the mouse reference genome (mm39/GRCm39) using BWA-MEM. Low-quality alignments (MAPQ < 30) and PCR duplicates were removed, and contact matrices were normalized using Knight–Ruiz (KR) normalization.
Genome-wide chromatin features were identified using Juicer Tools v2.20.00 on KR-normalized matrices. A/B compartments were inferred by principal component analysis (PCA) of contact matrices at 1 Mb resolution.
Topologically associating domains (TADs) were identified per replicate using Arrowhead at 10 kb resolution.
Chromatin loops were detected at 10 kb resolution using HiCCUPS.
Assembly: mm39
Supplementary files format and content: HiC matrices at multiple resolutions (.hic)

source_name: Cortex tissue

extract_protocol:
Peri-infarct cortical tissue and corresponding sham tissue were dissected, flash-frozen in liquid nitrogen. 36 mice were used to generate n = 4 pooled biological replicates/condition (sham, 6h reperfusion and 24h reperfusion), with each replicate comprising 3 randomly assigned animals.
Hi-C libraries were generated using the Arima-HiC kit (A510008) and the Arima Library Prep Module (A303011) following manufacturer’s protocols. Briefly, tissue was crosslinked, pulverized using liquid nitrogen, digested with the Arima enzyme cocktail, proximity-ligated, reverse-crosslinked and purified. DNA (∼3 µg) was fragmented to 200–600 bp, and 200 ng of biotin-enriched DNA was size-selected, indexed and amplified. Libraries were sequenced on an Illumina NovaSeqPlus platform (150 bp paired-end), with a target of ≥ 600 million reads per library.

treatment_protocol: All experimental procedures were approved by the University of Wisconsin Research Animal Resources and Care Committee and were conducted in accordance with the Guide for the Care and Use of Laboratory Animals (8th edition, 2011). Adult male C57BL/6J mice (27 ± 2 g; Jackson Laboratory) were subjected to transient middle cerebral artery occlusion (tMCAO) using a silicone-coated 6-0 monofilament (Doccol) under isoflurane anesthesia, as previously described. Core body temperature was maintained at 37 °C using a feedback-controlled heating pad throughout the procedure. After 1 h of occlusion, mice were euthanized at either 6 h or 24 h of reperfusion. Sham-operated mice underwent identical surgical procedures without arterial occlusion.

value: Cortex tissue

value: tMCAO


title: d1_Mock-2

city: Hong Kong

description: Library name: d1_M2

source_name: 5-day-old seedlings


title: A_1D91L

description: Library name: Sample 38


title: snMultiome(snATAC-seq) of human mid-fetal dlPFC sample H431DFCm

description:
Library name: H431DFCm_ATAC
snMultiome(snATAC-seq) of human mid-fetal dlPFC samples


title: E14 TKO ChIP AEBP2 rep2

description: Library name: E14_TKO_ChIP_AEBP2_rep2

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- (triple knockout)


title: WT_Mock-2

description: Library name: WT_M2


title: bulk RNA-seq of human E7-TCR-T cells vaccinated with UniCVac rep_2

description: Library name: E7_vac_2

value: T cell

value: E7-TCR-T cells

value: vaccinated with UniCVac


title: E14 TKO ChIP AEBP2 rep1

description: Library name: E14_TKO_ChIP_AEBP2_rep1


title: snMultiome(snATAC-seq) of human mid-fetal dlPFC sample H421DFCm2

description:
Library name: H421DFCm2_ATAC
snMultiome(snATAC-seq) of human mid-fetal dlPFC samples


title: tMCAO 24h_2

description: Library name: AL8-242


title: E14 WT ChIP AEBP2 rep2

description: Library name: E14_WT_ChIP_AEBP2_rep2

value: Wild type


title: snMultiome(snRNA-seq) of human mid-fetal dlPFC sample H421DFCm2

description:
Library name: H421DFCm2_GEX
snMultiome(snRNA-seq) of human mid-fetal dlPFC samples


title: B4G12 cells, HG+LV-FOXO1, D3,rep3

city: Qingdao

first: Hongran

last: Zhao

state: Shandong

address: ShiNanQu

institute: Shandong Eye Institute

description:
Library name: Sample6
OE_FOXO1_3

data_processing:
The genome of human genome version of hg38 was used as reference. The sequencing quality were assessed with FastQC (v0.11.5) and then low quality data were filtered using NGSQC (v2.3.3).The clean reads were then aligned to the reference genome using HISAT2 (v2.1.0)with default parameters. The processed reads from each sample were aligned using HISAT2 against the reference genome. The gene expression analyses were performed with StringTie (v1.3.3b). DESeq(v1.28.0) was used to analyze the DEGs between samples.
Assembly: hg38
Supplementary files format and content: Excel files include count and FPKM values for each sample

