title: Patient1_Second ICI-IA_TCR

description:
Library name: Synovial fluid cells isolated from second arthritis irAE_patient 1_TCR
10X Genomic


title: subcutaneously injected CT26 (shNC; control) rep1

status: Public on Jul 25 2026

type: SRA

city: Seoul

first: Seung-Pyo

last: Hong

address: 103 Daehak-ro

country: South Korea

institute: Seoul national university

description:
Library name: shNC-1
Column name in CR.count.txt : shNC1

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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

tag: tissue

value: Colon

tag: cell line

tag: cell type

value: Colon adenocarcinoma

tag: treatment

value: shNC; control


title: chr2_reverse_1D_D0_S3

city: Shenzhen

first: zengqi

last: wen

state: Guangdong

address: No. 66 Gongchang Road, Guangming District

department: Zhongshan School of Medicine

country: China

institute: Sun Yat-sen University Shenzhen Campus

description: Library name: chr2_reverse_1D_D0_S3

library_source: genomic

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.

molecule: genomic DNA

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

tag: genotype


title: Gene expression of 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

country: USA

institute: Indiana University

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

library_source: transcriptomic single cell

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

organism: Homo sapiens

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: Patient1_First ICI-IA_TCR

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 first arthritis irAE_patient 1_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

molecule: polyA RNA

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

tag: Sex

value: male

tag: age

value: 60-80 years old


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

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


title: sgAnkrd11_3, D5

city: Beijing

first: Wei

last: Xu

address: No. 3, 1 Beichengxi West Road, Chaoyang District, Beijing 100020, China

institute: Institute of Microbiology, Chinese Academy of Sciences

description: Library name: H3K27ac_sgAnkrd11_3

data_processing:
Run FastQC and MultiQC for raw data quality control
Perform adapter trimming with Trimmomatic (ILLUMINACLIP:adapter.fa:2:30:10:8:true; HEADCROP:9; SLIDINGWINDOW:4:15; MINLEN:36)
Align reads to mm39 genome using HISAT2
Process BAM files with SAMtools (-f 2; -q 30; grep -v chrM)
Merge biological replicates, generate BigWig files with bamCoverage
Assembly: mm39
Supplementary files format and content: Bw files store genome-wide coverage information for each sample
Library strategy: CUT&Tag

source_name: Spleen and pLN

extract_protocol:
100,000 cells were bound to concanavalin A-coated magnetic beads, sequentially incubated with H3K27ac primary antibody overnight at 4°C, goat anti-rabbit secondary antibody for 1 hour at room temperature, and then treated with pA/G-Tn5 transposase complex for 1 hour at room temperature. Tagmentation was initiated at 37°C for 1 hour, terminated with SDS, and DNA fragments were purified using magnetic beads.
DNA libraries for Cut&Tag assays were prepared using Hyperactive Universal CUT&Tag Assay Kit following manufacturer's protocols

value: Spleen and pLN

value: mouse primary cells

value: CD8+ T cells

value: Ankrd11 KO


title: chr2_reverse_1D_D0_S2

description: Library name: chr2_reverse_1D_D0_S2


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

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


title: sgAnkrd11_2, D5

description: Library name: H3K27ac_sgAnkrd11_2


title: Patient6_OA_GEX

description:
Library name: Synovial fluid cells isolated from Osteoarthritis_patient 6_GEX
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

value: female


title: chr2_reverse_1D_D0_S1

description: Library name: chr2_reverse_1D_D0_S1


title: Patient5_OA_GEX

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


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

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


title: 2G_D9_S4_rep2

description: Library name: 2G_D9_S4_rep2

value: Dox(1μg/mL) 9days


title: sgNTC_3, D5

description: Library name: H3K27ac_sgNTC_3

value: WT


title: Patient4_OA_GEX

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

value: 40-60 years old


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

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


title: 2G_D9_S3_rep2

description: Library name: 2G_D9_S3_rep2


title: sgNTC_2, D5

description: Library name: H3K27ac_sgNTC_2


title: Patient3_Second ICI-IA_GEX

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


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

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


title: CUT&TAG_sgAnkrd11, D5

description:
Library name: sgAnkrd11
Ankrd11 KO

data_processing:
Run FastQC and MultiQC for raw data quality control
Perform adapter trimming with Trimmomatic (ILLUMINACLIP:adapter.fa:2:30:10:8:true; HEADCROP:9; SLIDINGWINDOW:4:15; MINLEN:36)
Align reads to mm10 genome using HISAT2
Process BAM files with SAMtools (-f 2; -q 30; grep -v chrM)
Merge biological replicates, generate BigWig files with bamCoverage
Assembly: mm10
Supplementary files format and content: Bw files store genome-wide coverage information for each sample
Library strategy: CUT&Tag


title: Patient3_First ICI-IA_GEX

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


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

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


title: 2G_D9_S2_rep2

description: Library name: 2G_D9_S2_rep2


title: 2G_D9_S1_rep2

description: Library name: 2G_D9_S1_rep2


title: Patient2_Second ICI-IA_GEX

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


title: CUT&TAG_sgNTC, D5

description:
Library name: sgNTC
Control


title: sgAnkrd11, D5, rep2

description:
Library name: sgAnkrd11_2
Ankrd11 KO

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC Genomic Workbench (parameter- Quality limit:0,05)
Trimmed sequence reads were mapped to mm10 using CLC Genomic Workbench (Parameters-mismatch cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC Genomic Workbench
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific). 1μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacturer's protocols


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

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


title: 2G_D9_S4_rep1

description: Library name: 2G_D9_S4_rep1


title: Patient2_First ICI-IA_GEX

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


title: PvPBSS4

city: Riverside

first: Caroline

last: Roper

state: CA

address: 900 University avenue

institute: University of California, Riverside

description: Library name: 80_S15_R1_001_SE

data_processing:
Illumina reads were quality-filtered using HTStream. FastQC and MultiQC were used to verify the quality of the remaining reads. STAR was used to align trimmed sequences to the reference genome of V. vinifera (Genome: PN40024 v1, v.V1)
Assembly: Genome: PN40024 v1, v.V
Supplementary files format and content: star counts

organism: Vitis vinifera

source_name: petiole

growth_protocol: For all in planta bioassays, V. vinifera cv. Cabernet Sauvignon one-bud cuttings were rooted in vermiculite, potted in UC soil mix and amended with 5 g of controlled-release fertilizer (Scotts Osmocote Classic, N-P-K: 14-14-14). Vines were propagated in the greenhouse and trained vertically as a single shoot of approximately 6 feet tall.

extract_protocol:
The petioles of three plant replicates of a given treatment were pooled to yield one biological replicate (total of four biological replicate cDNA libraries). RNA extraction and cDNA preparation were performed as in Rapicavoli et al. (2018).
The cDNA libraries were sequenced using Illumina HiSeq 4000 sequences (DNA Technologies Core, University of California, Davis, CA, USA) as single-end 100-bp reads (Illumina).

treatment_protocol: P. viridiflava, A. vitis and PsJN were harvested from solid medium and suspended in sterile 1X PBS and adjusted to an OD600nm=0.25. For each treatment, grapevines were inoculated by droplet puncture with 10 µL of either P. viridiflava, A. vitis or PsJN on each side of the cane between the first and second node above the soil (Hill and Purcell 1995). Negative control plants were pre-treated with 1X PBS only. Plants were then challenge-inoculated with X. fastidiosa either 1 or 7 days after pre-treatment with an individual biocontrol agent.

