title: HepG2 ARID1B-KO RNA-seq, DMSO, rep1

description: Library name: HepG2_ARID1B-KO_DMSO_RNAseq_rep1


title: WSU-DLCL2_DOT1Li_Rep2

status: Public on Jun 19 2026

type: SRA

city: Amsterdam

first: Rachele

last: Niccolai

address: Plesmanlaan 121

department: Tumor Biology and Immunology

country: Netherlands

institute: The Netherlands Cancer Institute

description: Library name: Sample8.2

library_source: transcriptomic

data_processing:
FASTQ files were produced by BCL Convert using demultiplexing.
Sample distribution was based on indexing using IDT UDI indexes.
Seqpurge was used for adapter trimming.
RNA-seq data were aligned with STAR against reference genome GRCh38, and reads were counted and annotated per gene using GenSum (https://www.github.com/NKI-GCF/gensum) against Ensembl GRCh38.107.
DESeq2 package was used to normalize read counts and to obtain the differential gene expression of RNA-seq samples.
Assembly: hg38
Supplementary files format and content: tab-delimited txt files includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: SUDHL10, WSU-DLCL2, and SUDHL4 were maintained in IMDM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were lysed in RLT buffer (Qiagen).
RNA-seq libraries were prepared using the xGen polyA+ stranded RNA library kit, according to manufacturer’s protocol.

treatment_protocol: SUDHL10, WSU-DLCL2, and SUDHL4 GCB-DLBCL cell lines were treated for six days with the following concentrations of EPZ-5676 (DOT1Li): 100 nM for SUDHL10; and 250 nM for WSU-DLCL2 and SUDHL4; and the following concentration of GSK343 (EZH2i): 5 µM for SUDHL4. At day 3, 5x10^4 cells/ml were reseeded with fresh medium and inhibitors.

tag: cell line

tag: cell type

value: GCB-DLBCL

tag: treatment


title: WSU-DLCL2_DOT1Li_Rep1

description: Library name: Sample8.1


title: WSU-DLCL2_DMSO_Rep3

description: Library name: Sample7.3

value: DMSO


title: HepG2 WT RNA-seq, Sorafenib, rep3

city: Chapel Hill

first: Jacqueline

last: Brinkman

address: 120 Mason Farm Rd

department: Genetics

country: USA

institute: Unversity of North Carolina-Chapel Holl

description: Library name: HepG2_WT_Sorafenib_RNAseq_rep3

data_processing:
Quantification: Salmon (default parameters) against GRCh38/Ensembl 109. Gene-level summarization: tximeta v1.24.0 + tximport. Differential expression: DESeq2 v1.46.0, design ~genotype+treatment+genotype:treatment, apeglm shrinkage. Genes <10 counts in >=3 samples excluded.
Assembly: GRCh38 / Ensembl release 109
Supplementary files format and content: Per-sample Salmon quant.sf (tab-delimited: Name, Length, EffectiveLength, TPM, NumReads). Shared: DESeq2 raw count matrix, normalized count matrix, sample metadata table.

molecule: polyA RNA

growth_protocol: HepG2 (CVCL_0027) maintained at 37°C, 5% CO2 in DMEM/10% FBS/1% P-S.

extract_protocol:
1x10^6 cells pelleted (500xg, 1 min). Total RNA isolated with Monarch Total RNA Miniprep Kit (NEB T1010) with on-column DNase I digestion.
KAPA mRNA HyperPrep Kit (Roche #08098123702) from 750 ng total RNA. Fragmentation 6 min 94°C. Adapter ligation 7 µM stock. 9 PCR cycles. Paired-end 75 bp on Illumina NextSeq 100.

treatment_protocol: Sorafenib: 5 µM (Selleckchem S1040) 48 h. Vehicle: equivalent DMSO. ARID1B-KO by CRISPR/Cas9.

tag: genotype

value: WT

value: sorafenib 5 µM, 48 h


title: HepG2 WT RNA-seq, Sorafenib, rep2

description: Library name: HepG2_WT_Sorafenib_RNAseq_rep2


title: HepG2 WT RNA-seq, Sorafenib, rep1

description: Library name: HepG2_WT_Sorafenib_RNAseq_rep1


title: WSU-DLCL2_DMSO_Rep1

description: Library name: Sample7.1


title: HepG2 WT RNA-seq, DMSO, rep3

description: Library name: HepG2_WT_DMSO_RNAseq_rep3

value: DMSO vehicle (0.1% v/v)


title: HepG2 WT RNA-seq, DMSO, rep2

description: Library name: HepG2_WT_DMSO_RNAseq_rep2


title: SUDHL10_DOT1Li_Rep3

description: Library name: Sample6.3


title: HepG2 ARID1B-KO H3K4me3 CUT&RUN, Sorafenib, rep2

description: Library name: HepG2_ARID1B-KO_Sorafenib_H3K4me3_rep2

library_source: genomic

data_processing:
Bowtie2 alignment to GRCh38. MACS2 peak calling (-f BAMPE). MSPC consensus peaks. csaw normalization. DESeq2 differential occupancy. deepTools bigWig generation.
Assembly: GRCh38 / hg38
Supplementary files format and content: RPKM-normalized bigWig (*_rpkm.bw), csaw-scaled bigWig (*_scaled.bw), MACS2 narrowPeak (*_peaks.narrowPeak; absent for IgG controls). Note: scaled bigWig absent for HepG2_ARID1B-KO_Sorafenib_IgG_rep1 and rep2.
Library strategy: CUT&Run

molecule: genomic DNA

growth_protocol: HepG2 (CVCL_0027) and HLF (CVCL_2947) maintained at 37°C, 5% CO2 in DMEM/10% FBS/1% P-S.

extract_protocol:
CUT&RUN adapted from EpiCypher protocol. 200,000-500,000 cells, Concanavalin A beads, overnight primary antibody at 4°C (H3K4me3 CST #3076423; H3K27ac CST #2561016; ARID1B CST #65747 clone E1U7D; FOXA1; FOXA2; IgG CST #550038), guinea pig anti-rabbit secondary (Novus NBP1-72763 1:100), pAG-MNase 700 ng/ml 1 h 4°C, CaCl2 digestion on ice 30 min, stop buffer quench, Zymo D4014 cleanup.
KAPA HyperPrep Kit (Roche #07962363001). 14 PCR cycles. Paired-end 50 bp or 150 bp reads on Illumina NextSeq 1000 (HepG2) or NovaSeq X Plus 10B (HLF).

tag: antibody

tag: biological replicate


title: SUDHL10_DOT1Li_Rep2

description: Library name: Sample6.2


title: HepG2 WT RNA-seq, DMSO, rep1

description: Library name: HepG2_WT_DMSO_RNAseq_rep1


title: SUDHL10_DMSO_Rep3

description: Library name: Sample5.3


title: SUDHL10_DOT1Li_Rep1

description: Library name: Sample6.1


title: SUDHL10_DMSO_Rep2

description: Library name: Sample5.2


title: 20250925_210866960925_01_12

type: RNA

city: Madison

first: Daeun

last: Shim

state: Wisconsin

address: 1111 Highland Ave

institute: Daeun Shim

description: nCounter® Immune Exhaustion Panel Mouse

data_processing: Processed using Rosalind Bio platform (Inc R. Discovery Platform & Data Hub for Scientists | ROSALIND® [Internet]. [cited 2025 Dec 28]. https://www.rosalind.bio. Accessed 28 Dec 2025)

organism: Mus musculus

source_name: E.G7-OVA tumor

extract_protocol: Tumors were collected and stored at -80°C until radioactivity reached background. Then the samples were thawed, finely minced, and homogenized in TRIzol using a bead beater. Homogenates were centrifuged, and supernatants were collected for RNA isolation using Direct-zol RNA Miniprep Kit (Zymo Research, Irvine, CA, Cat # R2050). Gene expression analysis was performed using the nCounter Mouse Immune Exhaustion Panel (Brucker Spatial Biology, Bothell, WA, Cat # XT-M-EXHAUST-12) on the nCounter MAX system (Brucker Spatial Biology).

tag: strain

tag: group

value: OT-I CD8+ → pTVG-sOVA → RPT

tag: days post-rpt


title: SUDHL10_DMSO_Rep1

description: Library name: Sample5.1


title: GSK3B wild-type RKO ATAC-Seq 1

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: NO. 199 Renai Road

country: China

institute: Soochow University

description: Library name: GSK3B wild-type RKO ATAC-Seq 1

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform (Illumina, San Diego, California, United States) using the PE150 strategy.
The original ATAC-Seq reads were trimmed of adapter sequences using fastp. The trimmed reads were then aligned to the reference genome (hg38) using Bowtie2. Subsequently, duplicates, multi mapping reads, and low quality alignments were removed using SAMtools. Mitochondrial reads, chromosome Y alignments, and ENCODE blacklisted genomic regions were excluded. Peaks were called using MACS3 with the settings -f BAMPE -B --nomodel --SPMR --keep-dup 1.
Assembly: hg38
Supplementary files format and content: BigWig

source_name: RKO cells

extract_protocol:
ATAC sequencing service was provided by CloudSeq Biotech (Shanghai, China) with GenSeq® ATAC kit (GenSeq Inc.). Briefly, cells were lysed using cold lysis buffer. After lysis, nuclei were collected by centrifuging at 500 g for 10 min at 4℃. The pellet was transposed with transposome and tags were added on both sides of fragmented genomic DNA according to the manufacturer's instruction.
After tagmentation, the purified tagged DNA was used for PCR amplification with GenSeq® 2×HiFi PCR Mix (GenSeq Inc.). The libraries were quantified using Qubit fluorometric assay (ThermoFisher).