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen).
Total RNA samples that meet the following requirements were used in subsequent experiments: RNA integrity number (RIN) > 7.0 and a 28S:18S ratio > 1.8.RNA-seq libraries were generated and sequenced by CapitalBio Technology (Beijing, China). The triplicate samples of all assays were constructed an independent library, and do the following sequencing and analysis. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) was used to construct the libraries for sequencing. NEB Next Poly(A) mRNA Magnetic Isolation Module (NEB) kit was used to enrich the poly(A) tailed mRNA molecules from 1 μg total RNA. The mRNA was fragmented into ~200 base pair pieces. The first-strand cDNA was synthesized from the mRNA fragments reverse transcriptase and random hexamer primers, and then the second-strand cDNA was synthesized using DNA polymerase I and RNaseH. The end of the cDNA fragment was subjected to an end repair process that included the addition of a single “A” base, followed by ligation of the adapters. Products were purified and enriched by polymerase chain reaction (PCR) to amplify the library DNA. The final libraries were quantified using KAPA Library Quantification kit (KAPA Biosystems, South Africa) and an Agilent 2100 Bioanalyzer.

treatment_protocol: B4G12 cells, HG+LV-NC, D3

value: Human corneal endothelial cell lines

tag: transduction

value: lentivirus transduction

value: HG+LV-FOXO1, D3


title: A8LIV_2

description: Library name: Sample 35

source_name: Liver

value: Liver

value: liver metastatic tumor cells


title: tMCAO 6h _4

description: Library name: AL7-64


title: B4G12 cells, HG+LV-FOXO1, D3,rep2

description:
Library name: Sample5
OE_FOXO1_2


title: tMCAO 6h _2

description: Library name: AL5-62


title: E14 TKO AEBP2 short rescue CUTnTag H3K27me3 rep2

description: Library name: E14_TKO_AEBP2_Short_rescue_CUTnTag_H3K27me3_rep2

data_processing:
CUTnTag: Adaptor sequences were trimmed using Cutadapt, and the filtered reads were aligned to the mouse reference genome (mm10) with Bowtie2 using default parameters. Duplicate reads were identified and removed with Samtools markdup. Reads that failed to align to the mouse genome were subsequently mapped to the Drosophila genome (dm6), and the number of Drosophila-mapped reads was used to calculate the spike-in normalization factor.  ChIP-seq: and Libraries were prepared with NEB DNA library prep kit (NEB, E7645L) following the manufacturer’s protocol. Libraries were validated using the Tapestation HS D5000 screen tape.  RNA-seq: Adapter sequences were trimmed using Trimmomatic and reads were aligned to the hg38 reference genome using HISAT2. Transcript assembly was performed with StringTie for downstream analysis. Differential gene expression analysis was carried out using DESeq2 with p-value < 0.05 and log2 |fold change| > 1.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

value: Mouse embryonic stem cell

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- ; AEBP2-short rescue


title: A8LIV_1

description: Library name: Sample 34


title: B4G12 cells, HG+LV-FOXO1, D3,rep1

description:
Library name: Sample4
OE_FOXO1_1


title: A8BR_2

description: Library name: Sample 33

value: Breast


title: E14 TKO AEBP2 short rescue CUTnTag H3K27me3 rep1

description: Library name: E14_TKO_AEBP2_Short_rescue_CUTnTag_H3K27me3_rep1


title: tMCAO 6h _1

description: Library name: AL4-61


title: B4G12 cells, HG+LV-NC, D3, rep3

description:
Library name: Sample3
NC3

value: HG+LV-NC, D3


title: E14 TKO AEBP2 long rescue CUTnTag H3K27me3 rep2

description: Library name: E14_TKO_AEBP2_Long_rescue_CUTnTag_H3K27me3_rep2

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- ; AEBP2-long rescue


title: Sham_4

description: Library name: AL3-S2

value: Cortex tissue

value: Sham


title: B4G12 cells, HG+LV-NC, D3, rep2

description:
Library name: Sample2
NC2


title: A49LUN_2

description: Library name: Sample 25

source_name: Lung

value: Lung

value: lung metastatic tumor cells


title: E14 TKO AEBP2 long rescue CUTnTag H3K27me3 rep1

description: Library name: E14_TKO_AEBP2_Long_rescue_CUTnTag_H3K27me3_rep1


title: Sham_3

description: Library name: AL2-S2


title: E14 TKO CUTnTag H3K27me3 rep2

description: Library name: E14_TKO_CUTnTag_H3K27me3_rep2

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- (triple knockout)


