title: CasTuner XX sgTsix ctrl Day4 Rep1

status: Public on Jul 25 2026

city: Berlin

first: Edda

middle: G.

last: Schulz

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

country: Germany

institute: Max Planck Institute for Molecular Genetics

description:
Library name: XX_sgTsix_ctrl_D4_Rep1
500nM dTAG

data_processing:
Sequencing reads were trimmed with Trim Galore, with [--clip_R1 10 --three_prime_clip_R1 5 --clip_R2 15 --three_prime_clip_R2 5 --paired].
They were mapped using bsmapz with settings -m 0 -g 3 -n 1 -v 0.1 -w 10 to the reference fasta file that contains the amplicon sequences.
bam files were sorted and indexed with samtools, and merged if the sample was sequenced multiple times.
bam files were used for methylation calling by mcall command of MOABS package (Sun et al, 2014) [--trimWGBSEndRepairPE2Seq 0 --trimWGBSEndRepairPE1Seq 0 --reportCHX 0].
Assembly: mm10
Supplementary files format and content: bed files with MOABS methylation calls.

source_name: Embryonic stem cells

growth_protocol: The XXΔXIC-Cast (clone A6) are derived from the TX1072 cell line with a deletion around the Xist locus on the B6 and the Cast allele, respectively (chrX:103,183,145-103,955,698 mm10) (Pacini et al, 2020). TX1072 mouse ES cells and all derived cell lines were cultured in feeder-free 2i/FBS/LIF conditions (DMEM (Sigma-Aldrich D6429), 15% ES cell-grade foetal bovine serum (FBS, Pan Biotech P30-2602), 0.1 mM β-mercaptoethanol, 1000 U/mL LIF (Millipore), 3 mM GSK3 inhibitor CT-99021 (Axon Medchem) and 1 mM MEK inhibitor PD0325901 (Axon Medchem)). For CasTuner lines, 500nM dTAG-13 was added to the medium. They were plated at a density of 3.2 × 10^4 cells per cm^2 on gelatin-coated T25 flasks (Corning). The medium was changed daily, and the cells were split every two days.

extract_protocol:
Genomic DNA was extracted from harvested cells using the DNeasy Blood & Tissue kit (Qiagen). 1μg of DNA were bisulfite-converted with EZ DNA Methylation-Gold kit (Zymo). One fifth of the eluted DNA was used per amplicon PCR. Primers for bisulfite-converted DNA targeting the Xist-promoter proximal CpG island (chrX:103,482,090-103,482,350 mm10 from UCSC Genome Browser) were designed with MethPrimer2.0 (Li & Dahiya, 2002). PCR was performed with EpiTaq polymerase (Takara), using 25mM MgCl2. DNA was amplified for 27 cycles, at an annealing temperature of 53oC. PCR reactions of each sample were pooled (total volume for Xist amplicons) and cleaned with MinElute Reaction Cleanup kit (Qiagen) (2 columns per sample).
Libraries were prepared with NEBNext Ultra II DNA Library Prep kit (New England Biolabs), indexed with NEBNext Multiplex Oligos for Illumina Dual Index Set 1 (New England Biolabs) and cleaned with AMPure XP beads (Beckman Coulter). Concentration and size distribution of libraries were analyzed with Qubit 1x dsDNA HS (Thermo Fisher Scientific) and HS DNA D1000 Tapestation (Agilent), respectively. Libraries were sequenced 2x150bp paired-end with MiSeq, DNBSEQ G400 or Aviti sequencers.

treatment_protocol: Differentiation was induced by 2i/LIF withdrawal (DMEM (Sigma-Aldrich), 10% FBS (Gibco) and 0.1 mM β-mercaptoethanol). The cells were plated at a density of 2.1 × 10^4 cells per cm2, on 6-well plates coated with 10 μg/mL fibronectin (Corning 356008 or Serva 21370.03) in PBS for 1 hour. Once seeded for differentiation, the medium was changed every day and the cells were not split until harvesting.  The knock-down of Xist (in TX1072 XX and XO) and Tsix (in TX1072 XX) with CasTuner was induced with dTAG-13 removal from the culture medium for 6 days in total, and differentiation was induced during the last 4 days before harvesting.  Xist overexpression was induced with Doxycycline addition (1µg/ml) for two days, with and without differentiation.

value: Embryonic stem cells

value: CAST x C57BL/6

value: Differentiation by 2i/LIF withdrawal, dTAG-13 for CasTuner degradation

tag: timepoint

value: Differentiation Day 4


title: CasTuner XX sgTsix ctrl Day4 Rep2

type: SRA

description:
Library name: XX_sgTsix_ctrl_D4_Rep2
500nM dTAG

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: CasTuner XX sgTsix KD Day4 Rep1

description:
Library name: XX_sgTsix_KD_D4_Rep1
0nM dTAG

value: Differentiation by 2i/LIF withdrawal, KD by dTAG-13 removal


title: CasTuner XX sgTsix ctrl Day4 Rep3

description:
Library name: XX_sgTsix_ctrl_D4_Rep3
500nM dTAG


title: CD36 flox-2

status: Public on Jul 26 2026

city: Guangzhou

first: xialin

last: liu

address: Jinsui Road

country: China

institute: Zhongshan Opythalmic Center, Sun yat-sen University

description:
Library name: Sample2
WT3OD

library_source: transcriptomic

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

molecule: total RNA

source_name: isolated retinal cells

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

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

value: isolated retinal cells

value: CD11bintCD45+  microglia

value: CD36 flox


title: RH41 cells DMSO bio rep 2

city: Washington

first: Nikola

last: Knoll

state: DC

address: 3700 O St. NW

department: Oncology

country: USA

institute: Georgetown University

description: Library name: Sample 2

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

organism: Homo sapiens

source_name: soft tissue

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

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

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

value: soft tissue

value: fusion-positive rhabdomyosarcoma

value: WT

value: 7 days DMSO


title: T cells donor 3 control edit replicate 2

city: Oxford

first: Joseph

last: Hamley

address: John Radcliffe Hospital/Headley Way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
Library name: cd4_don3_control_rep2
Nucleotide percentage table around gRNA, split for reference and alternate chromosome

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

source_name: Blood

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

extract_protocol:
Qiagen DNAeasy kit
NEB Next Ultra II

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

value: Blood

value: CD4 T cell

value: CRISPR-Edited

value: Activated


title: CasTuner XX sgXist ctrl Day4 Rep1

description:
Library name: XX_sgXist_ctrl_D4_Rep1
500nM dTAG


title: XXdXIC ctrl ESC Rep1

description: Library name: XXdXIC_noDox_ESC_Rep1

value: TX1072 XXdXIC-Cast

value: ESCs


title: XXdXIC ctrl Day2 Rep3

description: Library name: XXdXIC_noDox_D2_Rep3

value: Embryonic stem cells

value: CAST x C57BL/6

value: Differentiation by 2i/LIF withdrawal

value: Differentiation Day 2


title: XXdXIC ctrl Day2 Rep2

description: Library name: XXdXIC_noDox_D2_Rep2


title: XXdXIC XistOverexpression ESC Rep3

description: Library name: XXdXIC_Dox_ESC_Rep3

value: Doxycycline


title: XXdXIC XistOverexpression Day2 Rep2

description: Library name: XXdXIC_Dox_D2_Rep2

value: Doxycycline, Differentiation by 2i/LIF withdrawal


title: Split dCas9-KRAB sgSTC ABA ctrl Day4 Rep2

description: Library name: sgSTC_ABA_ctrl_D4_Rep2

growth_protocol: TX1072 mouse ES cells and all derived cell lines were cultured in feeder-free 2i/FBS/LIF conditions (DMEM (Sigma-Aldrich D6429), 15% ES cell-grade foetal bovine serum (FBS, Pan Biotech P30-2602), 0.1 mM β-mercaptoethanol, 1000 U/mL LIF (Millipore), 3 mM GSK3 inhibitor CT-99021 (Axon Medchem) and 1 mM MEK inhibitor PD0325901 (Axon Medchem)). For CasTuner lines, 500nM dTAG-13 was added to the medium. They were plated at a density of 3.2 × 10^4 cells per cm^2 on gelatin-coated T25 flasks (Corning). The medium was changed daily, and the cells were split every two days.  WT F121.9 mouse ESCs and the derived deletion cell lines Rnf12-/- and Rnf12 -/- Rex1 -/- (DKO) were adapted to feeder-free 2i/LIF conditions (DMEM (GIBCO 11995065), 15% ES cell-grade foetal bovine serum (FBS, Pan Biotech P30-2602), 100 U/mL penicillin/streptomycin (Thermo Fisher Scientifc), 1x NEAA (Gibco 11140035), 0.1 mM β-mercaptoethanol, 1000 U/mL LIF (Millipore), 3 mM GSK3 inhibitor CT-99021 (Axon Medchem) and 1 mM MEK inhibitor PD0325901 (Axon Medchem)) for 5 passages. They were plated at a density of 3.2 × 10^4 cells per cm^2 on gelatin-coated T25 plates (Corning). The medium was changed daily, and the cells were split every two days.

treatment_protocol: Differentiation of all cell lines was induced by 2i/LIF withdrawal (DMEM (Sigma-Aldrich), 10% FBS (Gibco) and 0.1 mM β-mercaptoethanol). The cells were plated at a density of 2.1 × 10^4 cells per cm^2, on 6-well plates coated with 10 μg/mL fibronectin (Corning 356008 or Serva 21370.03) in PBS for 1 hour. Once seeded for differentiation, the medium was changed every day and the cells were not split until harvesting.  For the knock-down of Zfp36l1 and Zfp280c, the CasTuner system was induced with dTAG-13 removal for 6 days in total, the last 4 of which differentiation was also induced. The control condition was cultured with dTAG-13 and differentiated for 4 days. To knock-down the transcription of Rex1 and Zfp281, the dCas9-KRAB system was induced with ABA for 5 days in total, the last 4 of which differentiation was also induced. The safe-targeting control line with “STC” guides was cultured in the same conditions as the knock-down cell lines. To knock-down the transcription of Rnf12 and Zic3, the CasTuner system was induced by dTAG-13 removal for 7 days in total, and during the last 3 days differentiation was induced. The control condition was cultured with dTAG-13 and differentiated for 3 days.