value: RKO cells


title: 20250925_210866960925_01_10

description: nCounter® Immune Exhaustion Panel Mouse

value: OT-I CD8+ → pTVG4 → RPT


title: SUDHL4_Combo_Rep3

description: Library name: Sample4.3


title: 20250925_210866960925_01_09

description: nCounter® Immune Exhaustion Panel Mouse

value: OT-I CD8+ → pTVG4


title: 20250923_210866920925_01_11

description: nCounter® Immune Exhaustion Panel Mouse

value: OT-I CD8+ → pTVG-sOVA


title: 20250923_210866920925_01_10

description: nCounter® Immune Exhaustion Panel Mouse

value: OT-I CD8+ → pTVG4 ? RPT


title: SUDHL4_GSK343_Rep2

description: Library name: Sample3.2


title: 20250923_210866920925_01_09

description: nCounter® Immune Exhaustion Panel Mouse


title: SUDHL4_GSK343_Rep1

description: Library name: Sample3.1


title: SUDHL4_DOT1Li_Rep3

description: Library name: Sample2.3


title: 20250923_210866910925_01_12

description: nCounter® Immune Exhaustion Panel Mouse


title: SUDHL4_DOT1Li_Rep2

description: Library name: Sample2.2


title: SUDHL4_DOT1Li_Rep1

description: Library name: Sample2.1


title: 20250923_210866920925_01_12

description: nCounter® Immune Exhaustion Panel Mouse


title: 20250923_210866910925_01_11

description: nCounter® Immune Exhaustion Panel Mouse


title: SUDHL4_DMSO_Rep3

description: Library name: Sample1.3


title: 20250923_210866910925_01_09

description: nCounter® Immune Exhaustion Panel Mouse


title: 8 week old Langerin-DTA mice

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

description:
Library name: Adult_LC_DTA
10x genomics

library_source: transcriptomic single cell

data_processing:
The raw reads were aligned against the GRCm38 mouse reference genome using 10x Genomics Cell Ranger 8.01 pipeline (10x Genomics)
Assembly: GRCm38
Supplementary files format and content: matrix files

source_name: Skin biopsy

growth_protocol: Mice between 4-8 weeks old were aged matched each. Both male and female mice were used for experiments: 4 week old WT mice (5M, 3F), 8 week old WT mice (6M, 4F), 8 week old Langerin-DTA (4M, 6F). C57BL/6J (#000664), Langerin-DTA (#017949) were originally from Jackson Laboratory (JAX) (Bar Harbor, ME) and bred at our facility. The WT mice used in experiments involving Langerin-DTA mice were littermate controls obtained by breeding hemizygous Langerin-DTA males and WT females.

extract_protocol:
Excised ear was finely minced, digested with collagenase type II (616 U/mL; Worthington Biochemical Corporation), dispase (2.42 U/mL; Life Technologies), and DNAse1 (80 µg/mL; Sigma-Aldrich), incubated with 100 rpm at 37°C  for 30 minutes, triturated with glass pipettes, and then filtered. CD45-CD31+PDPN+ LECs, CD45-CD31+PDPN- BECs, CD45+ cells, and CD45-CD31- cells were sorted from 8-10 mice of each of the following conditions: 4 week old WT mice, 8 week old WT mice, 8 week old Langerin-DTA mice, and imiquimod-treated mice. For each condition, the sorted cell populations were pooled together at equal proportions and, per the manufacturer’s recommendations, 29,000 cells per sample were loaded into the 10x Chromium X controller to capture 20,000 cells.
The 3’ v4 GEM & Library construction kit(10x Genomics) was used to generate RNA libraries and sequenced with Illumina NovaSeq X platform to obtain ~30,000 reads per cell

tag: tissue

value: Skin biopsy

value: skin cells

value: Langerin-DTA

tag: age

value: 8 weeks

value: not treated


title: MM4014-D7-MCSF

city: Pittsburgh

first: Timothy

last: Billiar

state: PA

address: 200 Lothrop Street

department: Surgery

institute: University of Pittsburgh

description:
Library name: MM4014-D7-MCSF
scRNA-seq

data_processing:
We generated feature-barcode count matrix using cellranger count (mapped to GRCh38 human reference genome) for each sample separately. The outputs of the samples from the same donor were aggregated using cellranger aggr. The feature-barcode count matrix was processed using Seurat package.
Assembly: GRCh38
Supplementary files format and content: Ma-trauma.rds

source_name: PBMC

growth_protocol: On day 0, cryopreserved PBMCs were thawed and resuspended in complete media (RPMI164+ 10%FBS + penicillin (100U/mL) + streptomycin (100U/mL)) at 5 * 10^5 cell/mL at 37° with 5%CO2 overnight.

extract_protocol:
Blood samples were obtained from human study subjects. PBMCs were isolated by standard Ficoll centrifugation.
Flow isolated monocytes were further proceeded with scRNA libraries using Chromium Single Cell 3' Reagent Kits (v3.1, CG000315)

treatment_protocol: On day 1, GM-CSF (Sigma-Aldrich, Cat# G5035; final concentration: 50 ng/mL) or M-CSF (Sigma-Aldrich, Cat# H6916; final concentration: 50 ng/mL) were added to the media. On day 4, the same amount of fresh complete media with or without cytokines correspondingly were added to the cultured cells. Cells were harvested on day 7 (Accutase: Sigma-Aldrich, Cat# A6964).

value: PBMC

value: in vitro culture


title: 8 week old C57BL/6J (WT) mice

description:
Library name: Adult_WT
10x genomics


title: 20250923_210866920925_01_08

description: nCounter® Immune Exhaustion Panel Mouse

value: Untreated


title: MM4014-D7-Ctrl

description:
Library name: MM4014-D7-Ctrl
scRNA-seq


title: 4 week old C57BL/6J (WT) mice

description:
Library name: Young_WT
10x genomics

value: 4 weeks


title: 20250923_210866910925_01_10

description: nCounter® Immune Exhaustion Panel Mouse


title: MM4014-D3-MCSF

description:
Library name: MM4014-D3-MCSF
scRNA-seq


title: H1FX/S31A(repeat 2)

description:
Library name: H1FX/S31A(repeat 2)
Combined signal track for H1FX/S31A

data_processing:
The original ATAC-Seq reads were trimmed of adapter sequences using fastp. The trimmed reads were then aligned to the reference genome (hg38) using Bowtie2. Subsequently, duplicates, multi mapping reads, and low quality alignments were removed using SAMtools. Mitochondrial reads, chromosome Y alignments, and ENCODE blacklisted genomic regions were excluded. Peaks were called using MACS3 with the settings -f BAMPE -B --nomodel --SPMR --keep-dup 1.
Assembly: hg38
Supplementary files format and content: bigWig signal tracks generated from MACS3 callpeak bedGraph outputs with --SPMR using merged biological replicates for each condition

source_name: RKO

extract_protocol:
50000 cells were treated with cell lysis buffer then centrifuging for 10 min at 500g, supernatant (cytoplasm) was discarded and pellet (nuclei) was keeped. Transposition mix (Vazyme,TD711) was added to nuclei and incubated at 37℃ for 30 minutes on thermomixer at 1,000 rpm. Tagmented DNA was recovered using ATAC DNA Extract Beads (Vazyme,TD711) then amplified by PCR using indexed P5 and P7 primers.
The library products were enriched, quantified and finally sequenced on a DNBSEQ-T7 (MGI) platform using 150 bp paired end reads.

value: RKO


title: MM4014-D3-Ctrl

description:
Library name: MM4014-D3-Ctrl
scRNA-seq


title: H1FX/S31A(repeat 1)

description:
Library name: H1FX/S31A(repeat 1)
Combined signal track for H1FX/S31A


title: H1FX/S31A+GSK3B(repeat 2)

description:
Library name: H1FX/S31A+GSK3B(repeat 2)
Combined signal track for H1FX/S31A+GSK3B


title: GB24 Replicate 2 heavy polysome

city: Providence

first: Mattia

last: Pizzagalli

state: RI

address: 593 Eddy St

department: Neurosurgery Department

institute: Rhode Island Hospital

description:
Library name: GB24_Rep_2_heavy
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.

data_processing:
Salmon (v1.10.1) was used to quantify the abundance of transcripts. The novel transcriptome generated from Bambu was used as the genome annotation.
Assembly: hg38 v44
Supplementary files format and content: TPM of transcripts identified by Salmon using the novel transcriptome generated by Bambu
Library strategy: Ribo-Seq

source_name: Glioblastoma

growth_protocol: Cells are grown as neurospheres in GSC media (Neurobasal A with B27, Glutamax, Anti-Anti, 1 mg/mL heparin, 20 ng/mL EGF, 20 ng/mL FGF)

extract_protocol:
Extraction was performed by creative biolabs. Polysome fractions were isolated and purified mRNA was extracted using oligo(dT)-coated beads.
Libraries were constructed by Creative Biolabs using standard protocols

value: Glioblastoma

value: Glioblastoma Stem Cell

tag: batch


title: SUDHL4_Combo_Rep1

description: Library name: Sample4.1

value: GCB-DLBCL


title: 20250925_210866960925_01_08

description: nCounter® Immune Exhaustion Panel Mouse


title: GB24 Replicate 2 light polysome

description:
Library name: GB24_Rep_2_light
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: GB24 Replicate 2 total

description:
Library name: GB24_Rep_2_tot
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: H1FX/WT+GSK3B(repeat 1)

description:
Library name: H1FX/WT+GSK3B(repeat 1)
Combined signal track for H1FX/WT+GSK3B


title: SUDHL4_GSK343_Rep3

description: Library name: Sample3.3


title: GB24 Replicate 1 heavy polysome

description:
Library name: GB24_Rep_1_heavy
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: GB24 Replicate 2 monosome

description:
Library name: GB24_Rep_2_mono
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: H1FX/WT(repeat 2)

description:
Library name: H1FX/WT(repeat 2)
Combined signal track for H1FX/WT


title: GB24 Replicate 1 monosome

description:
Library name: GB24_Rep_1_mono
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: GB24 Replicate 1 light polysome

description:
Library name: GB24_Rep_1_light
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: H1FX/WT(repeat 1)

description:
Library name: H1FX/WT(repeat 1)
Combined signal track for H1FX/WT


title: H1FX/WT+GSK3B(repeat 2)

description:
Library name: H1FX/WT+GSK3B(repeat 2)
Combined signal track for H1FX/WT+GSK3B


title: 29304-28

type: genomic

city: North Brunswick Township

first: Jia

last: Xu

state: NJ

address: 675 US Highway One

institute: Genomic Prediction, Inc.

description:
No amplification
gDNA isolated from beES4 human ESC line (passage P3), derived from 5AA embryo injected (MII) with ABE RNP with HBG1/2 & PCSK9 sgRNAs

data_processing:
Affymetrix UK Biobank Axiom Array Manufacturer's Protocol
Primary data description: DNA copy number and genotyping

label: biotin

source_name: ESCs derived from ABE injected human embryo (at ICSI on day 0 of development)

growth_protocol: Thawing of human 2PN zygotes was performed using the Qinn's Advantage warming kit or using a one-step protocol with GMOPS-plus depending on the method of cryopreservation. Donated oocytes were warmed using the Cryotech warming kit. Embryos were cultured in Global total.

extract_protocol: Single cells, single polar bodies, or cytoplasmic fragments were placed into single PCR tubes containing 2 ul of Genomic Prediction's loading Buffer. Genomic DNA amplification was performed using amplification kit as indicated for each sample.

treatment_protocol: Cas9 or ABE ribonucleoprotein complex was assembled in vitro and injected at fertilization or at the 1-cell stage of embryo development. Zygotes were either at the 2PN stage or at the entry into the first mitosis.