title: Sham_2

description: Library name: AL1-S2


title: E14 TKO CUTnTag H3K27me3 rep1

description: Library name: E14_TKO_CUTnTag_H3K27me3_rep1


title: Sham_1

description: Library name: HiC-S1


title: BON-1 cells, Radioresistant R2

city: shanghai

first: jianyun

last: jiang

address: dong'an road 270

institute: fudan university shanghai cancer center

description:
Library name: Sample 11
Processed data files_2.txt
BR2

data_processing:
Read preprocessing / QC: Raw FASTQ files were quality-controlled to obtain clean reads (adapter/low-quality reads removed).  Alignment: Clean reads were aligned to the human reference genome GRCh38/hg38.  Quantification: Gene-level read counts were generated from the aligned reads to produce a count matrix for downstream analyses.  Gene detection: Gene detection sensitivity was evaluated using an expression threshold of FPKM ≥ 1.  Differential expression: Differential gene expression analysis was performed in R using DESeq2 based on gene-level raw counts.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Gene-level raw counts matrix (TSV), genes × samples, used for downstream DESeq2 analysis.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. RNA quantity and integrity were assessed using an Agilent 2100 Bioanalyzer, and only high-quality samples were used for downstream library preparation.
. Sequencing libraries were constructed using a poly(A) enrichment protocol and sequenced on an Illumina NovaSeq 6000 platform to generate 150-bp paired-end reads.

value: panNET cells

value: WT

tag: sample group

value: Radioresistant


title: tMCAO 24h_1

description: Library name: HiC-M24-1

tag: tissue

value: tMCAO


title: BON-1 cells, Radioresistant R1

description:
Library name: Sample 10
Processed data files_2.txt
BR1

tag: cell type


title: A49BR_2

description: Library name: Sample 21

value: breast tumor cells


title: E14 WT CUTnTag H3K27me3 rep1

description: Library name: E14_WT_CUTnTag_H3K27me3_rep1

tag: genotype

value: Wild type


title: D12_repC

description: Library name: JB_9

data_processing:
The reads were trimmed using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data. Fastq Screen v0.13.0 was used to screen for various types of contamination. Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a and assigned count estimates to genes with RSEM v1.3.3. Alignment options followed ENCODE standards for RNA-seq.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

extract_protocol:
RNA was extracted using RNEasy kits (Qiagen)
University of Michigan Advanced Genomics Core prepared polyA cDNA libraries.

treatment_protocol: Cells were treated with 1 uM 4-hydroxytamoxifen for 2 days to deplete PAX8 then subsequently treated with 1 ug/ml doxycycline.

value: Kidney

value: Proximal tubule

value: doxycycline (1 ug/ml)

tag: replicate

value: C


title: A49BR_1

description: Library name: Sample 20

value: Breast


title: Mus_musculus-WT-TNF_3

city: Toronto

first: Aleixo

last: Muise

state: ON

address: 686 Bay Street, 19-9400 I-M PGCRL

department: Cell Biology

institute: The Hospital for Sick Children

description:
Library name: Sample 18
WT-TNF-3_1

data_processing:
Raw reads in FASTQ format were processed using Fastp (version 0.23.1) for quality control. The raw RNAseq reads were aligned to the mouse genome (GRCm39) / zebrafish genome (GRCz11) using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2.
Assembly: Mus musculus (GRCm39 genome) zebrafish (GRCz11)
Supplementary files format and content: tab-delimited text files include the count values for each Sample. Rows = genes; Columns = samples.

source_name: small intestine organoid

growth_protocol: For Mus Musculus: Mouse small intestinal organoids were cultured in ENR medium in an incubator at 37°C with 5% CO₂.  For Danio rerio: For wt and all the mutants at 3dpf and 8dpf ,embryos were obtained via natural mating and cultured in embryo E3 buffer, raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.