value: petiole

tag: cultivar

value: Cabernet Sauvignon

tag: location

value: Systemic

tag: challenge

value: PBS

value: PV

tag: batch


title: sgAnkrd11, D5, rep1

description:
Library name: sgAnkrd11_1
Ankrd11 KO


title: Patient1_Second ICI-IA_GEX

description:
Library name: Synovial fluid cells isolated from second arthritis irAE_patient 1_GEX
10X Genomic

value: knee joint


title: PvPBSS3

description: Library name: 79_S16_R1_001_SE


title: 2G_D9_S3_rep1

description: Library name: 2G_D9_S3_rep1

value: Inner cell mass

value: embryonic stem cell


title: sgNTC, D5, rep2

description:
Library name: sgNTC_2
Control


title: 2G_D9_S2_rep1

description: Library name: 2G_D9_S2_rep1


title: sgNTC, D5, rep1

description:
Library name: sgNTC_1
Control


title: PvPBSS2

description: Library name: 78_S15_R1_001_SE


title: 2G_D9_S1_rep1

description: Library name: 2G_D9_S1_rep1


title: Patient1_First ICI-IA_GEX

description:
Library name: Synovial fluid cells isolated from first arthritis irAE_patient 1_GEX
10X Genomic

value: Synovial fluid cell

value: male

value: 60-80 years old


title: SW48(WT), Input

description: Library name: W3-Input

data_processing:
Raw reads were trimmed using Trimmomatic and aligned against the GRCh38 human genome by Bowtie2 (v2.5.1).
METTL3 and TEAD4 peaks were detected by MACS3 (v3.0.0b1).
Assembly: GRCh38
Supplementary files format and content: narrowPeak (except for Input sample)

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature, and the reaction was quenched with 0.125 M glycine. DNA was purified using the ChIP DNA Clean & Concentrator kit (D5205; Zymo Research).
Purified DNA was subjected to ChIP-qPCR analysis or prepared for sequencing using the NEBNext® Ultra™ II DNA Library Prep Kit (E7645S; NEB).

value: Colon

value: Colorectal adenocarcinoma

tag: sample type

value: input


title: PvPBSS1

description: Library name: 77_S14_R1_001_SE


title: sgAnkrd11, D5

description:
Library name: sgAnkrd11
Ankrd11 KO

data_processing:
Run FastQC and MultiQC for raw data quality control
Perform adapter trimming with Trimmomatic (ILLUMINACLIP:adapter.fa:2:30:10:8:true; HEADCROP:9; SLIDINGWINDOW:4:15; MINLEN:36)
Align reads to mm10 genome using HISAT2
Process BAM files with SAMtools (-f 2; -q 30; grep -v chrM)
Merge biological replicates, generate BigWig files with bamCoverage(--binSize 50)
Assembly: mm10
Supplementary files format and content: Bw files store genome-wide coverage information for each sample

extract_protocol:
50,000 cells per library were incubated with Lysis Buffer to lyse cellular membranes. A tagmentation mix containing Tn5 transposome was added and incubated at 37°C for 30 min, followed by Stop Buffer treatment to terminate the reaction. Fragmented DNA was purified using ATAC DNA Extract Beads.
DNA libraries for ATAC-seq were prepared using Hyperactive ATAC-Seq Library Prep Kit following manufacturer's protocols

value: Spleen and pLN

value: mouse primary cells

value: CD8+ T cells

value: Ankrd11 KO


title: 2G_D0_S4_rep1

description: Library name: 2G_D0_S4_rep1


title: SW48(WT), ChIP (TEAD4), rep 3

description: Library name: W3-TEAD4-3

value: ChIP (TEAD4)


title: ACHXfS4

description: Library name: 76_S13_R1_001_SE

value: petiole

value: Cabernet Sauvignon

value: Systemic

value: Xf

value: ACH


title: sgNTC, D5

description:
Library name: sgNTC
Control

value: WT


title: 2G_D0_S3_rep1

description: Library name: 2G_D0_S3_rep1

value: Inner cell mass

value: embryonic stem cell


title: CasTuner XO sgXist ctrl Day4 Rep3

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: XO_sgXist_ctrl_D4_Rep3
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 (CAST chrX)

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

tag: timepoint

value: Differentiation Day 4


title: SW48(WT), ChIP (TEAD4), rep 2

description: Library name: W3-TEAD4-2

value: Colon

value: Colorectal adenocarcinoma


title: ACHXfS3

description: Library name: 75_S13_R1_001_SE


title: 2G_D0_S2_rep1

description: Library name: 2G_D0_S2_rep1


title: SW48(WT), ChIP (TEAD4), rep 1

description: Library name: W3-TEAD4-1


title: ACHXfS2

description: Library name: 74_S14_R1_001_SE


title: CasTuner XO sgXist ctrl Day4 Rep2

description:
Library name: XO_sgXist_ctrl_D4_Rep2
500nM dTAG


title: 2G_D0_S1_rep1

description: Library name: 2G_D0_S1_rep1


title: ACHXfS1

description: Library name: 73_S13_R1_001_SE


title: CasTuner XO sgXist ctrl Day4 Rep1

description:
Library name: XO_sgXist_ctrl_D4_Rep1
500nM dTAG


title: HPF cell, TGFB, 72 hrs, LIGHT, 24 hrs, rep3

city: La Jolla

first: Michael

last: Croft

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

description: Library name: 230428_NG_Sample_30

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.1.2
Filtered reads were mapped against the human GRCh38 reference using STAR v2.6.1
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using FeatureCount v1.6.5 (“union” option) and features with 0 counts across all samples were removed
Assembly: GRCh38
Supplementary files format and content: tsv counts matrix with rows as genes and columns as samples

source_name: Lung

growth_protocol: Human pulmonary fibroblasts were cultured in fibroblast media, serum starved prior  cytokine treatment

extract_protocol:
Zymo Direct-zol
NEB mRNA Directional

treatment_protocol: Human pulmonary fibroblasts (HPF) stimulated with 50 ng/ml LIGHT, 25 ng/ml IL-13, and 100 ng/ml IL-17A and in combination of IL13 or Il17A with LIGHT. HPF were also pretreated with 5 ng/ml of TGFb followed by 50 ng/ml LIGHT treatment.

value: Lung

value: HPF

value: Fibroblasts

value: TGFB 72 hrs followed by LIGHT 24 hrs

value: batch 1


title: 12E_D21_S4_rep2

description: Library name: 12E_D21_S4_rep2

value: Dox(1μg/mL) 21days Puromycin (1μg/mL) 4days


title: HPF cell, TGFB, 72 hrs, LIGHT, 24 hrs, rep2

description: Library name: 230428_NG_Sample_29


title: ACHXfL4

description: Library name: 72_S13_R1_001_SE

value: petiole

value: Cabernet Sauvignon

value: Local

value: Xf


title: 12E_D21_S3_rep2

description: Library name: 12E_D21_S3_rep2

value: Inner cell mass

value: embryonic stem cell


title: CasTuner XO sgXist KD Day4 Rep3

description:
Library name: XO_sgXist_KD_D4_Rep3
0nM dTAG

value: Embryonic stem cells

value: CAST x C57BL/6 (CAST chrX)