value: Human ESCs


title: GB24 Replicate 1 total

description:
Library name: GB24_Rep_1_tot
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: 22550-25

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 3-C human embryo #7 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2

hyb_protocol: Affymetrix UK Biobank Axiom Array Manufacturer's Protocol

source_name: Blastomere from CRISPR/Cas9-injected human embryo (at 2PN stage on day 1 of development, D1); Sample collected on day D4

value: Preimplantation embryo


title: GB13 Replicate 2 heavy polysome

description:
Library name: GB13_Rep_2_heavy
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: SUDHL4_DMSO_Rep2

description: Library name: Sample1.2

value: DMSO


title: 22550-24

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 3-C human embryo #7 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2

scan_protocol: Affymetrix UK Biobank Axiom Array Manufacturer's Protocol


title: SUDHL4_DMSO_Rep1

description: Library name: Sample1.1


title: GB13 Replicate 2 light polysome

description:
Library name: GB13_Rep_2_light
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: GB13 Replicate 2 monosome

description:
Library name: GB13_Rep_2_mono
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: 22550-22

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #3 from 4-C human embryo #6 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2

label_protocol: Affymetrix UK Biobank Axiom Array Manufacturer's Protocol


title: 22550-21

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 4-C human embryo #6 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2


title: 20250923_210866910925_01_08

description: nCounter® Immune Exhaustion Panel Mouse


title: 22550-20

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 4-C human embryo #6 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2


title: GB13 Replicate 2 total

description:
Library name: GB13_Rep_2_tot
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: GB13 Replicate 1 heavy polysome

description:
Library name: GB13_Rep_1_heavy
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: 22550-19

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 2-C human embryo #5 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2


title: GB13 Replicate 1 light polysome

description:
Library name: GB13_Rep_1_light
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: GB13 Replicate 1 monosome

description:
Library name: GB13_Rep_1_mono
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: 22550-17

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #5 from 5-C human embryo #4 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2


title: 22550-18

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 2-C human embryo #5 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2


title: GB13 Replicate 1 total

description:
Library name: GB13_Rep_1_tot
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: 22550-16

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #4 from 5-C human embryo #4 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2


title: GB2 Replicate 2 heavy polysome

description:
Library name: GB2_Rep_2_heavy
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: GB2 Replicate 2 light polysome

description:
Library name: GB2_Rep_2_light
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: 22550-13

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 5-C human embryo #4 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2


title: GB2 Replicate 2 monosome

description:
Library name: GB2_Rep_2_mono
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: 22550-14

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 5-C human embryo #4 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2


title: 22550-15

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #3 from 5-C human embryo #4 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2


title: GB2 Replicate 2 total

description:
Library name: GB2_Rep_2_tot
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: HepG2 CRISPR screen Sorafenib_4uM, rep3

description: Library name: HepG2_CRISPRscreen_Sorafenib_4uM_rep3

data_processing:
MAGeCK count for sgRNA quantification. MAGeCK test for differential enrichment with non-targeting controls. 6 contrasts: DMSO vs T0, IC10 vs T0, IC50 vs T0, IC10 vs DMSO, IC50 vs DMSO, IC10 vs IC50.
Assembly: N/A (amplicon sequencing)
Supplementary files format and content: Shared files listed as supplementary files: count matrix, normalized counts, QC summary, MAGeCK gene/sgRNA summaries x6 contrasts, sgRNA library (tab-delimited + FASTA).
Library strategy: CRISPR Screen

extract_protocol:
Genomic DNA (Monarch Genomic DNA Purification Kit, NEB T3010). sgRNA amplification with Illumina adapters.
~6,000 sgRNA library in pLentiCRISPRv2. Lentiviral transduction MOI 0.25-0.3, puromycin 1 µg/ml 7 days. Single-end 75 bp, Illumina NextSeq 500.

treatment_protocol: Post-puromycin selection: T0 harvested day 0. DMSO, sorafenib 2.5 µM, sorafenib 4 µM for 28 days. Medium refreshed every 3 days.

value: WT (Cas9-expressing, unedited parental)

value: sorafenib 4 µM (~IC50 in HepG2 at 96 h), 28 days


title: 22550-11

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #4 from 5-C human embryo #3 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2


title: HepG2 CRISPR screen Sorafenib_4uM, rep2

description: Library name: HepG2_CRISPRscreen_Sorafenib_4uM_rep2


title: GB2 Replicate 1 heavy polysome

description:
Library name: GB2_Rep_1_heavy
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: HepG2 CRISPR screen Sorafenib_4uM, rep1

description: Library name: HepG2_CRISPRscreen_Sorafenib_4uM_rep1


title: 22550-10

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #3 from 5-C human embryo #3 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2


title: HepG2 CRISPR screen Sorafenib_2.5uM, rep3

description: Library name: HepG2_CRISPRscreen_Sorafenib_2.5uM_rep3

value: sorafenib 2.5 µM (~IC10 in HepG2), 28 days


title: GB2 Replicate 1 light polysome

description:
Library name: GB2_Rep_1_light
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: H1FX/S31A+GSK3B(repeat 1)

description:
Library name: H1FX/S31A+GSK3B(repeat 1)
Combined signal track for H1FX/S31A+GSK3B


title: H14, NSC, replicate 3

description:
Library name: H14_p18_PCS114_20250312
Neural stem cells were grown and total RNA was collected using trizol. 500 ng of total RNA was processed using ONT PCS114 PCR-cDNA sequencing kit according to manufacturer's recommendation and protocol.

data_processing:
Basecalling using dorado (rna004_130bps_sup@v5.0.0)
Filtering/processing using pychopper
Alignment using minimap (splice:hq)
Gene counts obtained from Bambu
Assembly: hg38 v44
Supplementary files format and content: Raw counts of annotated genes, as well as novel genes/transcripts identified by Bambu

source_name: Neural Stem Cell

extract_protocol:
Trizol extraction followed by purification/concentration using RNA Clean and Concentrator
cDNA-PCR Sequencing V14 kit (SQK-PCS114)

value: Neural Stem Cell


title: GB2 Replicate 1 monosome

description:
Library name: GB2_Rep_1_mono
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: HepG2 CRISPR screen Sorafenib_2.5uM, rep2

description: Library name: HepG2_CRISPRscreen_Sorafenib_2.5uM_rep2


title: 22550-09

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 5-C human embryo #3 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2


title: GB2 Replicate 1 total

description:
Library name: GB2_Rep_1_tot
GSCs were grown to ~70% confluency, when they were treated with cycloheximide (100 ug/mL) and incubated fro 15 min at 37deg. Cells were collected, washed three times using ice cold PBS with 1000 um/mL cycloheximide, after which supernatant was removed and cells were snap frozen. Samples were sent to Creative biolabs for processing and sequencing.


title: H14, NSC, replicate 1

description:
Library name: H14_p16_PCS114_20250212
Neural stem cells were grown and total RNA was collected using trizol. 500 ng of total RNA was processed using ONT PCS114 PCR-cDNA sequencing kit according to manufacturer's recommendation and protocol.


title: H14, NSC, replicate 2

description:
Library name: H14_p16_PCS114_20250407
Neural stem cells were grown and total RNA was collected using trizol. 500 ng of total RNA was processed using ONT PCS114 PCR-cDNA sequencing kit according to manufacturer's recommendation and protocol.


title: HepG2 CRISPR screen Sorafenib_2.5uM, rep1

description: Library name: HepG2_CRISPRscreen_Sorafenib_2.5uM_rep1


title: 22550-07

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #7 from 7-C human embryo #2 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2


title: 22550-08

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 5-C human embryo #3 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2


title: HepG2 CRISPR screen DMSO, rep3

description: Library name: HepG2_CRISPRscreen_DMSO_rep3

value: DMSO vehicle (0.1% v/v), 28 days


title: H9, NSC, replicate 3

description:
Library name: H9_p13_PCS114_20250403
Neural stem cells were grown and total RNA was collected using trizol. 500 ng of total RNA was processed using ONT PCS114 PCR-cDNA sequencing kit according to manufacturer's recommendation and protocol.


title: 22550-06

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #6 from 7-C human embryo #2 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2


title: p300 CUT&Tag, OCI-AML3 cells, siEP300, Day3, rep2

city: XIAMEN

first: Lanfen

last: Chen

state: Fujian Province

address: No.4221, Xiang'an South Roa

department: School of Life Sciences

institute: XIAMEN UNIVERSITY

description:
Library name: S10
cut-tag antibody: anti-p300 (Abcam, ab10483)

data_processing:
Raw sequencing reads were trimmed and filtered for quality using CutAdapt (v.2.6). Paired-end reads were aligned using Bowtie2 (v.2.3.5.1) (PMID: 22388286) against hg38 genome.
Aligned reads were sorted and non-uniquely mapping reads were marked using Picard (v.2.9.5) (http://broadinstitute.github.io/picard/). PCR duplicates, reads mapped to mitochondria or of low mapping quality were filtered using Samtools (v.1.9) (PMID: 19505943).
To correct for the fact that the Tn5 transposase binds as a dimer and inserts two adapters in the Tn5 tagmentation step, all positive-strand reads were shifted 4 bp downstream and all negative-strand reads were shifted 5 bp upstream to center the reads on the transposon binding event.
We then pooled the shifted reads by sample type and identified peaks using MACS2 (v.2.2.6) (PMID: 18798982) with a threshold of FDR-corrected p < 0.001 using the Benjamini-Hochberg procedure for multiple hypothesis correction. A union peak list for each experiment was created by combining all peaks in all samples; overlapping peaks were merged with minimum overlap > 0.5. The number of reads in each peak was determined with Diffbind (v.3.16.0) (PMID: 22217937).
Differentially expressed peaks were identified after edgeR normalization using a FDR cut-off of 0.05. Peaks were annotated using R package ChIPseeker (v.1.18.0) (PMID: 25765347).
Assembly: hg38
Supplementary files format and content: Supplementary files format and content: BigWig Track Format of each CUT&Tag sample.
Library strategy: CUT&Tag

source_name: Bone marrow

growth_protocol: OCI-AML3 cells were maintained in RPMI1640 complete medium with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
1 × 10^5 OCI-AML3 cells were collected and washed once with 500 μl wash buffer before they were bound to ConA beads for 10 min at 25 °C.
Cells were incubated with 1 mg of respective targeting antibodies at 4 °C overnight. 0.5 mg secondary antibody was added and incubated for 1 h at 25 °C. Then cells were washed three times with DIG wash buffer and incubated with 0.04 μM pA/G–Tnp for 1 h at 25 °C. Similarly, cells were washed three times with DIG 300 buffer, resuspended in tagmentation buffer and incubated at 37 °C for 1 h. Tagmentation was stopped by adding proteinase K, buffer LB and DNA extract beads. After incubation at 55 °C for 10 min, cells were plated on a magnet and unbound liquid was removed. Beads were gently rinsed twice with 80% ethanol and DNA was eluted with double-distilled water. libraries were barcoded using TruePrep™ Index Kit V2 for lllumina (Vazyme TD202) and amplified for 14 cycles. Final product was cleaned by VAHTS DNA Clean Beads at a 2 × ratio. Libraries were sequenced on a Novaseq 6000 in a 150 bp/150 bp Paired end run. An average of 20 × 106 paired reads was generated per sample.

