title: WNTi

city: Basel

first: Quan

last: Xu

address: Grenzacherstrasse 124

country: Switzerland

institute: Institute of Human Biology (IHB)

description: Library name: WNTi

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Cells from all samples were loaded to scanpy, and mitochondrial and ribosomal genes were removed. Cells with mitochondrial counts exceeding 20% were excluded, and only those with 4,000 to 10,000 detected genes were selected for downstream analysis. The counts for each cell were normalized to 10,000, followed by natural logarithm transformation.
Assembly: Human hg38
Supplementary files format and content: The scanpy h5ad files include normalized counts

source_name: Organoid

extract_protocol:
Organoids were dissociated to single cells using the Miltenyi Neural Tissue Dissociation kit (P).
Singe-cell RNA-seq libraries were generated using Chromium Next GEM Single Cell 3ʹ Kit v3.1 (1000268, 1000120, 1000215, 10x Genomics) according to 10x Genomics user manual CG000315 Rev F. Briefly, cell concentration, viability and percentage of aggregation of single-cell suspensions were quantified on the automatic cell counter Countess 3 FL (AMQAF2000, Thermo Fisher Scientific) with Trypan Blue Stain (T10282, Thermo Fischer Scientific). For each condition, cells were loaded into one lane of a Chromium Chip G (1000120, 10x Genomics) with a target recovery of 1000 - 10000 cells. Single-cell encapsulation, barcoding and library preparation were performed according to the manufacturer’s guidelines. Libraries were quantified with Qubit 1X dsDNA HS (Q33231, Thermo Fischer Scientific) and Bioanalyzer High Sensitivity DNA Kit (5067-4626, Agilent) and sequenced on the Illumina NovaSeq 6000 platform.

value: Organoid


title: Fetal

status: Public on Mar 12 2026

type: SRA

description:
Library name: Fetal
Visium HD Spatial for FFPE Probe Set v2.0

library_source: transcriptomic

data_processing:
FASTQ files were processed using the Space Ranger pipeline Version 3.1.2
Assembly: GRCh38
Supplementary files format and content: We are including the files generated by spaceRanger. Those include the filtered count matrix with barcode IDs and gene names and the image related files.
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: Adrenal gland

extract_protocol:
Tissue sections were destained, decrosslinked and immediately processed to Visium HD libraries according to the manufacturer’s protocol (CG000685 Visium HD Spatial Gene Expression User Guide, Rev A).
Dual-indexed libraries were generated and sequenced paired-end on the Illumina NovaSeq 6000 instrument (Illumina, 20028316) following the manufacturer’s guidelines (CG000685 Visium HD Spatial Gene Expression User Guide, Rev A) at a target read depth of 1300 read pairs per tissue-covered 8 um bin.

tag: tissue

value: Adrenal gland


title: FKBP-TASOR F8 ES, +dTAG

city: Oxford

first: Mafalda

last: Almeida

address: South Parks Rd

department: Biochemistry

country: United Kingdom

institute: University of Oxford

description: Library name: 208_TASORF8_27hdTAG_ES

library_source: other

data_processing:
The data processing pipeline for ChrRNA-seq followed procedures similar to those described by Nesterova et al. 2019 Briefly, raw FASTQ files containing paired-end reads were first aligned to a custom rRNA reference using Bowtie2 (v2.3.5.1) to remove rRNA contaminants. Reads mapping to rRNA were discarded, and the remaining unmapped read pairs were subsequently aligned to the N-masked mouse genome (mm10) using STAR (v2.5.2b). STAR was run with the following parameters: “--twopassMode Basic --outSAMstrandField intronMotif --outFilterMismatchNoverReadLmax 0.06 --outFilterMultimapNmax 1 --alignEndsType EndToEnd”. Only uniquely mapped reads were retained for downstream analyses. To distinguish allelic origin, alignments were split into Cast and 129S alleles using SNPsplit (v0.4.0dev, Babraham Institute)67 with the “--paired” option, based on annotated SNPs present bewteen the two strains. Allele-specific read counts were obtained using featureCounts (v1.5.2) with the parameters “-t transcript -g gene_id -s 2”. Alignments were sorted using Samtools (v1.16). For data visualisation, Bedtools (v2.30) was used to generate bigWig coverage tracks, which were then visualized using IGV (https://software.broadinstitute.org/software/igv/). Metagene profiles and heatmaps were created using deepTools (v3.5.2), supplemented with custom Python scripts. For biallelic (non-split) analyses, read counts were normalized to counts per million (CPM) mapped read pairs using the edgeR R package (v4.2.1). Only X-linked genes with at least 10 SNP-overlapping reads across all samples were considered for allelic ratio calculations. The allelic ratio was defined as Xi/(Xi + Xa), where Xi and Xa represent the inactive and active X chromosome alleles, respectively.
Assembly: mm10
Supplementary files format and content: txt

molecule: other

organism: Mus musculus

source_name: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

growth_protocol: mESC were grown in ESC medium at 37oC in a 5% CO2 incubator and passaged onto 0.1% gelatin-coated plates in feeder-dependent conditions every 2-3 days using TrypLE Express (Life Technologies). Mitomycin C-inactivated SNLP (STO mouse fibroblasts expressing Neomycin and Puromycin resistance and Lif genes) were used as feeder cells. Cells were pre-plated and passaged at least twice to remove feeders prior to cell collection for genomic experiments. ESC medium consisted of Dulbecco’s Modified Eagle Medium (DMEM; Life Technologies) supplemented with 10% Fetal Bovine Serum (FBS), 1x NEAA (Non-essential amino acids; Life Technologies), 2mM L-glutamine (Life Technologies), 1x Penicillin-Streptomycin (Life Technologies), 50µM b-mercaptoethanol (Life Technologies) and Leukemia Inhibitory Factor (LIF)-conditioned medium made in-house. Mouse embryonic stem cells were differentiated into NPC as previously described62,63. To obtain feederless mESC cell suspensions, mESC were collected using TrypLE and pre-plated four consecutive times for 40 min each. Cells were then washed in PBS twice to remove any traces of FBS and counted using a Countess® II FL Automated Cell Counter (Life Technologies). Cells were then resuspended in N2B27 medium (50% Neurobasal; 50% DMEM/F12 with 0.5x N2 and 0.25x B27, 1mM L-glutamine, 0.5x Penicillin-Streptomycin, 100μM b-mercaptoethanol, all from Life Technologies) supplemented with 1μg/mL of doxycycline to induce Xist expression simultaneously with the onset of differentiation, and plated at a density of 20,000 cells per cm2 in pre-gelatinized plates. Cells were fed daily from day 2 to day 7 of differentiation and fed also on day 1 for experiments in which this corresponded to the timepoint of 100 nM dTAG-13 addition. dTAG-13 treated NPC cultures were fed with media containing dTAG-13 from NPCd1 onwards until collection. On day 7, cells were dissociated by incubation with accutase (diluted 1:3 in PBS) (Merck Life Sciences) and counted. Three million cells were resuspended in N2B27 supplemented with doxycycline and 10 ng/mL EGF (cat# 315-09, Peprotech) and 10 ng/mL FGF2 (cat# 100-18B, Peprotech) and plated to grow in suspension in non-adherent bacterial petri dishes to promote embryoid body formation. On day 10, cells were recovered by centrifugation and plated onto pre-gelatinized dishes to expand more homogeneous neural stem cell cultures. At this point, neural stem cells were fed every other day and passaged as required using accutase (diluted 1:3 in PBS) (Merck Life Sciences) until the required timepoint. Cells were collected for different experiments at the appropriate timepoints (generally, NPCd1, d3 and d7 for ChIP experiments and multiple timepoints from NPCd1 to NPCd28 for chromatin-RNA) by washing with PBS and then incubating the cells at room temperature with accutase (diluted 1:3 in PBS) (Merck Life Sciences) until they were dissociated for collection.

extract_protocol:
Chromatin-RNA isolation and sequencing was as previously described. Briefly, cells were collected in a 15mL tube, washed with PBS and snap frozen immediately after PBS removal. Cells pellets were stored at -80oC until further processing. In order to purify chromatin-RNA, pellets were thawed on ice and resuspended in 800mL of hypotonic buffer HLBN (10mM NaCl, 2.5mM MgCl2, 10mM Tris pH 7.5, 0.1% NP40) and transferred to a 1.5mL tube. This solution was underlaid with a 480mL HLBN containing 24% sucrose to create a sucrose cushion for nuclear isolation by centrifugation at 1000g for 5min at 4oC. For fractionation, the nuclear pellet was then resuspended in 120mL NUN1 (20mM Tris pH8.0, 75mM NaCl, 0.5mM EDTA, 50% glycerol) freshly supplemented with 1mM DTT and protease inhibitors. After resuspension, 1200mL NUN2 (20mM HEPES pH7.6, 7.5mM MgCl2, 0.2mM EDTA, 0.3M NaCl, 1M urea, 1% NP40) freshly supplemented with 1mM DTT and protease inhibitors were added and mixed by gentle vortexing. Sample was incubated on ice for 15 min with occasional vortexing. After centrifugation for 10min at 15000rpm at 4oC, the supernatant containing the nucleoplasmic fraction was discarded and the chromatin pellet was resuspended in 200mL HSB (10mM Tris pH7.5, 500mM NaCl, 10mM MgCl2) supplemented with 2mL TURBO DNAse (Life Technologies) to digest the sample DNA by incubating at 37oC for at least 10min, shaking at 1400rpm. After this incubation, 2μL of 20% SDS and 4μL of proteinase K (20mg/ml) were added and the samples were incubated at 37oC for at least 30min for protein digestion. Chromatin-bound RNA was then purified using Trizol reagent according to manufacturer’s recommendations with addition of glycogen to aid precipitation of the RNA at -20oC overnight. Purified chromatin-RNA was subjected to a second round of TURBO DNAse treatment and a second round of Trizol reagent purification as previously described.
Chromatin-RNA concentrations were initially measured by Nanodrop to inform further dilution for quantification using Qubit HS RNA assay (Invitrogen) and quality control using RNA Pico 6000 Bioanalyser kit (Agilent). RNA Libraries were prepared for sequencing using the Illumina TruSeq stranded total RNA kit including the rRNA depletion according to the manufacturer’s instructions. Libraries were quantified and verified using Qubit High Sensitivity DNA (Invitrogen) and the Bioanalyser High Sensitivity DNA (Agilent) kits before pooling and paired-end sequencing on an Illumina NextSeq 500 machine using NextSeq 500/550 High-Output v2.5 Kit (150 cycles) (Illumina).

treatment_protocol: To induce Xist expression, medium was supplemented with 1µg/mL doxycycline. To induce protein degradation in lines expressing FKBP12F36V-tagged SETDB1, medium was supplemented with 100nM dTAG-13 (Tocris Bioscience).

tag: strain background

value: Cast x 129S

tag: cell line

tag: cell type

value: mESC

tag: genotype

tag: treatment

value: dTAG-13 for 27hours


title: scRNA-seq of multiplexed dissociated tumor tissues (BAP1 WT/KO; subcutaneous and ocular Melan-a models)

city: Singapore

first: Mona

middle: Meng

last: Wang

address: 20 College Rd, Singapore

country: Singapore

institute: Singaoire Eye Research Institute

description:
Library name: BAP1_scRNAseq_multiplexed_Subcutaneous_and_Ocular_model
10x Genomics Chromium Next GEM 3' v3.1

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were demultiplexed and converted to FASTQ format. For bulk RNA-seq data, reads were quality controlled, trimmed if necessary, and aligned to the mouse reference genome, followed by gene-level quantification. For single-cell RNA-seq data, raw base call files were processed using the Cell Ranger pipeline for alignment, barcode processing, and generation of gene–cell count matrices. For WGS and WES data, reads were aligned to the mouse reference genome, followed by duplicate marking, base quality recalibration, and variant calling.
Somatic variants in BAP1 knockout clones were identified by comparison against the Melan-a wild-type reference. Variant annotation was performed using standard annotation tools. Quality control metrics were assessed for all datasets prior to downstream analysis.
Assembly: Mouse reference genome GRCm38 (mm10) was used for read alignment and downstream analyses.
Supplementary files format and content: For single-cell RNA sequencing data, base call files were processed using the Cell Ranger pipeline to perform alignment, barcode processing, and generation of filtered gene–cell count matrices.
Supplementary files format and content: For whole-genome sequencing, whole-exome sequencing, and bulk RNA-seq datasets, raw FASTQ files are provided without additional downstream processing.

molecule: polyA RNA

source_name: tumor

growth_protocol: Melan-a cells (BAP1 wild-type and CRISPR-engineered BAP1 knockout clones) and B16F10 cells were cultured under standard conditions in a humidified incubator at 37 °C with 5% CO₂ using recommended growth media. Primary murine ocular melanocytes were isolated from mouse ocular tissue and cultured under melanocyte-supporting conditions prior to DNA extraction. For in vivo experiments, Melan-a wild-type or BAP1 knockout cells were injected into syngeneic mice via ocular or subcutaneous routes, and tumors were harvested at defined endpoints for downstream analyses.