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


title: HPF cell, TGFB, 72 hrs, LIGHT, 24 hrs, rep1

description: Library name: 230428_NG_Sample_28


title: ACHXfL3

description: Library name: 71_S12_R1_001_SE

value: ACH


title: CasTuner XO sgXist KD Day4 Rep2

description:
Library name: XO_sgXist_KD_D4_Rep2
0nM dTAG

value: Differentiation Day 4


title: HPF cell, TGFB, 72 hrs, rep3

description: Library name: 230428_NG_Sample_27

value: Lung

value: TGFB 72 hrs


title: 12E_D21_S2_rep2

description: Library name: 12E_D21_S2_rep2


title: ACHXfL2

description: Library name: 70_S11_R1_001_SE


title: CasTuner XO sgXist KD Day4 Rep1

description:
Library name: XO_sgXist_KD_D4_Rep1
0nM dTAG


title: 12E_D21_S1_rep2

description: Library name: 12E_D21_S1_rep2


title: HPF cell, TGFB, 72 hrs, rep2

description: Library name: 230428_NG_Sample_26

value: HPF

value: Fibroblasts


title: ACHXfL1

description: Library name: 69_S11_R1_001_SE


title: CasTuner XX sgTsix KD Day4 Rep2

description:
Library name: XX_sgTsix_KD_D4_Rep2
0nM dTAG

value: CAST x C57BL/6


title: 12E_D15_S4_rep2

description: Library name: 12E_D15_S4_rep2

value: Dox(1μg/mL) 15days Puromycin (1μg/mL) 4days


title: HPF cell, TGFB, 72 hrs, rep1

description: Library name: 230428_NG_Sample_25

value: batch 1


title: PBSXfS4

description: Library name: 68_S10_R1_001_SE

value: petiole

value: Cabernet Sauvignon

value: Systemic

value: PBS


title: CasTuner XX sgXist ctrl Day4 Rep3

description:
Library name: XX_sgXist_ctrl_D4_Rep3
500nM dTAG

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


title: PBSXfS3

description: Library name: 67_S9_R1_001_SE

value: Xf


title: HPF cell, IL17A, 72 hrs, LIGHT, 24 hrs, rep3

description: Library name: 231107_NG_Sample_18

value: IL17A 72 hrs followed by LIGHT 24 hrs


title: 12E_D15_S3_rep2

description: Library name: 12E_D15_S3_rep2

value: Inner cell mass

value: embryonic stem cell


title: 12E_D15_S2_rep2

description: Library name: 12E_D15_S2_rep2


title: F121.9 DKO Day4 Rep4

description: Library name: DKO_D4_Rep4

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: Embryonic stem cells

value: Differentiation by 2i/LIF withdrawal

value: Differentiation Day 4


title: PBSXfS2

description: Library name: 66_S9_R1_001_SE


title: HPF cell, IL17A, 72 hrs, LIGHT, 24 hrs, rep2

description: Library name: 231107_NG_Sample_17

value: Lung

value: HPF


title: F121.9 DKO Day4 Rep3

description: Library name: DKO_D4_Rep3


title: HPF cell, IL17A, 72 hrs, LIGHT, 24 hrs, rep1

description: Library name: 231107_NG_Sample_16

value: Fibroblasts


title: 12E_D15_S1_rep2

description: Library name: 12E_D15_S1_rep2

value: Dox(1μg/mL) 15days Puromycin (1μg/mL) 4days


title: PBSXfS1

description: Library name: 65_S8_R1_001_SE


title: F121.9 DKO Day4 Rep2

description: Library name: DKO_D4_Rep2


title: 12E_D9_S4_rep2

description: Library name: 12E_D9_S4_rep2

value: Dox(1μg/mL) 9days Puromycin (1μg/mL) 4days


title: HPF cell, IL17A, 72 hrs, rep3

description: Library name: 231107_NG_Sample_15

value: IL17A 72 hrs


title: PBSXfL4

description: Library name: 64_S7_R1_001_SE

value: petiole

value: Cabernet Sauvignon

value: Local


title: 12E_D9_S3_rep2

description: Library name: 12E_D9_S3_rep2


title: F121.9 RNF12-KO Day4 Rep4

description: Library name: RNF12-KO_D4_Rep4


title: HPF cell, IL17A, 72 hrs, rep2

description: Library name: 231107_NG_Sample_14


title: PBSXfL3

description: Library name: 63_S7_R1_001_SE

value: PBS


title: F121.9 RNF12-KO Day4 Rep3

description: Library name: RNF12-KO_D4_Rep3


title: 12E_D9_S2_rep2

description: Library name: 12E_D9_S2_rep2


title: HPF cell, IL17A, 72 hrs, rep1

description: Library name: 231107_NG_Sample_13


title: PBSXfL2

description: Library name: 62_S6_R1_001_SE

value: Xf


title: F121.9 RNF12-KO Day4 Rep2

description: Library name: RNF12-KO_D4_Rep2


title: HPF cell, IL13, 72 hrs, LIGHT, 24 hrs, rep3

description: Library name: 231107_NG_Sample_12

value: IL13 72hrs followed by LIGHT 24hrs


title: 12E_D9_S1_rep2

description: Library name: 12E_D9_S1_rep2

value: Inner cell mass


title: PBSXfL1

description: Library name: 61_S6_R1_001_SE


title: F121.9 WT Day4 Rep4

description: Library name: WT_D4_Rep4


title: 12E_D2_S4_rep2

description: Library name: 12E_D2_S4_rep2

value: embryonic stem cell

value: Dox(1μg/mL) 2days


title: HPF cell, IL13, 72 hrs, LIGHT, 24 hrs, rep2

description: Library name: 231107_NG_Sample_11


title: 12E_D2_S3_rep2

description: Library name: 12E_D2_S3_rep2


title: PsJNPBSS3

description: Library name: 59_S4_R1_001_SE

value: Systemic

value: PsJN


title: F121.9 WT Day4 Rep2

description: Library name: WT_D4_Rep2

value: Embryonic stem cells

value: Differentiation by 2i/LIF withdrawal

value: Differentiation Day 4


title: F121.9 WT Day4 Rep3

description: Library name: WT_D4_Rep3


title: 12E_D2_S2_rep2

description: Library name: 12E_D2_S2_rep2


title: PsJNPBSS2

description: Library name: 58_S5_R1_001_SE


title: HPF cell, IL13, 72 hrs, rep3

description: Library name: 231107_NG_Sample_9

value: Lung

value: HPF

value: Fibroblasts

value: IL13 72 hrs


title: XXdXIC ctrl Day2 Rep3

description: Library name: H3K9me3_XXdXIC_noDox_D2_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.