value: Differentiation by 2i/LIF withdrawal, 100μM ABA for CRISPR KD

value: Differentiation Day 4


title: Split dCas9-KRAB sgSTC ABA ctrl Day2 Rep3

description: Library name: sgSTC_ABA_ctrl_D2_Rep3


title: Split dCas9-KRAB sgSTC ABA ctrl Day2 Rep1

description: Library name: sgSTC_ABA_ctrl_D2_Rep1


title: A1_3

first: Yang

last: Ziqi

institute: Zhongshan opythalmic center

description: Library name: Sample6

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

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

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

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

value: microglial cell line

value: wild type

value: oxLDL 1 μg/ml, 24h

tag: batch


title: CD36 flox-1

description:
Library name: Sample1
WT1OS

value: isolated retinal cells

value: CD11bintCD45+  microglia

value: CD36 flox


title: CasTuner XX sgTsix KD Day4 Rep3

description:
Library name: XX_sgTsix_KD_D4_Rep3
0nM dTAG

value: Differentiation by 2i/LIF withdrawal, KD by dTAG-13 removal


title: Split dCas9-KRAB sgZfp281 ABA KD Day4 Rep2

description: Library name: sgZfp281_ABA_KD_D4_Rep2


title: Split dCas9-KRAB sgZfp281 ABA KD Day4 Rep1

description: Library name: sgZfp281_ABA_KD_D4_Rep1


title: Split dCas9-KRAB sgZfp281 ABA KD Day2 Rep2

description: Library name: sgZfp281_ABA_KD_D2_Rep2


title: Split dCas9-KRAB sgZfp281 ABA KD Day2 Rep1

description: Library name: sgZfp281_ABA_KD_D2_Rep1


title: XXdXIC XistOverexpression ESC Rep2

description: Library name: XXdXIC_Dox_ESC_Rep2

value: TX1072 XXdXIC-Cast


title: CasTuner XX sgXist KD Day4 Rep1

description:
Library name: XX_sgXist_KD_D4_Rep1
0nM dTAG


title: XXdXIC ctrl ESC Rep2

description: Library name: XXdXIC_noDox_ESC_Rep2

value: ESCs


title: CasTuner XX sgXist ctrl Day4 Rep2

description:
Library name: XX_sgXist_ctrl_D4_Rep2
500nM dTAG

value: Embryonic stem cells

value: Differentiation by 2i/LIF withdrawal, dTAG-13 for CasTuner degradation


title: Split dCas9-KRAB sgSTC ABA ctrl Day2 Rep2

description: Library name: sgSTC_ABA_ctrl_D2_Rep2

value: CAST x C57BL/6


title: XXdXIC XistOverexpression ESC Rep1

description: Library name: XXdXIC_Dox_ESC_Rep1


title: XXdXIC XistOverexpression Day2 Rep1

description: Library name: XXdXIC_Dox_D2_Rep1

value: Differentiation Day 2


title: Split dCas9-KRAB sgZfp281 ABA KD Day4 Rep3

description: Library name: sgZfp281_ABA_KD_D4_Rep3


title: XXdXIC ctrl ESC Rep3

description: Library name: XXdXIC_noDox_ESC_Rep3


title: Split dCas9-KRAB sgRex1 ABA KD Day4 Rep2

description: Library name: sgRex1_ABA_KD_D4_Rep2


title: Split dCas9-KRAB sgRex1 ABA KD Day4 Rep3

description: Library name: sgRex1_ABA_KD_D4_Rep3


title: Split dCas9-KRAB sgRex1 ABA KD Day2 Rep2

description: Library name: sgRex1_ABA_KD_D2_Rep2


title: Split dCas9-KRAB sgRex1 ABA KD Day2 Rep1

description: Library name: sgRex1_ABA_KD_D2_Rep1


title: CasTuner sgZfp280c ctrl Day4 Rep3

description:
Library name: sgZfp280c_ctrl_D4_Rep3
500nM dTAG


title: CasTuner sgZfp280c ctrl Day4 Rep1

description:
Library name: sgZfp280c_ctrl_D4_Rep1
500nM dTAG


title: CasTuner sgZfp280c KD Day4 Rep2

description:
Library name: sgZfp280c_KD_D4_Rep2
0nM dTAG


title: CasTuner sgZfp280c ctrl Day2 Rep3

description:
Library name: sgZfp280c_ctrl_D2_Rep3
500nM dTAG


title: Split dCas9-KRAB sgRex1 ABA KD Day4 Rep1

description: Library name: sgRex1_ABA_KD_D4_Rep1


title: XX 96h Rep1

description: Library name: XX_T96_Rep1

growth_protocol: TX1072 mouse ES cells were cultured in feeder-free 2i/FBS/LIF conditions (DMEM (Sigma-Aldrich), 15% ES cell-grade foetal bovine serum (FBS, Pan Biotech P30-2602), 0.1  mM β-mercaptoethanol, 1000 U/mL LIF (Millipore), 3 mM GSK3 inhibitor CT-99021 (Axon Medchem) and 1 mM MEK inhibitor PD0325901 (Axon Medchem)). They were plated at a density of 3.2 × 10^4 cells per cm^2 on gelatin-coated T25 plates (Corning). The medium was changed daily, and the cells were split every two days.

treatment_protocol: Differentiation was induced by 2i/LIF withdrawal (DMEM (Sigma-Aldrich), 10% FBS (Gibco) and 0.1 mM β-mercaptoethanol). The cells were plated at a density of 2.1 × 10^4 cells per cm^2, on 6-well plates coated with 10 μg/mL fibronectin (Corning 356008 or Serva 21370.03) in PBS for 1 hour. Once seeded in differentiation conditions, the medium was changed daily and the cells were not split until harvesting.

value: TX1072 XX

value: Differentiation by 2i/LIF withdrawal

value: 96 hours


title: CasTuner sgZfp280c KD Day2 Rep2

description:
Library name: sgZfp280c_KD_D2_Rep2
0nM dTAG


title: XX 72h Rep2

description: Library name: XX_T72_Rep2

value: 72 hours


title: CasTuner sgZfp280c KD Day2 Rep1

description:
Library name: sgZfp280c_KD_D2_Rep1
0nM dTAG


title: XX 72h Rep1

description: Library name: XX_T72_Rep1


title: XX 56h Rep3

description: Library name: XX_T56_Rep3

value: 56 hours


title: CasTuner XX sgXist KD Day4 Rep3

description:
Library name: XX_sgXist_KD_D4_Rep3
0nM dTAG

value: Differentiation Day 4


title: CasTuner sgZfp280c KD Day2 Rep3

description:
Library name: sgZfp280c_KD_D2_Rep3
0nM dTAG


title: CasTuner sgZfp280c ctrl Day2 Rep2

description:
Library name: sgZfp280c_ctrl_D2_Rep2
500nM dTAG


title: XX 96h Rep2

description: Library name: XX_T96_Rep2


title: CasTuner sgZfp36l1 ctrl Day4 Rep1

description:
Library name: sgZfp36l1_ctrl_D4_Rep1
500nM dTAG


title: XX 56h Rep1

description: Library name: XX_T56_Rep1


title: CasTuner sgZfp36l1 ctrl Day4 Rep3

description:
Library name: sgZfp36l1_ctrl_D4_Rep3
500nM dTAG


title: CasTuner XX sgXist KD Day4 Rep2

description:
Library name: XX_sgXist_KD_D4_Rep2
0nM dTAG


title: CasTuner sgZfp36l1 ctrl Day2 Rep3

description:
Library name: sgZfp36l1_ctrl_D2_Rep3
500nM dTAG


title: XX 48h Rep3

description: Library name: XX_T48_Rep3

value: 48 hours


title: XX 72h Rep3

description: Library name: XX_T72_Rep3


title: XX 56h Rep2

description: Library name: XX_T56_Rep2


title: XXdXIC ctrl Day2 Rep1

description: Library name: XXdXIC_noDox_D2_Rep1


title: CasTuner sgZfp36l1 KD Day4 Rep3

description:
Library name: sgZfp36l1_KD_D4_Rep3
0nM dTAG


title: XX 48h Rep1

description: Library name: XX_T48_Rep1


title: CasTuner sgZfp36l1 KD Day4 Rep2

description:
Library name: sgZfp36l1_KD_D4_Rep2
0nM dTAG


title: XX 36h Rep3

description: Library name: XX_T36_Rep3

value: 36 hours


title: XX 36h Rep2

description: Library name: XX_T36_Rep2


title: Split dCas9-KRAB sgZfp281 ABA KD Day2 Rep3

description: Library name: sgZfp281_ABA_KD_D2_Rep3

value: Differentiation by 2i/LIF withdrawal, 100μM ABA for CRISPR KD


title: CasTuner sgZfp36l1 KD Day4 Rep1

description:
Library name: sgZfp36l1_KD_D4_Rep1
0nM dTAG


title: CasTuner sgZfp36l1 KD Day2 Rep3

description:
Library name: sgZfp36l1_KD_D2_Rep3
0nM dTAG


title: XX 48h Rep2

description: Library name: XX_T48_Rep2


title: CasTuner sgZfp36l1 ctrl Day2 Rep2

description:
Library name: sgZfp36l1_ctrl_D2_Rep2
500nM dTAG


title: CasTuner sgZfp36l1 KD Day2 Rep2

description:
Library name: sgZfp36l1_KD_D2_Rep2
0nM dTAG


title: XX 24h Rep1

description: Library name: XX_T24_Rep1

value: 24 hours


title: XX 10h Rep3

description: Library name: XX_T10_Rep3

value: 10 hours


title: CasTuner sgZfp36l1 KD Day2 Rep1

description:
Library name: sgZfp36l1_KD_D2_Rep1
0nM dTAG

value: Differentiation by 2i/LIF withdrawal, KD by dTAG-13 removal


title: XX sgTsix ctrl Xist-noDox ESC Rep3

description: Library name: H3K9me3_XX_sgTsix_ctrl_noDox_ESC_Rep3

data_processing:
Sequencing reads were trimmed with Trim Galore 0.6.10.
Reads were mapped to mm10 using bowtie2 version 2.5.0 (Langmead and Salzberg 2012) with settings [--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 2000].
Unmapped reads were filtered out using samtools (v1.22) (Li et al. 2009) with options [view -F 0x04]. ENCODE Blacklisted regions (mm10-v2) (Amemiya et al. 2019) were removed using bedtools intersect -v (v2.30.0)(Quinlan and Hall 2010).
Coverage bigwig tracks were generated from filtered and sorted bam files using `bamCoverage` of the deepTools package (v3.5.6) (Ramírez et al. 2016), with options [--extendReads -bs 1 --normalizeUsing RPKM].
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
Cells were dissociated with accutase for 5 min, followed by media addition to stop dissociation. 10^5 cells were collected per CUT&Tag reaction and washed with 1ml wash buffer (20 mM HEPES–KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 10 mM sodium butyrate, protease Inhibitor and 1 mM PMSF). After washing, cells were resuspended in 100 μl wash buffer. For every 10^5 cells, 10μl of BioMag Plus Concanavalin A beads were used, after being equilibrated in excess of binding buffer (20 mM HEPES–KOH pH 7.5,10 mM KCl,1 mM CaCl2, 1 mM MnCl2) and concentrated in 10ul of binding buffer. The cells were incubated with Concanavalin A beads by rotating for 10 min at room temperature. The beads with the bound cells were separated with a magnet and resuspended in 100 μl of ice-cold antibody buffer (wash buffer with 0.05% digitonin and 2mM EDTA). 1 μl of primary antibody (H3K9me3, Active Motif #39161) was added and beads were incubated on a rotator for 3 h at 4 °C. The beads were magnetically separated and resuspended in 100 μl of ice-cold Dig-wash buffer (wash buffer with 0.05% digitonin) and 1 μl of secondary antibody (Guinea pig anti-rabbit, antibodies online ABIN101961) and incubated for 1 h at 4 °C on a rotator. Next, the beads were washed three times with ice-cold Dig-wash buffer, and resuspended in 100 μl ice-cold Dig-300 buffer (20 mM HEPES–KOH pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, 10 mM sodium butyrate and 1 mM PMSF and protease inhibitor) with 0.4 μl 3×FLAG–pA-Tn5 (5.5μM) (derived from Addgene 124601 and purified according to (Gjaltema et al, 2022)) preloaded with mosaic-end adaptors. Beads were incubated for 1 h at 4 °C on a rotator, and then washed four times with ice-cold Dig-300 buffer. While on ice, beads were resuspended in 50μl of tagmentation buffer (Dig-300 buffer, 10 mM MgCl2 and 0.125pM spike-in DNA). Spike-in DNA was prepared with PCR amplification of the Ampicillin resistance gene (AmpR) that also contains i5 and i7 primer binding sites on 5′ and 3′ ends, respectively. Tagmentation was carried out for 1 h at 37 °C. To stop tagmentation and solubilize DNA fragments, 2.25 μl of 0.5 M EDTA, 2.75 μl of 10% SDS and 0.5 μl of 20 mg/ml proteinase K were added, followed by vortexing for 5 s. Samples were incubated overnight at 55 °C followed by 30 min at 70 °C to inactivate proteinase K. The DNA fragments were purified with the ChIP DNA clean and concentrator kit (Zymo Research) and eluted in 25 μl of elution buffer.
Libraries for sequencing were prepared by amplifying the purified fragments with indexed primers and NEBNext HiFi 2× PCR Master Mix for 14 amplification cycles. Post-PCR cleanup was performed with AMPure XP beads (1x volume), and the final libraries were eluted in 27 µl of 10 mM Tris (pH 8.0). Libraries were sequenced PE75, PE100 or PE150.

treatment_protocol: Differentiation was induced by 2i/LIF withdrawal (DMEM (Sigma-Aldrich), 10% FBS (Gibco) and 0.1 mM β-mercaptoethanol). The cells were plated at a density of 2.1 × 10^4 cells per cm2, on 6-well plates coated with 10 μg/mL fibronectin (Corning 356008 or Serva 21370.03) in PBS for 1 hour. Once seeded for differentiation, the medium was changed every day and the cells were not split until harvesting.  The knock-down of Xist (in TX1072 XX and XO) and Tsix (in TX1072 XX) with CasTuner was induced with dTAG-13 removal from the culture medium for 6 days in total, and differentiation was induced during the last 4 days before harvesting. The knock-down of Tsix in the experiment of parallel Xist overexpression was induced for 4 days in total, without simultaneous differentiation.  Xist overexpression was induced with Doxycycline addition (1µg/ml) for two days, with and without differentiation.

