title: HUVECs, OSS_2

city: Shenzhen

first: Tianyu

last: Gao

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

description: Library name: OSS_3

data_processing:
Raw reads were trimmed 15 bp using Trimmomatic (version 0.36) , and then aligned to hg38 using Bowtie2 (version 2.3.5.1)  with default parameters. Only the uniquely mapped reads were preserved. The RPKM was calculated at 100 bp resolution using deeptools. The peaks were called using MACS2 (version 2.1.2)  with 0.05 as FDR threshold.
Assembly: GRCh38
Supplementary files format and content: BIGWIG

source_name: primary

extract_protocol:
HUVECs were subjected to different shear stress conditions for 72 hours and collected for ATAC-seq analysis. Cells were washed with PBS, and cell viability was assessed to be >90%. Cells were lysed with lysis buffer, and nuclei were isolated by centrifugation.
ATAC libraries were sequenced on Illumina NovaSeq X Plus.

value: primary

value: Human umbilical vein endothelial cells

value: WT

value: Oscillatory shear stress


title: HUVECs, LSS_2

status: Public on Jan 08 2026

type: SRA

country: China

description: Library name: LSS_2

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: Laminar shear stress


title: HUVECs, LSS_1

description: Library name: LSS_1


title: COTC022-1006-T-F-B

type: RNA

city: Bethesda

first: Christina

last: Mazcko

state: MD

address: 10 Center Drive Room 1B58

department: CCR

country: USA

institute: NCI

description: RNA was profiled using the Canine IO Panel

hyb_protocol: Gene expression profiling was performed using NanoString Canine Immuno-Oncology panel and nCounter instrument according to the manufacturer’s instructions.

data_processing: Normalization was accomplished using the nanostringr platform using the positive control normalization approach. Sample-specific correlation within each sample lane was also performed using CodeSet context (housekeeping gene) normalization

molecule: total RNA

organism: Canis lupus familiaris

source_name: FFPE

extract_protocol: RNA was extracted using RNeasy Mini reagents and protocol. RNA quality was determined by Agilent 2100 Bioanalyzer’s DV200 analysis.

treatment_protocol: Dogs with osteosarcoma were enrolled in COTC021/022 and received standard of care with or without adjuvant sirolimus (LeBlanc et al., Clinical Cancer Research 2021)

tag: sample site

value: Bone

tag: primary tumor or met

value: Primary Malignant Tumor Tissue


title: OSRC-2 cells,si-Control,day2,biol rep 1

city: Beijing

first: Qingjiang

last: Xu

address: Senior Department of Urology, Chinese PLA General Hospital, Beijing, China.

institute: Chinese PLA General Hospital

description:
Library name: sample1
NC_1

library_source: transcriptomic

data_processing:
CLC Genomics Workbenchv 11.0.1
Assembly: GRCH38
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Homo

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina® Stranded mRNA Prep Ligation following manufacturer's prolocols.

value: epithelial cell

value: si-Control

tag: time


title: HUVECs, OSS_1

description: Library name: OSS_2


title: OSRC-2 cells,si-Control,day2,biol rep 2

description:
Library name: sample2
NC_2


title: COTC022-1006-M-S-Kidney

source_name: Snap Frozen

value: Kidney

value: Metastatic Tumor Tissue


title: OSRC-2 cells,si-KLHDC4,day2,biol rep 1

description:
Library name: sample4
SI_1

value: KLHDC4 Knockdown


title: Control1

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  Ø MT% < 30%;   Ø Cell Gene Number < Median Gene Number * 2;  Ø Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mmu10(Ensembl release 100)
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

organism: Mus musculus

source_name: hippocampus

extract_protocol:
Each sample was placed in a sterile Petri dish on ice. Fat, fibrous and necrotic areas were removed, and the tissue was subsequently minced to smaller pieces of less than 3 mm. Samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with collagenase Ⅱ (Worthington) for 60 min at 37°C, with agitation. Subsequently, the sample was filtered using a 70-mm nylon mesh (Miltenyi #130-095-823). 10 ml of this cell suspension was counted by Trypan Blue to determine the concentration of live cells. The sample was then centrifuged at 300g and 4℃ for 5 min, and the supernatant was discarded. The cell pellet was resuspended in 1 ml freezing media (Gibco) for long term cryopreservation in liquid nitrogen. Throughout the dissociation procedure, cells were maintained on ice whenever possible, and the entire procedure was completed in less than 1 hr.
Cryopreserved single-cell suspensions were promptly thawed and prepared as outlined by the 10x Genomics Single Cell 3 v3.1 Reagent Kit user guide.