extract_protocol:
For bulk RNA-seq, total RNA was extracted from cultured cells using a column-based RNA isolation kit following the manufacturer’s instructions, including on-column DNase treatment. For whole-genome and whole-exome sequencing, genomic DNA was extracted using a standard phenol–chloroform or silica column–based method. For single-cell RNA sequencing, freshly isolated or fixed tumor tissues were mechanically and enzymatically dissociated into single-cell suspensions prior to library preparation according to the 10x Genomics fixed tissue workflow.
Bulk RNA-seq libraries were prepared from polyadenylated RNA using a stranded mRNA library preparation kit. Whole-genome sequencing libraries were prepared from genomic DNA using a PCR-free or low-cycle library preparation protocol. Whole-exome sequencing libraries were generated using a hybrid-capture–based exome enrichment kit. Single-cell RNA-seq libraries were constructed using the 10x Genomics Chromium platform following the manufacturer’s protocol for fixed tissue gene expression, generating barcoded single-cell cDNA libraries.

treatment_protocol: No drug or chemical treatments were applied. The primary experimental variables were BAP1 genotype (wild-type versus knockout) and tumor anatomical site (ocular versus subcutaneous).

value: tumor

value: whole tissue single-cell suspension

value: BAP1 WT and KO

value: No

tag: batch


title: Adult

description:
Library name: Adult
Visium HD Spatial for FFPE Probe Set v2.0


title: WNTi+MC2Ra+cAMPa+LXRa

description: Library name: IWR+FSK+ACTH+LXRa


title: cmnorhe_36_2

city: Beijing

first: Jinfang

address: No.50 Zhanghua Road, Haidian District

country: China

institute: Beijing Academy of Agricultural and Forestry Sciences

description: Library name: cmnorhe_36_2

data_processing:
Illumina NovaSeq X
fastx_toolkit_0.0.14/SeqPrep/Sickle were used for estimating sequencing quality to gain clean reads.
TopHat2 / HISAT2 were used to analysis the mapped data quality.
The mapped reads were spliced using StringTie or Cufflinks software
FPKM（Fragments Per Kilobases per Millionreads）values were used to show gene expression level.
Assembly: http://cucurbitgenomics.org/organism/18
Supplementary files format and content: text files include FPKM values for each Sample

organism: Citrullus lanatus

source_name: flesh

extract_protocol:
RNA was extracted from The homozygotes Cmnor; CmNOR/Cmnor heterozygotes and WT flesh were harveseted at 33 DAP,36 and 39 DAP  (days after pollination) and 6 days after storage with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed
The 36 libraries were built by TruseqTM RNA sample prep kit (Illumina, USA).

value: flesh

value: CmNOR/Cmnor heterozygotes

value: 36 days after pollination


title: WT_Recovery_D3

city: Seoul

first: Su-Hyung

last: Lee

state: Seoul

address: 120 Neungdong-ro, Gwangjin-gu

country: South Korea

institute: Konkuk University

description: Library name: 9727-BC-0003_S1_L005

data_processing:
Alignment was performed using PIPseeker (Fluent BioSciences). Downstream analysis was conducted using PartekFlow. Differential expression was filtered with adjusted P-value < 0.05 and |fold change| > 2.
Assembly: mm39 (GRCm39)
Supplementary files format and content: The processed data consists of digital gene expression matrices. For each sample, a sparse matrix is provided in Market Exchange Format (.mtx), accompanied by files for barcodes (.tsv) and features/genes (.tsv). The values represent raw UMIs (Unique Molecular Identifier) counts per gene per cell, generated via the PIPseeker alignment pipeline and PartekFlow analysis.

source_name: Stomach corpus epithelial cells

extract_protocol:
Corpus tissues were dissociated into single cells using TrypLE (Gibco) with 10nM Y27632 at 37°C for 5 min.
PIPseq™ T20 3’ Single Cell Capture and Lysis Kit (Fluent BioSciences). 25,000 cells were loaded per capture.

value: Stomach corpus epithelial cells

value: epithelial cell


title: WNTi+MC2Ra+cAMPa

description: Library name: IWR1+FSK+ACTH


title: FKBP-SETDB1 P2F7, dTAGd1, NPC d28

description: Library name: 172_SetP2F7_dTAGd1_NPCd28

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: doxycyline for 28 days coupled with differentiation, dTAG-13 for 27 days


title: WT_Injury_D1

description: Library name: 9727-BC-0002_S1_L005


title: WT_36_2

description: Library name: WT_36_2

growth_protocol: The homozygotes Cmnor; CmNOR/Cmnor heterozygotes and WT flesh were harveseted at 33 DAP,36 and 39 DAP  (days after pollination) and 6 days after storage

value: wild type


title: TGFBa

description: Library name: TGFBa

value: Organoid


title: WT_36_1

description: Library name: WT_36_1


title: cmnor_33_3

description: Library name: cmnor_33_3

value: Cmnor homozygotes

value: 33 days after pollination


title: Base

description: Library name: Base

value: Base


title: FKBP-TASOR F8 ES

description: Library name: 207_TASORF8_ES

value: Cast x 129S

value: mESC


title: WT_36_3

description: Library name: WT_36_3


title: FKBP-SETDB1 P2F7, Control, NPC d28

description: Library name: 171_SetP2F7_Control_NPCd28

value: doxycyline for 28 days coupled with differentiation


title: WT_Untreated

description: Library name: 9727-BC-0001_S1_L005


title: WT_Recovery_AREG_D3

description: Library name: 9727-BC-0004_S1_L005


title: cmnor_33_1

description: Library name: cmnor_33_1


title: FKBP-TASOR H4 ES, +dTAG+dox

description: Library name: 170_TASORH4_27hdTAG24hdox_ES

value: dTAG-13 for 27hours and doxycyline for 24hours


title: FKBP-TASOR H4 ES, +dox

description: Library name: 169_TASORH4_24hdox_ES

value: doxycyline for 24hours


title: cmnor_33_2

description: Library name: cmnor_33_2

value: flesh


title: ANG2

description: Library name: ANG2


title: cmnorhe_33_3

description: Library name: cmnorhe_33_3

value: CmNOR/Cmnor heterozygotes


title: Male_Placenta_0.1PCB_YesFA_36_05

city: Davis

first: Janine

last: LaSalle

state: California

address: 1275 Med Science Dr

country: USA

institute: University of California, Davis

description: Library name: 36_05_PLAC

data_processing:
Raw RNA-seq fastq files were processed by trimming adapters using Trim Galore (v0.6.5)
Trimmed sequence reads were aligned to the mouse genome (mm10)
Gene count quantification was done using STAR (v2.7.3a)
QC metrics were generated with MultiQC (v1.9).
Assembly: mm10
Supplementary files format and content: .xlsx format; normalized counts

extract_protocol:
Nucleic acids were extracted by homogenizing the same half of placenta and brain tissue using a TissueLyser II (Qiagen) followed by the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s instructions.
Isolated RNA underwent quantification and QC using a Bioanalyzer Eukaryotic Total RNA Nano Assay (Agilent). Libraries were constructed using the KAPA mRNA HyperPrep kit (Roche) and NEXTFLEX Unique Dual Index Barcodes (PerkinElmer). Libraries were pooled and sequenced on a NovaSeq 6000 S4 flow cell (Illumina) for 150 bp paired end reads resulting in approximately 25 million uniquely mapped reads per sample.

value: Placenta

tag: strain

tag: Sex

value: M

tag: pcb treatment

tag: folic acid_treatment

value: YES


title: Male_Placenta_0.1PCB_YesFA_36_02

description: Library name: 36_02_PLAC


title: Male_Placenta_0.1PCB_YesFA_36_04

description: Library name: 36_04_PLAC


title: BMPa

description: Library name: BMPa


title: Male_Placenta_0.1PCB_YesFA_35_05

description: Library name: 35_05_PLAC


title: FKBP-TASOR H4 ES, +dTAG

description: Library name: 168_TASORH4_27hdTAG_ES

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: dTAG-13 for 27hours


title: FKBP-MPP8 G1 ES, +dTAG+dox

description: Library name: 166_MPP8G1_27hdTAG24hdox_ES


title: WNTa

description: Library name: WNTa

value: CHIR


title: Pt 8 Pre-treatment ROI 6 TME

city: Houston

first: Ken

last: Chen

state: TX

address: 7007 Bertner Ave

institute: University of Texas MD Anderson Cancer Center

description: Library name: DSP-1001660035398-H-H05

data_processing:
Data was normalized with RUVg normalization with housekeeping genes (FCF1, DHX16, ABCF1, EDC3, ZNF143, HDAC3, CNOT10, SAP130, AGK, AMMECR1L, SF3A3, COG7, TMUB2, ZC3H14, DDX50, MRPS5, ZNF346, MTMR14, ERCC3, EIF2B4, TLK2, NUBP1, USP39, PRPF38A. NOL7, CNOT4).
Assembly: hg38
Supplementary files format and content: lab worksheet
Supplementary files format and content: dcc files
Library strategy: Spatial Transcriptomics

source_name: Abdomen

extract_protocol:
The slides were incubated overnight with the GeoMx Human whole transcriptome atlas (WTA) assay probe cocktail. The GeoMx Digital Spatial Platform (DSP) was used to scan the slides, followed by region-of-interest (ROI) selections performed by pathologists. Probe barcodes were UV cleaved and collected.
Libraries were paired-end sequenced (2x50) on a NovoSeq 6000.

value: Abdomen

tag: segment

value: TME

value: Pre-treatment

tag: roi

tag: patient


title: Male_Placenta_0.1PCB_YesFA_35_06

description: Library name: 35_06_PLAC


title: Organoid

description: Library name: Organoid

value: Organoid

value: Base


title: cmnorhe_33_1

description: Library name: cmnorhe_33_1

value: 33 days after pollination


title: Pt 8 Pre-treatment ROI 6 Tumor

description: Library name: DSP-1001660035398-H-H04

value: Tumor


title: FKBP-MPP8 G1 ES, +dox

description: Library name: 165_MPP8G1_24hdox_ES

value: Cast x 129S

value: mESC


title: WT_33_3

description: Library name: WT_33_3

value: flesh

value: wild type


title: Male_Placenta_0.1PCB_YesFA_32_07

description: Library name: 32_07_PLAC

value: Placenta


title: WT_33_2

description: Library name: WT_33_2


title: FKBP-TASOR H4 ES

description: Library name: 167_TASORH4_ES


title: Male_Placenta_0.1PCB_YesFA_32_04

description: Library name: 32_04_PLAC

value: M


title: cmnorhe_33_2

description: Library name: cmnorhe_33_2

value: CmNOR/Cmnor heterozygotes


title: FKBP-MPP8 G1 ES, +dTAG

description: Library name: 164_MPP8G1_27hdTAG_ES

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)


title: WT_33_1

description: Library name: WT_33_1


title: Male_Placenta_0.1PCB_YesFA_31_05

description: Library name: 31_05_PLAC

value: YES


title: Pt 8 Pre-treatment ROI 5 Tumor

description: Library name: DSP-1001660035398-H-H02


title: PBS control, WGBS screening

city: Coventry

first: Javier

last: Antunez Sanchez

address: Gibbet Hill Campus

department: Life Sciences

institute: University of Warwick

description: Library name: PBS

library_source: genomic

data_processing:
Initial quality assessment of raw sequencing data was performed using FastQC (v0.11.5). Adapter trimming and quality filtering were conducted using fastp (v0.23.2) with parameters --cut_right --cut_window_size 4 --cut_mean_quality 20 --length_required 40. Post-trimming quality was reassessed with FastQC to ensure the effectiveness of trimming. MultiQC (v1.17) was used to aggregate quality reports.
Bismark (v0.22.3) was used for processing the BS-seq reads. The Tomato reference genome SL4.0 was bisulfite-converted and indexed using the bismark_genome_preparation command. Trimmed single-end reads were aligned to the indexed reference genome using bismark with the --non_directional flag. PCR duplicates were removed using deduplicate_bismark with default settings. Methylation extraction was performed using bismark_methylation_extractor with the parameters --cytosine_report and --CX to generate comprehensive cytosine reports for all contexts (CpG, CHG, CHH).
BigWig files representing methylation levels were generated using a custom script, CX_report2bigwig.sh, which converts CX reports into BigWigs for visualisation.
Assembly: SL4.0 (GCA_000188115.5)
Supplementary files format and content: Bigwig files (.bw) of CG methylation
Supplementary files format and content: Bigwig files (.bw) of CHG methylation
Supplementary files format and content: Bigwig files (.bw) of CHH methylation
Supplementary files format and content: Tab separated values (.tsv) containing the mC rate in 100 kbp windows for all samples in all contexts (CG, CHG, CHH)

molecule: genomic DNA

organism: Solanum lycopersicum

source_name: PBS

growth_protocol: Plants were grown in a glasshouse under long day conditions (16 hr light, 8 hr dark, 23°C, 42% humidity). Three weeks after germination seedlings were transferred to 3 litre pots and grown to maturity

extract_protocol:
Around 100 mg of the whole plant tissue were collected, snap frozen in liquid nitrogen and stored at -80oC. Tissue samples were ground using TissueLyser II (Qiagen) with sterile RNAse-free glass beads. DNA was extracted using a QIAGEN Plant DNeasy kit as manufacture’s manual. The quality of the DNA was assessed using a NanoDrop spectrophotometer and Qubit fluorometer.
Bisulfite libraries were prepared from 100 ng of genomic DNA using the TruSeq Nano kit (Illumina, San Diego, CA, USA), following the manufacturer’s instructions, with the following modification: after adapter ligation and clean-up, samples were treated with bisulfite using the Epitect Plus kit (Qiagen, Hilden, Germany). The thermal cycle incubation was repeated once before clean-up. DNA fragments were then amplified using the Kapa HiFi HotStart Uracil+ PCR mix in 14 cycles of PCR (Kapa Biosystems, Wilmington, MA, USA). Bisulfite libraries were sequenced on an Illumina HiSeq 3000 instrument, generating 150 bp paired-end reads.