tag: Sex

value: female

value: 500nM dTAG, no Dox

value: ESCs

tag: antibody


title: XX 10h Rep2

description: Library name: XX_T10_Rep2

value: Embryonic stem cells

value: CAST x C57BL/6


title: XX 24h Rep2

description: Library name: XX_T24_Rep2

value: TX1072 XX


title: XX 10h Rep1

description: Library name: XX_T10_Rep1

value: Differentiation by 2i/LIF withdrawal


title: XX 36h Rep1

description: Library name: XX_T36_Rep1


title: XX ESCs Rep2

description: Library name: XX_T0_Rep2

value: 0 hours


title: XX sgTsix ctrl Xist-Dox ESC Rep1

description: Library name: H3K9me3_XX_sgTsix_ctrl_Dox_ESC_Rep1

value: 500nM dTAG, 1µg/ml Dox


title: XX ESCs Rep1

description: Library name: XX_T0_Rep1


title: XX sgTsix KD Xist-noDox ESC Rep3

description: Library name: H3K9me3_XX_sgTsix_KD_noDox_ESC_Rep3

value: 0nM dTAG, no Dox


title: XX sgTsix ctrl Xist-noDox ESC Rep2

description: Library name: H3K9me3_XX_sgTsix_ctrl_noDox_ESC_Rep2


title: XX sgTsix ctrl Xist-Dox ESC Rep3

description: Library name: H3K9me3_XX_sgTsix_ctrl_Dox_ESC_Rep3


title: XX sgTsix ctrl Xist-noDox ESC Rep1

description: Library name: H3K9me3_XX_sgTsix_ctrl_noDox_ESC_Rep1


title: XO 96h Rep2

description: Library name: XO_T96_Rep2

value: TX1072 XO

value: CAST x C57BL/6 (CAST chrX)

value: 96 hours


title: XX ESCs Rep3

description: Library name: XX_T0_Rep3


title: XX sgTsix ctrl Xist-Dox ESC Rep2

description: Library name: H3K9me3_XX_sgTsix_ctrl_Dox_ESC_Rep2


title: XX sgTsix KD Xist-noDox ESC Rep1

description: Library name: H3K9me3_XX_sgTsix_KD_noDox_ESC_Rep1


title: XO 96h Rep1

description: Library name: XO_T96_Rep1


title: XX sgTsix KD Xist-noDox ESC Rep2

description: Library name: H3K9me3_XX_sgTsix_KD_noDox_ESC_Rep2


title: XO 96h Rep3

description: Library name: XO_T96_Rep3


title: XO 72h Rep3

description: Library name: XO_T72_Rep3

value: 72 hours


title: XX sgTsix KD Xist-Dox ESC Rep3

description: Library name: H3K9me3_XX_sgTsix_KD_Dox_ESC_Rep3

value: 0nM dTAG, 1µg/ml Dox


title: XX sgTsix KD Xist-Dox ESC Rep1

description: Library name: H3K9me3_XX_sgTsix_KD_Dox_ESC_Rep1


title: XO 72h Rep1

description: Library name: XO_T72_Rep1


title: XO 56h Rep3

description: Library name: XO_T56_Rep3

value: 56 hours


title: XO 56h Rep2

description: Library name: XO_T56_Rep2


title: XO sgXist KD Day4 Rep3

description:
Library name: H3K9me3_XO_sgXist_KD_D4_Rep3
0nM dTAG

value: Differentiation by 2i/LIF withdrawal, KD by dTAG-13 removal

value: Differentiation Day 4


title: XO sgXist ctrl Day4 Rep2

description:
Library name: H3K9me3_XO_sgXist_ctrl_D4_Rep2
500nM dTAG

value: Differentiation by 2i/LIF withdrawal, dTAG-13 for CasTuner degradation


title: XO 48h Rep3

description: Library name: XO_T48_Rep3

value: 48 hours


title: XO sgXist KD Day4 Rep2

description:
Library name: H3K9me3_XO_sgXist_KD_D4_Rep2
0nM dTAG

value: Embryonic stem cells


title: XO 48h Rep2

description: Library name: XO_T48_Rep2


title: XO sgXist KD Day4 Rep1

description:
Library name: H3K9me3_XO_sgXist_KD_D4_Rep1
0nM dTAG


title: XO 36h Rep3

description: Library name: XO_T36_Rep3

value: 36 hours


title: XO 36h Rep2

description: Library name: XO_T36_Rep2


title: F121.9 WT Day4 Rep1

description: Library name: H3K9me3_WT_D4_Rep1

data_processing:
Sequencing reads were trimmed with Trim Galore 0.6.10.
Reads were mapped to mm10 using bowtie2 version 2.5.0 (Langmead and Salzberg 2012) with settings [--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 2000]. For samples targeting Zfp280c and Zfp36l1 the spike-in reads (mapping to AmpR gene) were filtered out with samtools view because they dominated the library.
Unmapped reads were filtered out using samtools (v1.22) (Li et al. 2009) with options [view -F 0x04]. ENCODE Blacklisted regions (mm10-v2) (Amemiya et al. 2019) were removed using bedtools intersect -v (v2.30.0)(Quinlan and Hall 2010).
Coverage bigwig tracks were generated from filtered and sorted bam files using `bamCoverage` of the deepTools package (v3.5.6) (Ramírez et al. 2016), with options [--extendReads -bs 1 --normalizeUsing RPKM].
Peaks were called in each condition and replicate separately using epic2 (Stovner & Sætrom, 2019) with settings [--keep-duplicates --gaps-allowed 1].
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: bed, peaks called by epic2 tool.
Library strategy: CUT&Tag

value: female


title: XO 36h Rep1

description: Library name: XO_T36_Rep1

value: Differentiation by 2i/LIF withdrawal


title: Split dCas9-KRAB sgSTC ABA ctrl Day4 Rep3

description: Library name: H3K9me3_sgSTC_ABA_ctrl_D4_Rep3

value: CAST x C57BL/6

value: Differentiation by 2i/LIF withdrawal, 100μM ABA for CRISPR KD


description: Library name: H3K9me3_sgSTC_ABA_ctrl_D4_Rep2


title: Split dCas9-KRAB sgSTC ABA ctrl Day4 Rep1

description: Library name: H3K9me3_sgSTC_ABA_ctrl_D4_Rep1


title: XO 24h Rep1

description: Library name: XO_T24_Rep1

value: 24 hours


description: Library name: H3K9me3_sgZfp281_ABA_KD_D4_Rep3


title: XO 10h Rep3

description: Library name: XO_T10_Rep3

value: TX1072 XO

value: 10 hours


description: Library name: H3K9me3_sgZfp281_ABA_KD_D4_Rep2


title: XO 10h Rep2

description: Library name: XO_T10_Rep2

value: CAST x C57BL/6 (CAST chrX)


description: Library name: H3K9me3_sgZfp281_ABA_KD_D4_Rep1


title: XO 10h Rep1

description: Library name: XO_T10_Rep1


description: Library name: H3K9me3_sgRex1_ABA_KD_D4_Rep3


title: XX sgTsix KD Xist-Dox ESC Rep2

description: Library name: H3K9me3_XX_sgTsix_KD_Dox_ESC_Rep2

value: ESCs


title: XO 72h Rep2

description: Library name: XO_T72_Rep2

value: 72 hours


title: XO sgXist ctrl Day4 Rep3

description:
Library name: H3K9me3_XO_sgXist_ctrl_D4_Rep3
500nM dTAG


title: XO ESCs Rep3

description: Library name: XO_T0_Rep3

value: 0 hours


title: XO sgXist ctrl Day4 Rep1

description:
Library name: H3K9me3_XO_sgXist_ctrl_D4_Rep1
500nM dTAG


title: H2AK119ub CUT&RUN in vector control matched to ASXL1 (1-1067) conditions

city: Changsha

first: Jiazheng

last: Lin

address: No. 27 Tianma Road

institute: Hunan university

description:
Library name: H2AK119ub_CUTRUN_Vector_1-1067
H2AK119ub CUT&RUN profiling in vector control cells matched to ASXL1 (1-1067), ASXL1 (1-1067) 34DN, and ASXL1 (1-1067) 36EQ conditions. Data were normalized using E. coli spike-in reads.

data_processing:
Raw paired-end FASTQ reads were quality-controlled and preprocessed using fastp v0.24.0 to remove adapters, low-quality bases, and low-quality reads. Clean reads were aligned to the mouse reference genome mm39 using Bowtie2 v2.5.4 with the --very-sensitive preset. Alignment files were processed using SAMtools and Picard to remove unmapped reads, secondary and supplementary alignments, low-mapping-quality reads (MAPQ < 30), PCR duplicates, and mitochondrial reads. Peaks were called independently for each sample from duplicate-removed, MAPQ >=30, chrM-excluded paired-end BAM files using MACS3 v3.0.3. Called peaks are provided in BED6+4 narrowPeak format.
Assembly: mm39
Supplementary files format and content: NarrowPeak format (BED6+4).
Library strategy: CUT&Run

source_name: bone marrow

growth_protocol: c-Kit+ cells were isolated from mouse bone marrow. After overnight prestimulation, cells were co-transduced with retroviruses expressing BAP1 together with empty vector or the indicated ASXL1 constructs. Cells were collected for ChIP-seq or CUT&RUN chromatin profiling.

extract_protocol:
Mouse c-Kit+ bone marrow cells were co-transduced with BAP1 and the indicated ASXL1 construct or empty vector. For ChIP-seq samples, chromatin was prepared from collected cells and immunoprecipitated using antibodies against HA for HA-tagged BAP1 or ASXL1. ChIP DNA was purified for sequencing library preparation. For CUT&RUN samples, nuclei were incubated with an antibody against H2AK119ub, followed by targeted nuclease cleavage and recovery of released chromatin fragments. Released DNA was purified for sequencing library preparation.
Sequencing libraries were prepared from purified ChIP-seq or CUT&RUN DNA fragments using standard Illumina-compatible library preparation procedures, including end repair, adapter ligation, PCR amplification, and library purification. Libraries were sequenced in paired-end mode on an Illumina platform.

treatment_protocol: c-Kit+ cells were isolated from mouse bone marrow and prestimulated overnight before retroviral transduction. Cells were co-transduced with retroviruses expressing BAP1 together with empty vector or the indicated ASXL1 constructs. For the ASXL1 (1-590) condition set, cells were transduced with empty vector, ASXL1 (1-590), ASXL1 (1-590) 10RA, or ASXL1 (1-590) 25RA. For the ASXL1 (1-1067) condition set, cells were transduced with empty vector, ASXL1 (1-1067), ASXL1 (1-1067) 34DN, or ASXL1 (1-1067) 36EQ. Cells were collected for ChIP-seq or CUT&RUN chromatin profiling.

value: bone marrow

value: Purified c-Kit+ cells

value: hematopoietic stem and progenitor cells (HSPCs)

value: mock

value: co-transduced with BAP1 and empty vector


description: Library name: H3K9me3_sgRex1_ABA_KD_D4_Rep2

value: Embryonic stem cells

value: Differentiation Day 4


title: XO 56h Rep1

description: Library name: XO_T56_Rep1

value: Differentiation by 2i/LIF withdrawal

value: 56 hours


title: H2AK119ub CUT&RUN in ASXL1 (1-1067) 36EQ

description:
Library name: H2AK119ub_CUTRUN_36EQ
H2AK119ub CUT&RUN profiling in mouse c-Kit+ bone marrow cells co-transduced with BAP1 and charge-neutralized ASXL1 (1-1067) 36EQ. Data were normalized using E. coli spike-in reads.

value: co-transduced with BAP1 and ASXL1 (1-1067) 36EQ


title: H2AK119ub CUT&RUN in ASXL1 (1-1067) 34DN

description:
Library name: H2AK119ub_CUTRUN_34DN
H2AK119ub CUT&RUN profiling in mouse c-Kit+ bone marrow cells co-transduced with BAP1 and charge-neutralized ASXL1 (1-1067) 34DN. Data were normalized using E. coli spike-in reads.

value: co-transduced with BAP1 and ASXL1 (1-1067) 34DN


title: XO ESCs Rep2

description: Library name: XO_T0_Rep2

value: TX1072 XO


description: Library name: H3K9me3_sgRex1_ABA_KD_D4_Rep1

value: female

value: CAST x C57BL/6

value: Differentiation by 2i/LIF withdrawal, 100μM ABA for CRISPR KD


title: XO 48h Rep1

description: Library name: XO_T48_Rep1

value: CAST x C57BL/6 (CAST chrX)

value: 48 hours


title: H2AK119ub CUT&RUN in ASXL1 (1-1067)

description:
Library name: H2AK119ub_CUTRUN_1-1067
H2AK119ub CUT&RUN profiling in mouse c-Kit+ bone marrow cells co-transduced with BAP1 and ASXL1 (1-1067). Data were normalized using E. coli spike-in reads.

value: bone marrow


title: XO ESCs Rep1

description: Library name: XO_T0_Rep1

value: 0 hours


title: F121.9 RNF12-KO Day4 Rep1

description: Library name: H3K9me3_RNF12-KO_D4_Rep1


title: F121.9 DKO Day4 Rep1

description: Library name: H3K9me3_DKO_D4_Rep1


title: DVGdeltaNP3

city: Rochester

first: Justin

last: Brennan

state: NY

address: 601 Elmwood Ave.