value: TX1072 XXdXIC-Cast

value: female

value: CAST x C57BL/6

value: Differentiation Day 2

tag: antibody


title: HPF cell, IL13, 72 hrs, LIGHT, 24 hrs, rep1

description: Library name: 231107_NG_Sample_10

value: IL13 72hrs followed by LIGHT 24hrs


title: 12E_D2_S1_rep2

description: Library name: 12E_D2_S1_rep2

value: Inner cell mass


title: HPF cell, IL13, 72 hrs, rep2

description: Library name: 231107_NG_Sample_8


title: PsJNPBSS1

description: Library name: 57_S4_R1_001_SE

value: petiole

value: Cabernet Sauvignon

value: PBS


title: 12E_D0_S4_rep2

description: Library name: 12E_D0_S4_rep2

value: embryonic stem cell


title: XXdXIC ctrl Day2 Rep2

description: Library name: H3K9me3_XXdXIC_noDox_D2_Rep2

value: Embryonic stem cells


title: HPF cell, IL13, 72 hrs, rep1

description: Library name: 231107_NG_Sample_7


title: 12E_D0_S3_rep2

description: Library name: 12E_D0_S3_rep2


title: XXdXIC ctrl Day2 Rep1

description: Library name: H3K9me3_XXdXIC_noDox_D2_Rep1

value: Differentiation by 2i/LIF withdrawal


title: PsJNXfS4

description: Library name: 56_S2_R1_001_SE

value: Systemic

value: Xf

value: PsJN


title: PsJNXfS3

description: Library name: 55_S6_R1_001_SE


title: HPF cell, PBS, 72hrs, LIGHT, 24 hrs, rep3

description: Library name: 231107_NG_Sample_6

value: Lung

value: HPF

value: Fibroblasts

value: PBS 72 hrs and LIGHT 24 hrs


title: XXdXIC XistOverexpression Day2 Rep3

description: Library name: H3K9me3_XXdXIC_Dox_D2_Rep3

value: TX1072 XXdXIC-Cast

value: female

value: CAST x C57BL/6

value: Doxycycline, Differentiation by 2i/LIF withdrawal


title: 12E_D0_S2_rep2

description: Library name: 12E_D0_S2_rep2

value: Inner cell mass


title: HPF cell, PBS, 72hrs, LIGHT, 24 hrs, rep2

description: Library name: 231107_NG_Sample_5


title: PsJNXfS2

description: Library name: 54_S2_R1_001_SE

value: petiole

value: Cabernet Sauvignon


title: XXdXIC XistOverexpression Day2 Rep2

description: Library name: H3K9me3_XXdXIC_Dox_D2_Rep2

value: Differentiation Day 2


title: 12E_D0_S1_rep2

description: Library name: 12E_D0_S1_rep2

value: embryonic stem cell


title: PsJNXfS1

description: Library name: 53_S1_R1_001_SE


title: HPF cell, PBS, 72hrs, LIGHT, 24 hrs, rep1

description: Library name: 231107_NG_Sample_4


title: XXdXIC XistOverexpression Day2 Rep1

description: Library name: H3K9me3_XXdXIC_Dox_D2_Rep1

value: Embryonic stem cells


title: HPF cell, PBS, 96 hrs, rep3

description: Library name: 231107_NG_Sample_3

value: PBS 96 hrs


title: 12E_D21_S4_rep1

description: Library name: 12E_D21_S4_rep1

value: Dox(1μg/mL) 21days Puromycin (1μg/mL) 4days


title: PsJNXfL4

description: Library name: 52_S4_R1_001_SE

value: Local

value: Xf

value: PsJN


title: XXdXIC ctrl ESC Rep3

description: Library name: H3K9me3_XXdXIC_noDox_ESC_Rep3

value: ESCs


title: 12E_D21_S3_rep1

description: Library name: 12E_D21_S3_rep1


title: PsJNXfL3

description: Library name: 51_S3_R1_001_SE


title: HPF cell, PBS, 96 hrs, rep2

description: Library name: 231107_NG_Sample_2

value: Lung

value: HPF

value: Fibroblasts


title: XXdXIC ctrl ESC Rep2

description: Library name: H3K9me3_XXdXIC_noDox_ESC_Rep2

value: TX1072 XXdXIC-Cast

value: female

value: CAST x C57BL/6


title: 12E_D21_S2_rep1

description: Library name: 12E_D21_S2_rep1

value: Inner cell mass


title: HPF cell, PBS, 96 hrs, rep1

description: Library name: 231107_NG_Sample_1


title: 12E_D21_S1_rep1

description: Library name: 12E_D21_S1_rep1


title: XXdXIC ctrl ESC Rep1

description: Library name: H3K9me3_XXdXIC_noDox_ESC_Rep1


title: PsJNXfL2

description: Library name: 50_S2_R1_001_SE

value: petiole

value: Cabernet Sauvignon


title: HPF cell, LIGHT and IL17A, 24 hrs, rep3

description: Library name: 230428_NG_Sample_18

value: IL17A and LIGHT 24 hrs


title: XXdXIC XistOverexpression ESC Rep3

description: Library name: H3K9me3_XXdXIC_Dox_ESC_Rep3

value: Embryonic stem cells

value: Doxycycline


title: PsJNXfL1

description: Library name: 49_S1_R1_001_SE


title: 12E_D15_S4_rep1

description: Library name: 12E_D15_S4_rep1

value: embryonic stem cell

value: Dox(1μg/mL) 15days Puromycin (1μg/mL) 4days


title: HPF cell, LIGHT and IL17A, 24 hrs, rep2

description: Library name: 230428_NG_Sample_17


title: PFPBSL4

description: Library name: 48_S20_R1_001_SE

value: Local

value: PBS

value: PF


title: XXdXIC XistOverexpression ESC Rep2

description: Library name: H3K9me3_XXdXIC_Dox_ESC_Rep2

value: ESCs


title: 12E_D15_S3_rep1

description: Library name: 12E_D15_S3_rep1


title: HPF cell, LIGHT and IL17A, 24 hrs, rep1

description: Library name: 230428_NG_Sample_16

value: Lung

value: HPF


title: PFPBSL3

description: Library name: 47_S19_R1_001_SE


title: XXdXIC XistOverexpression ESC Rep1

description: Library name: H3K9me3_XXdXIC_Dox_ESC_Rep1

value: TX1072 XXdXIC-Cast


title: 12E_D15_S2_rep1

description: Library name: 12E_D15_S2_rep1


title: HPF cell, IL17A, 24 hrs, rep3

description: Library name: 230428_NG_Sample_15

value: Fibroblasts

value: IL17A 24 hrs


title: PFPBSL2

description: Library name: 46_S20_R1_001_SE


title: 12E_D15_S1_rep1

description: Library name: 12E_D15_S1_rep1

value: Inner cell mass


title: HPF cell, IL17A, 24 hrs, rep2

description: Library name: 230428_NG_Sample_14


title: CasTuner XX sgXist ctrl  Day4 Rep3

description:
Library name: H3K9me3_XX_sgXist_ctrl_D4_Rep3
500nM dTAG

value: female

value: CAST x C57BL/6

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

value: Differentiation Day 4


title: HPF cell, IL17A, 24 hrs, rep1

description: Library name: 230428_NG_Sample_13


title: PFPBSL1

description: Library name: 45_S20_R1_001_SE

value: petiole

value: Cabernet Sauvignon


title: ACHPBSS4

description: Library name: 44_S18_R1_001_SE

value: Systemic

value: ACH


title: 12E_D9_S4_rep1

description: Library name: 12E_D9_S4_rep1

value: embryonic stem cell

value: Dox(1μg/mL) 9days Puromycin (1μg/mL) 4days


title: CasTuner XX sgXist ctrl  Day4 Rep1

description:
Library name: H3K9me3_XX_sgXist_ctrl_D4_Rep1
500nM dTAG

value: Embryonic stem cells


title: CasTuner XX sgXist ctrl  Day4 Rep2

description:
Library name: H3K9me3_XX_sgXist_ctrl_D4_Rep2
500nM dTAG


title: HPF cell, LIGHT and IL13, 24 hrs, rep3

description: Library name: 230428_NG_Sample_12

value: Lung

value: IL13 and LIGHT 24 hrs


title: 12E_D9_S3_rep1

description: Library name: 12E_D9_S3_rep1


title: ACHPBSS3

description: Library name: 43_S19_R1_001_SE

value: PBS


title: CasTuner XX sgXist KD  Day4 Rep3

description:
Library name: H3K9me3_XX_sgXist_KD_D4_Rep3
0nM dTAG

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


title: 12E_D9_S2_rep1

description: Library name: 12E_D9_S2_rep1


title: HPF cell, LIGHT and IL13, 24 hrs, rep2

description: Library name: 230428_NG_Sample_11

value: HPF

value: Fibroblasts


title: ACHPBSS2

description: Library name: 42_S19_R1_001_SE


title: CasTuner XX sgXist KD  Day4 Rep2

description:
Library name: H3K9me3_XX_sgXist_KD_D4_Rep2
0nM dTAG

value: female


title: 12E_D9_S1_rep1

description: Library name: 12E_D9_S1_rep1

value: Inner cell mass


title: ACHPBSS1

description: Library name: 41_S20_R1_001_SE


title: HPF cell, LIGHT and IL13, 24 hrs, rep1

description: Library name: 230428_NG_Sample_10


title: 12E_D2_S3_rep1

description: Library name: 12E_D2_S3_rep1

value: Dox(1μg/mL) 2days


title: CasTuner XX sgXist KD  Day4 Rep1

description:
Library name: H3K9me3_XX_sgXist_KD_D4_Rep1
0nM dTAG

value: CAST x C57BL/6

value: Differentiation Day 4


title: HPF cell, IL13 24 hrs, rep3

description: Library name: 230428_NG_Sample_9

value: IL13 24 hrs


title: ACHPBSL4

description: Library name: 40_S18_R1_001_SE

value: petiole

value: Cabernet Sauvignon

value: Local


title: CasTuner XX sgTsix ctrl  Day4 Rep3

description:
Library name: H3K9me3_XX_sgTsix_ctrl_D4_Rep3
500nM dTAG

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


title: 12E_D2_S2_rep1

description: Library name: 12E_D2_S2_rep1

value: embryonic stem cell


title: ACHPBSL3

description: Library name: 39_S19_R1_001_SE

value: ACH


title: HPF cell, IL13, 24 hrs, rep2

description: Library name: 230428_NG_Sample_8

value: Lung


title: CasTuner XX sgTsix ctrl  Day4 Rep2

description:
Library name: H3K9me3_XX_sgTsix_ctrl_D4_Rep2
500nM dTAG

value: Embryonic stem cells


title: 12E_D2_S1_rep1

description: Library name: 12E_D2_S1_rep1


title: HPF cell, IL13, 24 hrs, rep1

description: Library name: 230428_NG_Sample_7


title: ACHPBSL2

description: Library name: 38_S17_R1_001_SE

value: PBS


title: CasTuner XX sgTsix ctrl  Day4 Rep1

description:
Library name: H3K9me3_XX_sgTsix_ctrl_D4_Rep1
500nM dTAG


title: 12E_D0_S4_rep1

description: Library name: 12E_D0_S4_rep1


title: HPF cell, LIGHT, 24 hrs,rep3

description: Library name: 230428_NG_Sample_6

value: HPF

value: LIGHT 24 hrs


title: ACHPBSL1

description: Library name: 37_S18_R1_001_SE


title: 12E_D0_S3_rep1

description: Library name: 12E_D0_S3_rep1


title: CasTuner XX sgTsix KD  Day4 Rep3

description:
Library name: H3K9me3_XX_sgTsix_KD_D4_Rep3
0nM dTAG

value: female

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


title: HPF cell, LIGHT, 24 hrs, rep2

description: Library name: 230428_NG_Sample_5

value: Fibroblasts


title: PFXfS4

description: Library name: 36_S17_R1_001_SE

value: Systemic

value: Xf

value: PF


title: 12E_D0_S2_rep1

description: Library name: 12E_D0_S2_rep1

value: Inner cell mass


title: CasTuner XX sgTsix KD  Day4 Rep2

description:
Library name: H3K9me3_XX_sgTsix_KD_D4_Rep2
0nM dTAG

value: CAST x C57BL/6

value: Differentiation Day 4


title: HPF cell, LIGHT, 24 hrs, rep1

description: Library name: 230428_NG_Sample_4


title: CasTuner XX sgTsix KD  Day4 Rep1

description:
Library name: H3K9me3_XX_sgTsix_KD_D4_Rep1
0nM dTAG


title: PFXfS3

description: Library name: 35_S16_R1_001_SE

value: petiole

value: Cabernet Sauvignon


title: 12E_D0_S1_rep1

description: Library name: 12E_D0_S1_rep1

value: embryonic stem cell


title: HPF cell, PBS, 24 hrs, rep3

description: Library name: 230428_NG_Sample_3

value: Lung

value: PBS 24 hrs


title: jurkat replicate 3

status: Public on Jul 26 2026

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: jurkat_3
Raw junction counts & normalized bigwig per capture point

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

source_name: Blood

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

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

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

value: Blood

value: Jurkat

value: WT


title: PFXfS2

description: Library name: 34_S17_R1_001_SE


title: F121.9 RNF12-KO Day4 Rep4

description: Library name: H3K9me3_RNF12-KO_D4_Rep4

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: Embryonic stem cells

value: female

value: Differentiation by 2i/LIF withdrawal


title: Repliseq_10F_S4

description: Library name: Repliseq_10F_S4


title: HPF cell, PBS, 24 hrs, rep2

description: Library name: 230428_NG_Sample_2

value: HPF

value: Fibroblasts


title: PFXfS1

description: Library name: 33_S18_R1_001_SE

value: Systemic

value: Xf

value: PF


title: F121.9 RNF12-KO Day4 Rep3

description: Library name: H3K9me3_RNF12-KO_D4_Rep3

value: Differentiation Day 4


title: Repliseq_10F_S3

description: Library name: Repliseq_10F_S3

value: Inner cell mass


title: HPF cell, PBS, 24 hrs, rep1

description: Library name: 230428_NG_Sample_1


title: PBSPBSS4

description: Library name: 32_S17_R1_001_SE

value: petiole

value: Cabernet Sauvignon

value: PBS


title: F121.9 RNF12-KO Day4 Rep2

description: Library name: H3K9me3_RNF12-KO_D4_Rep2


title: Repliseq_10F_S2

description: Library name: Repliseq_10F_S2

value: embryonic stem cell


title: SW48(G12D/+), Input

description: Library name: G12D-Input

data_processing:
Raw reads were trimmed using Trimmomatic and aligned against the GRCh38 human genome by Bowtie2 (v2.5.1).
METTL3 and TEAD4 peaks were detected by MACS3 (v3.0.0b1).
Assembly: GRch38
Supplementary files format and content: narrowPeak (except for Input sample)

value: Colon

value: Colorectal adenocarcinoma


title: PBSPBSS3

description: Library name: 31_S16_R1_001_SE


title: F121.9 DKO Day4 Rep4

description: Library name: H3K9me3_DKO_D4_Rep4


title: Repliseq_10F_S1

description: Library name: Repliseq_10F_S1


title: SW48(G12D/+), ChIP (TEAD4), rep 3

description: Library name: G12D-TEAD4-3


title: PBSPBSS2

description: Library name: 30_S14_R1_001_SE


title: F121.9 DKO Day4 Rep3

description: Library name: H3K9me3_DKO_D4_Rep3


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

description:
Library name: CHR0407
10X Genomics

data_processing:
Raw scRNA-seq data was aligned to the GRCm39 and processed using the 10X Genomics Cell Ranger (v9.0.1).
Ambient RNA was removed using scAR and doublets were filtered by Solo.
Low quality cells were filtered based on median absolute deviations (MAD) and following criteria : cell with < 1,000 unique molecular identifier (UMI) counts and > 20,000 UMI counts; < 200 genes and > 7,000 genes; > 10% of mitochondrial gene expression in UMI counts.
Assembly: GRCm39
Supplementary files format and content: Cellranger output (filtered_feature_bc_matrix) : barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

extract_protocol:
Follwing FACS & MACS sorting using CD45, cells washed and measured cell viability.
scRNA-seq libraries were generated using the Chromium GEM-X Single Cell 3’ Reagent Kit v4 (10X Genomics) following the manufacturer’s instructions. Briefly, single cells were encapsulated in gel beads in emulsion (GEMs), lysed, and subjected to RNA barcoding, reverse transcription, and PCR amplification. Library quality control was performed with an Agilent 2100 Bioanalyzer (Agilent Technologies) at the Genomic Medicine Institute Research Service Center, and sequencing was conducted on an Illumina NovaSeqX 10B instrument.

value: Colon adenocarcinoma


title: SW48(G12D/+), ChIP (TEAD4), rep 2

description: Library name: G12D-TEAD4-2


title: PBSPBSS1

description: Library name: 29_S16_R1_001_SE


title: F121.9 WT Day4 Rep4

description: Library name: H3K9me3_WT_D4_Rep4

value: Embryonic stem cells


title: subcutaneously injected CT26 (shMettl3 knockdown)

description:
Library name: CHR0406
10X Genomics


title: SW48(G12D/+), ChIP (TEAD4), rep 1

description: Library name: G12D-TEAD4-1


title: PBSPBSL4

description: Library name: 28_S15_R1_001_SE

value: Local


title: F121.9 WT Day4 Rep3

description: Library name: H3K9me3_WT_D4_Rep3

value: female

value: Differentiation by 2i/LIF withdrawal


title: subcutaneously injected CT26 (shNC; control)

description:
Library name: CHR0405
10X Genomics


title: PBSPBSL3

description: Library name: 27_S15_R1_001_SE


title: F121.9 WT Day4 Rep2

description: Library name: H3K9me3_WT_D4_Rep2


title: SW48(G12D/+), ChIP (METTL3), rep 3

description: Library name: G12D-METTL3-3


title: Liver, EtOH-fed, Hepatocyte-specific YAP overexpression, 3

city: Boston

first: Yuchen

last: Liu

state: Massachusetts

address: 188 Longwood Avenue, REB 514B

institute: Harvard school of dental medicine

description:
Library name: IonCode_0129
YAP_OE_EtOH_3

data_processing:
Thermo Fisher Torrent Suite V5.10 used for basecalling.
Thermo Fisher Torrent Suite V5.10 used for alignment.
Thermo Fisher ampliSeqRNA V5.10 in Torrent Suite V5.10 used for reads counting and data normalization.
Assembly: AmpliSeq_Mouse_Transcriptome_v1.fasta
Supplementary files format and content: processed_data_CPM.csv: Comma-Separated Values file includes normalized CPM values for each Sample.