value: PBS

tag: line


title: FKBP-SETDB1 P2F7, dTAGd1, NPC d21

description: Library name: 162_SetP2F7_dTAGd1_NPCd21

value: NPC

value: doxycyline for 21 days coupled with differentiation, dTAG-13 for 20 days


title: Male_Placenta_0.1PCB_YesFA_31_04

description: Library name: 31_04_PLAC


title: FKBP-SETDB1 P2F7, dTAGd1, NPC d7

description: Library name: 160_SetP2F7_dTAGd1_NPCd7

value: doxycyline for 7 days coupled with differentiation, dTAG-13 for 6 days


title: B T2 + 20, young leaf, WGBS screening

description: Library name: B2_20

source_name: young leaves

value: young leaves

value: B T2 +


title: FKBP-MPP8 G1 ES

description: Library name: 163_MPP8G1_ES


title: FKBP-SETDB1 P2F7, Control, NPC d21

description: Library name: 161_SetP2F7_Control_NPCd21

value: doxycyline for 21 days coupled with differentiation


title: Pt 8 Pre-treatment ROI 3 Tumor

description: Library name: DSP-1001660035398-H-G10

value: Abdomen

value: Tumor

value: Pre-treatment


title: Pt 8 Pre-treatment ROI 4 TME

description: Library name: DSP-1001660035398-H-H01

value: TME


title: Pt 8 Pre-treatment ROI 5 TME

description: Library name: DSP-1001660035398-H-H03


title: Female_Placenta_0.1PCB_YesFA_36_03

description: Library name: 36_03_PLAC

value: F


title: Male_Placenta_0.1PCB_YesFA_31_02

description: Library name: 31_02_PLAC

value: Placenta


title: Pt 8 Pre-treatment ROI 3 TME

description: Library name: DSP-1001660035398-H-G11


title: Pt 8 Pre-treatment ROI 4 Tumor

description: Library name: DSP-1001660035398-H-G12


title: B T2 + 18, young leaf, WGBS screening

description: Library name: B2_18


title: B T2 + 16, young leaf, WGBS screening

description: Library name: B2_16


title: FKBP-SETDB1 P2F7, Control, NPC d7

description: Library name: 159_SetP2F7_Control_NPCd7

value: Cast x 129S

value: doxycyline for 7 days coupled with differentiation


title: FKBP-SETDB1 P2F7, dTAGd1, NPC d6

description: Library name: 158_SetP2F7_dTAGd1_NPCd6

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: doxycyline for 6 days coupled with differentiation, dTAG-13 for 5 days


title: B T2 + 14, young leaf, WGBS screening

description: Library name: B2_14


title: Negative control, WGBS screening

description: Library name: neg

source_name: water

value: water


title: Pt 8 Pre-treatment ROI 2 TME

description: Library name: DSP-1001660035398-H-G09


title: Female_Placenta_0.1PCB_YesFA_36_01

description: Library name: 36_01_PLAC

value: YES


title: B T2 + 13, young leaf, WGBS screening

description: Library name: B2_13


title: FKBP-SETDB1 P2F7, Control, NPC d6

description: Library name: 157_SetP2F7_Control_NPCd6

value: NPC

value: doxycyline for 6 days coupled with differentiation


title: Female_Placenta_0.1PCB_YesFA_35_01

description: Library name: 35_01_PLAC


title: Female_Placenta_0.1PCB_YesFA_35_02

description: Library name: 35_02_PLAC


title: Female_Placenta_0.1PCB_YesFA_32_08

description: Library name: 32_08_PLAC


title: B T2 + 10, young leaf, WGBS screening

description: Library name: B2_10

value: young leaves


title: FKBP-SETDB1 P2F7, Control, NPC d5

description: Library name: 155_SetP2F7_Control_NPCd5

value: doxycyline for 5 days coupled with differentiation


title: Pt 8 Pre-treatment ROI 1 TME

description: Library name: DSP-1001660035398-H-G07


title: Female_Placenta_0.1PCB_YesFA_32_03

description: Library name: 32_03_PLAC


title: B T2 + 9, young leaf, WGBS screening

description: Library name: B2_9

value: B T2 +


title: Female_Placenta_0.1PCB_YesFA_32_06

description: Library name: 32_06_PLAC


title: Pt 9 Pre-treatment ROI 3 TME

description: Library name: DSP-1001660035398-H-G05

source_name: Pelvic

value: Pelvic


title: B T2 + 5, young leaf, WGBS screening

description: Library name: B2_5


title: Female_Placenta_0.1PCB_YesFA_31_06

description: Library name: 31_06_PLAC


title: FKBP-SETDB1 P2F7, dTAGd1, NPC d4

description: Library name: 154_SetP2F7_dTAGd1_NPCd4

value: doxycyline for 4 days coupled with differentiation, dTAG-13 for 3 days


title: Pt 9 Pre-treatment ROI 2 TME

description: Library name: DSP-1001660035398-H-G04

value: Pre-treatment


title: B T2 + 1, young leaf, WGBS screening

description: Library name: B2_1


title: FKBP-SETDB1 P2F7, dTAGd1, NPC d5

description: Library name: 156_SetP2F7_dTAGd1_NPCd5

value: doxycyline for 5 days coupled with differentiation, dTAG-13 for 4 days


title: FKBP-SETDB1 P2F7, Control, NPC d4

description: Library name: 153_SetP2F7_Control_NPCd4

value: doxycyline for 4 days coupled with differentiation


title: B T2 - 9, young leaf, WGBS screening

description: Library name: B1_9

value: B T2 -


title: Pt 9 Pre-treatment ROI 1 TME

description: Library name: DSP-1001660035398-H-G03

value: TME


title: Female_Placenta_0.1PCB_YesFA_31_03

description: Library name: 31_03_PLAC

value: Placenta

value: F


title: FKBP-SETDB1 P2F7, dTAGd1, NPC d3

description: Library name: 152_SetP2F7_dTAGd1_NPCd3

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: doxycyline for 3 days coupled with differentiation, dTAG-13 for 2 days


title: Female_Placenta_0.1PCB_YesFA_31_01

description: Library name: 31_01_PLAC

value: YES


title: Pt 3 On-treatment ROI 3 TME

description: Library name: DSP-1001660035398-H-G02

value: On-treatment


title: Pt 8 Pre-treatment ROI 1 Tumor

description: Library name: DSP-1001660035398-H-G06

value: Abdomen

value: Tumor


title: B T2 - 8, young leaf, WGBS screening

description: Library name: B1_8

value: young leaves


title: Male_Placenta_0PCB_YesFA_20_01

description: Library name: 20_01_PLAC

value: M


title: Pt 8 Pre-treatment ROI 2 Tumor

description: Library name: DSP-1001660035398-H-G08


title: FKBP-SETDB1 P2F7, Control, NPC d2

description: Library name: 149_SetP2F7_Control_NPCd2

value: NPC

value: doxycyline for 2 days coupled with differentiation


title: Pt 3 On-treatment ROI 1 TME

description: Library name: DSP-1001660035398-H-F12


title: B T2 - 7, young leaf, WGBS screening

description: Library name: B1_7


title: Pt 3 On-treatment ROI 2 TME

description: Library name: DSP-1001660035398-H-G01


title: Pt 13 Pre-treatment ROI 6 TME

description: Library name: DSP-1001660035398-H-F11

source_name: Pelvis

value: Pelvis

value: Pre-treatment


title: FKBP-SETDB1 P2F7, dTAGd1, NPC d2

description: Library name: 150_SetP2F7_dTAGd1_NPCd2

value: doxycyline for 2 days coupled with differentiation, dTAG-13 for 1 day


title: FKBP-SETDB1 P2F7, Control, NPC d3

description: Library name: 151_SetP2F7_Control_NPCd3

value: doxycyline for 3 days coupled with differentiation


title: Male_Placenta_0PCB_YesFA_18_05

description: Library name: 18_05_PLAC

value: Placenta


title: FKBP-SETDB1 P2F7, Control, NPC d1

description: Library name: 148_SetP2F7_Control_NPCd1

value: doxycyline for 1 day coupled with differentiation


title: Male_Placenta_0PCB_YesFA_18_06

description: Library name: 18_06_PLAC


title: Pt 13 Pre-treatment ROI 6 Tumor

description: Library name: DSP-1001660035398-H-F10


title: B T1 11, young leaf, WGBS screening

description: Library name: B_11

value: B T1


title: Pt 13 Pre-treatment ROI 5 TME

description: Library name: DSP-1001660035398-H-F09

value: TME


title: Male_Placenta_0PCB_YesFA_18_03

description: Library name: 18_03_PLAC


title: FKBP-KAP1 A4A11 ES, +dTAG

description: Library name: 129_KAP1A4A11_27hdTAG_ES

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: mESC

value: dTAG-13 for 27hours


title: FKBP-KAP1 A4A11 ES, +dTAG+dox

description: Library name: 131_KAP1A4A11_27hdTAG24hdox_ES

value: dTAG-13 for 27hours and doxycyline for 24hours


title: Male_Placenta_0PCB_YesFA_13_05

description: Library name: 13_05_PLAC

value: YES


title: Pt 13 Pre-treatment ROI 5 Tumor

description: Library name: DSP-1001660035398-H-F08

value: Tumor


title: Male_Placenta_0PCB_YesFA_13_04

description: Library name: 13_04_PLAC

value: M


title: B T1 8, young leaf, WGBS screening

description: Library name: B_8

value: young leaves


title: FKBP-KAP1 A4A11 ES, +dox

description: Library name: 130_KAP1A4A11_24hdox_ES

value: doxycyline for 24hours


title: B T2 - 2, young leaf, WGBS screening

description: Library name: B1_2

value: B T2 -


title: Pt 13 Pre-treatment ROI 4 TME

description: Library name: DSP-1001660035398-H-F07

value: Pelvis

value: Pre-treatment


title: B T2 - 6, young leaf, WGBS screening

description: Library name: B1_6


title: Male_Placenta_0PCB_YesFA_18_04

description: Library name: 18_04_PLAC

value: Placenta


title: B T1 10, young leaf, WGBS screening

description: Library name: B_10


title: FKBP-TASOR H8 ES, +dTAG+dox

description: Library name: 127_TASORH8_27hdTAG24hdox_ES


title: B T1 6, young leaf, WGBS screening

description: Library name: B_6


title: B T2 - 3, young leaf, WGBS screening

description: Library name: B1_3


title: Pt 13 Pre-treatment ROI 3 TME

description: Library name: DSP-1001660035398-H-F05


title: FKBP-KAP1 A4A11 ES

description: Library name: 128_KAP1A4A11_ES


title: FKBP-TASOR H8 ES, +dox

description: Library name: 126_TASORH8_24hdox_ES


title: B T1 5, young leaf, WGBS screening

description: Library name: B_5


title: Pt 13 Pre-treatment ROI 2 TME

description: Library name: DSP-1001660035398-H-F03


title: Male_Placenta_0PCB_YesFA_13_03

description: Library name: 13_03_PLAC


title: Female_Placenta_0PCB_YesFA_20_02

description: Library name: 20_02_PLAC

value: F


title: Female_Placenta_0PCB_YesFA_20_03

description: Library name: 20_03_PLAC


title: FKBP-MPP8 E10 ES, +dTAG+dox

description: Library name: 123_MPP8E10_27hdTAG24hdox_ES


title: FKBP-TASOR H8 ES

description: Library name: 124_TASORH8_ES


title: A T3 11, young leaf, WGBS screening

description: Library name: A11_11

value: A T3


title: Pt 13 Pre-treatment ROI 4 Tumor

description: Library name: DSP-1001660035398-H-F06


title: B T1 2, young leaf, WGBS screening

description: Library name: B_2

value: B T1


title: FKBP-MPP8 E10 ES, +dox

description: Library name: 122_MPP8E10_24hdox_ES

value: Cast x 129S


title: FKBP-TASOR H8 ES, +dTAG

description: Library name: 125_TASORH8_27hdTAG_ES

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)