department: Microbiology & Immunology

institute: University of Rochester Medical Center

description: Library name: Sample 1

data_processing:
For total RNA extracted from DVG-ΔN stocks: reads were aligned to DVG-ΔN reference genome and WT virus genome (MT020881). The resulting BAM files were used for visualization in IGV. ViReMa then first aligned the obtained reads to the human reference genome GRCh38 human reference genome. Those subsequent unmapped reads were further applied to ViReMa (v0.25) to identify junction reads from cbDVGs. The final DVG junction reads from ViReMa were used to graph the cbDVG break and rejoin point distribution in R.
Assembly: GRCh38, SARS-CoV-2 reference (GenBank ID MT020881.1)
Supplementary files format and content: ViReMa file includes the break and rejoin points, and counts for each DVG detected.

organism: Severe acute respiratory syndrome coronavirus 2

source_name: Virus Stock

extract_protocol:
Total RNA was extracted from DVG-ΔN stocks using Trizol-LS according to the manufacturer's instructions. Total RNA was DNase digested and RNA was re-purified using lithium chloride.
RNA-sequencing of Total RNA from DVG-ΔN stocks was perfromed by Genewiz. RNA quality was assessed using the RNA Pico 6000 module on an Agilent Tapestation 2100 (Agilent Technologies) prior to cDNA library preparation. 100 ng of total cDNA libraries were prepared using the Illumina TruSeq Stranded Total RNA LT kit with Ribo-Zero Gold, according to the manufacturer’s instructions. Samples were run on Illumina NextSeq 500 to generate 150 bp, paired-end reads, resulting in 20-50 million reads per sample, with an average Q30 score ≥ 96.8%.

value: Virus Stock

value: DVG-ΔN


title: H2AK119ub CUT&RUN in ASXL1 (1-590) 25RA

description:
Library name: H2AK119ub_CUTRUN_25RA
H2AK119ub CUT&RUN profiling in mouse c-Kit+ bone marrow cells co-transduced with BAP1 and condensation-defective ASXL1 (1-590) 25RA. Data were normalized using E. coli spike-in reads.

value: Purified c-Kit+ cells

value: hematopoietic stem and progenitor cells (HSPCs)

value: mock

value: co-transduced with BAP1 and ASXL1 (1-590) 25RA


title: H2AK119ub CUT&RUN in ASXL1 (1-590) 10RA

description:
Library name: H2AK119ub_CUTRUN_10RA
H2AK119ub CUT&RUN profiling in mouse c-Kit+ bone marrow cells co-transduced with BAP1 and condensation-impaired ASXL1 (1-590) 10RA. Data were normalized using E. coli spike-in reads.

value: co-transduced with BAP1 and ASXL1 (1-590) 10RA


title: CasTuner sgZic3 ctrl Day3 Rep3

description:
Library name: sgZic3_ctrl_D3_Rep3
500nM dTAG

value: Embryonic stem cells

value: Differentiation by 2i/LIF withdrawal, dTAG-13 for CasTuner degradation

value: Differentiation Day 3


title: dvgb-P4_001.fastq.gz

description:
Library name: Sample 35
dvgb-P4_R1_001

data_processing:
For infected A549-ACE2 cells: quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32. Gene-level expression quantification was performed 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. Differential expression was done with edgeR v4.0.16 using standard practice including filtering for low-expressed genes with edgeR::filterByExprwith default values. Functional enrichment, when available, is performed using gene set enrichment analysis with gseapy v0.12 using the MSigDB Hallmark gene set.
For total RNA extracted from DVG-B stocks: reads were aligned to DVG-B reference genome and WT virus genome (MT020881). The resulting BAM files were used for visualization in IGV. ViReMa then first aligned the obtained reads to the human reference genome GRCh38 human reference genome. Those subsequent unmapped reads were further applied to ViReMa (v0.25) to identify junction reads from cbDVGs. The final DVG junction reads from ViReMa were used to graph the cbDVG break and rejoin point distribution in R.
Assembly: GRCh38, SARS-CoV-2 reference (GenBank ID MT020881.1)
Supplementary files format and content: DVG7TD refers to infections comparing SARS-CoV-2 (Hong Kong strain, HK), DVG-B, DVG-A and co-infections at with SARS-CoV-2 and DVG-B or DVG-A. L6Y3VG refers to infections comparing SARS-CoV-2, DVG-B and SARS-CoV-2ΔN. Expression matricies are provided. DVGB_Virema refers to ViReMa break/rejoin point analysis of the DVG-B stocks.

growth_protocol: A549-ACE2 cells were maintained in DMEM supplemented with 10% fetal bovine serum and gentamicin. Cultured in a humidified atmosphere at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from infected cells using Trizol according to the manufacturer's instructions. Total RNA was extracted from DVG-B stocks using Trizol-LS according to the manufacturer's instructions. Total RNA was DNase digested and RNA was re-purified using lithium chloride.
RNA-sequencing of infected A549-ACE2 cells was performed by Plasmidsaurus. For sequencing library preparation, Poly-A mRNA capture and reverse transcription for cDNA synthesis: oligo-dT primer to capture just the mRNA (contains sample barcode, UMI, and Read 1 sequences). Second strand synthesis and tagmentation: double stranded-cDNA is generated. Tagmentation creates fragments and incorporates Read 2 sequence. Illumina library amplification: adds unique dual indices (UDI = i5, i7) and P5/P7 sequences.
RNA-sequencing of Total RNA from DVG-B stocks was perfromed by Genewiz. RNA quality was assessed using the RNA Pico 6000 module on an Agilent Tapestation 2100 (Agilent Technologies) prior to cDNA library preparation. 100 ng of total cDNA libraries were prepared using the Illumina TruSeq Stranded Total RNA LT kit with Ribo-Zero Gold, according to the manufacturer’s instructions. Samples were run on Illumina NextSeq 500 to generate 150 bp, paired-end reads, resulting in 20-50 million reads per sample, with an average Q30 score ≥ 96.8%.

treatment_protocol: A549-ACE2 cells were singly, or co-, infected with SARS-CoV-2 (Hong Kong strain, HK), DVG-B or DVG-A at MOI=1 for 24 hours. Alternatively, A549-ACE2 cells were singly infected with SARS-CoV-2, DVG-B or SARS-CoV-2ΔN at MOI=1 for 24 hours. Infections were carried out in DMEM supplemented with 5% fetal bovine serum and gentamicin in a humidified atmosphere at 37°C with 5% CO2.

value: DVG-B


title: H2AK119ub CUT&RUN in ASXL1 (1-590)

description:
Library name: H2AK119ub_CUTRUN_1-590
H2AK119ub CUT&RUN profiling in mouse c-Kit+ bone marrow cells co-transduced with BAP1 and ASXL1 (1-590). Data were normalized using E. coli spike-in reads.


title: CasTuner sgZic3 ctrl Day3 Rep2

description:
Library name: sgZic3_ctrl_D3_Rep2
500nM dTAG

value: CAST x C57BL/6


title: ASXL1 ChIP-seq in ASXL1 (1-590) 10RA

description:
Library name: ASXL1_ChIPseq_10RA
ASXL1 ChIP-seq profiling using an anti-ASXL1 antibody in mouse c-Kit+ bone marrow cells co-transduced with BAP1 and condensation-impaired ASXL1 (1-590) 10RA.

data_processing:
Raw paired-end FASTQ reads were quality-controlled and preprocessed using fastp v0.24.0 to remove adapters, low-quality bases, and low-quality reads. Clean reads were aligned to the mouse reference genome mm39 using Bowtie2 v2.5.4 with the --very-sensitive preset. Alignment files were processed using SAMtools and Picard to remove unmapped reads, secondary and supplementary alignments, low-mapping-quality reads (MAPQ < 30), PCR duplicates, and mitochondrial reads. Peaks were called independently for each sample from duplicate-removed, MAPQ >=30, chrM-excluded paired-end BAM files using MACS3 v3.0.3. Called peaks are provided in BED6+4 narrowPeak format.
Assembly: mm39
Supplementary files format and content: NarrowPeak format (BED6+4).

value: co-transduced with BAP1 and HA-ASXL1 (1-590) 10RA


title: ASXL1 ChIP-seq in ASXL1 (1-590)

description:
Library name: ASXL1_ChIPseq_1-590
ASXL1 ChIP-seq profiling using an anti-ASXL1 antibody in mouse c-Kit+ bone marrow cells co-transduced with BAP1 and ASXL1 (1-590).

value: co-transduced with BAP1 and HA-ASXL1 (1-590)


title: dvgB-P3_001.fastq.gz

description:
Library name: Sample 34
dvgB-P3_R1_001


title: XO 24h Rep3

description: Library name: XO_T24_Rep3

value: TX1072 XO

value: CAST x C57BL/6 (CAST chrX)

value: Differentiation by 2i/LIF withdrawal

value: 24 hours


title: CasTuner sgZic3 ctrl Day3 Rep1

description:
Library name: sgZic3_ctrl_D3_Rep1
500nM dTAG


title: H2AK119ub CUT&RUN in vector control matched to ASXL1 (1-590) conditions

description:
Library name: H2AK119ub_CUTRUN_Vector_1-590
H2AK119ub CUT&RUN profiling in vector control cells matched to ASXL1 (1-590), ASXL1 (1-590) 10RA, and ASXL1 (1-590) 25RA conditions. Data were normalized using E. coli spike-in reads.

value: bone marrow

value: co-transduced with BAP1 and empty vector


title: BAP1 ChIP-seq in ASXL1 (1-590) 10RA

description:
Library name: BAP1_ChIPseq_10RA
BAP1 ChIP-seq profiling using an anti-BAP1 antibody in mouse c-Kit+ bone marrow cells co-transduced with BAP1 and condensation-impaired ASXL1 (1-590) 10RA.

value: Purified c-Kit+ cells

value: hematopoietic stem and progenitor cells (HSPCs)

value: co-transduced with HA-BAP1 and ASXL1 (1-590) 10RA


title: L6Y3VG_DeltaN_rep1.fastq.gz

description:
Library name: Sample 33
L6Y3VG_1_DeltaN_rep1


title: BAP1 ChIP-seq in ASXL1 (1-590)

description:
Library name: BAP1_ChIPseq_1-590
BAP1 ChIP-seq profiling using an anti-BAP1 antibody in mouse c-Kit+ bone marrow cells co-transduced with BAP1 and ASXL1 (1-590).

value: mock

value: co-transduced with HA-BAP1 and ASXL1 (1-590)


title: CasTuner sgZic3 KD Day3 Rep3

description:
Library name: sgZic3_KD_D3_Rep3
0nM dTAG

value: Embryonic stem cells

value: Differentiation by 2i/LIF withdrawal, KD by dTAG-13 removal


title: XO 24h Rep2

description: Library name: XO_T24_Rep2


title: G8-10-3

city: Beijing

first: sijia

address: Xiannongtan Street, Xicheng District

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College

description: Library name: Sample 18

data_processing:
Raw fastq reads were quality-controlled using FastQC v0.11.9; low-quality reads, adapters and N-containing sequences were trimmed by Trimmomatic v0.39 to obtain clean reads.
Clean reads were aligned to human reference genome GRCh38 (hg38) using HISAT2 v2.1.0, and mapping bam files were sorted and indexed with Samtools v1.15.
Gene expression quantification (FPKM/raw count) was performed using StringTie v2.2.1, and read counts matrix of all samples was generated for differential analysis.
Differentially expressed genes (DEGs) were screened by DESeq2 R package, threshold: |log2FC| ≥ 1, adjusted P-value < 0.05.
Functional enrichment analyses including GO, KEGG and GSEA were conducted based on DEGs using clusterProfiler R package.
Assembly: Human GRCh38
Supplementary files format and content: Gene read count matrix file (readcount.xlsx): Excel spreadsheet containing raw read counts of all detected genes across 18 samples. Rows represent individual genes, columns correspond to each biological replicate sample.

source_name: kidney

growth_protocol: Human renal proximal tubular epithelial HK2 cells were cultured in DMEM/F12 complete medium supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin and 100 μg/mL streptomycin. Cells were maintained at 37 °C in a humidified incubator containing 5% CO2, and passaged at 80% confluence.

extract_protocol:
Total RNA was extracted from cell pellets using TRIzol reagent following manufacturer’s instructions. RNA purity was measured by Nanodrop 2000, and RNA integrity was verified with Agilent 2100 Bioanalyzer (RIN > 7.0). PolyA mRNA was enriched from total RNA using oligo(dT) magnetic beads.
RNA-seq libraries were constructed with Illumina TruSeq RNA Library Prep Kit. Enriched mRNA was fragmented into 200–300 bp short fragments, reverse-transcribed to first-strand cDNA, then synthesized to double-strand cDNA. After end repair, A-tailing and adapter ligation, fragments were amplified by PCR and purified for paired-end sequencing.