tag: tissue

value: hippocampus

value: air


title: COTC022-1006-M-F-Rib

value: Rib


title: HUVECs, Static_1

description: Library name: Static_1


title: Section D 3 hpf rep 3

city: Vestec by Prague

first: Radek

last: Sindelka

address: Průmyslová 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

description: Library name: zebrafish_1000_cells_D_3

data_processing:
Low-quality reads and adaptor sequences were removed using fastp (v0.23.4) . Ribosomal RNA sequences were removed using Ribodetector (v0.3.1) and mitochondrial reads with SortMeRNA (v4.3.6). The reads were then aligned to the Danio rerio genome (NCBI: GCF_000002035.6, access date: Jan 2025) using STAR (v2.7.11). Library strandedness was verified using checkstrandedness (v1.0.1) and alignment quality using Qualimap (v2.3). Gene-level counts were generated with HTSeq-count (v2.0.4).
Normalized number of reads was generated using DESeq2.
Raw counts were initially filtered to keep transcripts with counts greater than 30 in at least one sample.
Ortholog mapping was done using a combination of ProteinOrtho (v6.0.31), Ensembl BioMart (v.2.56.1), orthogene (v.1.6.1) and gene symbol matching.
Assembly: GRCz11 (GCF_000002035.6)
Supplementary files format and content: The Excel files contain non-normalized and normalized read counts for each sample (rows contain genes, columns contain samples), and include only data from samples processed after outlier removal.
Supplementary files format and content: - "01_drerio_all_samples_non_normalized.xlsx" contains the non-normalized reads for all samples.
Supplementary files format and content: - "02_drerio_all_samples_normalized.xlsx" contains the normalized reads for all samples.
Supplementary files format and content: - "03_drerio_total_altered_counts_per_stage_non_normalized.xlsx"  contains the non-normalized reads for the summarized total transcripts per stage.
Supplementary files format and content: - "04_drerio_total_altered_counts_per_stage_normalized.xlsx" contains the normalized reads for the summarized total transcripts per stage.
Supplementary files format and content: - "05_drerio_alteration_between_the_sections_at_4_cells_stage_normalized.xlsx" contains the normalized reads for 4-cell stage samples.
Supplementary files format and content: - "06_drerio_alteration_between_the_sections_at_64_cells_stage_normalized.xlsx" contains the normalized reads for 64-cell stage samples.
Supplementary files format and content: - "07_drerio_alteration_between_the_sections_at_1000_cells_stage_normalized.xlsx" contains the normalized reads for 1000-cells stage samples.
Supplementary files format and content: - "08_ortholog_analysis_gene_symbols.xlsx" contains the ortholog mapping between Oncorhynchus mykiss, Salvelinus fontinalis and Danio rerio for differentially localized transcripts.

organism: Danio rerio

source_name: 1000 cells

extract_protocol:
The samples were homogenized in 300 μl of TRIReagent® (Sigma-Aldrich, USA) and total RNA was extracted according to the manufacturer’s protocol. LiCl precipitation was performed to remove inhibitors present in the yolky vegetal hemisphere. The concentration of RNA was measured using NanoDrop-2000 (ThermoFisher, USA) and sample quality was assessed using 5200 Fragment Analyzer (Agilent, USA).
Libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, USA) and adaptors and indexes were provided with NEBNext® Multiplex Oligos for Illumina® (96 Index Primers) (New England Biolabs, USA). 20 ng of a total RNA was used for library preparation. Ribosomal RNA depletion was performed using Ribocop rRNA Depletion Kit V1.3 (Lexogen, Austria).