source_name: Liver

extract_protocol:
Total RNA was isolated from cells or liver tissues using RNAzol Reagent or TRI Reagent (Sigma-Aldrich) according to the manufacturer’s instructions. cDNA was synthesized using the SuperScript™ VILO™ cDNA Synthesis Kit (Thermo Fisher Scientific).
Libraries were prepared using the Ion AmpliSeq™ Transcriptome Mouse Gene Expression Panel, Chef-Ready Kit on Ion Chef (Thermo Fisher Scientific) according to the manufacturer's instruction.

treatment_protocol: Hepatocyte-specific Yap knockout (Yap KO) was achieved injection of AAV-TBG-Cre (0.5 × 10¹¹ GC/mouse) into 8-week-old Yapfl/fl mice. Hepatocyte-specific YAP overexpression (YAP OE) was induced by retro-orbital injection of AAV-TBG-YAP-P2A-EGFP (2 × 10¹¹ GC/mouse) into 8-week-old Yapfl/fl mice.  Control mice received an dose of AAV-TBG-GFP (2 × 10¹¹ GC/mouse). 2 weeks after AAV injection, mice were subjected to a modified chronic-plus-binge ethanol feeding protocol, also known as the NIAAA model (Bertola et al., 2013). Briefly, mice were first acclimated to a Lieber–DeCarli control liquid diet (F1259SP, Bio-Serv) for 5 days. The ethanol-fed group was then switched to a Lieber–DeCarli ethanol liquid diet (F1258SP, Bio-Serv) and maintained on the diet for 4 weeks. At the end of the feeding period, ethanol-fed mice received a single oral gavage of ethanol (5 g/kg body weight, 33% v/v ethanol), whereas control mice received an isocaloric maltose-dextrin solution. Mice were euthanized 9 hours after gavage.

value: Liver

value: Yap fl/fl

value: AAV-TBG-YAP, EtOH-fed


title: SW48(G12D/+), ChIP (METTL3), rep 2

description: Library name: G12D-METTL3-2


title: PBSPBSL2

description: Library name: 26_S14_R1_001_SE


title: Liver, EtOH-fed, Hepatocyte-specific YAP overexpression, 2

description:
Library name: IonCode_0114
YAP_OE_EtOH_2


title: CasTuner sgZfp36l1 ctrl Day4 Rep3

description:
Library name: H3K9me3_sgZfp36l1_ctrl_D4_Rep3
500nM dTAG

value: CAST x C57BL/6

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


title: CasTuner sgZfp36l1 ctrl Day4 Rep2

description:
Library name: H3K9me3_sgZfp36l1_ctrl_D4_Rep2
500nM dTAG

value: Differentiation Day 4


title: Liver, EtOH-fed, Hepatocyte-specific YAP overexpression, 1

description:
Library name: IonCode_0106
YAP_OE_EtOH_1


title: SW48(G12D/+), ChIP (METTL3), rep 1

description: Library name: G12D-METTL3-1


title: SW48(WT) rep 2, Input

description: Library name: W3_Input

data_processing:
Raw reads were trimmed using Trimmomatic (v 0.39) and an in-house method after checking the quality of raw FASTQ files using FastQC (v0.11.9).
Trimmed reads were aligned against the GRCh38 human genome by STAR (v2.7.8a) and gene expression value quantified by RSEM (v1.3.3).
m6A peaks and differentially methylated peaks were identified by exomePeak2 (v.1.3.7) and RADAR (v0.2.4).
Assembly: GRCh38
Supplementary files format and content: exomepeak2 file (Mod.csv, except for Input smaple)
Library strategy: MeRIP-Seq

extract_protocol:
mRNA extracted by Dynabeads™ mRNA Purification Kit (61006, Thermo Fisher) was fragmented with RNA fragmentation reagent (AM8740, Thermo Fisher Scientific) at 94°C for 3 min and then 0.5 M EDTA was added immediately
The input RNA and purified m6A containing RNA were used as starting materials to construct libraries with SMARTer Stranded RNA-Seq Kit (634838, Takara-Clontech) according to the standard protocol