treatment_protocol: OCI-AML3 cells were transfected at 1 × 105 cells/ ml using Lipofectamine RNAi MAX (Invitrogen) following the manufacturer's recommendations. The final concentration of the siRNA molecules is 10 nM. Collect the cells and extract total RNA after 3 days.

value: Bone marrow

value: acute myeloid leukemia blast

value: WT


title: H9, NSC, replicate 2

description:
Library name: H9_p13_PCS114_20250218
Neural stem cells were grown and total RNA was collected using trizol. 500 ng of total RNA was processed using ONT PCS114 PCR-cDNA sequencing kit according to manufacturer's recommendation and protocol.


title: p300 CUT&Tag, OCI-AML3 cells, siEP300, Day3, rep1

description:
Library name: S10_1
cut-tag antibody: anti-p300 (Abcam, ab10483)


title: 22550-05

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #5 from 7-C human embryo #2 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2


title: HepG2 CRISPR screen DMSO, rep2

description: Library name: HepG2_CRISPRscreen_DMSO_rep2


title: H9, NSC, replicate 1

description:
Library name: H9_p10_PCS114_20250707
Neural stem cells were grown and total RNA was collected using trizol. 500 ng of total RNA was processed using ONT PCS114 PCR-cDNA sequencing kit according to manufacturer's recommendation and protocol.


title: HepG2 CRISPR screen DMSO, rep1

description: Library name: HepG2_CRISPRscreen_DMSO_rep1


title: p300 CUT&Tag, OCI-AML3 cells, siKAT7, Day3, rep2

description:
Library name: S9
cut-tag antibody: anti-p300 (Abcam, ab10483)


title: 22550-04

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #4 from 7-C human embryo #2 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2


title: GB24, GSC, replicate 3

description:
Library name: GB24_p26_PCS114_20250621
Glioblastoma stem cells were grown as neurospheres and total RNA was collected using trizol. 500 ng of total RNA was processed using ONT PCS114 PCR-cDNA sequencing kit according to manufacturer's recommendation and protocol.


title: HepG2 CRISPR screen T0, rep3

description: Library name: HepG2_CRISPRscreen_T0_rep3

value: baseline (pre-selection, post-puromycin); timepoint 0


title: p300 CUT&Tag, OCI-AML3 cells, siKAT7, Day3, rep1

description:
Library name: S9_1
cut-tag antibody: anti-p300 (Abcam, ab10483)


title: 22550-03

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #3 from 7-C human embryo #2 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2


title: GB24, GSC, replicate 2

description:
Library name: GB24_p22_PCS114_20241212
Glioblastoma stem cells were grown as neurospheres and total RNA was collected using trizol. 500 ng of total RNA was processed using ONT PCS114 PCR-cDNA sequencing kit according to manufacturer's recommendation and protocol.


title: HepG2 CRISPR screen T0, rep2

description: Library name: HepG2_CRISPRscreen_T0_rep2


title: 22550-02

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 7-C human embryo #2 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2


title: 22550-01

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 7-C human embryo #2 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2


title: p300 CUT&Tag, OCI-AML3 cells, siControl, Day3, exp2, rep2

description:
Library name: C7
cut-tag antibody: anti-p300 (Abcam, ab10483)

value: siControl


title: HepG2 CRISPR screen T0, rep1

description: Library name: HepG2_CRISPRscreen_T0_rep1


title: GB13, GSC, replicate 3

description:
Library name: GB13_p17_PCS114_20241204
Glioblastoma stem cells were grown as neurospheres and total RNA was collected using trizol. 500 ng of total RNA was processed using ONT PCS114 PCR-cDNA sequencing kit according to manufacturer's recommendation and protocol.


title: KAT7 CUT&Tag, OCI-AML3 cells, siEP300, Day3, rep2

description:
Library name: S8
cut-tag antibody: anti-KAT7 (Cell Signaling Technology, 8418)


title: GB24, GSC, replicate 1

description:
Library name: GB24_p16_PCS114_20250430
Glioblastoma stem cells were grown as neurospheres and total RNA was collected using trizol. 500 ng of total RNA was processed using ONT PCS114 PCR-cDNA sequencing kit according to manufacturer's recommendation and protocol.


title: p300 CUT&Tag, OCI-AML3 cells, siControl, Day3, exp2, rep1

description:
Library name: C7_1
cut-tag antibody: anti-p300 (Abcam, ab10483)


title: 22547-23

description:
Other option: Treff method - Phi29 mediated amplification
1-C human embryo #1 injected with CRISPR/Cas9 RNP with HBG1/2 & PCSK9 sgRNAs_Experiment CRISPR-BE2

source_name: CRISPR/Cas9-injected human zygote (at 2PN stage on day 1 of development); Sample collected on day D1


title: GB13, GSC, replicate 2

description:
Library name: GB13_p13_PCS114_20241114
Glioblastoma stem cells were grown as neurospheres and total RNA was collected using trizol. 500 ng of total RNA was processed using ONT PCS114 PCR-cDNA sequencing kit according to manufacturer's recommendation and protocol.


title: shUSP7_H3K27me3_rep2

description: Library name: Sample6.2

data_processing:
Fastq raw data were analyzed using the snakemake-based pipeline CUTEmake using default parameters.
Briefly, reads have been mapped on the human genome (GRCh38.v102/Hg38) using bowtie2.
We further used peaks generated from GoPeaks for ChromHMM analyses.
For visualisation, the signals were normalized using DESeq2 by applying the “Greenlist” method as previously described (de Mello FN et al., Briefings in Bioinformatics, 2024)
For the density profiles at gene transcription start sites (TSS), signal scores were obtained using deeptools computeMatrix and plotted using Rseb (v0.3.4).
Assembly: Hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: IMDM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
5 x 105 cells per condition were harvested and processed according to the manufacturer’s instructions for CUT&Tag-IT Assay Kit (Active Motif).
Libraries were prepared following manufacturer’s instructions of CUT&Tag-IT Assay Kit (Active Motif)

treatment_protocol: Cells were treated with EPZ-5676 (DOT1Li) for 6 days. At day 3, 5x10^4 cells/ml were reseeded with fresh medium and inhibitors. Oci-Ly7 cells containing dox-inducible shRNA targeting USP7 were treated with 2 µg/ml doxycycline for three days.

value: H3K27me3, Cell Signaling; cat. No. 9733S


title: KAT7 CUT&Tag, OCI-AML3 cells, siEP300, Day3, rep1

description:
Library name: S8_1
cut-tag antibody: anti-KAT7 (Cell Signaling Technology, 8418)


title: WSU-DLCL2_DMSO_Rep2

description: Library name: Sample7.2


title: shUSP7_H3K27me3_rep1

description: Library name: Sample6.1


title: 22549-33

description:
No amplification
gDNA isolated from beES2 human ESC line (passage P3), derived from 5AA embryo injected with ABE RNP with HBG1/2 & PCSK9 sgRNAs

source_name: ESCs derived from ABE-injected human embryo (at 2PN stage on day 1 of development, D1)


title: KAT7 CUT&Tag, OCI-AML3 cells, siKAT7, Day3, rep2

description:
Library name: S7
cut-tag antibody: anti-KAT7 (Cell Signaling Technology, 8418)


title: 22549-32

description:
No amplification
gDNA isolated from beES1 human ESC line (passage P3), derived from 6AA embryo injected with ABE RNP with HBG1/2 & PCSK9 sgRNAs


title: GB13, GSC, replicate 1

description:
Library name: GB13_p12_PCS114_20241121
Glioblastoma stem cells were grown as neurospheres and total RNA was collected using trizol. 500 ng of total RNA was processed using ONT PCS114 PCR-cDNA sequencing kit according to manufacturer's recommendation and protocol.

value: Glioblastoma


title: KAT7 CUT&Tag, OCI-AML3 cells, siKAT7, Day3, rep1

description:
Library name: S7_1
cut-tag antibody: anti-KAT7 (Cell Signaling Technology, 8418)


title: GB11, GSC, replicate 3

description:
Library name: GB11_p34_PCS114_20250217
Glioblastoma stem cells were grown as neurospheres and total RNA was collected using trizol. 500 ng of total RNA was processed using ONT PCS114 PCR-cDNA sequencing kit according to manufacturer's recommendation and protocol.

value: Glioblastoma Stem Cell


title: DOT1Li_H3K27me3_rep2

description: Library name: Sample4.2

value: GCB-DLBCL


title: GB11, GSC, replicate 2

description:
Library name: GB11_p19_PCS114_20250217
Glioblastoma stem cells were grown as neurospheres and total RNA was collected using trizol. 500 ng of total RNA was processed using ONT PCS114 PCR-cDNA sequencing kit according to manufacturer's recommendation and protocol.


title: KAT7 CUT&Tag, OCI-AML3 cells, siControl, Day3, exp2, rep2

description:
Library name: C6
cut-tag antibody: anti-KAT7 (Cell Signaling Technology, 8418)


title: 22548-37

description:
Other option: Treff method - Phi29 mediated amplification
Human blastocyst (multiple cells), embryo #4 injected with ABE mRNA and PCSK9 sgRNA_Experimental Group BEx

source_name: Human blastocyst (multiple cells) developed from ABE-injected human embryo (at 2PN stage on day 1 of development, D1); Sample collected on day D7


title: shUSP7_H2AK119ub1_rep2

description: Library name: Sample5.2

value: H2AK119ub1, Cell signaling; cat. No. 8240S


title: shUSP7_H2AK119ub1_rep1

description: Library name: Sample5.1


title: 22548-36

description:
Other option: Treff method - Phi29 mediated amplification
Complete human morula (multiple cells), embryo #3 injected with ABE mRNA and PCSK9 sgRNAs_Experimental Group BEx

source_name: Complete human morula developed from ABE-injected human embryo (at 2PN stage on day 1 of development, D1); Sample collected on day D6

value: Preimplantation embryo


title: 20250925_210866960925_01_11

description: nCounter® Immune Exhaustion Panel Mouse

value: OT-I CD8+ → pTVG-sOVA


title: KAT7 CUT&Tag, OCI-AML3 cells, siControl, Day3, exp2, rep1

description:
Library name: C6_1
cut-tag antibody: anti-KAT7 (Cell Signaling Technology, 8418)


title: GB11, GSC, replicate 1

description:
Library name: GB11_p16_PCS114_20241124
Glioblastoma stem cells were grown as neurospheres and total RNA was collected using trizol. 500 ng of total RNA was processed using ONT PCS114 PCR-cDNA sequencing kit according to manufacturer's recommendation and protocol.