tag: section

value: Section D

tag: biological replicate


title: COTC022-1006-M-F-Lung A

value: Lung


title: Cas12a, sample 6

city: Frederick

first: Thomas

last: Gonatopoulos-Pournatzis

address: Building 560

institute: National Cancer Institute

description:
Library name: Sample6_Cas12a
10x Genomics

data_processing:
Cell Ranger Software v8.0.1 was used for the demultiplexing, barcoded processing, gene counting and identifying transfected hgRNA from each cell. The unified feature-barcode matrix for all the sequencing runs was generated by using cellranger aggr.
Assembly: hg38
Supplementary files format and content: Tab-delimited value file and matrix file
Supplementary files format and content: Feature reference input file for Cell Ranger
Supplementary files format and content: Comma-separated files containing cell barcode and targeting guide information

molecule: polyA RNA

growth_protocol: HAP1 cells expressing SpCas9 and opCas12a17 were cultured in Dulbecco’s modified Eagle’s medium (DMEM) with high glucose and pyruvate (Gibco #11995073), supplemented with 10% heat-inactivated fetal bovine serum (HI-FBS) (Gibco #16140071) and 1% penicillin-streptomycin (Gibco #15140122). Cells were cultured at 37°C in a humidified atmosphere with 5% CO2 in a HERA VIOS incubator (ThermoFisher Scientific). Cells were passaged every 3rd day by collecting cells with 0.25% trypsin-EDTA (Gibco #25200056), counting and reseeding them in culture media on TC plastic. Cell confluence and viability was monitored using the EVOS™ M5000 Imaging System (Invitrogen) and the Vi-Cell BLU Cell Viability Analyzer (Beckman Coulter), respectively.

extract_protocol:
For single cell capture and sequencing library construction the protocol described in the 10x Genomics User Guide ‘Chromium Next GEM Single Cell 3’ Reagents Kits v3.1 (Dual Index)’ (CG000316 RevD) was followed. GEM generation and barcoding was performed using a 10x Genomics Chromium or Chromium X device.
Gene expression libraries were constructed as recommended by 10x Genomics. The CRISPR screening library construction was performed as described in the user guide, whereby 11 cycles with 5 µL input were performed for the feature PCR, and 9 cycles with 10 µL input were applied for the sample index PCR. To enhance Cas12a capture, a customized Cas12a screening library protocol was applied as described in the associated manuscript.

treatment_protocol: Three million HAP1 cells were seeded in 6-well plates and transduced with the lentiviral exon deletion library or focused hgRNA constructs at a low MOI of 0.1. For the exon deletion screen, a total of 24 million cells (8x 3 million) were transduced, reaching a 2,400x library coverage. 24 hours post-transduction, cells were selected with 2 µg/mL puromycin for ~40 hours. Transduced cells were collected and seeded at 1 million cells in 6-well plates (T0). 24 hours later (T1), cells were collected, counted and a single cell suspension was prepared following the wash steps described in the 10x Genomics Demonstrated Protocol ‘Single Cell Suspensions from Cultured Cell Lines for Single Cell RNA Sequencing’ (CG00054 RevB).