treatment_protocol: HK2 cells were seeded and cultured to 70% confluence before drug intervention. For compound pretreatment, cells were incubated with 2.5 μM or 10 μM (d)-G4/(d)-G8 for 2 h, followed by co-incubation with 15 μM cisplatin for 48 h. Model group received only 15 μM cisplatin for 48 h, and control group was cultured with normal medium without any compound or cisplatin treatment.

value: kidney


title: L6Y3VG_DeltaN_rep2.fastq.gz

description:
Library name: Sample 32
L6Y3VG_2_DeltaN_rep2


title: CasTuner sgZic3 KD Day3 Rep2

description:
Library name: sgZic3_KD_D3_Rep2
0nM dTAG

value: CAST x C57BL/6

value: Differentiation Day 3


city: Anhui,

first: HanLin

last: Bai

address: Bengbu Medical University

department: Department of Anesthesiology

institute: The First Affiliated Hospital of Bengbu Medical University

description:
Library name: LX2_E3
RNA-seq of human hepatic stellate LX-2 cells transfected with ATP6AP1-targeting siRNA, replicate 3

data_processing:
Raw sequencing reads in FASTQ format were first subjected to quality control and adapter trimming using FastQC and Trimmomatic software to remove low-quality bases, ambiguous reads, and residual sequencing adapters. Clean high-quality reads were aligned to the human reference genome using HISAT2. Gene expression quantification was performed with featureCounts to generate raw read count matrices. Differential expression analysis between ATP6AP1 siRNA knockdown and non-targeting siRNA control groups was implemented via DESeq2 R package.
Assembly: GRCh38 (hg38), Ensembl release 109
Supplementary files format and content: Excel workbook gene_count_matrix.xlsx containing gene-level processed expression values across six samples.

source_name: Liver

extract_protocol:
Total RNA extraction from cultured LX-2 hepatic stellate cells was performed using TRIzol reagent following the manufacturer’s standard protocol. Briefly, cell pellets were homogenized in TRIzol lysis buffer, followed by chloroform phase separation and isopropanol precipitation. RNA pellets were washed with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA integrity and concentration were assessed via agarose gel electrophoresis and Nanodrop spectrophotometry; RNA integrity number (RIN) ≥7.0 was required for subsequent library construction.
mRNA was enriched from qualified total RNA using oligo(dT) magnetic beads to deplete ribosomal RNA. Purified mRNA was fragmented into short fragments under elevated temperature. First-strand cDNA was synthesized with random hexamer primers and reverse transcriptase, followed by second-strand cDNA synthesis using DNA polymerase I. End repair, A-tailing, and adapter ligation were sequentially conducted. Fragments with suitable insert sizes were purified, enriched by PCR amplification, and quantified for paired-end RNA-seq library sequencing.

value: Liver

value: Hepatic stellate cell

value: ATP6AP1 transient knockdown

value: Transfection with siRNA targeting human ATP6AP1


title: G8-10-2

description: Library name: Sample 17


title: L6Y3VG_DeltaN_rep3.fastq.gz

description:
Library name: Sample 31
L6Y3VG_3_DeltaN_rep3


title: G8-10-1

description: Library name: Sample 16


title: CasTuner sgZic3 KD Day3 Rep1

description:
Library name: sgZic3_KD_D3_Rep1
0nM dTAG


description:
Library name: LX2_E2
RNA-seq of human hepatic stellate LX-2 cells transfected with ATP6AP1-targeting siRNA, replicate 2


title: L6Y3VG_DVG-B_rep1.fastq.gz

description:
Library name: Sample 30
L6Y3VG_4_DVG-B_rep1

value: DVG-B


description:
Library name: LX2_E1
RNA-seq of human hepatic stellate LX-2 cells transfected with ATP6AP1-targeting siRNA, replicate 1


title: CasTuner sgRnf12 ctrl Day3 Rep3

description:
Library name: sgRnf12_ctrl_D3_Rep3
500nM dTAG

value: Differentiation by 2i/LIF withdrawal, dTAG-13 for CasTuner degradation


title: G8-2-5-3

description: Library name: Sample 15


title: L6Y3VG_DVG-B_rep2.fastq.gz

description:
Library name: Sample 29
L6Y3VG_5_DVG-B_rep2


title: G8-2-5-2

description: Library name: Sample 14


title: CasTuner sgRnf12 ctrl Day3 Rep2

description:
Library name: sgRnf12_ctrl_D3_Rep2
500nM dTAG


description:
Library name: LX2_C3
RNA-seq of human hepatic stellate LX-2 cells transfected with non-targeting control siRNA, replicate 3

value: wild type

value: Transfection with non-targeting negative control siRNA


description:
Library name: LX2_C2
RNA-seq of human hepatic stellate LX-2 cells transfected with non-targeting control siRNA, replicate 2


title: L6Y3VG_DVG-B_rep3.fastq.gz

description:
Library name: Sample 28
L6Y3VG_6_DVG-B_rep3


title: CasTuner sgRnf12 ctrl Day3 Rep1

description:
Library name: sgRnf12_ctrl_D3_Rep1
500nM dTAG


title: G8-2-5-1

description: Library name: Sample 13


title: L6Y3VG_DVG-B_rep4.fastq.gz

description:
Library name: Sample 27
L6Y3VG_7_DVG-B_rep4


title: CasTuner sgRnf12 KD Day3 Rep3

description:
Library name: sgRnf12_KD_D3_Rep3
0nM dTAG


description:
Library name: LX2_C1
RNA-seq of human hepatic stellate LX-2 cells transfected with non-targeting control siRNA, replicate 1


title: G4-10-3

description: Library name: Sample 12


title: RBE PBX1 CUT&Tag replicate 3

city: DaLian

first: Luo

last: Kai

state: Liaoning Province

address: No. 467, Zhongshan Road, Shahekou District, Dalian 116011, China

institute: The Second Hospital of Dalian Medical University

description:
Library name: RBE_3_PBX1_CUTTAG
RBE; untreated; anti-PBX1 CUT&Tag; biological replicate 3; antibody: Proteintech 18204-1-AP (rabbit polyclonal; RRID: AB_10951860); no input control was generated in the CUT&Tag workflow; IgG control status unknown.

data_processing:
Raw reads were evaluated with FastQC v0.11.8 and filtered with fastp v0.19.5 to remove adapters, 3-prime low-quality bases, and reads shorter than 40 bp.
Clean reads were aligned to the hg38 reference genome using Bowtie2 v2.3.4.3. Only uniquely mapped reads were retained for downstream analysis; BAM processing and mapping-quality filtering were performed with Sambamba v0.6.7.
deepTools v3.4.1 was used for coverage and enrichment evaluation. bigWig files represent genome-wide signal tracks from unique, duplicate-marked reads.
PBX1 enrichment peaks were called with MACS2 v2.2.6.
Motif analysis was performed with HOMER v4.11.1. Peak annotation used PeakAnnotator v1.4, ANNOVAR (2018-04-16), and BEDTools v2.28.0.
Assembly: hg38
Supplementary files format and content: bigWig files contain genome-wide PBX1 CUT&Tag signal tracks for individual biological replicates.

source_name: RBE

extract_protocol:
CUT&Tag was performed on HUCCT1 and RBE cell samples. Cells or nuclei were bound to ConA magnetic beads. Exact starting cell number and fixation status were not recorded in the available report.
CUT&Tag libraries were reported to be prepared using the NovoNGS CUT&Tag 4.0 High-Sensitivity Kit (for Illumina; Novoprotein). A rabbit polyclonal anti-PBX1 antibody was used (Proteintech, 18204-1-AP; RRID: AB_10951860). The standard workflow included primary antibody incubation at 4C overnight, secondary antibody incubation at room temperature for 1 h, pA-Tn5-mediated tagmentation, PCR amplification, and library quality control. Libraries were sequenced on an Illumina NovaSeq platform with 150-bp paired-end reads. Exact antibody amount, input cell number, fixation status, and PCR cycle count were unknown.

treatment_protocol: Cells were untreated. Culture conditions were not recorded in the available report.

value: RBE

value: unknown

value: untreated


title: L6Y3VG_Mock_rep1.fastq.gz

description:
Library name: Sample 26
L6Y3VG_8_Mock_rep1

value: Mock


title: CasTuner sgRnf12 KD Day3 Rep2

description:
Library name: sgRnf12_KD_D3_Rep2
0nM dTAG

value: Embryonic stem cells


title: G4-10-2

description: Library name: Sample 11


title: L6Y3VG_Mock_rep3.fastq.gz

description:
Library name: Sample 25
L6Y3VG_10_Mock_rep3


title: RBE PBX1 CUT&Tag replicate 2

description:
Library name: RBE_2_PBX1_CUTTAG
RBE; untreated; anti-PBX1 CUT&Tag; biological replicate 2; antibody: Proteintech 18204-1-AP (rabbit polyclonal; RRID: AB_10951860); no input control was generated in the CUT&Tag workflow; IgG control status unknown.


title: CasTuner sgRnf12 KD Day3 Rep1

description:
Library name: sgRnf12_KD_D3_Rep1
0nM dTAG

value: Differentiation by 2i/LIF withdrawal, KD by dTAG-13 removal


title: G4-10-1

description: Library name: Sample 10

value: kidney


title: L6Y3VG_HK_rep1.fastq.gz

description:
Library name: Sample 24
L6Y3VG_11_HK_rep1


title: CasTuner sgZic3 ctrl Day3 Rep1

description:
Library name: H3K9me3_sgZic3_ctrl_D3_Rep1
500nM dTAG

value: female

value: CAST x C57BL/6


title: RBE PBX1 CUT&Tag replicate 1

description:
Library name: RBE_1_PBX1_CUTTAG
RBE; untreated; anti-PBX1 CUT&Tag; biological replicate 1; antibody: Proteintech 18204-1-AP (rabbit polyclonal; RRID: AB_10951860); no input control was generated in the CUT&Tag workflow; IgG control status unknown.


title: G4-2-5-3

description: Library name: Sample 9


title: L6Y3VG_HK_rep2.fastq.gz

description:
Library name: Sample 23
L6Y3VG_12_HK_rep2


title: HUCCT1 PBX1 CUT&Tag replicate 3

description:
Library name: HUCCT1_3_PBX1_CUTTAG
HUCCT1; untreated; anti-PBX1 CUT&Tag; biological replicate 3; antibody: Proteintech 18204-1-AP (rabbit polyclonal; RRID: AB_10951860); no input control was generated in the CUT&Tag workflow; IgG control status unknown.


title: G4-2-5-2

description: Library name: Sample 8


title: CasTuner sgZic3 KD Day3 Rep2

description:
Library name: H3K9me3_sgZic3_KD_D3_Rep2
0nM dTAG

value: Differentiation Day 3


title: HUCCT1 PBX1 CUT&Tag replicate 2

description:
Library name: HUCCT1_2_PBX1_CUTTAG
HUCCT1; untreated; anti-PBX1 CUT&Tag; biological replicate 2; antibody: Proteintech 18204-1-AP (rabbit polyclonal; RRID: AB_10951860); no input control was generated in the CUT&Tag workflow; IgG control status unknown.


title: DVG7TD_HK+DVG-B 3.fastq.gz

description:
Library name: Sample 22
DVG7TD_15_HK+DVG-B 3


title: CasTuner sgZic3 KD Day3 Rep1

description:
Library name: H3K9me3_sgZic3_KD_D3_Rep1
0nM dTAG


title: DVG7TD_HK+DVG-B 2.fastq.gz

description:
Library name: Sample 21
DVG7TD_14_HK+DVG-B 2


title: G4-2-5-1

description: Library name: Sample 7


title: HUCCT1 PBX1 CUT&Tag replicate 1

description:
Library name: HUCCT1_1_PBX1_CUTTAG
HUCCT1; untreated; anti-PBX1 CUT&Tag; biological replicate 1; antibody: Proteintech 18204-1-AP (rabbit polyclonal; RRID: AB_10951860); no input control was generated in the CUT&Tag workflow; IgG control status unknown.


title: Model-3

description: Library name: Sample 6


title: CasTuner sgRnf12 ctrl Day3 Rep1

description:
Library name: H3K9me3_sgRnf12_ctrl_D3_Rep1
500nM dTAG


title: XXdXIC XistOverexpression Day2 Rep3

description: Library name: XXdXIC_Dox_D2_Rep3

value: TX1072 XXdXIC-Cast

value: Doxycycline, Differentiation by 2i/LIF withdrawal

value: Differentiation Day 2


title: DVG7TD_HK+DVG-B 1.fastq.gz

description:
Library name: Sample 20
DVG7TD_13_HK+DVG-B 1


title: RBE siPBX1 replicate 3

description:
Library name: RBE_siPBX1_3
RBE; siRNA-mediated PBX1 knockdown; biological replicate 3; sequencing report indicates S4 flow cell.