title: DOT1Li_H3K27me3_rep1

description: Library name: Sample4.1


title: GB2, GSC, replicate 3

description:
Library name: GB2_p34_PCS114_20250408
Glioblastoma stem cells were grown as neurospheres and total RNA was collected using trizol. 500 ng of total RNA was processed using ONT PCS114 PCR-cDNA sequencing kit according to manufacturer's recommendation and protocol.


title: NPM1c CUT&Tag, OCI-AML3 cells, siEP300, Day3, rep2

description:
Library name: S6
cut-tag antibody: anti-NPM1c (ABclonal, 8457)


title: 22548-33

description:
No amplification
ES cells from the ICM outgrowth of 5AA human blastocyst; embryo injected with ABE RNP with HBG1/2 & PCSK9 sgRNAs_Experimental Group BEx

source_name: ESCs from outgrowth of ABE-injected human embryo (at 2PN stage on day 1 of development, D1)

value: Human ESCs


title: SUDHL4_Combo_Rep2

description: Library name: Sample4.2


title: DOT1Li_H2AK119ub1_rep2

description: Library name: Sample3.2


title: GB2, GSC, replicate 2

description:
Library name: GB2_p25_PCS114_20241204
Glioblastoma stem cells were grown as neurospheres and total RNA was collected using trizol. 500 ng of total RNA was processed using ONT PCS114 PCR-cDNA sequencing kit according to manufacturer's recommendation and protocol.


title: 22548-30

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 4-C human embryo #2 injected with ABE mRNA and PCSK9 sgRNA_Experimental Group BEx

source_name: Blastomere from ABE-injected human embryo (at 2PN stage on day 1 of development, D1); Sample collected on day D5


title: DOT1Li_H2AK119ub1_rep1

description: Library name: Sample3.1


title: NPM1c CUT&Tag, OCI-AML3 cells, siEP300, Day3, rep1

description:
Library name: S6_1
cut-tag antibody: anti-NPM1c (ABclonal, 8457)


title: 22548-26

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #4 from 5-C human embryo #1 injected with ABE mRNA and PCSK9 sgRNA_Experimental Group BEx


title: U87MG cells, S/G(+)_2

status: Public on Jun 20 2026

city: Busan

first: Jong-Ho

last: Lee

address: 37 Nakdong-daero 550 Beon-gil

country: South Korea

institute: Dong-A University

data_processing:
ExDEGA  GraphicPlus_v2.1
Bowtie2
Supplementary files format and content: Read Count.xlsx

growth_protocol: U87MG epithelial cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QuantSeq 3' mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: U87MG epithelial cells were cultured with serine/glycine-containing complete media or equivalent media lacking serine/glycine for 24h.

value: glioblastoma cell line

tag: cell state

value: Naïve

value: with serine and glycine DMEM

tag: time

value: Day 1


title: ATAC, Ctrl, Smad2_KO1, rep 1

city: Toronto

first: Giacomo

last: Furlan

state: ONTARIO

address: 25 Orde St

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

description:
Library name: Sample 5
Smad2_KO_1A

data_processing:
Read quality was assessed using FastQC. Paired-end reads were trimmed using Trim Galore, and only high-quality reads passing these steps were retained for downstream analysis.
Reads were aligned to the Mus musculus reference genome (mm10) using Bowtie2 (v2.4.1). Unaligned reads, mitochondrial reads, and PCR duplicates were removed at this stage.
Peak calling was performed with MACS3 (v3.0.3), using --nomodel and --nolambda parameters. Peaks overlapping with mouse ENCODE blacklist regions were excluded.
Differential accessibility analysis was performed in R using the DiffBind package (v3.16.0). Regions were considered significantly differentially accessible with a false discovery rate (FDR) < 0.05 and an absolute log₂ fold change > 1.
Genomic regions were annotated to nearby genes using GREAT (McLean et al., 2010), with the following settings: proximal = ±5 kb from transcription start site (TSS); distal = up to 1000 kb.
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing normalized counts for all peaks in all samples

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured on gelatin-coated plates in standard serum/LIF medium consisting of DMEM GlutaMAX supplemented with sodium pyruvate, 15% fetal bovine serum, 0.1 mM non-essential amino acids, 50 U mL-1 penicillin–streptomycin, 0.1 mM 2-mercaptoethanol, and 1,000 U mL-1 ESGRO LIF.

extract_protocol:
50,000 live cells were collected and resuspended in cold resuspension buffer (RSB: 10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl₂) supplemented with 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin. Following lysis, nuclei were washed in RSB containing 0.1% NP-40 and subjected to tagmentation using the transposition mixture: 25 μL of 2× TD buffer, 2.5 μL of Tn5 transposase (100 nM final concentration), 16.5 μL of 1× PBS, 0.5 μL of 1% digitonin, 0.5 μL of 10% Tween-20, and 5 μL of nuclease-free water. After transposition, DNA was purified using the Zymo DNA Clean & Concentrator-5 Kit.
Library amplification was carried out as per protocol (Corces et al., 2017). Amplified libraries were purified using AMPure XP beads with a double-sided size selection to remove both primer dimers and large fragments (>1000 bp). Final libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit, pooled at equimolar concentrations, and sequenced on a NovaSeq X platform with a 10B flow cell, generating 150 bp paired-end reads.

treatment_protocol: To induce in vitro pausing, 200nM of the mTOR inhibitor INK128 was added to the culture medium for 12 hours.

value: embryonic stem cells

value: KO

value: Ctrl


title: ATAC, Ctrl, Smad2_KO1, rep 3

description:
Library name: Sample 7
Smad2_KO_1C


title: N2 adult day 8, DMSO, rep 1, trial 3

city: Eugene

first: Patrick

last: Phillips

state: OR

address: 5289 University of Oregon

department: Institute of Ecology and Evolution

institute: University of Oregon

description:
Library name: N2_8_DMSO_r1_tr3
N2_additional_controls.featureCounts.txt

data_processing:
Subread v2.0.2 was used to build a custom C. elegans reference genome package with default parameters.
Sequenced reads contained in single-end FASTQ files were mapped to the WBcel235 reference genome using Subread with parameter -t 0.
Uniquely mapped reads were assigned to genes using the Subread featureCounts package with parameters -t exon -g gene_id.
Assembly: WBcel235 (build 108)
Supplementary files format and content: Tab-delimited tables of raw gene counts for every gene and sample, for (1) two-group comparisons in wild type at each age, (2) additional wild type control series, and (3) skn-1 and daf-16 mutants at two ages.

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: C. elegans N2, PX991 (daf-16(fx107)), and EU1 (skn-1(zu67)) strains were maintained at 20°C and 80% RH on 60 mm nematode growth medium (NGM) plates seeded with E. coli OP50-1.

extract_protocol:
Worms were picked into 0.2 mL tubes containing 45 µL lysis buffer, 4 µL RNA-secure, 5 µL proteinase K and flash frozen with liquid nitrogen.
Libraries were prepared using the KAPA mRNA HyperPrep kit (KK8580 from Kapa Biosystems) as per manufacture protocol except that the total volume was adjusted to 1/4 per reaction.

treatment_protocol: Sulforaphane (Santa Cruz Biotech, sc-207495D) was mixed with DMSO (dimethyl sulfoxide) to create a stock solution. Stock solutions (DMSO for the controls) were then diluted with water to create working solutions and distributed onto 35 mm NGM plates containing 51 µM FUdR and previously seeded with OP50-1. Plates were treated with compound solutions such that the final volume was assumed equal to the volume of agar and the final concentration of DMSO was 0.25%. Worms were synchronized and added to treatment plates beginning on day 1 of adulthood. Biological replicates were aged and collected in tandem, with the exception of EU1, where biological replicates 4, 5, and 6 were temporally independent. Approximately 50 worms total were collected per age, intervention, and replicate.

value: whole worm

value: adult day 8

value: WT

value: DMSO control


title: Muc13 KO mouse cornea_2

city: Bengbu

first: Jing

last: Wu

address: Donghai road 2600

institute: Bengbu Medical University

description:
Library name: Sample 2
The corneal tissue of Muc13 KO mouse.

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLCgenomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork(parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarityraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Cornea

growth_protocol: Male SPF Muc13-/- and WT mice (6 weeks old) were maintained on a 12-h light/dark cycle. Corneas were collected post-mortem and subjected to transcriptomic profiling via RNA-seq.

extract_protocol:
Total RNA of cells or tissues were isolated with RNA extraction reagent (Servicebio, Cat#: G3013). cDNA was synthesized from 1 μg of total RNA with SweScript RT II First Strand cDNA Synthesis Kit (Servicebio, Cat#: G3333.). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kitollowing manufacturer's protocols.

value: Cornea

value: Muc13 knock out


title: Round spermatids, Bearded dragon, HiC, rep1

status: Public on Jun 22 2026

city: Cerdanyola del Vallès

first: Laia

last: Marín-Gual

address: Campus UAB

country: Spain

institute: Universitat Autònoma de Barcelona

description: Library name: RS_BeardedDragon_HiC_rep1

data_processing:
BBDuk (version 09/2019) was used for quality check and trimming. Basically, adapters and low-quality reads (i.e. reads with a minimum length of 35 bp and a minimum Phred quality score of 20) were removed. High-quality reads were then mapped against the tammar wallaby (PRJNA1235426) and bearded dragon (PviZW2.1) genomes using the GEM (version 3.6.1) mapper from TADbit (version 1.0.1).
Assembly: PRJNA1235426 (tammar wallaby), PviZW2.1 (bearded dragon)
Supplementary files format and content: GInteraction tables of Hi-C data at a 50 Kbp resolution, which include interaction values between all genomic bins genome-wide.