title: PFXfL4

description: Library name: 24_S12_R1_001_SE

value: petiole

value: Xf

value: PF


title: CasTuner sgZfp36l1 ctrl Day4 Rep1

description:
Library name: H3K9me3_sgZfp36l1_ctrl_D4_Rep1
500nM dTAG


title: SW48(WT) rep 2, MeRIP

description: Library name: W3_MeRIP


title: Liver, Pair-fed, Hepatocyte-specific YAP overexpression, 3

description:
Library name: IonCode_0128
YAP_OE_Pair_3

value: AAV-TBG-YAP, Pair-fed


title: PFXfL3

description: Library name: 23_S12_R1_001_SE

value: Cabernet Sauvignon


title: CasTuner sgZfp36l1 KD Day4 Rep3

description:
Library name: H3K9me3_sgZfp36l1_KD_D4_Rep3
0nM dTAG

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


title: Liver, Pair-fed, Hepatocyte-specific YAP overexpression, 2

description:
Library name: IonCode_0113
YAP_OE_Pair_2


title: PBSPBSL1

description: Library name: 25_S12_R1_001_SE

value: PBS


title: SW48(WT) rep 1, Input

description: Library name: W1_Input

value: Colon

value: Colorectal adenocarcinoma


title: PFXfL2

description: Library name: 22_S11_R1_001_SE

value: Local


title: CasTuner sgZfp36l1 KD Day4 Rep2

description:
Library name: H3K9me3_sgZfp36l1_KD_D4_Rep2
0nM dTAG

value: Embryonic stem cells

value: female


title: Liver, Pair-fed, Hepatocyte-specific YAP overexpression, 1

description:
Library name: IonCode_0105
YAP_OE_Pair_1

value: Liver

value: Yap fl/fl


title: SW48(WT) rep 1, MeRIP

description: Library name: W1_MeRIP


title: PFXfL1

description: Library name: 21_S10_R1_001_SE


title: Liver, EtOH-fed, Hepatocyte-specific Yap knockout, 3

description:
Library name: IonCode_0127
Yap_KO_EtOH_3

value: AAV-TBG-CRE, EtOH-fed


title: CasTuner sgZfp36l1 KD Day4 Rep1

description:
Library name: H3K9me3_sgZfp36l1_KD_D4_Rep1
0nM dTAG

value: CAST x C57BL/6


title: SW48(G12V/+), Input

description: Library name: G12V_Input


title: PsJNPBSS4

description: Library name: 60_S10_R1_001_SE

value: Systemic

value: PsJN


title: PFPBSS4

description: Library name: 20_S11_R1_001_SE

value: petiole


title: CasTuner sgZfp280c ctrl Day4 Rep3

description:
Library name: H3K9me3_sgZfp280c_ctrl_D4_Rep3
500nM dTAG

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

value: Differentiation Day 4


title: A1_1

city: Guangzhou

first: Yang

last: Ziqi

address: Jinsui Road

institute: Zhongshan opythalmic center

description: Library name: Sample4

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


title: RNA_mESC_Gabpa_12h_dTAG_rep2

first: Hang

last: Yang

state: Beijing

address: No.1 West Beichen Road,Chaoyang District

institute: CAS

description: Library name: RNA_mESC_Gabpa_12h_dTAG_rep2

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

source_name: cell line

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

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

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

value: cell line

value: mESCs

value: GabpadTAG/dTAG

value: treated with dTAG13 for 12 hours


title: EU_OMA_SUP,replicate2,scRNAseq

city: shanghai

first: yiqin

last: zhang

address: No. 910, Hengshan Rd

institute: International Peace Maternity and Child Health Hospital

description: 10x Genomics

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

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

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

value: Endometriosis


title: Liver, EtOH-fed, Hepatocyte-specific Yap knockout, 2

description:
Library name: IonCode_0112
Yap_KO_EtOH_2

value: Liver


title: PFPBSS3

description: Library name: 19_S10_R1_001_SE

value: Cabernet Sauvignon

value: PBS

value: PF


title: CasTuner sgZfp280c ctrl Day4 Rep2

description:
Library name: H3K9me3_sgZfp280c_ctrl_D4_Rep2
500nM dTAG

value: Embryonic stem cells

value: female

value: CAST x C57BL/6


title: Liver, EtOH-fed, Hepatocyte-specific Yap knockout, 1

description:
Library name: IonCode_0104
Yap_KO_EtOH_1

value: Yap fl/fl

value: AAV-TBG-CRE, EtOH-fed


title: SW48(G12V/+), MeRIP

description: Library name: G12V_MeRIP

value: Colon

value: Colorectal adenocarcinoma


title: PFPBSS2

description: Library name: 18_S9_R1_001_SE

value: petiole

value: Systemic


title: SW48(G12D/+), Input

description: Library name: G12D_Input


title: Liver, Pair-fed, Hepatocyte-specific Yap knockout, 3

description:
Library name: IonCode_0126
Yap_KO_Pair_3

value: AAV-TBG-CRE, Pair-fed


title: CasTuner sgZfp280c ctrl Day4 Rep1

description:
Library name: H3K9me3_sgZfp280c_ctrl_D4_Rep1
500nM dTAG

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

value: Differentiation Day 4


title: SW48(G12D/+), MeRIP

description: Library name: G12D_MeRIP


title: Liver, Pair-fed, Hepatocyte-specific Yap knockout, 2

description:
Library name: IonCode_0111
Yap_KO_Pair_2


title: CasTuner sgZfp280c KD Day4 Rep3

description:
Library name: H3K9me3_sgZfp280c_KD_D4_Rep3
0nM dTAG

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


title: PFPBSS1

description: Library name: 17_S8_R1_001_SE


title: HT tumor, ST14KO

city: Taipei

first: Yi-Lin

last: Chiu

address: No. 161, Sec. 6, Minquan E. Rd., Neihu Dist.

country: Taiwan

institute: National Defense Medical Center

description: Library name: Sample2

data_processing:
Raw sequencing reads were assessed for quality using FastQC. Adapter sequences and low-quality bases were trimmed using vendor-provided preprocessing workflows.
Transcript-level quantification was performed using Salmon (v1.10.0) and kallisto (v0.46.1), both employing lightweight mapping strategies (quasi-mapping for Salmon and pseudoalignment for kallisto).
Assembly: GRCh38
Supplementary files format and content: Expression values were reported as TPM (transcripts per million) and estimated counts. No read alignment to the genome was performed.

source_name: Tumor tissue

growth_protocol: Human HT B-cell lymphoma cells (1.5 × 10⁷), including wild type and ST14 knockout, were implanted subcutaneously into male CAnN.Cg-Foxn1nu/CrlNarl mice (4 weeks old).

extract_protocol:
Tumors were lysed in QIAzol Lysis Reagent(QIAGEN), and RNA purified with RNeasy Mini Kit (QIAGEN).
Total RNA (1 µg) was used for library construction. Poly(A)+ mRNA was isolated using oligo(dT) magnetic beads and fragmented using divalent cations at elevated temperature. First- and second-strand cDNA synthesis was performed using random primers. Double-stranded cDNA underwent end repair, A-tailing, and adaptor ligation. Size selection was performed using magnetic beads, followed by PCR amplification with indexed primers. Library preparation was performed by Genewiz on an Illumina NovaSeq 6000 platform using 2×150 bp paired-end mode.

treatment_protocol: Tumor size was monitored twice weekly; mice were euthanized if volumes exceeded 2000 mm³.

value: Tumor tissue

value: HT

value: B-cell lymphoma


title: PvXfL4

description: Library name: 16_S8_R1_001_SE

value: Cabernet Sauvignon

value: Local

value: Xf

value: PV


title: Liver, Pair-fed, Hepatocyte-specific Yap knockout, 1

description:
Library name: IonCode_0103
Yap_KO_Pair_1

value: Liver

value: Yap fl/fl


title: CasTuner sgZfp280c KD Day4 Rep2

description:
Library name: H3K9me3_sgZfp280c_KD_D4_Rep2
0nM dTAG

value: Embryonic stem cells

value: female

value: CAST x C57BL/6


title: Liver, EtOH-fed, control, 3

description:
Library name: IonCode_0131
Ctrl_EtOH_3

value: AAV-TBG-GFP, EtOH-fed


title: HT tumor, parental

description: Library name: Sample1

value: WT


title: CasTuner sgZfp280c KD Day4 Rep1

description:
Library name: H3K9me3_sgZfp280c_KD_D4_Rep1
0nM dTAG


title: N008 cells,siTOX 3

city: Shanghai

first: Luju

last: Jiang

state: State...

address: Dongchuan Road 800, Minhang, Shanghai, China

institute: Shanghai Jiaotong University

description: Library name: Sample21

data_processing:
CLC Genomics Workbench v11.0.1
Assembly: GRCh38 (hg38) from the Genome Reference Consortium
Supplementary files format and content: txt files include fpkm values for each sample

growth_protocol: N008 cell was maintained in primary Schwann cell media (iCell bioscience, Shanghai, China) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin according to ATCC protocols.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: human primary Schwann cell

value: TOX knockdown


title: PvXfL3

description: Library name: 15_S7_R1_001_SE

data_processing:
Illumina reads were quality-filtered using HTStream. FastQC and MultiQC were used to verify the quality of the remaining reads. STAR was used to align trimmed sequences to the reference genome of V. vinifera (Genome: PN40024 v1, v.V1)
Assembly: Genome: PN40024 v1, v.V
Supplementary files format and content: star counts

value: petiole


title: PvXfL2

description: Library name: 14_S6_R1_001_SE


title: Liver, EtOH-fed, control, 2

description:
Library name: IonCode_0115
Ctrl_EtOH_2


title: TX-Maged1-2tag Xist-Off Rep3

description:
Library name: TX-Maged1-2tag_Xist-Off_Rep3_H3K9me3
sorted mScarletI3-high/mStayGold-high

growth_protocol: TX-Maged1-2tag 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.

extract_protocol:
Cells were dissociated with Accutase for 5 mins, followed by media addition to stop dissociation. They were sorted with a BD FACS Aria II flow cytometer (BD Biosciences) with a 100μm nozzle and a 5B-3YG-2R-1DB laser configuration for mScarlet-I3 (615/20) and mStaygold (510/20). The sideward and forward scatter areas were used for live cell gating. The height and width of the forward scatter and subsequently the height and width of the sideward scatter were used for singlet/doublet differentiation. Sorted cells were centrifuged, resuspended in cell culture medium andcounted. 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 100μL 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 (derived from Addgene 124601) 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 50uL of tagmentation buffer (Dig-300 buffer, 10 mM MgCl2 and 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 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 cm^2, on 6-well plates coated with 10 μg/mL fibronectin (Corning 356008) in PBS for 1 hour. Once seeded in differentiation conditions, the medium was changed every day and the cells were not split until harvesting.

value: Differentiation by 2i/LIF withdrawal


title: N008 cells,siTOX 2

description: Library name: Sample20


title: PvXfL1

description: Library name: 13_S5_R1_001_SE


title: Liver, EtOH-fed, control, 1

description:
Library name: IonCode_0110
Ctrl_EtOH_1


title: TX-Maged1-2tag Xist-Off Rep2

description:
Library name: TX-Maged1-2tag_Xist-Off_Rep2_H3K9me3
sorted mScarletI3-high/mStayGold-high


title: N008 cells,siTOX 1

description: Library name: Sample19


title: PsJNPBSL4

description: Library name: 12_S5_R1_001_SE

value: PBS

value: PsJN


title: Liver, Pair-fed, control, 3

description:
Library name: IonCode_0125
Ctrl_Pair_3

value: AAV-TBG-GFP, Pair-fed


title: N008 cells,siSNTB1 3

description: Library name: Sample18

value: SNTB1 knockdown


title: TX-Maged1-2tag Xist-Off Rep1

description:
Library name: TX-Maged1-2tag_Xist-Off_Rep1_H3K9me3
sorted mScarletI3-high/mStayGold-high


title: PsJNPBSL3

description: Library name: 11_S9_R1_001_SE

value: Cabernet Sauvignon

value: Local


title: TX-Maged1-2tag Xist-Cast Rep3

description:
Library name: TX-Maged1-2tag_Xist-Cast_Rep3_H3K9me3
sorted mScarletI3-high/mStayGold-low


title: T cells donor 3 control edit replicate 1

description:
Library name: cd4_don3_control_rep1
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.