title: Pt 13 Pre-treatment ROI 3 Tumor

description: Library name: DSP-1001660035398-H-F04


title: B T1 3, young leaf, WGBS screening

description: Library name: B_3


title: Female_Placenta_0PCB_YesFA_20_04

description: Library name: 20_04_PLAC


title: FKBP-MPP8 E10 ES

description: Library name: 120_MPP8E10_ES

value: mESC


title: Pt 13 Pre-treatment ROI 1 Tumor

description: Library name: DSP-1001660035398-H-E12


title: Female_Placenta_0PCB_YesFA_13_02

description: Library name: 13_02_PLAC


title: Pt 13 Pre-treatment ROI 2 Tumor

description: Library name: DSP-1001660035398-H-F02


title: Female_Placenta_0PCB_YesFA_18_01

description: Library name: 18_01_PLAC


title: B T1 4, young leaf, WGBS screening

description: Library name: B_4


title: A T3 10, young leaf, WGBS screening

description: Library name: A11_10


title: Female_Placenta_0PCB_YesFA_18_02

description: Library name: 18_02_PLAC


title: FKBP-MPP8 E10 ES, +dTAG

description: Library name: 121_MPP8E10_27hdTAG_ES

value: dTAG-13 for 27hours


title: Pt 13 Pre-treatment ROI 1 TME

description: Library name: DSP-1001660035398-H-F01

value: TME


title: Pt 11 Pre-treatment ROI 6 TME

description: Library name: DSP-1001660035398-H-E11

source_name: Liver

value: Retroperitoneum


title: TsixStop NPCd21

description: Library name: 111_TsixStop_NPCd21

source_name: Tsix Stop on 129 allele leading to non-random X inactivation upon differentiation

value: NPC


title: Female_Placenta_0PCB_YesFA_13_01

description: Library name: 13_01_PLAC

value: YES


title: A T3 8, young leaf, WGBS screening

description: Library name: A11_8

value: young leaves


title: A T3 5, young leaf, WGBS screening

description: Library name: A11_5


title: Pt 11 Pre-treatment ROI 6 Tumor

description: Library name: DSP-1001660035398-H-E10

value: Tumor


title: Female_Placenta_0PCB_YesFA_12_03

description: Library name: 12_03_PLAC


title: Pt 11 Pre-treatment ROI 5 TME

description: Library name: DSP-1001660035398-H-E09


title: Female_Placenta_0PCB_YesFA_12_01

description: Library name: 12_01_PLAC


title: TsixStop NPCd6

description: Library name: 109_TsixStop_NPCd6

value: Tsix Stop on 129 allele leading to non-random X inactivation upon differentiation


title: TsixStop NPCd7

description: Library name: 110_TsixStop_NPCd7


title: Pt 11 Pre-treatment ROI 5 Tumor

description: Library name: DSP-1001660035398-H-E08


title: A T2 8, young leaf, WGBS screening

description: Library name: A1_8

value: A T2


title: Male_Placenta_6PCB_NoFA_57_08

description: Library name: 57_08_PLAC

value: M

value: NO


title: TsixStop NPCd3

description: Library name: 106_TsixStop_NPCd3


title: Pt 11 Pre-treatment ROI 4 TME

description: Library name: DSP-1001660035398-H-E07

value: Pre-treatment


title: TsixStop NPCd4

description: Library name: 107_TsixStop_NPCd4


title: A T2 7, young leaf, WGBS screening

description: Library name: A1_7


title: Female_Placenta_0PCB_YesFA_12_02

description: Library name: 12_02_PLAC

value: Placenta

value: F


title: A T1 22, young leaf, WGBS screening

description: Library name: A_22

value: A T1


title: Male_Placenta_6PCB_NoFA_57_03

description: Library name: 57_03_PLAC


title: A T2 2, young leaf, WGBS screening

description: Library name: A1_2


title: A T2 6, young leaf, WGBS screening

description: Library name: A1_6


title: Pt 11 Pre-treatment ROI 3 TME

description: Library name: DSP-1001660035398-H-E05


title: A T3 3, young leaf, WGBS screening

description: Library name: A11_3

value: A T3


title: Pt 11 Pre-treatment ROI 4 Tumor

description: Library name: DSP-1001660035398-H-E06


title: FKBP-SETDB1 G6D2 ES, +dTAG+dox

description: Library name: 99_SetG6D2_27hdTAG24hdox_ES

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: mESC

value: dTAG-13 for 27hours and doxycyline for 24hours


title: A T2 4, young leaf, WGBS screening

description: Library name: A1_4


title: TsixStop NPCd5

description: Library name: 108_TsixStop_NPCd5

value: NPC


title: Pt 11 Pre-treatment ROI 1 Tumor

description: Library name: DSP-1001660035398-H-D12

value: Retroperitoneum


title: Male_Placenta_6PCB_NoFA_51_06

description: Library name: 51_06_PLAC


title: Male_Placenta_6PCB_NoFA_57_01

description: Library name: 57_01_PLAC


title: Pt 13 On-treatment ROI 6 TME

description: Library name: DSP-1001660035398-H-D11

value: Ovary

value: TME

value: On-treatment


title: Pt 11 Pre-treatment ROI 2 TME

description: Library name: DSP-1001660035398-H-E03


title: A T1 15, young leaf, WGBS screening

description: Library name: A_15

value: young leaves


title: A T1 21, young leaf, WGBS screening

description: Library name: A_21


title: Pt 11 Pre-treatment ROI 2 Tumor

description: Library name: DSP-1001660035398-H-E02

value: Tumor


title: Pt 11 Pre-treatment ROI 3 Tumor

description: Library name: DSP-1001660035398-H-E04


title: Male_Placenta_6PCB_NoFA_51_03

description: Library name: 51_03_PLAC

value: M

value: NO


title: A T1 12, young leaf, WGBS screening

description: Library name: A_12


title: TsixStop NPCd1

description: Library name: 104_TsixStop_NPCd1

value: Tsix Stop on 129 allele leading to non-random X inactivation upon differentiation


title: Male_Placenta_6PCB_NoFA_51_07

description: Library name: 51_07_PLAC

value: Placenta


title: Male_Placenta_6PCB_NoFA_51_02

description: Library name: 51_02_PLAC


title: FKBP-SETDB1 G6D2 ES, +dox

description: Library name: 98_SetG6D2_24hdox_ES

value: doxycyline for 24hours


title: Male_Placenta_6PCB_NoFA_51_05

description: Library name: 51_05_PLAC


title: Pt 11 Pre-treatment ROI 1 TME

description: Library name: DSP-1001660035398-H-E01

value: Pre-treatment


title: A T1 4, young leaf, WGBS screening

description: Library name: A_4

value: A T1


title: FKBP-SETDB1 A12A10 ES, +dox

description: Library name: 94_SetA12A10_24hdox_ES

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)


title: Pt 13 On-treatment ROI 6 Tumor

description: Library name: DSP-1001660035398-H-D10


title: Female_Placenta_6PCB_NoFA_57_06

description: Library name: 57_06_PLAC

value: F


title: Female_Placenta_6PCB_NoFA_57_05

description: Library name: 57_05_PLAC


title: Male_Placenta_6PCB_NoFA_51_01

description: Library name: 51_01_PLAC


title: A T1 1, young leaf, WGBS screening

description: Library name: A_1


title: TsixStop NPCd2

description: Library name: 105_TsixStop_NPCd2

value: NPC


title: TsixStop ES

description: Library name: 100_TsixStop_ES

value: mESC


title: Pt 13 On-treatment ROI 5 Tumor

description: Library name: DSP-1001660035398-H-D08

source_name: Ovary

value: Ovary


title: Pt 13 On-treatment ROI 4 TME

description: Library name: DSP-1001660035398-H-D07

value: TME


title: FKBP-SETDB1 A12A10 ES, +dTAG+dox

description: Library name: 95_SetA12A10_27hdTAG24hdox_ES

value: dTAG-13 for 27hours and doxycyline for 24hours


title: A T1 14, young leaf, WGBS screening

description: Library name: A_14

value: young leaves


title: Female_Placenta_6PCB_NoFA_57_07

description: Library name: 57_07_PLAC


title: Pt 13 On-treatment ROI 5 TME

description: Library name: DSP-1001660035398-H-D09

value: On-treatment


title: WT 6, young leaf, WGBS screening

description: Library name: WT_6

value: WT


title: FKBP-SETDB1 A12A10 ES Rep2

description: Library name: 92_SetA12A10_ES_Rep2


title: Pt 13 On-treatment ROI 4 Tumor

description: Library name: DSP-1001660035398-H-D06

value: Tumor


title: FKBP-SETDB1 G6D2 ES, +dTAG

description: Library name: 97_SetG6D2_27hdTAG_ES

value: dTAG-13 for 27hours


title: Female_Placenta_6PCB_NoFA_57_02

description: Library name: 57_02_PLAC

value: Placenta

value: NO


title: A T1 17, young leaf, WGBS screening

description: Library name: A_17


title: FKBP-SETDB1 A12A10 ES, +dTAG

description: Library name: 93_SetA12A10_27hdTAG_ES


title: FKBP-SETDB1 G6D2 ES Rep2

description: Library name: 96_SetG6D2_ES_Rep2


title: WT 4, young leaf, WGBS screening

description: Library name: WT_4


title: FKBP-SETDB1 P2F7 ES, +dox

description: Library name: 90_SetP2F7_24hdox_ES

value: doxycyline for 24hours


title: FKBP-SETDB1 P2F7 ES, +dTAG+dox

description: Library name: 91_SetP2F7_27hdTAG24hdox_ES


title: FKBP-SETDB1 P2F7 ES, +dTAG

description: Library name: 89_SetP2F7_27hdTAG_ES


title: Female_Placenta_6PCB_NoFA_57_04

description: Library name: 57_04_PLAC


title: Pt 13 On-treatment ROI 3 TME

description: Library name: DSP-1001660035398-H-D05


title: FKBP-SETDB1 P2F7 ES

description: Library name: 88_SetP2F7_ES


title: WT 3, young leaf, WGBS screening

description: Library name: WT_3


title: NTS, leaf, RNA, rep2

description: Library name: NTS_2

data_processing:
Adapter trimming and quality filtering were conducted using fastp (v0.23.2) with the parameters --cut_right --cut_window_size 4 --cut_mean_quality 20 --length_required 40
Trimmed reads were aligned to the Tomato reference genome SL4.0 using STAR aligner (v2.7.9a). The reference genome was indexed with STAR using the gene annotation file (ITAG4.1_gene_models.gtf) and the parameter --sjdbOverhang 150. Alignment was performed with the parameters ‘--outSAMtype BAM SortedByCoordinate, --quantMode GeneCounts --outWigType bedGraph’ which generated sorted BAM files, gene count files, and coverage bedGraph files that were converted to BigWig format using bedGraphToBigWig.
For TE quantification, trimmed reads were realigned in two-pass mode. Multi-mapping was permitted (--outFilterMultimapNmax 100 --winAnchorMultimapNmax 200) so that reads originating from repetitive elements would be retained. BAM files were analysed with TEcount (TEtranscripts v2.2.4) in multi-mapping mode (--mode multi) and without strand specification (--stranded no). ITAG4.1 Gene models and RepeatModeler-derived solLyc_ITAG4.0_RepeatModeler_repeats_light_TE.gtf were provided for quantification.
Assembly: SL4.0 (GCA_000188115.5)
Supplementary files format and content: Bigwig files (.bw) of the RNA-seq coverage scaled to Reads Per Million (RPM)
Supplementary files format and content: Tab delimited files (.tsv) for the unstranded counts for each Sample to Genes
Supplementary files format and content: Tab delimited files (.tsv) for the unstranded counts for each Sample to TEs and Genes

source_name: expanded leaf

extract_protocol:
Around 100 mg of the whole plant tissue were collected, snap frozen in liquid nitrogen and stored at -80oC. Tissue samples were ground using TissueLyser II (Qiagen) with sterile RNAse-free glass beads. RNA samples were extracted using the RNeasy plant mini kit (Qiagen). RNA quantity was measured by NanoDrop (Thermo Fisher Scientific). Genomic DNA in RNA samples was removed by a TURBO DNA-free kit (Thermo Fisher Scientific).
For mRNA-seq analysis, total RNA (10 µg) from each sample was used to purify polyA+ mRNA, which was then used for cDNA synthesis and amplification. RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit from Illumina (San Diego, CA). Sequencing of RNA libraries was carried out on an Illumina NextSeq 500 instrument (75 bp single-end).