extract_protocol:
For Mus Musculus: Total RNA was extracted using TRNzol reagent (TIANGEN). 0.45μg of high-quality RNA was used for RNA-seq library construction.  For Danio rerio: RNA were extracted using RNAeasy mini kit(Qiagen). 600ng of total RNA were used for the construction of sequencing libraries.
For Mus Musculus: RNA libraries for RNA-Seq were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following the manufacturer’s instructions.  For Danio rerio: RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo-Zero Plus protocol to generate polyA-enriched, rRNA-depleted libraries.

treatment_protocol: For Mus Musculus: Three days after seeding in 24-well plates, the organoids were stimulated with TNF (10 ng/ml) for 15 hours.  For Danio rerio: Wt and all the mutants at 3dpf and 8dpf were anethetized with tricaine and underwent tailfin-cut genotyping.The wildtype and mutants were pooled (n=15), repectively.

value: small intestine organoid

tag: treatment

value: TNF


title: BON-1 cells, Parental R3

description:
Library name: Sample 9
Processed data files_2.txt
BP3

tag: cell line

value: Parental


title: D12_repB

description: Library name: JB_8

value: B


title: BON-1 cells, Parental R2

description:
Library name: Sample 8
Processed data files_2.txt
BP2


title: A39LIV_2

description: Library name: Sample 19

value: Liver

value: liver metastatic tumor cells


title: Mus_musculus-WT-TNF_2

description:
Library name: Sample 17
WT-TNF-2_1


title: D12_repA

description: Library name: JB_7

value: A


title: BON-1 cells, Parental R1

description:
Library name: Sample 7
Processed data files_2.txt
BP1

value: panNET cells

value: WT


title: A8LUN_2

description: Library name: Sample 37

value: Lung

value: lung metastatic tumor cells


title: tMCAO 24h_3

description: Library name: AL9-243

value: Cortex tissue

value: tMCAO


title: UC-35

city: Boston

first: Minyi

last: Lee

address: 72 East Concord Street, E632

institute: Boston University Chobanian & Avedisian School of Medicine

description: Library name: UC-35

data_processing:
Demultiplexing and creation of FASTQ files were automatically performed using the Illumina BaseSpace platform with default parameters.
Reads were aligned to the Genome Reference Consortium human build 38 (GRCh38) using STAR v2.6.0c.
Both gene and transcript level counts were calculated using RSEM v1.3.1 with annotation from Ensembl build 107.
Genes were filtered for analysis based on counts per million (CPM) reads mapped across all samples. Genes with CPM counts greater than 1 in more than 10% of the total number of patients were used in subsequent analyses. CPM was calculated using the calcNormFactors and cpm functions from the edgeR package (version 4.4.1).
Assembly: hg38
Supplementary files format and content: counts.tsv: tab-separated values (TSV) file containing 5737 x 120 matrix of "expected_count" values computed by RSEM

source_name: Nasal brushing

extract_protocol:
Total RNA was isolated from nasal brushings using the miRNeasy Mini Kit (Qiagen, Valencia, CA).
Libraries were generated using the Illumina TruSeq RNA Exome kit.

value: Nasal brushing

tag: median tin

tag: cancer status

value: Cancer

tag: age

tag: gender

value: female

tag: smoking status

value: FORMER

tag: sequencing batch


title: A8LUN_1

description: Library name: Sample 36


title: A39LIV_1

description: Library name: Sample 18


title: Mus_musculus-WT-TNF_1

description:
Library name: Sample 16
WT-TNF-1_1

value: small intestine organoid


title: E14 WT ChIP AEBP2 rep1

description: Library name: E14_WT_ChIP_AEBP2_rep1

value: Mouse embryonic stem cell

value: Wild type


title: tMCAO 6h _3

description: Library name: AL6-63


title: D6_repC

description: Library name: JB_6

value: Kidney

value: Proximal tubule

value: 4-hydroxytamoxifen (1 uM)