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: RH41 cells DMSO bio rep 1

city: Washington

first: Nikola

last: Knoll

state: DC

address: 3700 O St. NW

department: Oncology

institute: Georgetown University

description: Library name: Sample 1

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

source_name: soft tissue

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

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

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

value: soft tissue

value: fusion-positive rhabdomyosarcoma

value: 7 days DMSO


title: Liver, Pair-fed, control, 2

description:
Library name: IonCode_0109
Ctrl_Pair_2

value: Liver

value: Yap fl/fl


title: PsJNPBSL2

description: Library name: 10_S3_R1_001_SE

extract_protocol:
The petioles of three plant replicates of a given treatment were pooled to yield one biological replicate (total of four biological replicate cDNA libraries). RNA extraction and cDNA preparation were performed as in Rapicavoli et al. (2018).
The cDNA libraries were sequenced using Illumina HiSeq 4000 sequences (DNA Technologies Core, University of California, Davis, CA, USA) as single-end 100-bp reads (Illumina).

value: petiole


title: N008 cells,siSNTB1 2

description: Library name: Sample17

value: human primary Schwann cell


title: Liver, Pair-fed, control, 1

description:
Library name: IonCode_0101
Ctrl_Pair_1


title: TX-Maged1-2tag Xist-Cast Rep2

description:
Library name: TX-Maged1-2tag_Xist-Cast_Rep2_H3K9me3
sorted mScarletI3-high/mStayGold-low

value: Embryonic stem cells

value: female

value: CAST x C57BL/6

value: Differentiation by 2i/LIF withdrawal


title: N008 cells,siSNTB1 1

description: Library name: Sample16

value: SNTB1 knockdown


title: PsJNPBSL1

description: Library name: 9_S8_R1_001_SE

value: Cabernet Sauvignon

value: Local

value: PBS

value: PsJN


title: N008 cells,siNAV2 3

description: Library name: Sample15

value: NAV2 knockdown


title: TX-Maged1-2tag Xist-Cast Rep1

description:
Library name: TX-Maged1-2tag_Xist-Cast_Rep1_H3K9me3
sorted mScarletI3-high/mStayGold-low


title: Arabidopsis scl28 mutant rosette region at bolt, rep4

city: Auckland

first: Zhiwei

last: Luo

state: Auckland

address: 120 Mt Albert Road

country: New Zealand

institute: PLANT AND FOOD RESEARCH

description: Library name: scl_R6

data_processing:
RNA-seq reads were processed using nf-core/rnaseq v3.10 (https://doi: 10.5281/zenodo.1400710) of the nf-core pipeline (Ewels et al., 2020), and the filtered raw reads were mapped to Arabidopsis genome TAIR10 (https://www.arabidopsis.org/index.jsp). Raw read counts were processed using DESeq2 R package (Love et al., 2014).
Assembly: Arabidopsis genome TAIR10
Supplementary files format and content: txt

organism: Arabidopsis thaliana

source_name: tissue at the rosette region, leaves, stem and roots are removed.

growth_protocol: Arabidopsis seeds of scl28, ckx3 ckx5, Atd14 and WT were stratified in the dark at 4°C for two days then sowed and grown in a growth room under long-day conditions (16/8-hour light/dark cycle) using Heliospectra LX601C's LED units (each unit has lights of three wavelengths: 450 nm, 660 nm, and 735 nm) and the photon flux densities on the pot surface are between 120 and 172 µmol m-2 s-1, with an average density of 150 µmol m-2 s-1. The temperature of the growth room was maintained at 20 – 22°C

extract_protocol:
Total RNA was extracted from the powder using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO, USA) according to the instruction manual and treated with DNase using On-Column DNase I Digestion Set (Sigma-Aldrich, St. Louis, MO, USA). The quantities and purity of the extracted RNA samples were measured using a NanoDrop™ 1000 Spectrophotometer (Thermofisher, Waltham, MA, USA) and RNA integrity was checked using the RNA 6000 Nano kit and a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).
NEBNext® Ultra™ RNA Library Prep Kit

value: scl28 knock out


title: PvPBSL4

description: Library name: 8_S7_R1_001_SE

value: PV


title: TX-Maged1-2tag Xist-B6 Rep3

description:
Library name: TX-Maged1-2tag_Xist-B6_Rep3_H3K9me3
sorted mScarletI3-low/mStayGold-high


title: TX-Maged1-2tag Xist-B6 Rep2

description:
Library name: TX-Maged1-2tag_Xist-B6_Rep2_H3K9me3
sorted mScarletI3-low/mStayGold-high


title: N008 cells,siNAV2 2

description: Library name: Sample14


title: Arabidopsis scl28 mutant rosette region at bolt, rep3

description: Library name: scl_R5

value: tissue at the rosette region, leaves, stem and roots are removed.


title: Arabidopsis scl28 mutant rosette region at bolt, rep2

description: Library name: scl_R4


title: PvPBSL3

description: Library name: 7_S3_R1_001_SE


title: N008 cells,siNAV2 1

description: Library name: Sample13


title: PvPBSL2

description: Library name: 6_S5_R1_001_SE


title: PvPBSL1

description: Library name: 5_S1_R1_001_SE


title: TX-Maged1-2tag Xist-B6 Rep1

description:
Library name: TX-Maged1-2tag_Xist-B6_Rep1_H3K9me3
sorted mScarletI3-low/mStayGold-high


title: N008 cells,siCBFB 3

description: Library name: Sample12

value: CBFB knockdown


title: TX-Maged1-2tag unsorted Rep3

description:
Library name: TX-Maged1-2tag_unsorted_Rep3_H3K9me3
unsorted


title: Arabidopsis scl28 mutant rosette region at bolt, rep1

description: Library name: scl_R2


title: Arabidopsis d14-7 mutant rosette region at bolt, rep4

description: Library name: d14_R4

value: d14-7 knock out


title: N008 cells,siCBFB 2

description: Library name: Sample11


title: TX-Maged1-2tag unsorted Rep2

description:
Library name: TX-Maged1-2tag_unsorted_Rep2_H3K9me3
unsorted


title: PvXfS4

description: Library name: 4_S4_R1_001_SE

value: petiole

value: Systemic

value: Xf


title: N008 cells,siCBFB 1

description: Library name: Sample10

value: human primary Schwann cell


title: Arabidopsis d14-7 mutant rosette region at bolt, rep3

description: Library name: d14_R3


title: PvXfS3

description: Library name: 3_S3_R1_001_SE


title: Arabidopsis d14-7 mutant rosette region at bolt, rep2

description: Library name: d14_R2


title: TX-Maged1-2tag unsorted Rep1

description:
Library name: TX-Maged1-2tag_unsorted_Rep1_H3K9me3
unsorted

value: Embryonic stem cells

value: female

value: CAST x C57BL/6


title: N008 cells,siATF3 3

description: Library name: Sample9

value: ATF3 knockdown


title: PvXfS2

description: Library name: 2_S2_R1_001_SE

value: Cabernet Sauvignon


title: Arabidopsis d14-7 mutant rosette region at bolt, rep1

description: Library name: d14_R1


title: N008 cells,siATF3 2

description: Library name: Sample8


title: PvXfS1

description: Library name: 1_S1_R1_001_SE


title: Split dCas9-KRAB sgSTC ABA ctrl Day4 Rep1

description: Library name: sgSTC_ABA_ctrl_D4_Rep1

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.

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.

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

value: Differentiation Day 4