organism: Pogona vitticeps

source_name: Round spermatids

extract_protocol:
In nuclei Hi-C was adapted from previously described protocols.  Briefly, germ cells were incubated in lysis buffer containing 10 mM Tris, 10 mM NaCl, 0.2% Igepal and 1xPIC for 20 minutes at 4ºC. Subsequently, germ cells were incubated with 0.5% SDS in 1xNEBuffer 2 for 10 minutes at 4ºC and the reaction was quenched by adding 10% Triton X-100 and incubating for 30 minutes at 37ºC. Germ cells were then centrifuged at 5,000 xg for 5 minutes at 4ºC and resuspended in 300 µl 1xNEBuffer 2 containing 400 U of MboI. Chromatin was digested overnight at 37ºC and assessed the following day by comparing a digested and a non-digested control. Germ cells were then incubated at 65ºC for 20 minutes to inactivate the restriction enzyme and the reparation mix (0.05mM dCTP, 0.05mM dTTP, 0.5mM dGTP, 0.05mM biotin-dATP, 50U Klenow in 1xNEBuffer 2) was directly added into the cell suspension. Chromatin was repaired and biotinylated for 90 minutes at 37ºC, and then the enzyme was heat-inactivated at 65ºC for 10 minutes. Prior to ligation, germ cells were centrifuged for 5 minutes at 5,000 xg at 4ºC, resuspended in ligation buffer (0.8% Triton X-100, 0.1 mg/ml BSA, 10,000 U T4 DNA ligase in 1xNEB T4 ligase buffer) and incubated overnight at 16ºC. Lastly, germ cells were incubated with RNAse A for 15 minutes at 37ºC, and then with proteinase K overnight at 65ºC to reverse the crosslink, followed by a DNA extraction with Phenol:Chloroform. DNA concentration was quantified by Qubit and quality was assessed by running a 0.8% agarose gel.
For library preparation, samples were sonicated into fragments of 300 – 500 bp. The biotinylated fragments were pulled down using Dynabeades MyOne Streptavidin T1 beads, which were pre-washed with 2xbinding buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 2 M NaCl) and incubated with sonicated fragments for 30 minutes in rotation. Beads were then separated on a magnetic rack and washed with 1xbinding Buffer. Ends repair, adaptor ligation and amplification were performed with the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® according to manufacturer’s recommendations. For size selection, DNA fragments were incubated with AMPure beads in a 1:1 proportion for 10 minutes at room temperature. Beads were then washed twice with 70% ethanol and DNA was eluted with Tris buffer for 10 minutes at room temperature. DNA concentration was quantified by Qubit and fragment size was assessed by running a Bioanalyzer. Libraries were submitted for Illumina sequencing (paired-end 150bp each side on NovaSeq 6000).

value: Round spermatids

tag: Sex

value: Male


title: GB2, GSC, replicate 1

description:
Library name: GB2_p20_PCS114_20241114
Glioblastoma stem cells were grown as neurospheres and total RNA was collected using trizol. 500 ng of total RNA was processed using ONT PCS114 PCR-cDNA sequencing kit according to manufacturer's recommendation and protocol.

value: Glioblastoma

value: Glioblastoma Stem Cell


title: NPM1c CUT&Tag, OCI-AML3 cells, siKAT7, Day3, rep2

description:
Library name: S5
cut-tag antibody: anti-NPM1c (ABclonal, 8457)

value: Bone marrow

value: acute myeloid leukemia blast


title: U87MG cells, S/G(-)_2

value: glioblastoma cell line

value: Naïve

value: without serine and glycine DMEM


title: DMSO_H3K27me3_rep2

description: Library name: Sample2.2

value: GCB-DLBCL

value: H3K27me3, Cell Signaling; cat. No. 9733S


title: 22548-25

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #3 from 5-C human embryo #1 injected with ABE mRNA and PCSK9 sgRNA_Experimental Group BEx

value: Preimplantation embryo


title: female, high fat diet, replicate 1

city: Bronx

first: Ronald

last: Cutler

state: NY

address: 1300 Morris Park Ave

department: Genetics & Biochemistry

institute: Albert Einstein College of Medicine

description: Library name: FHF1

data_processing:
Raw sequence data were processed using the nf-core RNA-Seq pipeline (version 3.19.0). Reads were aligned to the GRCm39 mouse reference genome using the STAR aligner and gene quantification was performed against the GENCODE vM37 primary assembly annotation with RSEM to obtain gene expression counts.
Assembly: GRCm39
Supplementary files format and content: tab delimited text file that includes counts/TPM for each gene and sample

source_name: liver

extract_protocol:
Total RNA was isolated from approximately 20 mg of homogenized whole-liver powder using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
1 µg of total RNA per sample was submitted to Azenta Life Sciences for library preparation using the NEBNext Ultra RNA Library Prep Kit (New England Biolabs) followed by sequencing on the NovaSeq platform (Illumina).

treatment_protocol: Male and female C57BL/6J mice (Jackson Laboratory, #000664) were obtained at 6 weeks of age and assigned to either a normal chow (NC; LabDiet 5053; 4.5% of calories from fat) or a high fat (HF; Research Diets, D12492; 60% of calories from fat) diet for 10 weeks. Mice were group-housed in a temperature-controlled room with ad libitum access to food and water under a 12 h light/12 h dark cycle (lights on at 07:00, Zeitgeber time 0).

value: liver

value: wt

value: high fat diet


title: DMSO_H3K27me3_rep1

description: Library name: Sample2.1


title: female, high fat diet, replicate 2

description: Library name: FHF2


title: NPM1c CUT&Tag, OCI-AML3 cells, siControl, Day3, exp2, rep2

description:
Library name: C5
cut-tag antibody: anti-NPM1c (ABclonal, 8457)

value: WT

value: siControl


title: NPM1c CUT&Tag, OCI-AML3 cells, siKAT7, Day3, rep1

description:
Library name: S5_1
cut-tag antibody: anti-NPM1c (ABclonal, 8457)


title: 22548-23

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 5-C human embryo #1 injected with ABE mRNA and PCSK9 sgRNA_Experimental Group BEx


title: DMSO_H2AK119ub1_rep2

description: Library name: Sample1.2

value: H2AK119ub1, Cell signaling; cat. No. 8240S


title: 22548-24

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 5-C human embryo #1  injected with ABE mRNA and PCSK9 sgRNA_Experimental Group BEx


title: NPM1c CUT&Tag, OCI-AML3 cells, siControl, Day3, exp2, rep1

description:
Library name: C5_1
cut-tag antibody: anti-NPM1c (ABclonal, 8457)


title: DMSO_H2AK119ub1_rep1

description: Library name: Sample1.1


title: 22547-02

description:
Other option: Treff method - Phi29 mediated amplification
Complete human morula, embryo injected with ABE RNP with HBG1/2 & PCSK9 sgRNAs_Experimental Group BEx


title: female, high fat diet, replicate 3

description: Library name: FHF3


title: 22547-01

description:
Other option: Treff method - Phi29 mediated amplification
TE biopsy from 5AA human embryo injected with ABE RNP with HBG1/2 & PCSK9 sgRNAs_Experimental Group BEx

source_name: TE biopsy from ABE-injected human embryo (at 2PN stage on day 1 of development, D1); Sample collected on day D6


title: p300 CUT&Tag, OCI-AML3 cells, siNPM1c-AM, Day9, rep1

description:
Library name: S4_1
cut-tag antibody: anti-p300 (Abcam, ab10483)


title: female, normal diet, replicate 1

description: Library name: FNC1

value: normal diet


title: WT_5_2%

city: Houston

first: Jeanine

middle: L

last: Van Nostrand

state: TX

address: One Baylor Plaza M502C Van Nostrand

department: Molecular and Cellular Biology

institute: Baylor College of Medicine, Houston

description:
Library name: WT_5_2_
WT_5_2%

data_processing:
FastQ generation and demux with BCL Convert v4.3.6 and fqtk v0.3.1.
Read-filtering using FastP v0.24.0: poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp.
Alignment to the appropriate reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads.
Coordinate sorting of BAM files using samtools v1.22.1.
UMI based de-duplication: Removal of PCR and optical duplicates using UMICollapse v1.1.0.
Mapping QC: Alignment quality metrics, strand specificity, and read distribution across genomic features using RSeQC v5.0.4 and Qualimap v2.3.
Generation of comprehensive QC report using MultiQC v1.32.
Gene-expression quantification using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file.
Sample-sample correlations for sample-sample heatmap and PCA were calculated on normalized counts (TMM, trimmed mean of M-values) using Pearson correlation.
Assembly: GRCm39_114
Supplementary files format and content: Counts and Counts per million

source_name: T-antigen immortalized MEFs

growth_protocol: Complete media with 10% CO2 at 37C

extract_protocol:
RNA/DNA Shield (Zymo); Bead based extraction by plasmidsaurus
convert mRNA into complementary DNA (cDNA) via reverse transcription and second-strand synthesis, followed by tagmentation, library indexing, and amplification.

treatment_protocol: 10% CO2 or 2% CO2 for 24 hours

value: T-antigen immortalized MEFs

value: Mouse embryonic fibroblast

value: Wildtype


title: WT_4_2%

description:
Library name: WT_4_2_
WT_4_2%


title: 22531-85

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #12 from 12-C human embryo #4 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5

source_name: Blastomere from ABE-injected human embryo (at 2PN stage on day 1 of development, D1); Sample collected on day D4


title: female, normal diet, replicate 2

description: Library name: FNC2


title: WT_3_2%

description:
Library name: WT_3_2_
WT_3_2%


title: 22531-83

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #10 from 12-C human embryo #4 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: female, normal diet, replicate 3

description: Library name: FNC3


title: WT_2_2%

description:
Library name: WT_2_2_
WT_2_2%


title: 22531-81

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #8 from 12-C human embryo #4 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: male, high fat diet, replicate 1

description: Library name: MHF1


title: 22531-80

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #7 from 12-C human embryo #4 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: KAT7 CUT&Tag, OCI-AML3 cells, siNPM1c-AM, Day9, rep1

description:
Library name: S13_1
cut-tag antibody: anti-KAT7 (Cell Signaling Technology, 8418)

value: Bone marrow

value: acute myeloid leukemia blast


title: WT_5_10%

description:
Library name: WT_5_10_
WT_5_10%


title: 22531-78

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #5 from 12-C human embryo #4 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: male, high fat diet, replicate 2

description: Library name: MHF2


title: KAT7 CUT&Tag, OCI-AML3 cells, siControl, Day9, rep2

description:
Library name: C13
cut-tag antibody: anti-KAT7 (Cell Signaling Technology, 8418)


title: 22531-76

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #3 from 12-C human embryo #4 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: male, high fat diet, replicate 3

description: Library name: MHF3


title: KAT7 CUT&Tag, OCI-AML3 cells, siControl, Day9, rep1

description:
Library name: C13_1
cut-tag antibody: anti-KAT7 (Cell Signaling Technology, 8418)


title: WT_3_10%

description:
Library name: WT_3_10_
WT_3_10%


title: 22531-75

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 4 12-C human embryo #4 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: NPM1c CUT&Tag, OCI-AML3 cells, siNPM1c-AM, Day9, rep2

description:
Library name: S12
cut-tag antibody: anti-NPM1c (ABclonal, 8457)