data_processing:
Raw reads were filtered with fastp v0.19.7 using parameters: fastp -g -q 5 -u 50 -n 15 -l 150.
Clean reads were aligned to the GRCh38/hg38 reference genome with HISAT2, and SAM files were converted to BAM with samtools.
Gene-level read counts were generated using featureCounts from the Subread package; reads with mapping quality <10, unpaired alignments, and multi-mapping reads were filtered.
Differential expression analysis was performed with DESeq2 in R v4.3.3.
Assembly: GRCh38 / hg38
Supplementary files format and content: Tab-delimited text files containing gene-level raw read counts for each sample.
Supplementary files format and content: GRCh38.p12 gene annotation; GTF header: genome-build GRCh38.p12, genome-build-accession NCBI:GCA_000001405.27, genebuild-last-updated 2018-07

extract_protocol: Poly(A)+ mRNA was enriched using Oligo(dT) beads. RNA-seq libraries were prepared for paired-end sequencing. Exact library preparation kit and strand specificity were unknown.

value: siRNA-mediated PBX1 knockdown


title: Model-2

description: Library name: Sample 5


title: CasTuner sgRnf12 KD Day3 Rep2

description:
Library name: H3K9me3_sgRnf12_KD_D3_Rep2
0nM dTAG


title: DVG7TD_HK+DVG-A 3.fastq.gz

description:
Library name: Sample 19
DVG7TD_24_HK+DVG-A 3


title: CasTuner sgRnf12 KD Day3 Rep1

description:
Library name: H3K9me3_sgRnf12_KD_D3_Rep1
0nM dTAG


title: RBE siPBX1 replicate 2

description:
Library name: RBE_siPBX1_2
RBE; siRNA-mediated PBX1 knockdown; biological replicate 2; sequencing report indicates S4 flow cell.


title: DVG7TD_HK+DVG-A 2.fastq.gz

description:
Library name: Sample 18
DVG7TD_23_HK+DVG-A 2


title: RBE siPBX1 replicate 1

description:
Library name: RBE_siPBX1_1
RBE; siRNA-mediated PBX1 knockdown; biological replicate 1; sequencing report indicates S4 flow cell.


title: Model-1

description: Library name: Sample 4


title: Uterine tissue, CeTA@GPP, 2 weeks, rep5

city: Guangzhouo

first: Peixian

last: Cheng

address: No. 63 Duobao Road, Liwan District, Guangzhou, Guangdong Province, China.

institute: The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China

description:
Library name: Sample20
C520

data_processing:
The raw sequencing data were first subjected to quality control and filtering. The main filtering criteria included removal of reads containing 3′ adaptor sequences using fastp, removal of reads with an average quality score lower than Q20, removal of reads containing more than 10% ambiguous bases, and removal of reads shorter than 20 bp after adaptor trimming and quality filtering. High-quality clean reads were obtained after the above filtering steps. FastQC was then used to further evaluate base quality. Clean reads were aligned to the rat reference genome Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa using HISAT2. The distribution of reads mapped to the genome was summarized, and the number of mapped reads and transcript length in each sample were normalized. HTSeq was used to calculate the read count values mapped to each gene, which were used as the raw gene expression levels. To correct for the effects of sequencing depth and gene length on expression estimation, gene expression levels were normalized using FPKM, namely Fragments Per Kilobase of transcript per Million fragments mapped.
Assembly: Aligned to the rat reference genome Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa using HISAT2.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Rattus norvegicus

source_name: Uterine

extract_protocol:
Total RNA was extracted from rat uterine tissue samples. RNA concentration and purity were subsequently assessed, and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer.
During library construction, poly(A)-tailed mRNA was first enriched from total RNA using oligo(dT) magnetic beads. The enriched mRNA was then fragmented into approximately 300 bp fragments by ion-mediated fragmentation. cDNA was synthesized using RNA as the template. After PCR amplification, libraries with an approximate size of 450 bp were selected. Library quality was then assessed using an Agilent 2100 Bioanalyzer.

treatment_protocol: The IUA rat models were established using a combined mechanical injury and infection method. A total of 20 female Sprague-Dawley rats (180–220 g, 6–8 weeks old) were randomly divided into four groups (5 rats per group): sham surgery group (Sham), IUA model group (IUA), IUA + GPP group (GPP), and IUA + CeTA@GPP group (CeTA@GPP). After anesthesia, the lower abdomen was sterilized and incised with a 3 cm longitudinal incision to expose both sides of the uterus. A 2 mm incision was made near the cervix on both sides of the uterus. A uterine curette was inserted through the incision into the uterine cavity and used to scrape the endometrium until it became noticeably congested and roughened. Subsequently, a 1-0 surgical suture pre-soaked in a 6 mg/L LPS solution at 4 °C for 24 h was implanted into the uterine cavity. The suture tail was led through the abdominal wall and secured to the skin surface for removal 48 h post-surgery. After placement of the LPS-containing suture, 100 μL of GPP or CeTA@GPP hydrogel was injected into the uterine cavity using a syringe through the uterine incision, whereas the IUA group did not receive any injection. Subsequently, the uterus and abdomen were sutured layer by layer. After the operation, the rats were placed in a warm cage to maintain their body temperature until they regained consciousness. All rats received penicillin injections (50,000 units per day) for 3 consecutive days after the operation. The rats were sacrificed 2 weeks after the operation, and uterine tissue samples were collected from the four groups for RNA-seq analysis.

value: Uterine

tag: strain

value: Sprague-Dawley


title: Control-3

description: Library name: Sample 3


title: RBE siNC replicate 3

description:
Library name: RBE_siNC_3
RBE; negative control siRNA; biological replicate 3; sequencing report indicates S4 flow cell.

value: negative control siRNA


title: DVG7TD_HK+DVG-A 1.fastq.gz

description:
Library name: Sample 17
DVG7TD_22_HK+DVG-A 1


title: Uterine tissue, CeTA@GPP, 2 weeks, rep4

description:
Library name: Sample19
C519


title: DVG7TD_DVG-B 4.fastq.gz

description:
Library name: Sample 16
DVG7TD_12_DVG-B 4

value: DVG-B


title: Control-2

description: Library name: Sample 2


title: RBE siNC replicate 2

description:
Library name: RBE_siNC_2
RBE; negative control siRNA; biological replicate 2; sequencing report indicates S4 flow cell.

value: RBE

value: unknown


title: Control-1

description: Library name: Sample 1


title: DVG7TD_DVG-B 3.fastq.gz

description:
Library name: Sample 15
DVG7TD_11_DVG-B 3


title: RBE siNC replicate 1

description:
Library name: RBE_siNC_1
RBE; negative control siRNA; biological replicate 1; sequencing report indicates S4 flow cell.


title: Uterine tissue, CeTA@GPP, 2 weeks, rep3

description:
Library name: Sample18
C507


title: Uterine tissue, CeTA@GPP, 2 weeks, rep2

description:
Library name: Sample17
C506


title: Uterine tissue, CeTA@GPP, 2 weeks, rep1

description:
Library name: Sample16
C503


title: CasTuner sgZic3 ctrl Day3 Rep3

description:
Library name: H3K9me3_sgZic3_ctrl_D3_Rep3
500nM dTAG

value: Differentiation by 2i/LIF withdrawal, dTAG-13 for CasTuner degradation


title: DVG7TD_DVG-B 2.fastq.gz

description:
Library name: Sample 14
DVG7TD_10_DVG-B 2


title: CasTuner sgZic3 ctrl Day3 Rep2

description:
Library name: H3K9me3_sgZic3_ctrl_D3_Rep2
500nM dTAG

value: Embryonic stem cells


title: DVG7TD_DVG-B 1.fastq.gz

description:
Library name: Sample 13
DVG7TD_9_DVG-B 1


title: HUCCT1 siPBX1 replicate 3

description:
Library name: Hucct1_siPBX1_3
HUCCT1; siRNA-mediated PBX1 knockdown; biological replicate 3; sequencing report indicates S4 flow cell.


title: Uterine tissue, GPP, 2 weeks, rep5

description:
Library name: Sample15
H593


title: HUCCT1 siPBX1 replicate 2

description:
Library name: Hucct1_siPBX1_2
HUCCT1; siRNA-mediated PBX1 knockdown; biological replicate 2; sequencing report indicates S4 flow cell.


title: DVG7TD_DVG-A 3.fastq.gz

description:
Library name: Sample 12
DVG7TD_21_DVG-A 3

value: DVG-A


title: HUCCT1 siPBX1 replicate 1

description:
Library name: Hucct1_siPBX1_1
HUCCT1; siRNA-mediated PBX1 knockdown; biological replicate 1; sequencing report indicates S4 flow cell.


title: CasTuner sgZic3 KD Day3 Rep3

description:
Library name: H3K9me3_sgZic3_KD_D3_Rep3
0nM dTAG

value: Differentiation by 2i/LIF withdrawal, KD by dTAG-13 removal


title: Uterine tissue, GPP, 2 weeks, rep4

description:
Library name: Sample14
H592


title: DVG7TD_DVG-A 2.fastq.gz

description:
Library name: Sample 11
DVG7TD_20_DVG-A 2


title: CasTuner sgRnf12 ctrl Day3 Rep3

description:
Library name: H3K9me3_sgRnf12_ctrl_D3_Rep3
500nM dTAG

value: female


title: HUCCT1 siNC replicate 3

description:
Library name: Hucct1_siNC_3
HUCCT1; negative control siRNA; biological replicate 3; sequencing report indicates S4 flow cell.


title: Uterine tissue, GPP, 2 weeks, rep3

description:
Library name: Sample13
H590


title: CasTuner sgRnf12 ctrl Day3 Rep2

description:
Library name: H3K9me3_sgRnf12_ctrl_D3_Rep2
500nM dTAG

value: CAST x C57BL/6


title: DVG7TD_DVG-A 1.fastq.gz

description:
Library name: Sample 10
DVG7TD_19_DVG-A 1


title: DVG7TD_HK 5.fastq.gz

description:
Library name: Sample 9
DVG7TD_18_HK 7


title: Uterine tissue, GPP, 2 weeks, rep2

description:
Library name: Sample12
H589


title: HUCCT1 siNC replicate 1

description:
Library name: Hucct1_siNC_1
HUCCT1; negative control siRNA; biological replicate 1; sequencing report indicates S4 flow cell.


title: HUCCT1 siNC replicate 2

description:
Library name: Hucct1_siNC_2
HUCCT1; negative control siRNA; biological replicate 2; sequencing report indicates S4 flow cell.


title: CasTuner sgRnf12 KD Day3 Rep3

description:
Library name: H3K9me3_sgRnf12_KD_D3_Rep3
0nM dTAG

value: Differentiation Day 3


title: Uterine tissue, GPP, 2 weeks, rep1

description:
Library name: Sample11
H583


title: DVG7TD_HK 4.fastq.gz

description:
Library name: Sample 8
DVG7TD_17_HK 6


title: HK-2_sg_replicate3, target gene sgRNA knockdown

description:
Library name: sg-3
sg-3

data_processing:
Raw sequencing reads were filtered to remove low-quality reads, reads containing adapters and ambiguous N bases to obtain CleanData using fastp software.
Clean reads were aligned to human reference genome using HISAT2.
Gene-level read counts were quantified by featureCounts.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited plain text file (.txt). Contains raw read counts of all protein-coding genes across all samples. First column: Ensembl gene ID; subsequent columns represent raw counts for each library.

molecule: polyA RNA

growth_protocol: Human HK-2 renal proximal tubular epithelial cells were cultured in DMEM/F12 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Cells were maintained at 37 °C in a humidified incubator containing 5% CO₂.

extract_protocol:
Total RNA was isolated from cultured HK-2 cells using Trizol reagent following the manufacturer’s instructions. RNA integrity was verified, and RNA purity and concentration were determined by spectrophotometry.
mRNA was enriched from total RNA using oligo (dT) magnetic beads. Fragmentation buffer was used to interrupt mRNA into short fragments. First-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. After end repair, A-tailing and adapter ligation, fragments were purified and enriched by PCR amplification to construct the cDNA library. The libraries were sequenced on Illumina NovaSeq 6000 platform with paired-end 150 bp strategy.

treatment_protocol: HK-2 cells were transfected with target sgRNA (knockdown group) or non-targeting scrambled sgRNA (negative control group). Cells were harvested at the designated time point after transfection for total RNA extraction.

value: kidney


title: Uterine tissue, IUA, 2 weeks, rep5

description:
Library name: Sample10
M599


title: C57BL/6J, UIR_BA3, Day14

city: Hefei City, Anhui Province

first: Shuangyu

last: Li

address: 81 Meishan Road

institute: Anhui Medical University

description: Library name: UIR_BA3

data_processing:
Raw sequencing reads were quality-controlled and trimmed using CLC Genomics Workbench v11.0.1 to remove low-quality bases and adapter sequences.
Assembly: Tab-delimited plain text file containing raw gene read counts of all 6 samples, with rows as gene symbols and columns as individual samples.
Supplementary files format and content: Tab-delimited plain text file containing normalized FPKM expression values for all detected genes across six mouse renal tissue samples.