value: expanded leaf

value: A T1

value: Non Transgenic Sibling


title: WT 2, young leaf, WGBS screening

description: Library name: WT_2


title: Pt 13 On-treatment ROI 2 TME

description: Library name: DSP-1001660035398-H-D03


title: Female_Placenta_6PCB_NoFA_51_04

description: Library name: 51_04_PLAC

value: F


title: Male_Placenta_1PCB_NoFA_49_07

description: Library name: 49_07_PLAC

value: M


title: Pt 13 On-treatment ROI 2 Tumor

description: Library name: DSP-1001660035398-H-D02


title: Pt 11 On-treatment ROI 5 TME

description: Library name: DSP-1001660035398-H-C11

value: Liver


title: Male_Placenta_1PCB_NoFA_47_06

description: Library name: 47_06_PLAC


title: WT 1, young leaf, WGBS screening

description: Library name: WT_1


title: Pt 13 On-treatment ROI 1 TME

description: Library name: DSP-1001660035398-H-D01

value: Ovary


title: FKBP-SETDB1 G6D2 ES

description: Library name: 86_SetG6D2_ES

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: mESC


title: Pt 13 On-treatment ROI 3 Tumor

description: Library name: DSP-1001660035398-H-D04

value: On-treatment


title: Male_Placenta_1PCB_NoFA_49_03

description: Library name: 49_03_PLAC


title: Pt 13 On-treatment ROI 1 Tumor

description: Library name: DSP-1001660035398-H-C12


title: NTS, leaf, RNA, rep1

description: Library name: NTS_1


title: TET3, leaf, RNA, rep2

description: Library name: TET3_2


title: Male_Placenta_1PCB_NoFA_47_02

description: Library name: 47_02_PLAC


title: FKBP-SETDB1 G6D2, dTAGd1, NPC d28

description: Library name: 82_SetG6D2_dTAGd1_diffd28

value: NPC

value: doxycyline for 28 days coupled with differentiation, dTAG-13 for 27 days


title: Male_Placenta_1PCB_NoFA_43_06

description: Library name: 43_06_PLAC


title: Male_Placenta_1PCB_NoFA_49_02

description: Library name: 49_02_PLAC


title: Pt 11 On-treatment ROI 5 Tumor

description: Library name: DSP-1001660035398-H-C10

value: Tumor


title: FKBP-SETDB1 A12A10 ES

description: Library name: 85_SetA12A10_ES


title: Female_Placenta_1PCB_NoFA_49_05

description: Library name: 49_05_PLAC

value: Placenta


title: TET3, leaf, RNA, rep1

description: Library name: TET3_1


title: FKBP-SETDB1 G6D2, Control, NPC d28

description: Library name: 81_SetG6D2_Control_diffd28

value: doxycyline for 28 days coupled with differentiation


title: Pt 11 On-treatment ROI 4 TME

description: Library name: DSP-1001660035398-H-C09

value: TME


title: WT, leaf, RNA, rep2

description: Library name: WT_2

value: expanded leaf

value: WT


title: Female_Placenta_1PCB_NoFA_49_04

description: Library name: 49_04_PLAC

value: NO


title: Pt 11 On-treatment ROI 4 Tumor

description: Library name: DSP-1001660035398-H-C08


title: Female_Placenta_1PCB_NoFA_47_07

description: Library name: 47_07_PLAC

value: F


title: Salmonella Typhimurium Δpimt, mid log, biol rep 3

city: Bareilly

first: Mahindhan

last: R

state: Uttar Pradesh

address: Division of Biochemistry, IVRI, Izatnagar

department: Division of Biochemistry

country: India

institute: ICAR-Indian Veterinary Research Institute

description:
Library name: Sample 6
Column name in Processed data file: pimt_3

data_processing:
Raw data from the Illumina platform were recorded in a FASTQ file. The quality of the reads was assessed using FastQC v0.12.1. The reads were passed through fastp v0.23.4 to remove adaptors, low-quality bases (Q< 36 bp). The trimmed reads were then passed through SortMeRNA v4.3.7 and were used against all eight rRNA databases provided to filter and remove rRNA reads.
Assembly: S. Typhimurium reference genome and annotation were downloaded from NCBI  (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/006/945/GCA_000006945.2_ASM694v2/). The trimmed & filtered reads were mapped to the reference genome using HISAT2 v2.2.1
Supplementary files format and content: Excel file contains filtered and normalized gene level expression data for all samples

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: whole cell

growth_protocol: S.Typhimurium wild-type and Δpimt mutant strains were grown in LB broth media at 37°C/ 180 rpm until mid-logarithmic phase (OD₆₀₀ ≈ 1). Cultures (10 mL) were harvested by centrifugation, and bacterial pellets were immediately frozen and stored at −80 °C until further processing.

extract_protocol:
Frozen bacterial pellets were subjected to RNA extraction using the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions. RNA was quantified using a Qubit fluorometer, and RNA integrity was assessed using High Sensitivity RNA ScreenTape to determine RIN values.
1000 ng of RNA sample was used for ribodepletion by using NEBNext rRNA depletion kit Bacteria (Cat. no. NEB E7850X). The NEBNextâ Ultra II Directional RNA Library prep kit for Illumina (Cat. no. E7760L) was used to construct double-stranded cDNA libraries from the rRNA-depleted RNA, using RNA fragmentation. First strand cDNA synthesis with random primers, second strand cDNA synthesis, end repair of double-stranded cDNA, adapter ligation, removal of excess adapter using sample purification beads, PCR enrichment of adapter-ligated DNA and clean-up of PCR products were done as instructed by the manufacturer’s protocol. The cleaned libraries were quantified on a Qubit fluorometer, and appropriate dilutions were loaded on a D1000 screen tape to determine the size range of the fragments and the average library size.

value: whole cell

value: pimt mutant


title: WT, leaf, RNA, rep1

description: Library name: WT_1

value: A T1


title: Pt 11 On-treatment ROI 3 TME

description: Library name: DSP-1001660035398-H-C07

value: Liver


title: FKBP-SETDB1 A12A10, Control, NPC d28

description: Library name: 79_SetA12A10_Control_diffd28

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)


title: FKBP-SETDB1 G6D2, dTAGd1, NPC d7

description: Library name: 65_SetG6D2_dTAGd1_diffd7

value: doxycyline for 7 days coupled with differentiation, dTAG-13 for 6 days


title: Salmonella Typhimurium Δpimt, mid log, biol rep 2

description:
Library name: Sample 5
Column name in Processed data file: pimt_2


title: Female_Placenta_1PCB_NoFA_49_01

description: Library name: 49_01_PLAC


title: Female_Placenta_1PCB_NoFA_47_01

description: Library name: 47_01_PLAC


title: Salmonella Typhimurium Δpimt, mid log, biol rep 1

description:
Library name: Sample 4
Column name in Processed data file: pimt_1


title: Salmonella Typhimurium, mid log, biol rep 3

description:
Library name: Sample 3
Column name in Processed data file: ST_3

value: Wild type


title: Female_Placenta_1PCB_NoFA_47_05

description: Library name: 47_05_PLAC


title: FKBP-SETDB1 G6D2, dTAGd1, NPC d6

description: Library name: 64_SetG6D2_dTAGd1_diffd6

value: NPC

value: doxycyline for 6 days coupled with differentiation, dTAG-13 for 5 days


title: FKBP-SETDB1 G6D2, dTAGd1, NPC d5

description: Library name: 63_SetG6D2_dTAGd1_diffd5

value: doxycyline for 5 days coupled with differentiation, dTAG-13 for 4 days


title: Pt 11 On-treatment ROI 2 Tumor

description: Library name: DSP-1001660035398-H-C04

value: Tumor

value: On-treatment


title: FKBP-SETDB1 G6D2, dTAGd1, NPC d4

description: Library name: 62_SetG6D2_dTAGd1_diffd4

value: doxycyline for 4 days coupled with differentiation, dTAG-13 for 3 days


title: Salmonella Typhimurium, mid log, biol rep 2

description:
Library name: Sample 2
Column name in Processed data file: ST_2


title: Female_Placenta_1PCB_NoFA_43_03

description: Library name: 43_03_PLAC

value: Placenta


title: Pt 11 On-treatment ROI 1 TME

description: Library name: DSP-1001660035398-H-C03

value: TME


title: FKBP-SETDB1 G6D2, dTAGd1, NPC d2

description: Library name: 60_SetG6D2_dTAGd1_diffd2

value: doxycyline for 2 days coupled with differentiation, dTAG-13 for 1 day


title: FKBP-SETDB1 A12A10, dTAGd1, NPC d28

description: Library name: 80_SetA12A10_dTAGd1_diffd28

value: doxycyline for 28 days coupled with differentiation, dTAG-13 for 27 days


title: Female_Placenta_1PCB_NoFA_43_01

description: Library name: 43_01_PLAC

value: F

value: NO


title: FKBP-SETDB1 G6D2, dTAGd1, NPC d3

description: Library name: 61_SetG6D2_dTAGd1_diffd3

value: doxycyline for 3 days coupled with differentiation, dTAG-13 for 2 days


title: CMS_spleen

city: Philadelphia

first: James

last: Garifallou

state: Pennsylvania

address: 3615 Civic Center Boulevard, ARC1014

department: Neonatology

institute: Children's Hospital of Philadelphia

data_processing:
Data was demultiplexed and processed using the cellranger mkfastq and count pipelines (10x genomics, v.6.1.2) for demultiplexing, alignment of sequencing reads to the rattus norvegicus transcriptome (mRatBN7.2)
Secondary analysis was performed using the Seurat package (v.5.0) (19) within the R computing environment. Spleen and pancreas datasets were analyzed separately. Each dataset was filtered for cell quality to include cells with greater than or equal to 250 UMIs, 250 genes expressed, and mitochondrial content less than 20 percent. Data was merged, normalized, and the top 2000 variable features were used for principal component analysis. The harmony package in R (20) was used on the PCA to account for per library batch effects in downstream UMAP and clustering (resolution 0.5). Small clusters expressing high levels of collagen and red blood cell genes were determined to be contaminating clusters and were removed from dataset. Cell types were annotated using canonical marker genes.
Assembly: mRatBN7.2
Supplementary files format and content: cell ranger feature barcode matrices
Supplementary files format and content: processed Seurat Object .RDS objects

organism: Rattus

source_name: spleen

extract_protocol:
The pancreas and spleens were isolated from postnatal day 1 (PD1) rats as described above.  Cells were isolated from 5 males and 5 females as described above.  Cells were pooled to generate 2 pancreas and 2 spleen samples from both males and females.  Cells were resuspended in 50uL BV buffer and 100uL buffer and 1uL FcR block was added and incubated at 4°C for 5 minutes.  Cd45 antibody (BD Biosciences 561586) was added and incubated at 4°C for 30 minutes.  Cells were washed in PBS and spun down at 500G at 4°C for 5 minutes.  Cells were resuspended in PBS and 1uL Live/Dead Violet dye (Invitrogen L23105) for at 4°C for 20 minutes.  Cells were washed in PBS and spun down at 500G at 4°C for 5 minutes.  Cells were resuspended in buffer. Cells were sorted by the FACSAria II and CD45+ Live cells were collected in 10% FBS in DMEM.  28,000-63,000 cells were collected for each pancreas sample and 100,000 cells were collected for each spleen sample.  Cells were spun at 500G at 4°C for 5 minutes and resuspended in PBS. Viability was then confirmed to be above 85% and cells were counted.
Next generation sequencing libraries were prepared at The Center for Applied Genomics at Children’s Hospital of Philadelphia using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v2 as per manufacturer instructions (PN-120237).  cDNA and library preparation quality were confirmed with the Agilent Bioanalyzer High Sensitivity Kit and final concentration was determined with a KAPA Library Quantification Kit (PN-07960140001).  Libraries were individually indexed, pooled, and sequenced on the Illumina Hiseq2500 using SBS chemistry v4 in a paired-end, single indexing run.