value: C


title: QGP-1 cells, shSIRT7 R3

description:
Library name: Sample 6
Processed data files_1.txt
S3

value: panNET cells

value: SIRT7 knockdown


title: A39BR_1

description: Library name: Sample 17

value: Breast

value: breast tumor cells


title: Mus_musculus-WT-Ctrl_3

description:
Library name: Sample 15
WT-Ctrl-3_1

value: WT

value: NO


title: D6_repB

description: Library name: JB_5

value: B


title: QGP-1 cells, shSIRT7 R2

description:
Library name: Sample 5
Processed data files_1.txt
S2


title: A36LUN_2

description: Library name: Sample 16

value: Lung

value: lung metastatic tumor cells


title: Mus_musculus-WT-Ctrl_2

description:
Library name: Sample 14
WT-Ctrl-2_1


title: D6_repA

description: Library name: JB_4

value: A


title: QGP-1 cells, shSIRT7 R1

description:
Library name: Sample 4
Processed data files_1.txt
S1


title: A8BR_1

description: Library name: Sample 32


title: Mus_musculus-WT-Ctrl_1

description:
Library name: Sample 13
WT-Ctrl_1

value: small intestine organoid


title: A36LUN_1

description: Library name: Sample 15


title: D0_repC

description: Library name: JB_3


title: QGP-1 cells, shControl R3

description:
Library name: Sample 3
Processed data files_1.txt
C3


title: A49LUN_1

description: Library name: Sample 24


title: B4G12 cells, HG+LV-NC, D3, rep1

description:
Library name: Sample1
NC1

value: Human corneal endothelial cell lines

value: lentivirus transduction

value: HG+LV-NC, D3


title: A36LIV_2

description: Library name: Sample 14

value: Liver

value: liver metastatic tumor cells


title: Mus_musculus-BKO-TNF_3

description:
Library name: Sample 12
BKO-TNF-3_1

value: cIAP2 Knockout

value: TNF


title: QGP-1 cells, shControl R2

description:
Library name: Sample 2
Processed data files_1.txt
C2

value: panNET cells


title: D0_repB

description: Library name: JB_2

value: Kidney

value: Proximal tubule


title: BON-1 cells, Radioresistant R3

description:
Library name: Sample 12
Processed data files_2.txt
BR3

value: WT

value: Radioresistant


title: A49LIV_2

description: Library name: Sample 23


title: A36LIV_1

description: Library name: Sample 13


title: Mus_musculus-BKO-TNF_2

description:
Library name: Sample 11
BKO-TNF-2_1


title: QGP-1 cells, shControl R1

description:
Library name: Sample 1
Processed data files_1.txt
C1


title: A33LUN_2

description: Library name: Sample 12


title: D0_repA

description: Library name: JB_1


title: D12_T_repC

description: Library name: GD_9937_12

growth_protocol: PT-22 cells were cultured in DMEM supplemented with 3% fetal bovine serum and penicillin/streptomycin.

treatment_protocol: Cells were treated with 1 micromolar 4-hydroxytamoxifen for 2 days to deplete PAX8.

value: 4-hydroxytamoxifen (1 uM)

value: C


title: Mus_musculus-BKO-TNF_1

description:
Library name: Sample 10
BKO-TNF-1_1


title: A549 cell, siARID1A_IgG_rep2

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

institute: Southeast University

description: Library name: siARID1A, IgG CUT_Tag-2

data_processing:
Raw reads were trimmed using fastp (v0.23.2) in paired-end mode.Trimmed reads were aligned to human hg38 genome using Bowtie (v.2.4.2) with the parameters '--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10-X 700'. For spike-in normalization, the reads were also aligned to the E. coli genome by Bowtie (v.2.4.2) with the options ‘--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700’. Duplicated reads were then filtered using SAMtools (v.1.9). Reads adjusted to total reads were aligned to E. coli genome using bedtools(v2.30.0). Peak identification was performed using SEACR(v1.3). Adjusted reads were then converted to strand-specific bigwig files with the bamCoverage command from deepTools(v3.5.2). The coverage heatmaps were created using plotHeatmap from deepTools (v.3.5.2)
Assembly: GRCh38
Supplementary files format and content: bigwig, bed
Library strategy: CUT&Tag

growth_protocol: A549 cells  were maintained in RPMI 1640 supplemented with 10% (v/v) fetal bovine serum (FBS) and 1%penicillin/streptomycin at 37 °C in a humidified incubator containing 5% CO2.

extract_protocol:
For each CUT&Tag reaction, 2 × 10⁵ EDTA-free A549 cells were immobilized on Protein A magnetic beads (Cat. No. N259-YH01-01S) and incubated with 1 μg primary antibody overnight at 4 °C without agitation. On the following day, a secondary antibody (10 μg/mL) was added to amplify the signal. Subsequently, 1 μL ChiTag® pAG-Transposome (Cat. No. N2) was added and activated, and tagmented DNA was enriched using Tagment DNA Extract Beads (Cat. No. N240). Five nanograms of DNA were then used for sequencing library preparation with the NovoNGS® DNA Library FlashPrep Kit for Illumina® (Cat. No. N231).
Five nanograms of DNA were then used for sequencing library preparation with the NovoNGS® DNA Library FlashPrep Kit for Illumina® (Cat. No. N231).