extract_protocol:
Total RNA was extracted from mouse renal cortical tissue using the RNeasy Mini Plus Kit (Qiagen) following the manufacturer’s instructions. RNA integrity was assessed via agarose gel electrophoresis and Nanodrop spectrophotometry. A total of 1.3 μg qualified total RNA per sample was reserved for subsequent library construction.
mRNA was enriched from total RNA using oligo(dT) magnetic beads. Strand-specific RNA-seq libraries were generated with the SMARTER mRNA-Seq Library Prep Kit strictly according to the manufacturer’s standard protocols. Library fragment size was verified and quantified before sequencing.

value: Primary mouse renal cortical tissue

value: Renal cortical tissue (mixed tubular, interstitial cells)

value: Wild-type

value: Unilateral renal ischemia-reperfusion surgery + daily intraperitoneal Brucine A (1 mg/kg) injection for 14 days

value: 14 days after UIR surgery


title: C57BL/6J, UIR_BA2, Day14

description: Library name: UIR_BA2


title: DVG7TD_HK 3.fastq.gz

description:
Library name: Sample 7
DVG7TD_16_HK 5


title: DVG7TD_HK 2.fastq.gz

description:
Library name: Sample 6
DVG7TD_8_HK 4


title: Uterine tissue, IUA, 2 weeks, rep4

description:
Library name: Sample9
M511

value: Uterine

value: Sprague-Dawley


title: HK-2_sg_replicate2, target gene sgRNA knockdown

description:
Library name: sg-2
sg-2


title: HK-2_sg_replicate1, target gene sgRNA knockdown

description:
Library name: sg-1
sg-1


title: C57BL/6J, UIR_BA1, Day14

description: Library name: UIR_BA1


title: Uterine tissue, IUA, 2 weeks, rep3

description:
Library name: Sample8
M508


title: C57BL/6J, UIR3, Day14

description: Library name: UIR3

value: Unilateral renal ischemia-reperfusion surgery + daily intraperitoneal vehicle injection for 14 days


title: DVG7TD_HK 1.fastq.gz

description:
Library name: Sample 5
DVG7TD_7_HK 3


title: HK-2_NC_replicate3, non-targeting sgRNA control

description:
Library name: NC-3
NC-3


title: Uterine tissue, IUA, 2 weeks, rep2

description:
Library name: Sample7
M504


title: C57BL/6J, UIR2, Day14

description: Library name: UIR2


title: DVG7TD_Mock 4.fastq.gz

description:
Library name: Sample 4
DVG7TD_4_Mock 4

value: Mock


title: Uterine tissue, IUA, 2 weeks, rep1

description:
Library name: Sample6
M502


title: HK-2_NC_replicate2, non-targeting sgRNA control

description:
Library name: NC-2
NC-2


title: C57BL/6J, UIR1, Day14

description: Library name: UIR1


title: DVG7TD_Mock 3.fastq.gz

description:
Library name: Sample 3
DVG7TD_3_Mock 3


title: HK-2_NC_replicate1, non-targeting sgRNA control

description:
Library name: NC-1
NC-1


title: Uterine tissue, Sham, 2 weeks, rep5

description:
Library name: Sample5
S555


title: BSseq_XO_d4_r2

description: Library name: BSseq_XO_d4_r2

data_processing:
Adaptor and quality trimming was performed using Trim Galore (v0.6.4).
Reads were aligned to mm10 using BSMAPz.
bam files were sorted with samtools (v1.10) and duplicate reads removed using Picard (v2.7.1).
bedGraph files were generated using Methyldackel (v0.3.0) [extract –minDepth 2].
Lastly, blackliseted regions and mitochondrial reads were removed.
Assembly: mm10
Supplementary files format and content: bedGraph files containing per-base CpG methylation (merged or biological replicates)

source_name: XO ESCs

extract_protocol:
Whole Genome Bisulfite Sequencing (WGBS) for XO and XXΔXICB6 was performed in parallel, as described in (Mutzel et al, 2025). XXΔXICB6 data were published in (Mutzel et al, 2025). Briefly, XO B7 and XXΔXICB6 mES cells were differentiated for 0, 2 or 4 days and genomic DNA was extracted with the DNeasy Blood and Tissue Kit (Qiagen). Bisulfite-converted DNA libraries were prepared using the Accel-NGS Methyl-Seq DNA library kit (SWIFT BIOSCIENCES). Specifically, 200ng (in 50 μl lowTE) of purified DNA were fragmented to ~350 bp using the Covaris S2 system (10% duty cycle, intensity 5 for 2 × 45 s in Covaris AFA tubes) followed by a concentration step with Zymo columns (DNA Clean & Concentrator). 20 μl of DNA were used for bisulfite conversion overnight with the Zymo EZ-DNA methylation Gold Kit. Bisulfite-converted DNA was fully denatured by 2 min incubation at 95 °C and immediately transferred to ice. To anneal a truncated adapter, 15 μl of denatured DNA was mixed with 25 μl of Adaptase reaction mix (SWIFT) and incubated for 15 min at 37 °C, 2 min at 95 °C, and then cooled to 4 °C. Extension and second strand synthesis by using a primer complementary to the truncated adapter was performed mixing the Adaptase reaction mix with 44 μl of extension reaction mix (SWIFT) and incubation at 98 °C for 1 min, 62 °C for 2 min, 65 °C for 5 min and cooling to 4 °C. The samples were cleaned with 1.2 volumes of Ampure XP beads, 80% ethanol and eluted in 15 μl. Ligation of the second (truncated) adapter was performed at 25 °C for 15 min followed by an additional bead clean up with 1 volume of AmpureXP beads and 80% ethanol.
Samples were individually indexed using unique dual indexed primer sets with 6 cycles of the following PCR program: 30s @ 98 °C, 6 cycles of 15s @ 98 °C, 30s @ 60 °C, 60s @ 68 °C, followed by a final 5 min incubation step at 68 °C. Libraries were cleaned up with 1 volume of Ampure XP beads. Quality was assessed using Agilent’s Bioanalyzer and concentration was determined by qPCR. Libraries were pooled equimolarly and sequenced on a NovaSeq 6000 S2 flowcell (Illumina) in paired end 150 mode to yield ~ 120-278mio fragments.

value: XO ESCs

value: TX1072 XO B7

value: XO embryonic stem cells

value: CAST x C57BL/6 (CAST chrX)

value: Differentiation by 2i/LIF withdrawal


title: DVG7TD_Mock 2.fastq.gz

description:
Library name: Sample 2
DVG7TD_2_Mock 2


title: Uterine tissue, Sham, 2 weeks, rep4

description:
Library name: Sample4
S554


title: Patient6_OA_BCR

city: Houston

first: Roza

last: Nurieva

state: TX

address: 7455 Fannin St,, Unit 906

department: Immunology

institute: The University of Texas MD Anderson Cancer Center

description:
Library name: Synovial fluid cells isolated from Osteoarthritis_patient 6_BCR
10X Genomic

data_processing:
Demultiplexed and analyzed using the 10X Genomics Cell Ranger software v3.1.0 with default settings. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files (barcodes, features), comma-separated values files (clonotypes, contig annoation) and matrix files (gene expression matrix) from Cell Ranger
Library strategy: BCR-Seq

source_name: knee joint

extract_protocol:
cryopreserved SF cells were thawed, washed, and resuspended in 1X PBS with 0.05% RNase-free bovine serum albumin (ThermoFisher Scientific) to a final volume of less than 35 µL. Cell counts were determined using trypan blue exclusion and counted on a Countess II FL automated cell counter (Life Technologies).
The cDNA was used to create a gene expression library using the Chromium Single Cell 5’ Library Construction Kit (Cat No: 1000020, 10XGenomics, CA, USA) or for TCR enrichment/library preparation with the Chromium Single Cell V(D)J Enrichment Kit for Human T cells (Cat No: 1000005, 10XGenomics, CA, USA). Quality control steps, including cDNA amplification and library preparation, were performed using the Qubit™ 1X dsDNA HS Assay (Thermo Fisher Scientific) and Bioanalyzer High-Sensitivity DNA Analysis (Agilent) to assess concentration and quality. Library concentrations were confirmed with quantitative PCR using the KAPA Library Quantification Kit (Roche), and samples were normalized to 10 nM for pooling.

value: knee joint

value: Synovial fluid cell

value: female

tag: age

value: 60-80 years old


title: BSseq_XO_d4_r1

description: Library name: BSseq_XO_d4_r1


title: DVG7TD_Mock 1.fastq.gz

description:
Library name: Sample 1
DVG7TD_1_Mock 1


title: Patient5_OA_BCR

description:
Library name: Synovial fluid cells isolated from Osteoarthritis_patient 5_BCR
10X Genomic


title: Uterine tissue, Sham, 2 weeks, rep3

description:
Library name: Sample3
S518


title: BSseq_XO_d2_r2

description: Library name: BSseq_XO_d2_r2


title: chr2_reverse_5E_D9_S4

city: Shenzhen

first: zengqi

last: wen

state: Guangdong

address: No. 66 Gongchang Road, Guangming District

department: Zhongshan School of Medicine

institute: Sun Yat-sen University Shenzhen Campus

description: Library name: chr2_reverse_5E_D9_S4

data_processing:
Raw paired-end sequencing reads were trimmed using cutadapt to remove adapter sequences and low-quality bases.
Trimmed reads were aligned to the mouse reference genome GRCm38/mm10 using Bowtie2.
Aligned reads were sorted, PCR duplicates were marked, and duplicate reads, low-quality alignments, and reads outside the selected mm10 genomic regions were removed.
Genome-wide read coverage was calculated from filtered alignments and normalized to reads per million mapped reads. RPM-normalized signal tracks were exported as bigWig files.
Filtered paired-end fragments were counted in fixed genomic windows, and window-level signals were normalized to reads per million fragments.
Replication timing signal was calculated as log2((S1 + S2) / (S3 + S4)) using the four S-phase fractions.
Replication timing profiles were quantile-normalized across samples and smoothed using LOESS. The smoothed replication timing profiles were exported as bedGraph files.
Assembly: GRCm38/mm10
Supplementary files format and content: Processed bigWig files contain duplicate-removed, RPM-normalized genome-wide Repli-seq read coverage tracks for individual S-phase fractions. Processed bedGraph files contain quantile-normalized and LOESS-smoothed replication timing profiles calculated from S1-S4 Repli-seq fraction signals.

source_name: Inner cell mass

growth_protocol: R1 mouse embryonic stem cells were cultured under standard mouse embryonic stem cell culture conditions and maintained before Repli-seq sample preparation.

extract_protocol:
Cells were pulse-labeled with BrdU and sorted into four S-phase fractions, S1 to S4, based on DNA content. Genomic DNA was extracted from each sorted fraction, and BrdU-labeled nascent DNA was enriched for Repli-seq library preparation.
Sequencing libraries were prepared from enriched BrdU-labeled nascent DNA using standard sequencing library preparation procedures. Libraries were sequenced on a DNBSEQ-T7 platform using paired-end sequencing.

treatment_protocol: Cells were collected at the indicated time points and treatment conditions as described in the sample metadata. Samples labeled D0, D2, D9, D15, or D21 indicate the corresponding collection time points.