value: spleen

value: CD45+ Immune cells


title: Male_Placenta_0.1PCB_NoFA_30_05

description: Library name: 30_05_PLAC

value: M


title: Pt 2 On-treatment ROI 6 Tumor

description: Library name: DSP-1001660035398-H-B12

source_name: Lung

value: Lung


title: FKBP-SETDB1 G6D2, Control, NPC d4

description: Library name: 56_SetG6D2_Control_diffd4

source_name: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: Cast x 129S

value: NPC

value: doxycyline for 4 days coupled with differentiation


title: FKBP-SETDB1 G6D2, Control, NPC d6

description: Library name: 58_SetG6D2_Control_diffd6

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: doxycyline for 6 days coupled with differentiation


title: Salmonella Typhimurium, mid log, biol rep 1

description:
Library name: Sample 1
Column name in Processed data file: ST_1

value: whole cell

value: Wild type


title: FKBP-SETDB1 G6D2, Control, NPC d7

description: Library name: 59_SetG6D2_Control_diffd7

value: doxycyline for 7 days coupled with differentiation


title: Female_Placenta_1PCB_NoFA_43_02

description: Library name: 43_02_PLAC

value: Placenta


title: Pt 11 On-treatment ROI 2 TME

description: Library name: DSP-1001660035398-H-C05

value: Liver

value: TME

value: On-treatment


title: Pt 11 On-treatment ROI 1 Tumor

description: Library name: DSP-1001660035398-H-C02

value: Tumor


title: IMS_spleen

value: spleen


title: FKBP-SETDB1 G6D2, Control, NPC d3

description: Library name: 55_SetG6D2_Control_diffd3

value: doxycyline for 3 days coupled with differentiation


title: FKBP-SETDB1 G6D2, Control, NPC d5

description: Library name: 57_SetG6D2_Control_diffd5

value: doxycyline for 5 days coupled with differentiation


title: CFS_spleen

value: CD45+ Immune cells


title: IMP_pancreas

source_name: pancreas

value: pancreas


title: Pt 2 On-treatment ROI 6 TME

description: Library name: DSP-1001660035398-H-C01

value: Lung


title: Pt 2 On-treatment ROI 5 TME

description: Library name: DSP-1001660035398-H-B11


title: Pt 2 On-treatment ROI 4 Tumor

description: Library name: DSP-1001660035398-H-B08


title: Male_Placenta_0.1PCB_NoFA_27_01

description: Library name: 27_01_PLAC

value: M

value: NO


title: CMP_pancreas


title: Male_Placenta_0.1PCB_NoFA_30_01

description: Library name: 30_01_PLAC


title: Male_Placenta_0.1PCB_NoFA_27_02

description: Library name: 27_02_PLAC


title: Pt 2 On-treatment ROI 4 TME

description: Library name: DSP-1001660035398-H-B09


title: IFP_pancreas


title: FKBP-SETDB1 G6D2, Control, NPC d2

description: Library name: 54_SetG6D2_Control_diffd2

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: NPC

value: doxycyline for 2 days coupled with differentiation


title: Male_Placenta_0.1PCB_NoFA_30_04

description: Library name: 30_04_PLAC

value: Placenta


title: Pt 2 On-treatment ROI 3 TME

description: Library name: DSP-1001660035398-H-B07


title: Pt 2 On-treatment ROI 5 Tumor

description: Library name: DSP-1001660035398-H-B10


title: Pt 11 On-treatment ROI 3 Tumor

description: Library name: DSP-1001660035398-H-C06

value: Liver


title: Female_Placenta_0.1PCB_NoFA_30_08

description: Library name: 30_08_PLAC

value: F


title: FKBP-SETDB1 G6D2, Control, NPC d1

description: Library name: 53_SetG6D2_Control_diffd1

value: doxycyline for 1 day coupled with differentiation


title: Female_Placenta_0.1PCB_NoFA_30_07

description: Library name: 30_07_PLAC


title: FKBP-SETDB1 A12A10, dTAGd1, NPC d6

description: Library name: 51_SetA12A10_dTAGd1_diffd6

value: doxycyline for 6 days coupled with differentiation, dTAG-13 for 5 days


title: FKBP-SETDB1 A12A10, dTAGd1, NPC d7

description: Library name: 52_SetA12A10_dTAGd1_diffd7

value: doxycyline for 7 days coupled with differentiation, dTAG-13 for 6 days


title: CFP_pancreas


title: Pt 2 On-treatment ROI 2 Tumor

description: Library name: DSP-1001660035398-H-B04

value: Tumor

value: On-treatment


title: Pt 2 On-treatment ROI 3 Tumor

description: Library name: DSP-1001660035398-H-B06


title: J3411 LPi_3

city: Pozuelo de Alracon

first: Juan

middle: Carlos

last: del Pozo

state: Madrid

address: Campus de Montegancedo, UPM

department: Biotechnology

country: Spain

institute: Centro de Biotecnología y Genómica de Plantas

description: Library name: Lateral Root cap LPi_3

data_processing:
Basecalls performed using CASAVA version 1.4
For reads alignment, FastQC (v0.11.9) (26) and multiqc (v1.7) (27) were used for quality control analyses.
Assembly: Reads count to a reference  genome  (TAIR 42.gff3) using the STAR aligner (v2.5.3a)
Supplementary files format and content: To identify differential expressed gene (DEGs), first the HTSeq (v1.99.2) was used with the intersection 'union' option to generate read counts per gene based on RNA-seq mapped reads and Araport11 annotation. Normalization and statistical analysis of differential gene expression was performed using the DESeq2 Bioconductor package in R (v1.38.3). Genes were considered differentially expressed (DE), either up- or down-regulated, if they had a log2 fold change [log2-FC] > 0.58 with an adjusted P value ≤ 0.05

organism: Arabidopsis thaliana

source_name: root cells

growth_protocol: seedlings grown at 22ºC in half strength MS medium with high or low phsophate for 6 days in a growth chamber with 16 hour of light and 8 hour of darkness

extract_protocol:
Total  RNA was isolated from Arabidopsis plants using the Trizol reagent and RNeasy columns (Qiagen). Quantity and quality measurements were taken using a NanoDrop spectrophotometer and Bioanalyzer.
cDNA synthesis and library preparation for all the samples were performed with the  SMART-Seq v4 Ultra Low Input RNA kit (Takara, Mountain View, CA, USA) and the SMARTer® ThruPLEX® DNA-Seq Kit (Takara) kits following the manufacture’s instructions.

treatment_protocol: Control seedlings were grown in MS medium with high phosphate (HPi) and treatment was grown with 5 uM of phsophate (LPi) for 6 days. Afterwards, different cell types were shorted by fluorescence-activated cell sorting (FACS)

value: root cells

value: lateral root cap

value: Wild Type

value: grown 6 days in a hal stregth MS medium without Phosphate_replicate_3


title: Skin_PD2

type: RNA

first: Hanjae

address: 103, Daehak-ro, Jongno-gu

institute: Seoul National University

hyb_protocol: Hybridization of the probes was performed on the automated Xenium Analyzer platform. In brief, cycles of fluorescent probe binding, imaging, and probe removal were conducted, and the probe signals were captured. For further details, refer to the Xenium protocol: Xenium In Situ Gene Expression User Guide.

scan_protocol: A round of imaging was performed on the automated Xenium Analyzer platform.

data_processing: DAPI-based cell segmentation was performed using Xenium Analyzer’s onboard analysis, and the gene count matrix was curated. The raw data was subsequently processed with Xenium Ranger software to adjust the processing options.

label: Xenium probe

source_name: Mouse dorsal skin

label_protocol: The Xenium mouse custom and brain panel probe sets were used.

extract_protocol: Formalin-fixed paraffin-embedded (FFPE) tissue sections (5 μm thick) were prepared for each time point.

tag: developmental stage

value: Postnatal day 2


title: Female_Placenta_0.1PCB_NoFA_30_06

description: Library name: 30_06_PLAC

value: NO


title: FKBP-SETDB1 A12A10, dTAGd1, NPC d4

description: Library name: 49_SetA12A10_dTAGd1_diffd4

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: doxycyline for 4 days coupled with differentiation, dTAG-13 for 3 days


title: Female_Placenta_0.1PCB_NoFA_27_07

description: Library name: 27_07_PLAC

value: Placenta


title: Pt 2 On-treatment ROI 1 Tumor

description: Library name: DSP-1001660035398-H-B02

value: Lung


title: Skin_E18.5

value: Embryonic day 18.5


title: Pt 2 On-treatment ROI 1 TME

description: Library name: DSP-1001660035398-H-B03

value: TME


title: Female_Placenta_0.1PCB_NoFA_30_02

description: Library name: 30_02_PLAC

value: F


title: J3411 LPi_1

description: Library name: Lateral Root cap LPi_1

value: grown 6 days in a hal stregth MS medium without Phosphate_replicate_1


title: Female_Placenta_0.1PCB_NoFA_30_03

description: Library name: 30_03_PLAC


title: FKBP-SETDB1 A12A10, dTAGd1, NPC d5

description: Library name: 50_SetA12A10_dTAGd1_diffd5

value: NPC

value: doxycyline for 5 days coupled with differentiation, dTAG-13 for 4 days


title: J3411 LPi_2

description: Library name: Lateral Root cap LPi_2

value: root cells

value: grown 6 days in a hal stregth MS medium without Phosphate_replicate_2


title: J3411 HPi_2

description: Library name: Lateral Root cap HPi_2

value: lateral root cap

value: Wild Type

value: grown 6 days in a hal stregth MS medium with Phosphate_replicate_2


title: Pt 9 On-treatment ROI 6 TME

description: Library name: DSP-1001660035398-H-A12

source_name: LOV

value: LOV

value: On-treatment


title: FKBP-SETDB1 A12A10, dTAGd1, NPC d3

description: Library name: 48_SetA12A10_dTAGd1_diffd3

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: doxycyline for 3 days coupled with differentiation, dTAG-13 for 2 days


title: J3411 HPi_1

description: Library name: Lateral Root cap HPi_1

value: grown 6 days in a hal stregth MS medium with Phosphate_replicate_1


title: Pt 2 On-treatment ROI 2 TME

description: Library name: DSP-1001660035398-H-B05

value: Lung


title: SHR::GFP LPi_3

description: Library name: stele LPi_3

value: stele

value: grown 6 days in a hal stregth MS medium without Phosphate_replicate_3


title: Female_Placenta_0.1PCB_NoFA_27_06

description: Library name: 27_06_PLAC

value: Placenta

value: F

value: NO


title: J3411 HPi_3

description: Library name: Lateral Root cap HPi_3

value: root cells

value: grown 6 days in a hal stregth MS medium with Phosphate_replicate_3


title: Pt 9 On-treatment ROI 6 Tumor

description: Library name: DSP-1001660035398-H-A11

value: Tumor


title: FKBP-SETDB1 A12A10, dTAGd1, NPC d2

description: Library name: 47_SetA12A10_dTAGd1_diffd2

value: NPC

value: doxycyline for 2 days coupled with differentiation, dTAG-13 for 1 day


title: FKBP-SETDB1 A12A10, Control, NPC d7

description: Library name: 46_SetA12A10_Control_diffd7

value: doxycyline for 7 days coupled with differentiation


title: Female_Placenta_0.1PCB_NoFA_27_04

description: Library name: 27_04_PLAC


title: Pt 9 On-treatment ROI 3 TME

description: Library name: DSP-1001660035398-H-A07

value: LOV

value: TME

value: On-treatment


title: FKBP-SETDB1 A12A10, Control, NPC d3

description: Library name: 42_SetA12A10_Control_diffd3

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: doxycyline for 3 days coupled with differentiation


title: SHR::GFP LPi_1

description: Library name: stele LPi_1

value: stele

value: Wild Type

value: grown 6 days in a hal stregth MS medium without Phosphate_replicate_1


title: Pt 9 On-treatment ROI 5 Tumor

description: Library name: DSP-1001660035398-H-A10


title: Female_Placenta_0.1PCB_NoFA_27_05

description: Library name: 27_05_PLAC

value: Placenta

value: F


title: FKBP-SETDB1 A12A10, Control, NPC d6

description: Library name: 45_SetA12A10_Control_diffd6

value: doxycyline for 6 days coupled with differentiation


title: Pt 9 On-treatment ROI 4 TME

description: Library name: DSP-1001660035398-H-A09


title: Female_Placenta_0.1PCB_NoFA_27_03

description: Library name: 27_03_PLAC

value: NO


title: Pt 9 On-treatment ROI 2 TME

description: Library name: DSP-1001660035398-H-A05


title: FKBP-SETDB1 A12A10, Control, NPC d5

description: Library name: 44_SetA12A10_Control_diffd5

value: doxycyline for 5 days coupled with differentiation


title: FKBP-SETDB1 A12A10, Control, NPC d4

description: Library name: 43_SetA12A10_Control_diffd4

value: NPC

value: doxycyline for 4 days coupled with differentiation


title: SHR::GFP HPi_2

description: Library name: stele HPi_2

value: root cells

value: grown 6 days in a hal stregth MS medium with Phosphate_replicate_2


title: Male_Placenta_0PCB_NoFA_10_03

description: Library name: 10_03_PLAC

value: M


title: SHR::GFP LPi_2

description: Library name: stele LPi_2

value: grown 6 days in a hal stregth MS medium without Phosphate_replicate_2


title: SHR::GFP HPi_1

description: Library name: stele HPi_1

value: grown 6 days in a hal stregth MS medium with Phosphate_replicate_1


title: Pt 9 On-treatment ROI 4 Tumor

description: Library name: DSP-1001660035398-H-A08

value: LOV

value: Tumor

value: On-treatment


title: FKBP-SETDB1 A12A10, Control, NPC d2

description: Library name: 41_SetA12A10_Control_diffd2

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: doxycyline for 2 days coupled with differentiation