value: Human Lung Cancer Cell Line

value: ARID1A knockdown

tag: cut&tag antibody

value: IgG （CST, #2729）


title: A33LUN_1

description: Library name: Sample 11

value: Lung

value: lung metastatic tumor cells


title: Mus_musculus-BKO-Ctrl_3

description:
Library name: Sample 9
BKO-Ctrl-3_1

value: small intestine organoid

value: NO


title: D12_T_repB

description: Library name: GD_9937_11

value: B


title: A33LIV_2

description: Library name: Sample 10

value: Liver

value: liver metastatic tumor cells


title: A549 cell, siARID1A_IgG_rep1

description: Library name: siARID1A, IgG CUT_Tag-1


title: Mus_musculus-BKO-Ctrl_2

description:
Library name: Sample 8
BKO-Ctrl-2_1

value: cIAP2 Knockout


title: A549 cell, siARID1A_antiYTHDF1_rep2

description: Library name: siARID1A, YTHDF1 CUT_Tag-2

value: YTHDF1 (Abacm, #ab220162)


title: Mus_musculus-BKO-Ctrl_1

description:
Library name: Sample 7
BKO-Ctrl_1


title: E14 WT CUTnTag H3K27me3 rep2

description: Library name: E14_WT_CUTnTag_H3K27me3_rep2

value: Mouse embryonic stem cell

value: Wild type


title: D12_T_repA

description: Library name: GD_9937_10

value: Kidney

value: Proximal tubule

value: A


title: A49LIV_1

description: Library name: Sample 22


title: A33LIV_1

description: Library name: Sample 9


title: D6_T_repC

description: Library name: GD_9937_9

value: 4-hydroxytamoxifen (1 uM)

value: C


title: A549 cell, siARID1A_antiYTHDF1_rep1

description: Library name: siARID1A, YTHDF1 CUT_Tag-1

value: Human Lung Cancer Cell Line

value: ARID1A knockdown


title: Mus_musculus-312HZ-TNF_3

description:
Library name: Sample 6
312HZ-TNF-3_1

value: cIAP2H312Y/+ Knock in

value: TNF


title: D6_T_repB

description: Library name: GD_9937_8


title: A549 cell, siARID1A_antiARID1A_rep2

description: Library name: siARID1A, ARID1A CUT_Tag-2


title: A23LUN_1

description: Library name: Sample 7

value: Lung

value: lung metastatic tumor cells


title: D6_T_repA

description: Library name: GD_9937_7


title: Mus_musculus-312HZ-TNF_2

description:
Library name: Sample 5
312HZ-TNF-2_1

value: small intestine organoid


title: A23LIV_2

description: Library name: Sample 6

value: Liver

value: liver metastatic tumor cells


title: D2_T_repC

description: Library name: GD_9937_6


title: Mus_musculus-312HZ-TNF_1

description:
Library name: Sample 4
312HZ-TNF-1_1


title: A549 cell,YTHDF1-KO_IgG_rep2

description: Library name: YTHDF1-KO, IgG CUT_Tag-2

value: YTHDF1 knockout

value: IgG （CST, #2729）


title: A23LIV_1

description: Library name: Sample 5


title: A549 cell, siARID1A_antiARID1A_rep1

description: Library name: siARID1A, ARID1A CUT_Tag-1


title: Mus_musculus-312HZ-Ctrl_3

description:
Library name: Sample 3
312HZ-Ctrl-3_1

value: NO


title: D2_T_repB

description: Library name: GD_9937_5

value: Kidney

value: B


title: A549 cell,YTHDF1-KO_IgG_rep1

description: Library name: YTHDF1-KO, IgG CUT_Tag-1


title: A18LUN_2

description: Library name: Sample 4


title: D2_T_repA

description: Library name: GD_9937_4

value: Proximal tubule

value: A


title: Mus_musculus-312HZ-Ctrl_2

description:
Library name: Sample 2
312HZ-Ctrl-2_1


title: A549 cell,YTHDF1-KO_antiARID1A_rep2

description: Library name: YTHDF1-KO, ARID1A CUT_Tag-2


title: A18LUN_1

description: Library name: Sample 3


title: CTRL_repC

description: Library name: GD_9937_3

value: C


title: A18LIV_2

description: Library name: Sample 2


title: A549 cell,YTHDF1-KO_antiARID1A_rep1

description: Library name: YTHDF1-KO, ARID1A CUT_Tag-1

value: Human Lung Cancer Cell Line


title: Mus_musculus-312HZ-Ctrl_1

description:
Library name: Sample 1
312HZ-Ctrl_1


title: CTRL_repB

description: Library name: GD_9937_2


title: A4490_A4418_22_RNA_B4_E9-5

city: Utrecht

first: Jop

last: Kind

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Library name: A4490_A4418_22_RNA_B4_E9-5