title: male, high fat diet, replicate 4

description: Library name: MHF4


title: WT_2_10%

description:
Library name: WT_2_10_
WT_2_10%


title: NPM1c CUT&Tag, OCI-AML3 cells, siNPM1c-AM, Day9, rep1

description:
Library name: S12_1
cut-tag antibody: anti-NPM1c (ABclonal, 8457)


title: male, normal diet, replicate 1

description: Library name: MNC1


title: 22531-74

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 4 12-C human embryo #4 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: 22531-73

description:
Other option: Treff method - Phi29 mediated amplification
Cells and cell fragments from day 4 24-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5

source_name: Cells and cell fragments from ABE-injected human embryo (at 2PN stage on day 1 of development, D1); Sample collected on day D4


title: male, normal diet, replicate 2

description: Library name: MNC2


title: CD1 Sample

city: Albany

first: Melinda

last: Larsen

address: 1400 Washington Ave

institute: University at Albany

description:
Library name: CD1
10X Genomics

data_processing:
Initial processing steps included aligning to the GRCm39-8 genome with the addition of tdTomato and Cre transcripts and generating counts files, which was completed using CellRanger version 8.0.0.
Background noise was removed using CellBender (Fleming et al. 2023). Data files were imported using Seurat v5.0.1 in R v4.3.1 (R Project for Statistical Computing, 2021; Stuart et al., 2019)
Dead or apoptotic cells were removed if >25% of unique molecular identifiers (UMIs) mapped to mitochondrial genes.
Any cells with less than 200 or over 9,000 genes were excluded.
Integration was performed on 2 datasets to create one dataset. Clusters were calculated following the default pipeline (Seurat Guided Clustering Tutorial, 2023). All analysis of the integrated dataset was performed using the Seurat package in combination with other R packages.
Assembly: GRCm39-8
Supplementary files format and content: output_CellBender_FPR_0.01_filtered.h5

source_name: Submandibular Salivary Gland

extract_protocol:
For enrichment of stromal cell populations, Three mice were used for each timepoint with the mouse’s right submandibular and sublingual gland both being harvested. Excess fat and interstitial tissue were removed. The glands were then transferred to a dish containing 1X PBS, liberase TL Research Grade low Thermolysin (Roche 05401020001) at 0.25 mg/ml, DNase I (Stemcell Technologies 07900) at 15mg/ml, and dispase (Gibco 17105-041) at 0.53 u/ml and microdissected for 10 minutes. The sample was then incubated in a 37°C incubator for 15 minutes then triturated 1200 times . After trituration, the sample was incubated for an additional 5 minutes in a 37°C incubator and triturated once more. A 15 mL conical tube was placed on ice and the entire sample was transferred to the conical tube and incubated for 10 minutes. The supernatant was isolated and transferred to a fresh conical tube containing equal volume of DMEM/F12 (Gibco 11039-021) with 10% FBS (Gibco 10082-147) and was centrifuged for 5 minutes at 150xg 4C. The supernatant was removed and discarded, and the cell pellet was resuspended in 2 ml of isolation buffer composed of sterile-filtered Ca2+- and Mg2+-free 1X PBS, 0.1% bovine serum albumin, and 2 mM ethylenediaminetetraacetic acid. 5 μg of EpCAM (Invitrogen 14-5791-81) and Ter119 (Invitrogen 14-5921-82) was added to the cell suspension and incubated at 4°C on a rocker set on low speed for 10 minutes. the cell suspension was washed using isolation buffer and centrifuged at 150xg for 5 minutes at 4C. The supernatant was discarded, and the cell pellet was resuspended in 1 mL of isolation buffer. For depletion of epithelial and red blood cells, 25 μL of sheep anti-rat Dynabeads, which bind to the EpCAM- and Ter119 Ter119-labeled cells, (Invitrogen 11035) were added. The cell suspension was transferred to a 35 mm dish before incubating at 4C for 20 minutes on a rocker set at low speed. The sample was placed on a microcentrifuge magnet for 2 minutes, and the supernatant was collected. One additional epithelial and red blood cell depletion was performed. The sample was then depleted of dead cells using a dead cell removal kit (Miltenyi Biotec 130-090-101), following manufacturer’s instructions.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

treatment_protocol: Genetic Model Vs Control, No treatments

value: Submandibular Salivary Gland

value: Stromal Enriched

value: Control Mouse


title: male, normal diet, replicate 3

description: Library name: MNC3


title: NPM1c CUT&Tag, OCI-AML3 cells, siControl, Day9, rep1

description:
Library name: C12_1
cut-tag antibody: anti-NPM1c (ABclonal, 8457)


title: NPM1c CUT&Tag, OCI-AML3 cells, siControl, Day9, rep2

description:
Library name: C12
cut-tag antibody: anti-NPM1c (ABclonal, 8457)


title: NOD Sample

description:
Library name: NOD
10X Genomics

value: NOD/ShiltJ

value: Genetic Mouse Model


title: IgG CUT&Tag, OCI-AML3 cells, siNPM1c, Day9

description:
Library name: IgG_2
cut-tag antibody: Normal Rabbit IgG(Cell Signaling Technology, 2729)


title: 22531-71

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #21 from 24-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5

value: Preimplantation embryo


title: GSK3B knockout RKO RNA-Seq 3

description: Library name: GSK3B knockout RKO RNA-Seq 3

data_processing:
Sequencing reads were mapped to the human reference genome (hg38) with TopHat software. Then, read counts were calculated using GFOLD software. Differentially expressed genes were identified with the limma-edgeR workflow.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include reads count for each Sample

source_name: RKO

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen, CA, USA) following the manufacturer's guidelines. The purity and concentration of the RNA were measured with a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Subsequently, libraries were prepared with the VAHTS Universal V6 RNA-seq Library Prep Kit in accordance with the manufacturer's instructions. The sequencing of the RNA-Seq libraries was carried out on an illumina X10 platform, generating 150 bp paired-end reads.

value: RKO


title: IgG CUT&Tag, OCI-AML3 cells, siNPM1c, Day3

description:
Library name: IgG_1
cut-tag antibody: Normal Rabbit IgG(Cell Signaling Technology, 2729)

source_name: Bone marrow


title: Pooled snRNAseq samples

first: Alexandra

last: Moffat

state: Ontario

address: 2075 Bayview Ave

institute: Sunnybrook Research Institute

description:
Library name: Pool_135
Nuclei from biological replicate samples N1, N2 and N3 were pooled prior to sequencing (Pool_135). This sample represents computationally demultiplexed nuclei from the pooled library. Raw FASTQ files are associated with the pooled sample (Pool_135).

data_processing:
snRNA-seq data from three biological replicates was analyzed using R (v4.5.2) (https://www.r-project.org/; https://cran.r-project.org/bin/windows/base/old/). Quality control, normalization, integration, clustering, and visualization were performed using Seurat (v5.4.0) ( https://satijalab.org/seurat/) following standard workflows. Nuclei with mitochondrial transcript content greater than 5% were excluded, as were nuclei with fewer than 562 or more than 10 000 detected genes, and those with total UMI counts exceeding 100 000. After filtering, 3 000 highly variable features were selected. Gene expression was normalized using SCTransform (https://cran.r-project.org/web/packages/sctransform/citation.html), with simultaneous regression of cell cycle effects. Cell cycle phases were assigned using Seurat’s Cell Cycle Scoring method (https://satijalab.org/seurat/articles/cell_cycle_vignette.html), based on established S-phase (43 genes) and G2/M-phase (54 genes) markers. Nuclei exhibiting low scores for both gene sets were classified as G1. Biological replicates were integrated using Harmony (v1.2.4) 66 on the first 100 principal components. Dimensionality reduction was performed using Principal Component Analysis (PCA), and the top 25 principal components were used for Uniform Manifold Approximation and Projection (UMAP) embedding and graph-based clustering at a resolution of 1.5. Expression patterns of canonical lineage markers and the zsGreen reporter were visualized using FeaturePlot, overlaying normalized expression values onto UMAP embeddings. Differential gene expression analysis was performed using the Wilcoxon rank-sum test implemented in Seurat, comparing zsGreen-positive and zsGreen-negative nuclei within each cell type using the SCTransform assay and a minimum expression threshold of 10% of cells per gene. Gene Ontology biological process and KEGG pathway enrichment analyses were conducted using clusterProfiler (v4.16.0) 67, applying Benjamini–Hochberg correction for multiple testing and using all genes tested in differential expression analyses as the background universe.
Cell-type composition differences between zsGreen-positive and zsGreen-negative cells were assessed using scCODA (v0.1.9) 68. Cell counts were aggregated per cell type and biological replicate across two conditions (three replicates per condition), and the model was fitted using default parameters. Trajectory analysis was performed using Monocle3 (v1.4.26) 69. Processed single-cell data (https://allen-developmental-mouse-atlas.s3.amazonaws.com/scRNA/DevVIS_scRNA_processed.h5ad) were obtained from a previously published dataset 3. Cells were subset to developmental stages E11.5–P1 based on the SynchronizedAge metadata annotation prior to downstream analysis. Data processing and trajectory inference followed the Monocle3 workflow, with dimensionality reduction performed using principal component analysis (PCA) retaining the top 30 principal components, followed by UMAP embedding. All other parameters were used at their default settings.
Assembly: Mouse
Supplementary files format and content: barcodes,matrix and raw files

molecule: nuclear RNA

source_name: Adult Brain Cortex

extract_protocol:
At 2 months of age (post-natal day 58), mice were cervically dislocated. Brains were kept on ice and harvested into cold 1X PBS. The cortex was microdissected under the microscope isolated and flash frozen in liquid nitrogen. Nuclei isolation was performed by Princess Margaret Genomics Centre (PMGC). Nuclei extraction was performed on 54.5 - 64.6mg of flash frozen tis-sue per brain as per the manufacturer's instructions (Nuclei Isolation Kit, CG000505, 10x Ge-nomics) until step l on page 31, after which suspended in nuclei separation buffer and anti-nucleus microbeads (Miltenyi, 130-132-997). Isolated nuclei were processed using the GEM-X Flex Sam-ple Preparation v2 Kit (PN-1000781). For each reaction, 1.96-2.44x106 nuclei were recovered. To perform the Flex assay, we used Chromium GEM-X Flex Gene Expression protocol (CG000780, 10X Genomics). 10,000 nuclei were targeted per sample. Samples were pooled in equal amounts based on nuclei counts prior to loading on the Chromium. For Flex, samples were pooled prior to library prep.
Custom probes were used to identify zsGreen and iCre. Probe sequences: iCre_1 AGGATCTGCACACAGACAGGAGCATCTTCCAGGTGTGTTCAGAGAAGGCC; iCre_2 CTCTGATTCTGGCAATTTCGGCAATGCGCAGCAGGGTGTTGTAGGCAATG; iCre_3 CAGAACAGGTAGTTGTTGGGGTCATCAGCCACACCAGACACAGAGATCCA. Probe sequences: zsGreen_1 GCGGGGCAGGAGTTCTTGAAGTAGTCGACGATGTCCTGGGGG-TACTCGGT; zsGreen_2 CGTAGAACTTGGACTCGTGGTACATGCAGTTCTCCTCCAC-GCTCACGGTG; zsGreen_3 GGGATGATCTTCTCGCAGGAGGGCTCCCAGTT-GTCGGTCATCTTCTTCAT. Library preparation was performed using the GEM-X Flex GEM & Library Kit, 4 rxns (PN-1000782). Equal molar amounts of each library for all samples were pooled and sequenced at an expected depth of 35,000 reads/nuclei using the Illumina Novaseq X 100 cycles sequencing system (Princess Margaret Centre for Research and Genomics). Nuclei were pooled prior to library preparation (Pool_135) and sequenced as a single library. Cells were computationally demultiplexed into N1, N2, and N3 .All samples share the same raw FASTQ files.