title: Pt 9 On-treatment ROI 2 Tumor

description: Library name: DSP-1001660035398-H-A04


title: Pt 9 On-treatment ROI 1 TME

description: Library name: DSP-1001660035398-H-A03

value: TME


title: Pt 9 On-treatment ROI 3 Tumor

description: Library name: DSP-1001660035398-H-A06


title: Male_Placenta_0PCB_NoFA_6_02

description: Library name: 6_02_PLAC

value: Placenta


title: J0661 LPi_2

description: Library name: pericycle LPi_2

value: pericycle

value: Wild Type


title: FKBP-SETDB1 A12A10, Control, NPC d1

description: Library name: 40_SetA12A10_Control_diffd1

value: NPC

value: doxycyline for 1 day coupled with differentiation


title: J0661 LPi_3

description: Library name: pericycle LPi_3

value: root cells

value: grown 6 days in a hal stregth MS medium without Phosphate_replicate_3


title: SHR::GFP HPi_3

description: Library name: stele HPi_3

value: stele

value: grown 6 days in a hal stregth MS medium with Phosphate_replicate_3


title: FKBP-SETDB1 G6D2, dTAGd1, NPC d20

description: Library name: 32_SetG6D2_dTAGd1_diffd20

value: doxycycline for 20 days coupled with differentiation, dTAG-13 for 19 days


title: Male_Placenta_0PCB_NoFA_1_06

description: Library name: 1_06_PLAC

value: M

value: NO


title: Male_Placenta_0PCB_NoFA_10_01

description: Library name: 10_01_PLAC


title: FKBP-SETDB1 A12A10, dTAGd1, NPC d20

description: Library name: 27_SetA12A10_dTAGd1_diffd20


title: Male_Placenta_0PCB_NoFA_1_05

description: Library name: 1_05_PLAC


title: FKBP-SETDB1 G6D2, Control, NPC d20

description: Library name: 31_SetG6D2_Control_diffd20

value: doxycycline for 20 days coupled with differentiation


title: Human FF-EVs, Young, Rep 3

city: Lone Tree

first: Ye

last: Yuan

state: Colorado

address: 10290 RidgeGate Circle

department: Research

institute: Colorado Center for Reproductive Medicine

description: Library name: FF_EV_miRNA_Y3

data_processing:
Data were analyzed using the CLC Genomics Workbench software, version 21 (www.qiagenbioinformatics.com). Trimming of raw sequencing reads was based on quality score (Q‐score >30), ambiguous nucleotides (maximum two nucleotides allowed), read length (≥15 nucleotides), and removal of adapter sequences.
Small-RNA reads were annotated against human precursor and mature miRNAs listed in the mirBase database (release 22) using the Quantify miRNA tools with default software parameters applied.
Normalization of raw expression data was performed using the trimmed mean of M-values (TMM) normalization method and presented as transcripts per million (TPM) for genes.
Normalization of raw expression data was performed using the trimmed mean of M-values (TMM) normalization method and presented as TMM-adjusted counts per million (CPM) for miRNAs. A miRNA with a CPM ≥ 10 in at least 2 replicates was considered expressed.
The CLC Genomics Workbench Differential Expression tool was used for the expression analysis comparison of the two groups (Young v. Aged). Differential expression of miRNA was defined as a fold change ≥ 2, p-value ≤ 0.05, and false discovery rate (FDR) ≤ 0.10.
Assembly: mirBase database (release 22)
Supplementary files format and content: Comma delimited file (CSV) that includes raw counts and normalized counts (CPM = Counts per million) for each sample. It also includes fold change, p-value, and false discovery rate
Supplementary files format and content: Comma delimited file (CSV) that includes filtered list of differentially expressed (DE) miRNA with FC ≥2, p-value ≤ 0.05, and FDR ≤ 0.10.

source_name: follicular fluid extracellular vesicles

extract_protocol:
Follicular fluid EV samples were thawed on ice and total RNA was isolated using an Exosomal RNA Isolation Kit (Norgen Biotek Corp., Cat. 58000) according to the manufacturer’s instructions. The RNA integrity and concentration were measured using an Agilent 2100 Bioanalyzer (Agilent Technologies, CA) and a NanoDrop™ 2000 Spectrophotometer (ThermoFisher Scientific, Cat. ND-2000), respectively.
The isolated total RNA was sent to Novogene Co. LTD (California, USA) for library preparation and sequencing. The small-RNA libraries were constructed using the TruSeq Small RNA Library Prep Kit (Illumina RS-200) according to the manufacturer’s instructions. Library quantity and quality measurements were taken using a Qubit® DNA HS Assay Kit on a Qubit® 2.0 Fluorometer and an Agilent DNA High Sensitivity Kit in an Agilent 2100 Bioanalyzer, respectively. Library concentrations were calculated using quantitative PCR, then pooled in equimolar ratios, and sequenced on a NovaSeq6000 sequencing instrument (Illumina) as single-end, 50-base reads for miRNA sequencing.

value: follicular fluid extracellular vesicles

value: Young (< 32 y.o.)


title: Female_Placenta_0PCB_NoFA_6_01

description: Library name: 6_01_PLAC

value: F


title: Male_Placenta_0PCB_NoFA_1_03

description: Library name: 1_03_PLAC


title: Pt 9 On-treatment ROI 1 Tumor

description: Library name: DSP-1001660035398-H-A02

value: LOV

value: Tumor

value: On-treatment


title: Male_Placenta_0PCB_NoFA_1_02

description: Library name: 1_02_PLAC

value: Placenta


title: J0661 HPi_3

description: Library name: pericycle HPi_3

value: pericycle

value: Wild Type


title: J0661 LPi_1

description: Library name: pericycle LPi_1

value: root cells

value: grown 6 days in a hal stregth MS medium without Phosphate_replicate_1


title: Female_Placenta_0PCB_NoFA_6_03

description: Library name: 6_03_PLAC


title: J0661 HPi_2

description: Library name: pericycle HPi_2

value: grown 6 days in a hal stregth MS medium with Phosphate_replicate_2


title: Female_Placenta_0PCB_NoFA_10_02

description: Library name: 10_02_PLAC


title: Human FF-EVs, Young, Rep 1

description: Library name: FF_EV_miRNA_Y1


title: Human FF-EVs, Aged, Rep 3

description: Library name: FF_EV_miRNA_A3


title: FKBP-SETDB1 P2F7 ES, dTAG+dox, Input, double crosslinking

description: Library name: xxC076_dTSETDB1P2F7_dTAGdox_input

data_processing:
ChIP-sequencing analysis was performed using previously established pipelines45. For calibrated ChIP-seq experiments, raw fastq reads were mapped using Bowtie2 (v.2.3.5.1)67 to the 129S1xCast N-masked mm10 genome concatenated with the dm6 Drosophila genome using the following parameters: “--very-sensitive --no-discordant --no-mixed -X 2000”. Unmapped reads were then removed. PCR duplicates were identified and removed using picard-tools “MarkDuplicates” (Broad Institute) and remaining reads were then assigned to each allele using SNPsplit68. To calculate calibration factors, mm10 and dm6 mapped reads for each sample and input were counted using SAMtools (v.1.16)69. Calibration factors for cChIP-seq were then calculated according to the derived formula for occupancy ratio (ORi)70. In order to generate calibrated bigwig files for mouse chrX, bam files were initially filtered using the “intersect” function from BEDtools (v.2.30.0)71 to generate a bam file containing mouse chrX reads only. During the generation of the iXist-ChrXCast cell line using CRISPR-Cas9–facilitated homology-directed recombination, two SNPs (mm10, chrX:103482682 A/T and mm10, chrX:103482895 A/T) between the Cast and 129 alleles became uninformative, as both X alleles were converted to the 129 allele (T at both positions). Consequently, any reads spanning these two sites are no longer allele-specific as intended and were therefore removed from the allelic BAM files. BAM files were then sorted and indexed using SAMtools69 and bigWig files were finally generated using deepTools (v.3.5.1)72 bamCoverage per 10 million reads considering the calibration factors. For KAP1 and MPP8 (non-calibrated), ChIP signal was calculated from one million library size normalized values. BigWig files were then visualized using IGV (https://software.broadinstitute.org/software/igv/)73. To quantify the number of ChIP reads per kb over the Xist locus (chrX: 103460373-103483233), we used the function “bigWigAverageOverBed” from UCSCTools.
Assembly: mm10; dm6
Supplementary files format and content: bigWig

growth_protocol: mESC were grown in ESC medium at 37oC in a 5% CO2 incubator and passaged onto 0.1% gelatin-coated plates in feeder-dependent conditions every 2-3 days using TrypLE Express (Life Technologies). Mitomycin C-inactivated SNLP (STO mouse fibroblasts expressing Neomycin and Puromycin resistance and Lif genes) were used as feeder cells. Cells were pre-plated and passaged at least twice to remove feeders prior to cell collection for genomic experiments. ESC medium consisted of Dulbecco’s Modified Eagle Medium (DMEM; Life Technologies) supplemented with 10% Fetal Bovine Serum (FBS), 1x NEAA (Non-essential amino acids; Life Technologies), 2mM L-glutamine (Life Technologies), 1x Penicillin-Streptomycin (Life Technologies), 50µM b-mercaptoethanol (Life Technologies) and Leukemia Inhibitory Factor (LIF)-conditioned medium made in-house.

extract_protocol:
For RNA polymerase II calibrated ChIP-seq (cChIP-seq), 5x107 mESCs were pooled with 1x107 Drosophila cells after collection, washed in PBS wash and counted using a Countess II FL Automated Cell Counter (Life Technologies). Cells were crosslinked for 10min with 1% formaldehyde. The reaction was quenched using glycine for additional 10min before recovering the cells by centrifugation at 1000g for 5min at 4oC. After a PBS wash, supernatant was removed and cells were snap frozen and stored at -80oC until use. Cell pellets were thawed on ice, resuspended in 1mL of FA-Lysis Buffer (50 mM HEPES pH7.9, 150 mM NaCl, 2 mM EDTA, 0.5 mM EGTA, 0.5% NP-40, 0.1%  Sodium deoxycholate, 0.1% SDS) supplemented with protease inhibitors, 1 mM AEBSF, 10 mM NaF and incubated on ice for 10min prior to sonication using a Bioruptor Pico Sonicator (Diagenode) for 30 cycles (30sec on/off). Post-sonication chromatin was spun at maximum speed for 10min at 4oC and the supernatant was transferred to a new 1.5mL tube. For each IP, 300µg of chromatin were diluted to a total volume of 1mL in FA-Lysis Buffer and precleared by incubation with 40µL of pre-blocked rProtein A Sepharose™ Fast Flow bead slurry (Amersham) for 1h at 4oC with rotation. Pre-cleared chromatin was aliquoted in 1.5mL Protein lobind tubes and incubated overnight at 4oC with rotation with the corresponding antibody (15µL Anti-Rbp1 NTD, D8L4Y, Cell Signaling Technologies; 12.5µL Anti-Rbp1 Ser5P, D9N5I, Cell Signaling Technologies; 12.5µL Anti-Rbp1 Ser2P, E1Z3G, Cell Signaling Technologies). 10% of pre-cleared chromatin was kept as input. After incubation, 40µL of pre-blocked rProtein A Sepharose™ Fast Flow bead slurry (Amersham) were added to each sample and incubated for a minimum of 3h at 4oC followed by single 5min washes at 4oC with FA-Lysis, FA-Lysis 500 (same composition as FA-Lysis Buffer but with 500mM NaCl) and DOC (10 mM Tris pH8.0, 250 mM LiCl, 2 mM EDTA, 0.5% NP-40, 0.5% Sodium deoxycholate) buffers and two washes with TE pH8.0. The DNA was then eluted from the beads by incubation at 30oC for 30 min shaking at 1000rpm with 1% SDS, 100 mM NaHCO3 elution buffer and separated from the beads by centrifugation. IP and input samples were reverse crosslinked overnight and RNAse- and Proteinase K-treated, and the DNA was further purified using the ChIP DNA Clean and Concentrator Kit (Zymo Research) according to manufacturer’s instructions. For KAP1 and MPP8 ChIP-seq, 5x107 mESC cells were collected in PBS and double crosslinked by incubating with 2mM DSG for 50min at room temperature followed by an additional 12min with 1% formaldehyde. The reaction was quenched by addition of glycine and further incubation with rotation for 10min. Cells were pelleted by centrifugation, washed once with PBS and the pellet was snap frozen and stored at -80oC. To prepare chromatin, the cell pellets were thawed on ice and lysed in 10mL of LB1 (50mM HEPES-KOH pH 7.9, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X-100) supplemented with protease inhibitors for 10min, rotating at 4oC. Nuclei were recovered by centrifugation and resuspended in 10mL LB2 (10mM Tris pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) with protease inhibitors and incubated rotating for 10min. After centrifugation, the pellet was resuspended in 1mL of LB3 (10mM Tris pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-lauroylsarcosine) with protease inhibitors per 5x 107 cells and subjected to sonication using a Bioruptor Pico (Diagenode) for 30 cycles (30 sec on/off). After sonication, samples were spun for 2 min 2000rpm at 4oC and the supernatant was collected into a new tube to which 110µL of LB3 with 10% Triton X-100 were added and mixed by inversion. Chromatin was spun at maximum speed for 10 min and the supernatant was collected into a new tube, snap frozen and stored. For immunoprecipitation, chromatin was thawed on ice and 110µL were taken per reaction and diluted in 990µL ChIP dilution buffer (1% Triton X-100, 1mM EDTA, 20 mM Tris pH 8.0, 150 mM NaCl). Chromatin was precleared by incubation with pre-blocked rProtein A Sepharose™ Fast Flow beads (Amersham) for 1 hour (40μL bead slurry/mL of chromatin) at 4oC and 100μL set aside as input. Antibodies (KAP1, Abcam, ab22553, 5µg; MPP8, Proteintech, 16796-1-AP, 7µg) were added to 1mL of precleared chromatin each and incubated overnight at 4oC with rotation. Samples were then incubated for 4h with 40µL of pre-blocked rProtein A Sepharose™ Fast Flow beads (Amersham) followed by single 4min washes with Low Salt (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris pH 8.0, 150mM NaCl), High Salt (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris pH 8.0, 500mM NaCl), LiCl (0.25M LiCl, 1% NP-40, 1% Deoxycholate, 1mM EDTA, 10mM Tris pH 8.0) wash buffers and two washes with 1xTE. The DNA was then eluted from the beads by incubation at 25oC for 30 min shaking at 1000rpm with 1% SDS, 100 mM NaHCO3 elution buffer and separated from the beads by centrifugation. IP and input samples were reverse crosslinked overnight and RNAse- and Proteinase K-treated, and the DNA was further purified using the ChIP DNA Clean and Concentrator Kit (Zymo Research) according to manufacturer’s instructions.
ChIP and input DNA was quantified using the Qubit High Sensitivity DNA kit (Invitrogen) and submitted to library preparation using the the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions. Libraries were quantified using the Qubit High Sensitivity DNA kit (Invitrogen) and their length was estimated using the Bioanalyzer High Sensitivity DNA kit (Agilent) before pooling and subjected to paired-end sequencing on an Illumina NextSeq 500 machine using NextSeq 500/550 High-Output v2.5 Kit (150 cycles) (Illumina).