data_processing:
Counts for the open chromatin and transcriptional read-outs were obtained by running the cellranger-arc count pipeline with default settings.
Assembly: mm10
Supplementary files format and content: cellranger output files: atac_fragments.tsv.gz (ATAC) and filtered_feature_bc_matrix.h5 (RNA); sample annotations: table containing detailed sample information for all single-cell samples

source_name: Limb

growth_protocol: 10x multiome data collection was performed using C57Bl.6/J mice that were sourced from Inotiv and G4 ESCs (XY, 129S6/SvEvTac x C57BL/6Ncr F1 hybrid)

extract_protocol:
Embryos were isolated from the uteri of pregnant mothers between 8.5 and 13.5 days after the plug date. Embryos were dissected on ice in HBBS (for 8.5-day embryos) or PBS (for 9.5-13.5-day embryos), and staged based on morphology, size, and/or somite number.Samples were processed to create single cell suspensions differently depending on stage. Whole E8.5 embryos were pooled by precise somite number and transferred for tissue dissociation in 200 μl TrypLE Express (Gibco,12604013; Gibco) at 37 °C and triturated by pipetting at 10-20 minutes intervals for a total of 40 minutes. By contrast, tissues from E9.5 to E13.5 embryos were microdissected and pooled as needed. Tissues were then dissociated with Trypsin-EDTA (Thermo Fisher, 25300096; Thermo Fisher) and trituration by pipetting at 37°C at 2-3 minute intervals until no visible clumps remained (~5-15 minutes). Digestion was immediately halted by addition of 10% FCS/PBS. Following disassociation, all samples were cleared of  cell clumps by filtration (40 μm, Flowmi Cell Strainer, Scienceware) and then pelleted by centrifugation at 300 g for 5 minutes at 4°C. Cells were resuspended in 1:1 ratio of F1 [40% FCS/60% DMEM] and F2 solution [20%DMSO/40%FCS/40% DMEM] and cryopreserved.
Cryopreserved single-cell suspensions were used to prepare nuclei according to 10x Genomics guidelines with few modifications. Briefly, cells were thawed at 37°C and immediately washed twice with warm ESC media by centrifugation at 400 g for 10 minutes at RT. Pipetting was performed as gently as possible to ensure cell viability. Cells were then transferred onto ice and washed twice with cold 0.04%BSA/PBS by centrifugation at 400 g for 10 minutes at 4°C. After the final wash, the pellet was thoroughly resuspended in lysis buffer diluent (lysis buffer without tween, NP-40, or digitonin) [10 mM Tris-HCl (pH 7.4) (Roth, 9090.3), 10 mM NaCl (Invitrogen, AM9760G), 3 mM MgCl₂ (Roth, 2189.1), 1% BSA (Sigma, 810531), 1 mM DTT (have to check), DEPC water] to generate single cell-suspension. An equal volume of 2x concentrated lysis buffer [20 mM Tris-HCl (pH 7.4), 20 mM NaCl, 6 mM MgCl₂ , 0.20% Tween-20 (Serva, 37470), 0.20% NP40 substitute (have to check), 0.02% Digitonin (Milipore, 30410), 2% BSA, 2 mM DTT, DEPC water]  was added to the cell suspension, mixed by inversion, left to incubate on ice for  3 (embryonic tissues) or 5 minutes (ESCs). Nuclei were then washed three times with Wash buffer by centrifugation at 500g for 5 minutes at 4°C. Prior to the last centrifugation, samples were cleared of cell clumps by filtration (40 μm, Flowmi Cell Strainer, Scienceware). Nuclei were resuspended in 10x Genomics diluted nucleus buffer (PN-2000207), quantified using a haemocytometer and adjusted to 3,220 nuclei per μl. In total, 5 μl of diluted nuclei were subsequently used for the transposase reaction. All steps were performed on a RNAse-Zap treated bench. All buffers were supplemented with 1 U/μl RNAse inhibitor (1:1 ratio of Invitrogen, AM2684 and AM2694; Invitrogen). The final libraries were sequenced on the Illumina NovaSeq 6000 or NovaSeq X Plus platform with paired-end 50/50bp, 28/90bp or 50/90bp read length.