value: Adult Brain Cortex

value: Neurons

value: Brain cells

tag: library type

value: cDNA


title: GSK3B knockout RKO RNA-Seq 2

description: Library name: GSK3B knockout RKO RNA-Seq 2


description:
Library name: Vehicle-treated BMDN H3K36me2 ChIP-Seq 2
Combined signal track for Vehicle-treated BMDN H3K36me2

data_processing:
Reads were aligned to the reference genome (mm10) using Bowtie2. Subsequently, duplicates, multi mapping reads, and low quality alignments were removed using SAMtools. Mitochondrial reads, chromosome Y alignments, and ENCODE blacklisted genomic regions were excluded. Peaks were called using MACS3 with the settings -f BAMPE -B --nomodel --SPMR --keep-dup 1. For histone modification ChIP-Seq, peak calling was performed  with --broad option enabled.
Assembly: mm10
Supplementary files format and content: bigWig signal tracks generated from MACS3 callpeak bedGraph outputs with --SPMR using merged biological replicates for each condition (except for Input samples)

source_name: neutrophil

extract_protocol:
The chromatin immunoprecipitation (ChIP) protocol was performed to analyze histone modifications. Briefly, cells were collected and treated with 1% formaldehyde for 10 minutes at room temperature to induce crosslinking. After sonication, an anti-H3K36me2 antibody was used for immunoprecipitation, and then the DNA was extracted and purified using the Universal DNA Purification Kit.
Libraries were constructed from ChIP samples using the VAHTS Universal DNA Library Prep Kit for Illumina V3 and then sequenced on the NovaSeq X platform by Annoroad Gene Tech (Beijing) Co., Ltd.

value: neutrophil


title: GSK3B knockout RKO RNA-Seq 1

description: Library name: GSK3B knockout RKO RNA-Seq 1


title: 22531-68

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #18 from 24-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: Lymph Node, Classical PTC, 3B

city: Los Angeles

first: Anthony

last: Nguyen

address: 8700 Beverly Blvd, Department of Radiation Oncology

institute: Cedars-Sinai Medical Center

description: Library name: 3B

data_processing:
Demultiplexed fastq files for gene expression libraries were processed by Cellranger (v4.0.0)
Assembly: GRCh38-3.0.0
Supplementary files format and content: Cell Ranger output files : filtered_feature_bc_matrix.h5

source_name: Lymph node

extract_protocol:
Following CD45-positive selection, samples were diluted to 1000 cells/uL and processed according to the Single Cell 3’ v1 assay (10x Genomics) with a targeted 10,000 cell recovery.
Gene expression libraries were prepared according to the Single Cell 3’ v1 protocol (10x Genomics) and were sequenced using paired-end 150bp reads on the Novaseq 6000 (Illumina) through the CSMC Applied Genomics, Computation & Translational Core

value: Lymph node


title: Tumor, Classical PTC, 3A

description: Library name: 3A

source_name: Tumor

value: Tumor


description:
Library name: Vehicle-treated BMDN H3K36me2 ChIP-Seq 1
Combined signal track for Vehicle-treated BMDN H3K36me2


title: 22531-67

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #17 from 24-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5

data_processing:
Affymetrix UK Biobank Axiom Array Manufacturer's Protocol
Primary data description: DNA copy number and genotyping

extract_protocol: Single cells, single polar bodies, or cytoplasmic fragments were placed into single PCR tubes containing 2 ul of Genomic Prediction's loading Buffer. Genomic DNA amplification was performed using amplification kit as indicated for each sample.


title: DMF-treated BMDN H3K36me2 ChIP-Seq 2

description:
Library name: DMF-treated BMDN H3K36me2 ChIP-Seq 2
Combined signal track for DMF-treated BMDN H3K36me2


title: GSK3B wild-type RKO RNA-Seq 2

description: Library name: GSK3B wild-type RKO RNA-Seq 2


title: 22531-66

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #16 from 24-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: DMF-treated BMDN H3K36me2 ChIP-Seq 1

description:
Library name: DMF-treated BMDN H3K36me2 ChIP-Seq 1
Combined signal track for DMF-treated BMDN H3K36me2


title: Lymph Node, Tall Cell Variant

description: Library name: 1A


title: GSK3B wild-type RKO RNA-Seq 1

description: Library name: GSK3B wild-type RKO RNA-Seq 1


title: 22531-65

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #15 from 24-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: Lymph Node, Anaplastic

description: Library name: 13B


title: HS-PSS cells, 30uM PER, day7

city: Shinjuku-ku

first: Masahiro

last: Yo

state: TOKYO

address: 35 Shinanomachi

country: Japan

institute: Keio University

description:
Library name: Samlpe 9
H30

data_processing:
Raw FASTQ files were trimmed for adapters by Cutadapt and Salmon was used to generate the Transcripts Per Million (TPM) and estimated counts using the transcript index from GRCh38 (Gencode v33). Heatmaps of gene expression were drawn on the log2(TPM + 1) value.
Assembly: hg38
Supplementary files format and content: tab-separated text file includes raw counts for each sample

source_name: prostate

extract_protocol:
We extracted RNA from patient samples of schwannoma and cultured cell lines (YST-1 and TIG-1) before and after adding of PER using the ISOGEN (Nippon Gene, Japan).
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. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: prostate

value: HS-PSS

value: schwannoma

value: 30uM PER, day7


title: Vehicle-treated BMDN Input ChIP-Seq 1

first: Xiaoqin

last: Yang

address: NO. 199 Renai Road

institute: Soochow University

description: Library name: Vehicle-treated BMDN Input ChIP-Seq 1


title: HS-PSS cells, 10uM PER, day7

description:
Library name: Samlpe 8
H10

value: 10uM PER, day7


title: Tumor, Anaplastic

description: Library name: 13A


title: 22531-63

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #13 from 24-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: DMF-treated BMDN Input ChIP-Seq 2

description: Library name: DMF-treated BMDN Input ChIP-Seq 2


title: Multiome, testis, KO2, ATAC

status: Public on Jun 21 2026

city: Ithaca

first: Andrew

last: Grimson

address: 526 Campus Rd

department: Molecular and Cell Biology

institute: Cornell University

description:
Library name: KO2_ATAC
10x Next GEM Multiome libraries

library_source: genomic single cell

data_processing:
Libraries were processed using the cellranger-arc count pipeline
Assembly: mm10
Supplementary files format and content: atac_fragments.tsv.gz files
Supplementary files format and content: filtered_feature_bc_matrix.h5 files

source_name: testis

extract_protocol:
Single cell suspensions from wild-type and Ago413-/- testis were obtained following the method described by Ascenção et al. Testis from 2-5 mice from the same genotype were collected, the tunica albuginea was removed, and tubules were placed in 10 ml of preheated (37°C) DMEM-F12 containing 2 mg of Collagenase 1A (Sigma) for 2 minutes with manual shaking. Digestion was stopped by two washes of the tubules with DMEM-F12. Next, the tubules were incubated in 10 ml of DMEM-F12 with 5 mg of trypsin (Sigma) and 7 mg/ml of DNAse I (Sigma) at 37°C with constant shaking (150 rpm) until the length of the tubules was about 1 mm (approximately 10 minutes). Digestion was stopped by addition of 3 ml of Fetal Bovine Serum (FBS, Sigma) and 30 ml of DMEM F-12. Digested tubules were strained on a 100 μm strainer and centrifuged at 15°C for 5 minutes at 600g. Before proceeding with nuclei isolation, spermatozoa were removed from the germ cell suspension samples by negative selection Magnetic Activated Cell Sorting (MACS) using an antibody against the acrosomal protein ACRV1 coupled with anti-rabbit IgG MicroBeads (Miltenyi Biotec) and following the protocol provided by the manufacturer. Briefly, cells were labeled with anti ACRV1 antibody (1:50 concentration) by incubation of 108 cells in MACS buffer (0.5% BSA, 2mM EDTA in PBS, pH7.2) for 15 minutes. Then, the labelled cells were incubated with anti-rabbit IgG MicroBeads for 20 minutes on ice and loaded into an LS Column (Miltenyi Biotec) previously rinsed with MACS buffer. After depletion of spermatozoa by retention in the column, cells were collected from the negative fraction by centrifugation at 1500rpm for 5 minutes at 4C and proceeded with nuclei isolation using 10X Genomics Demonstrated Protocol CG000365 Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing.
Single cell RNA and ATAC sequencing libraries were prepared at the Cornell Genomics Facility using the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit.Nuclei were processed on the 10X Genomics Chromium System, targeting a total of 10000 cells per sample. Quality control was evaluated using a Fragment Analyzer

value: testis

value: male

value: enriched germ cell suspension

tag: background strain

value: ATAC


title: HS-PSS cells, control

description:
Library name: Samlpe 7
H0

tag: cell line

value: control


title: Lymph Node, Classical PTC, 12B

description: Library name: 12B


title: WT_1_10%

description:
Library name: WT_1_10_
WT_1_10%

value: T-antigen immortalized MEFs

tag: cell type

value: Mouse embryonic fibroblast

value: Wildtype


title: 22531-62

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #12 from 24-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5

value: Preimplantation embryo


title: DMF-treated BMDN Input ChIP-Seq 1

city: Suzhou

description: Library name: DMF-treated BMDN Input ChIP-Seq 1

value: neutrophil


title: Tumor, Classical PTC, 12A

description: Library name: 12A


title: YST-1 cells, 30uM PER, day7

description:
Library name: Samlpe 6
Y30

source_name: right arm

value: right arm

tag: treatment


title: 22531-61

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #11 from 24-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: Lymph Node, Diffuse Sclerosing Variant

description: Library name: 11B

value: Lymph node