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: mESC

value: dTAG-13 for 27hours and doxycycline for 24 hours

tag: chip antibody

tag: spike-in


title: FKBP-SETDB1 P2F7 ES, dox, Input, double crosslinking

description: Library name: xxC075_dTSETDB1P2F7_dox_input

tag: strain background

value: doxycycline for 24hours


title: Human FF-EVs, Young, Rep 2

description: Library name: FF_EV_miRNA_Y2

tag: tissue

value: follicular fluid extracellular vesicles


title: J0661 HPi_1

description: Library name: pericycle HPi_1

tag: cell line

tag: cell type

value: grown 6 days in a hal stregth MS medium with Phosphate_replicate_1


title: Female_Placenta_0PCB_NoFA_1_07

description: Library name: 1_07_PLAC

value: F

value: NO


title: FKBP-SETDB1 A12A10, Control, NPC d20

description: Library name: 25_SetA12A10_Control_diffd20

value: NPC

tag: genotype

tag: treatment

value: doxycycline for 20 days coupled with differentiation


title: Female_Placenta_0PCB_NoFA_1_04

description: Library name: 1_04_PLAC

value: Placenta

tag: strain


title: Human FF-EVs, Aged, Rep 2

description: Library name: FF_EV_miRNA_A2


title: FKBP-SETDB1 P2F7 ES, Control, Input, double crosslinking

description: Library name: xxC074_dTSETDB1P2F7_ES_input


title: Male_Brain_0.1PCB_YesFA_36_05

description: Library name: 36_05_BRAIN

value: Brain

tag: Sex

value: M

value: Yes


title: J0571 LPi_3

description: Library name: cortex LPi_3

value: root cells

value: cortex

value: Wild Type

value: grown 6 days in a hal stregth MS medium without Phosphate_replicate_3


title: FKBP-SETDB1 P2F7 ES, dTAG+dox, KAP1

description: Library name: xxC073_dTSETDB1P2F7_dTAGdox_KAP1

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: mESC

value: anti-KAP1 (Abcam, Cat# ab22553)


title: J0571 LPi_1

description: Library name: cortex LPi_1

value: grown 6 days in a hal stregth MS medium without Phosphate_replicate_1


title: FKBP-SETDB1 P2F7 ES, Control, KAP1

description: Library name: xxC071_dTSETDB1P2F7_ES_KAP1


title: Female_Placenta_0PCB_NoFA_1_01

description: Library name: 1_01_PLAC

value: F

tag: pcb treatment


title: SCLC_2_TCR

first: Yu

address: No.1 Shuaifuyuan Wangfujing Dongcheng District

department: Department of Neurosurgery

institute: Peking Union Medical College Hospital

description:
Library name: 1357_TCR
TCR VDJ transcripts library enriched from total cDNA

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were madeusing the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-.gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Human GRCh38
Supplementary files format and content: Cell Ranger multi output files: 5GEX_barcodes.tsv.gz, 5GEX_features.tsv.gz, 5GEX_matrix.mtx.gz
Supplementary files format and content: Cell Ranger multi output files: clonetypes.csv, contig_annotations.csv.
Library strategy: TCR-Seq

source_name: Brain Metastasis

extract_protocol:
Briefly, tissues were cut into approximately 1-2 mm3 pieces in the RPMI-1640 medium (Gibco), and enzymatically digested with gentleMACS (Miltenyi) using program 37C_m_TDK_2 on a rotor at 37°C, according to manufacturer’s instruction. The dissociated cells were subsequently passed through a 100 µm SmartStrainer and centrifuged at 400 g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi) and incubated on ice for 1-2 min to lyse red blood cells. After washing twice with 1× PBS (Gibco), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 2% fetal bovine serum (FBS, Gibco)). Single cell suspensions were stained with antibodies against 7AAD for FACS sorting, performed on a BD Melody instrument. Based on FACS analysis, single cells were sorted into 1.5 ml tubes and determine cell viability and cell concentration using a Countstar Automated Cell Counter.
Cells were loaded by using the 10x Chromium Single Cell V(D)J Reagent Kits v2. Cells were captured in droplets to generate nanoliter-scale Gel bead in EMulsion (GEMs). GEMs were then reverse transcribed in a C1000 Touch Thermal Cycler (Bio-Rad programmed at 53℃ for 45 min, 85℃ for 5 min, and held at 4℃. After reverse transcription and cell barcoding, emulsions were broken and cDNA was isolated and purified with Cleanup Mix containing DynaBeads and SPRIselect reagent (Thermo Fisher Scientific), followed by PCR amplification. Amplified cDNA was then used for both 5’ gene expression library construction and TCR/BCR V(D)J targeted enrichment performed with the Chromium Single Cell V(D)J Enrichment Kit (10x Genomics), followed by V(D)J library construction. For RNA-seq library construction, amplified cDNA was fragmented and end-repaired, double-sided size-selected, PCR-amplified with sample indexing primers, and double-sided size-selected. For TCR/BCR library construction, TCR/BCR transcripts were enriched from amplified cDNA by PCR. Subsequently, enriched PCR product was fragmented and end-repaired, size-selected, PCR-amplified with sample-indexing primers, and size-selected. Libraries prepared according to the manufacturer’s user guide were then purified and profiled for quality assessment. Single-cell RNA and TCR/BCR V(D)J libraries were sequenced by an Illumina NovaSeq 6000 sequencer with 150 bp paired-end reads (performed by Analytical Bioscience Limited, Beijing).

value: Brain Metastasis

tag: primary tumor

value: Small cell lung cancer

tag: group

value: Obese

tag: library type

value: TCR


title: FKBP-SETDB1 P2F7 ES, dox, KAP1

description: Library name: xxC072_dTSETDB1P2F7_dox_KAP1

value: doxycycline for 24hours


title: J0571 LPi_2

description: Library name: cortex LPi_2

value: grown 6 days in a hal stregth MS medium without Phosphate_replicate_2


title: J0571 HPi_3

description: Library name: cortex HPi_3

value: grown 6 days in a hal stregth MS medium with Phosphate_replicate_3


title: Male_Brain_0.1PCB_YesFA_36_04

description: Library name: 36_04_BRAIN

value: Brain

value: M

tag: folic acid_treatment

value: Yes


title: Male_Brain_0.1PCB_YesFA_36_02

description: Library name: 36_02_BRAIN


title: SCLC_2_GEX

description:
Library name: 1357_GEX
GEX (5' mRNA library)

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were madeusing the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-.gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Human GRCh38
Supplementary files format and content: Cell Ranger multi output files: 5GEX_barcodes.tsv.gz, 5GEX_features.tsv.gz, 5GEX_matrix.mtx.gz
Supplementary files format and content: Cell Ranger multi output files: clonetypes.csv, contig_annotations.csv.

value: mRNA


title: J0571 HPi_2

description: Library name: cortex HPi_2

value: root cells

value: cortex

value: Wild Type

value: grown 6 days in a hal stregth MS medium with Phosphate_replicate_2


title: SCLC_1_TCR

description:
Library name: pt8179_TCR
TCR VDJ transcripts library enriched from total cDNA


title: Human FF-EVs, Aged, Rep 1

description: Library name: FF_EV_miRNA_A1

value: follicular fluid extracellular vesicles


title: Male_Brain_0.1PCB_YesFA_35_06

description: Library name: 35_06_BRAIN


title: J0571 HPi_1

description: Library name: cortex HPi_1

value: grown 6 days in a hal stregth MS medium with Phosphate_replicate_1


title: SCLC_1_GEX

description:
Library name: pt8179_GEX
GEX (5' mRNA library)

value: Brain Metastasis


title: WER::GFP LPi_3

description: Library name: epidermis LPi_3

value: epidermis

value: grown 6 days in a hal stregth MS medium without Phosphate_replicate_3


title: FKBP-SETDB1 P2F7 ES, Control, MPP8

description: Library name: xxC068_dTSETDB1P2F7_ES_MPP8

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: mESC

value: anti-MPP8 (Proteintech, Cat# 16796-1-AP)


title: Male_Brain_0.1PCB_YesFA_35_05

description: Library name: 35_05_BRAIN

value: Brain


title: FKBP-SETDB1 A12A10 ES, dTAG+dox, Input, double crosslinking

description: Library name: xxC064_dTSETDB1A12A10_dTAGdox_input

value: dTAG-13 for 27hours and doxycycline for 24 hours


title: RNCC_2_TCR

description:
Library name: pt2441_Tumor_2_TCR
TCR VDJ transcripts library enriched from total cDNA

value: Clear cell renal carcinoma

value: Normal weighted

value: TCR


title: FKBP-SETDB1 A12A10 ES, dox, Input, double crosslinking

description: Library name: xxC063_dTSETDB1A12A10_dox_input

value: doxycycline for 24hours


title: RNCC_2_GEX

description:
Library name: pt2441_Tumor_2_GEX
GEX (5' mRNA library)

value: mRNA


title: WER::GFP LPi_2

description: Library name: epidermis LPi_2

value: root cells

value: Wild Type

value: grown 6 days in a hal stregth MS medium without Phosphate_replicate_2


title: FKBP-SETDB1 P2F7 ES, dox, MPP8

description: Library name: xxC069_dTSETDB1P2F7_dox_MPP8


title: FKBP-SETDB1 P2F7 ES, dTAG+dox, MPP8

description: Library name: xxC070_dTSETDB1P2F7_dTAGdox_MPP8


title: WER::GFP LPi_1

description: Library name: epidermis LPi_1

value: grown 6 days in a hal stregth MS medium without Phosphate_replicate_1


title: Male_Brain_0.1PCB_YesFA_32_04

description: Library name: 32_04_BRAIN

value: M

value: Yes


title: Male_Brain_0.1PCB_YesFA_31_05

description: Library name: 31_05_BRAIN


title: RNCC_1_TCR

description:
Library name: pt2441_Tumor_1_TCR
TCR VDJ transcripts library enriched from total cDNA

value: Brain Metastasis


title: FKBP-SETDB1 A12A10 ES, Control, Input, double crosslinking

description: Library name: xxC062_dTSETDB1A12A10_ES_input

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)


title: FKBP-SETDB1 A12A10 ES, dTAG+dox, KAP1

description: Library name: xxC061_dTSETDB1A12A10_dTAGdox_KAP1

value: mESC

value: anti-KAP1 (Abcam, Cat# ab22553)


title: WER::GFP HPi_3

description: Library name: epidermis HPi_3

value: epidermis

value: grown 6 days in a hal stregth MS medium with Phosphate_replicate_3


title: Male_Brain_0.1PCB_YesFA_32_07

description: Library name: 32_07_BRAIN

value: Brain


title: WER::GFP HPi_2

description: Library name: epidermis HPi_2

value: grown 6 days in a hal stregth MS medium with Phosphate_replicate_2


title: Male_Brain_0.1PCB_YesFA_31_02

description: Library name: 31_02_BRAIN


title: RNCC_1_GEX

description:
Library name: pt2441_Tumor_1_GEX
GEX (5' mRNA library)

value: Clear cell renal carcinoma

value: Normal weighted


title: WER::GFP HPi_1

description: Library name: epidermis HPi_1

value: root cells

value: grown 6 days in a hal stregth MS medium with Phosphate_replicate_1


title: RECT_1_GEX

description:
Library name: pt6822_GEX
GEX (5' mRNA library)

value: Rectal cancer

value: mRNA


title: RECT_1_TCR

description:
Library name: pt6822_TCR
TCR VDJ transcripts library enriched from total cDNA

value: TCR


title: FKBP-SETDB1 A12A10 ES, dox, KAP1

description: Library name: xxC060_dTSETDB1A12A10_dox_KAP1

value: doxycycline for 24hours


title: Male_Brain_0.1PCB_YesFA_31_04

description: Library name: 31_04_BRAIN

value: M

value: Yes