value: Limb

tag: Stage

value: wt


title: A549 cell,YTHDF1-KO_antiYTHDF1_rep2

description: Library name: YTHDF1-KO, YTHDF1 CUT_Tag-2

value: YTHDF1 (Abacm, #ab220162)


title: A18LIV_1

description: Library name: Sample 1


title: A4490_A4418_10_ATAC_C10_E9-5

description: Library name: A4490_A4418_10_ATAC_C10_E9-5


title: CTRL_repA

first: Jeffrey

last: Beamish

address: 1500 E. Medical Center Drive, SPC 5364

institute: University of Michigan

description: Library name: GD_9937_1


title: K562, sgMulti1, DISCOVER-seq, rep1

city: Zurich

first: Charles

middle: D

last: Yeh

state: ZH

address: Otto-stern-weg 7

department: D-BIOL

country: Switzerland

institute: ETH Zurich

description: Library name: NCOX2_DISCOVERseq_sgMulti1

data_processing:
Illumina NGS adapter trimming (cutadapt)
filtering for known amplicon contaminants (if any) (cutadapt)
alignment to human genome (bowtie2)
conversion to coverage (deepTools bamCoverage) with parameters (--normalizeUsing CPM --extendReads --minMappingQuality 10 --samFlagInclude 64 --binSize 50)
Assembly: hg38
Supplementary files format and content: bigWig with CPM normalization

source_name: blood

growth_protocol: RPMI 1640 base media supplemented to 10% with fetal bovine serum, GlutaMAX, and 1X PenStrep. Cells were cultured at +37C in 5%CO2 in log phase growth.

extract_protocol:
chromatin immunoprecipitation
NEBNext Ultra™ II DNA Library Prep Kit for Illumina

treatment_protocol: DSB induction by CRISPR/Cas9 Nucleofection

value: blood

value: myelogenous leukemia

value: CRISPR/Cas9, sgMulti1

tag: batch


title: A549 cell,YTHDF1-KO_antiYTHDF1_rep1

description: Library name: YTHDF1-KO, YTHDF1 CUT_Tag-1


title: A4490_A4418_21_RNA_B3_E8-5

description: Library name: A4490_A4418_21_RNA_B3_E8-5

source_name: Whole embryo

value: Whole embryo


title: stimulated microglia replicate 3

city: Halle

first: Martin

middle: Sebastian

last: Staege

address: Ernst-Grube-Str. 40

department: Paediatrics I

country: Germany

institute: Martin Luther University Halle-Wittenberg

description:
Library name: treated 3
column name in raw_counts_All_Samples.txt: T3

data_processing:
reads were mapped to murine genome mm39 using HISAT2
mapped reads were quantified using featureCounts
data processing was performed on the galaxy server (https://usegalaxy.org/)
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw fragment counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM for each sample

source_name: brain

growth_protocol: Cells were seeded in complete DMEM/F12 in a 75 cm2 cell culture flask coated with 0.1% poly-L-ornithine. Flasks were washed with complete DMEM/F12 after overnight incubation and stimulated with 20% L-929 conditioned medium in complete DMEM/F12 on day 8, 13, 21 and 29 after isolation. Microglia were collected by shaking the flasks for 5.5 h at 70 rpm and subsequently aspirating the cell suspension.

extract_protocol:
Total RNA was isolated from cell pellets or lysates using the Nucleospin RNA XS isolation kit (Machery-Nagel).
RNA libraries were constructed by BMKGENE, Berlin, Germany using standard protocolls.

treatment_protocol: For stimulation, microglia were cultured in the presence of 100ng/mL human TGFbeta, 100 ng/mL human IL34 and 100 ng/mLCX3CL1.

tag: strain

value: brain

value: microglia

value: 1-3 days

value: stimulated with TGFbeta, IL34 and CX3CL1


title: A549 cell, Wide type, WT_IgG_rep2

description: Library name: WT, IgG CUT_Tag-2

value: WT

value: IgG （CST, #2729）


title: A4490_A4418_09_ATAC_E8-5

description: Library name: A4490_A4418_09_ATAC_E8-5


title: K562, sgHBB, DISCOVER-seq, rep1

description: Library name: NCOX2_DISCOVERseq_sgHBB

value: CRISPR/Cas9, sgHBB


title: microglia control replicate 3

description:
Library name: untreated 3
column name in raw_counts_All_Samples.txt: U3

value: control