value: Inner cell mass

value: embryonic stem cell

value: Dox(1μg/mL) 9days


title: Patient4_OA_BCR

description:
Library name: Synovial fluid cells isolated from Osteoarthritis_patient 4_BCR
10X Genomic

value: 40-60 years old


title: Uterine tissue, Sham, 2 weeks, rep2

description:
Library name: Sample2
S517

value: Uterine


title: BSseq_XO_d2_r1

description: Library name: BSseq_XO_d2_r1


title: chr2_reverse_5E_D9_S3

description: Library name: chr2_reverse_5E_D9_S3


title: Uterine tissue, Sham, 2 weeks, rep1

description:
Library name: Sample1
S512

value: Sprague-Dawley


title: Patient3_Second ICI-IA_BCR

description:
Library name: Synovial fluid cells isolated from second arthritis irAE_patient 3_BCR
10X Genomic

value: male


title: chr2_reverse_5E_D9_S2

description: Library name: chr2_reverse_5E_D9_S2


title: BSseq_XO_d0_r2

description: Library name: BSseq_XO_d0_r2


title: Patient3_First ICI-IA_BCR

description:
Library name: Synovial fluid cells isolated from first arthritis irAE_patient 3_BCR
10X Genomic


title: PANC-1 cells, IgG CUT&Tag

city: Shanghai

first: taochen

last: he

address: 180 Fenglin Road, Shanghai, China

institute: Zhongshan Hospital Fudan University

description: Library name: P1_IgG_1

data_processing:
Raw sequencing reads were subjected to quality control to remove adaptor sequences and low-quality reads. Clean paired-end reads were aligned to the human reference genome (GRCh38) using Bowtie2. PCR duplicates were removed, and genome-wide coverage tracks were generated from the aligned reads and converted to BigWig (.bw) format for visualization and downstream analysis.
Assembly: GRCh38
Supplementary files format and content: BigWig (.bw) files containing normalized genome-wide CUT&Tag signal tracks mapped to the human reference genome (GRCh38). The files represent genome-wide read coverage and are suitable for visualization in genome browsers and downstream analyses.
Library strategy: CUT&Tag

growth_protocol: PANC-1 human pancreatic ductal adenocarcinoma cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Approximately 1 × 10^5 PANC-1 cells were immobilized on concanavalin A-coated magnetic beads and processed according to the CUT&Tag protocol. Cells were incubated with an anti-H2BK120ub1 antibody or normal rabbit IgG, followed by incubation with a secondary antibody and Protein A-Tn5 transposome. After tagmentation, DNA fragments were released, purified, and used for library preparation according to the manufacturer's instructions.
CUT&Tag libraries were generated by pA-Tn5-mediated tagmentation according to the manufacturer's protocol. Tagmented DNA fragments were PCR-amplified, purified, and assessed for library quality. Libraries were sequenced on an Illumina NovaSeq X Plus platform to generate paired-end 150 bp reads.

treatment_protocol: PANC-1 cells were cultured under standard conditions and harvested at approximately 80% confluence. No additional treatment or stimulation was applied prior to CUT&Tag library preparation.

value: pancreatic cancer cell

value: Empty vector

value: IgG CUT&Tag


title: BSseq_XO_d0_r1

description: Library name: BSseq_XO_d0_r1

value: XO ESCs

value: TX1072 XO B7

value: XO embryonic stem cells


title: chr2_reverse_5E_D9_S1

description: Library name: chr2_reverse_5E_D9_S1


title: Patient2_Second ICI-IA_BCR

description:
Library name: Synovial fluid cells isolated from second arthritis irAE_patient 2_BCR
10X Genomic

value: knee joint


title: PANC-1 cells, H2BK120ub1 CUT&Tag

description: Library name: P1_H2B_1

value: H2BK120ub1 CUT&Tag


title: chr2_reverse_5E_D0_S4

description: Library name: chr2_reverse_5E_D0_S4


title: subcutaneously injected CT26 (shMettl3 knock + Cd73 high-expression) rep3

city: Seoul

first: Seung-Pyo

last: Hong

address: 103 Daehak-ro

country: South Korea

institute: Seoul national university

description:
Library name: Cd73-5
Column name in CR.count.txt : Cd73_5

data_processing:
Raw RNA-seq reads were evaluated for quality using FastQC and trimmed using Trimmomatic. Processed reads were aligned against the mm10 mouse reference genome by STAR (v2.7.11b) and expression value were quantified by RSEM.
Assembly: mm10
Supplementary files format and content: tab-delimited txt file includes RSEM expected count for each Sample

source_name: Colon

extract_protocol:
Total RNA was isolated from cells using RNeasy Plus Mini Kit (74106, Qiagen) in accordance with the manufacturer’s instructions
RNA-seq libraries were constructed using the VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina according to the manufacturer’s instructions

value: Colon

value: Colon adenocarcinoma

value: shMettl3 knock + Cd73 high-expression


title: ADT expression NK cells samples treated by TNBC-exosomes and one untreated NK cells sample, Well8

city: Indiana University

first: Reza

last: Shahbazi

address: 980 W Walnut st

institute: Indiana University

description:
Library name: Well 8_FB
Anti-body expression of NK cells  samples treated by exosomes extracted from 17 different TNBC cell-lines and one untreated NK cells sample, Well8

library_source: other

data_processing:
All raw input data were distributed across 8 wells, meaning each well contained a portion of the sequencing data for all samples. The Cell Ranger pipeline (version 7.2.0) from 10x Genomics was used to process the raw sequencing data, including quality filtering, alignment to the human reference genome (GRCh38), cell barcode assignment, and generation of unique molecular identifier (UMI) counts to produce the gene expression matrix. Data from all wells were then aggregated to generate a unified H5 gene expression file for each individual sample.
Assembly: hg38
Supplementary files format and content: h5 files includes gene expression

molecule: protein

source_name: NK cell

growth_protocol: Triple-Negative Breast Cancer Panel 3 cell lines (TCP-1003) were obtained from the American Type Culture Collection (ATCC) and cultured in RPMI-1640 media supplemented with 10% exosome-depleted fetal bovine serum (Gibco) and 1% penstrep. Cells were passaged using TrypLE express enzyme (Gibco™) upon reaching 70-80% confluency. The conditioned media was collected for exosome isolation. +B63B64B62B62:B64

extract_protocol:
After incubation with exosomes, cells were harvested, washed, and stained with the TotalSeq™-C anti-human Hashtag antibodies (BioLegend), following the manufacturer’s recommended titration and staining protocol. Non-coding RNAs were isolated from exosomes derived from 17 TNBC cell lines as well as from plasma samples of 28 TNBC patients and 7 healthy donors, using the MagMAX™ mirVana™ Total RNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol. The isolated RNA, enriched for small and non-coding RNAs, was quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific), and RNA quality was assessed with an Agilent Bioanalyzer 2100 (Agilent Technologies).
For single cell RNA-seq, following staining, cells were counted and loaded onto the Chromium X system (10x Genomics) using the Chromium Single Cell 5′ High Throughput (HT) Immune Profiling Kit. Single-cell Gel Bead-In-Emulsions (GEMs) were generated, and barcoded cDNA libraries, including gene expression and antibody-derived tag (ADT) libraries, were constructed according to the manufacturer’s instructions. The resulting libraries were sequenced on an Illumina NovaSeq 6000 platform using an S4 flow cell to a targeted depth of ~50,000 reads per cell. For noncoding RNAs, library preparation was performed using the NEXTFLEX® Small RNA-Seq Kit v4 with Unique Dual Indices (UDIs) (Revvity), which includes 3′ and 5′ adapter ligation, reverse transcription, PCR amplification, and size selection steps optimized for non-coding RNA capture. Prepared libraries were quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and validated for size distribution using the Agilent Bioanalyzer. Sequencing was conducted on an Illumina platform following standard procedures for small RNA libraries.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from healthy donor leukopaks by Lymphoprep (STEMCELL Technologies) density gradient centrifugation. NK cells were then purified using the EasySep™ Human NK Cell Negative Isolation Kit (STEMCELL Technologies) according to the manufacturer’s instructions. Cells were resuspended in RPMI 1640 supplemented with 10% FBS and 10 ng/mL recombinant human IL-2 and IL-15 (STEMCELL Technologies). Following 24h incubation, NK cells were washed and treated with tumor-derived exosomes isolated from 17 distinct TNBC cell lines. Exosome exposure was carried out for 48 hours before cells were harvested for downstream analyses.

value: NK cell


title: subcutaneously injected CT26 (shMettl3 knock + Cd73 high-expression) rep2

description:
Library name: Cd73-3
Column name in CR.count.txt : Cd73_3


title: chr2_reverse_5E_D0_S3

description: Library name: chr2_reverse_5E_D0_S3

value: Inner cell mass

value: embryonic stem cell


title: Patient2_First ICI-IA_BCR

description:
Library name: Synovial fluid cells isolated from first arthritis irAE_patient 2_BCR
10X Genomic

value: Synovial fluid cell

value: 60-80 years old


title: Patient6_OA_TCR

description:
Library name: Synovial fluid cells isolated from Osteoarthritis_patient 6_TCR
10X Genomic

data_processing:
Demultiplexed and analyzed using the 10X Genomics Cell Ranger software v3.1.0 with default settings. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files (barcodes, features), comma-separated values files (clonotypes, contig annoation) and matrix files (gene expression matrix) from Cell Ranger
Library strategy: TCR-Seq

value: female


title: ADT expression NK cells samples treated by TNBC-exosomes and one untreated NK cells sample, Well7

description:
Library name: Well 7_FB
Anti-body expression of NK cells  samples treated by exosomes extracted from 17 different TNBC cell-lines and one untreated NK cells sample, Well7


title: Patient5_OA_TCR

description:
Library name: Synovial fluid cells isolated from Osteoarthritis_patient 5_TCR
10X Genomic


title: subcutaneously injected CT26 (shMettl3 knock + Cd73 high-expression) rep1

description:
Library name: Cd73-2
Column name in CR.count.txt : Cd73_2


title: ADT expression NK cells samples treated by TNBC-exosomes and one untreated NK cells sample, Well6

description:
Library name: Well 6_FB
Anti-body expression of NK cells  samples treated by exosomes extracted from 17 different TNBC cell-lines and one untreated NK cells sample, Well6


title: subcutaneously injected CT26 (shMettl3 knockdown) rep3

description:
Library name: shM3-6
Column name in CR.count.txt : shM3_6

value: shMettl3 knockdown


title: chr2_reverse_5E_D0_S2

description: Library name: chr2_reverse_5E_D0_S2


title: chr2_reverse_5E_D0_S1

description: Library name: chr2_reverse_5E_D0_S1


title: Patient4_OA_TCR

description:
Library name: Synovial fluid cells isolated from Osteoarthritis_patient 4_TCR
10X Genomic

value: 40-60 years old


title: ADT expression NK cells samples treated by TNBC-exosomes and one untreated NK cells sample, Well5

description:
Library name: Well 5_FB
Anti-body expression of NK cells  samples treated by exosomes extracted from 17 different TNBC cell-lines and one untreated NK cells sample, Well5


title: subcutaneously injected CT26 (shMettl3 knockdown) rep2

description:
Library name: shM3-4
Column name in CR.count.txt : shM3_4


title: chr2_reverse_1D_D9_S4

description: Library name: chr2_reverse_1D_D9_S4

value: Dox(1μg/mL) 9days


title: Patient3_Second ICI-IA_TCR

description:
Library name: Synovial fluid cells isolated from second arthritis irAE_patient 3_TCR
10X Genomic

value: male


title: ADT expression NK cells samples treated by TNBC-exosomes and one untreated NK cells sample, Well4

description:
Library name: Well 4_FB
Anti-body expression of NK cells  samples treated by exosomes extracted from 17 different TNBC cell-lines and one untreated NK cells sample, Well4


title: subcutaneously injected CT26 (shMettl3 knockdown) rep1

description:
Library name: shM3-2
Column name in CR.count.txt : shM3_2


title: Patient3_First ICI-IA_TCR

description:
Library name: Synovial fluid cells isolated from first arthritis irAE_patient 3_TCR
10X Genomic


title: chr2_reverse_1D_D9_S3

description: Library name: chr2_reverse_1D_D9_S3


title: ADT expression NK cells samples treated by TNBC-exosomes and one untreated NK cells sample, Well3

description:
Library name: Well 3_FB
Anti-body expression of NK cells  samples treated by exosomes extracted from 17 different TNBC cell-lines and one untreated NK cells sample, Well3


title: subcutaneously injected CT26 (shNC; control) rep4

description:
Library name: shNC-4
Column name in CR.count.txt : shNC4

value: shNC; control


title: Patient2_Second ICI-IA_TCR

description:
Library name: Synovial fluid cells isolated from second arthritis irAE_patient 2_TCR
10X Genomic


title: chr2_reverse_1D_D9_S2

description: Library name: chr2_reverse_1D_D9_S2


title: ADT expression NK cells samples treated by TNBC-exosomes and one untreated NK cells sample, Well2

description:
Library name: Well 2_FB
Anti-body expression of NK cells  samples treated by exosomes extracted from 17 different TNBC cell-lines and one untreated NK cells sample, Well2


title: subcutaneously injected CT26 (shNC; control) rep3

description:
Library name: shNC-3
Column name in CR.count.txt : shNC3


title: chr2_reverse_1D_D9_S1

description: Library name: chr2_reverse_1D_D9_S1


title: Patient2_First ICI-IA_TCR

description:
Library name: Synovial fluid cells isolated from first arthritis irAE_patient 2_TCR
10X Genomic


title: ADT expression NK cells samples treated by TNBC-exosomes and one untreated NK cells sample, Well1

description:
Library name: Well 1_FB
Anti-body expression of NK cells  samples treated by exosomes extracted from 17 different TNBC cell-lines and one untreated NK cells sample, Well1


title: subcutaneously injected CT26 (shNC; control) rep2

description:
Library name: shNC-2
Column name in CR.count.txt : shNC2


title: chr2_reverse_1D_D0_S4

description: Library name: chr2_reverse_1D_D0_S4