title: Section B 3 hpf rep 3

description: Library name: zebrafish_1000_cells_B_3

value: Section B


title: Control2

description: 10x Genomics


title: Cas12a, sample 8

description:
Library name: Sample8_Cas12a
10x Genomics


title: Cas12a, sample 7

description:
Library name: Sample7_Cas12a
10x Genomics


title: Section E 3 hpf rep 3

description: Library name: zebrafish_1000_cells_E_3

value: Section E


title: Control3

description: 10x Genomics


title: OSRC-2 cells,si-Control,day2,biol rep 3

description:
Library name: sample3
NC_3

value: WT


title: Cas12a, sample 4

description:
Library name: Sample4_Cas12a
10x Genomics


title: Section C 3 hpf rep 3

description: Library name: zebrafish_1000_cells_C_3

value: Section C


title: Cas12a, sample 5

description:
Library name: Sample5_Cas12a
10x Genomics


title: COTC022-1006-M-F-Lung


title: COTC022-0904-M-F-T6

value: T6 Vertebra


title: Section A 3 hpf rep 3

description: Library name: zebrafish_1000_cells_A_3

value: Section A


title: Cas12a, sample 2

description:
Library name: Sample2_Cas12a
10x Genomics


title: CRISPR,sample 7

description:
Library name: Sample7_CRISPR
10x Genomics


title: Section D 3 hpf rep 2

description: Library name: zebrafish_1000_cells_D_2


title: CRISPR,sample 2

description:
Library name: Sample2_CRISPR
10x Genomics


title: CRISPR,sample 6

description:
Library name: Sample6_CRISPR
10x Genomics


title: Cas12a, sample 1

description:
Library name: Sample1_Cas12a
10x Genomics


title: CRISPR,sample 5

description:
Library name: Sample5_CRISPR
10x Genomics


title: COTC022-0904-M-F-Heart

value: Heart


title: CRISPR,sample 3

description:
Library name: Sample3_CRISPR
10x Genomics


title: COTC022-0802-T-F-B

value: Bone

value: Primary Malignant Tumor Tissue


title: Section E 3 hpf rep 2

description: Library name: zebrafish_1000_cells_E_2


title: CRISPR,sample 1

description:
Library name: Sample1_CRISPR
10x Genomics


title: Section E 3 hpf rep 1

description: Library name: zebrafish_1000_cells_E_1


title: Gene expression, sample 8

description:
Library name: Sample8_GEX
10x Genomics

data_processing:
Cell Ranger Software v8.0.1 was used for the demultiplexing, barcoded processing, gene counting and identifying transfected hgRNA from each cell. The unified feature-barcode matrix for all the sequencing runs was generated by using cellranger aggr.
Assembly: hg38
Supplementary files format and content: Tab-delimited value file and matrix file


title: HUVECs, Static_2

description: Library name: Static_2

value: primary

value: Human umbilical vein endothelial cells


title: CRISPR,sample 4

description:
Library name: Sample4_CRISPR
10x Genomics


title: COTC022-0802-T

source_name: RNAlater


title: CRISPR,sample 8

description:
Library name: Sample8_CRISPR
10x Genomics


title: COTC022-0628-M-F-Lung

value: Metastatic Tumor Tissue


title: COTC022-0802-M-S-Lung


title: Section B 3 hpf rep 2

description: Library name: zebrafish_1000_cells_B_2


title: Gene expression, sample 6

description:
Library name: Sample6_GEX
10x Genomics


title: Section C 3 hpf rep 2

description: Library name: zebrafish_1000_cells_C_2


title: Gene expression, sample 1

description:
Library name: Sample1_GEX
10x Genomics


title: Cas12a, sample 3

description:
Library name: Sample3_Cas12a
10x Genomics


title: Gene expression, sample 7

description:
Library name: Sample7_GEX
10x Genomics


title: Section D 3 hpf rep 1

description: Library name: zebrafish_1000_cells_D_1


title: COTC022-0628-M-F-Kidney

description: RNA was profiled using the Canine IO Panel

value: Kidney


title: MSC, bovine 23, clone 108, adipogenic

city: Roslin

first: F. Xavier

last: Donadeu

address: Easter Bush

country: United Kingdom

institute: University of edinburgh

description:
NovaSeq 2x150 bp sequencing
Bo23C108

data_processing:
Raw sequence data converted to fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software
Trimming for adapters and poor quality reads was performed using Trimmomatic v0.36
Mapping performed using STAR aligner v2.5.2b
Gene hit counts calculated using feature Counts from the Subread package v1.5.2
Assembly: ARS-UCD1.2.110_ENSEMBL
Supplementary files format and content: raw_counts: comma separated values containing raw read counts and associated hgnc symbols for each sample

organism: Bos taurus

source_name: mesenchymal stem cell

growth_protocol: MSC cultures were generated by enzymatic digestion of bovine adipose tissues followed by in vitro expansion of MSCs, and clones were generated by single cell sorting in media containing 10% FBS and bFGF (5 ng/ml). To determine adipogenic capacity, clones underwent standard adipogenic differentiation then were stained with Oil Red O and quantified. Subset of adipogenic (showing high positive ORO staining) and non-adipogenic (no ORO staining) clones were analysed.

extract_protocol:
RNA was extracted using TRIzol and further purified using QIAGEN RNeasy columns
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufaturer's instructions

tag: animal

value: mesenchymal stem cell

value: adipogenic


title: Gene expression, sample 4

description:
Library name: Sample4_GEX
10x Genomics


title: COTC022-0620-T-F-B


title: MSC, bovine 22, clone 121, adipogenic

description:
NovaSeq 2x150 bp sequencing
Bo22C121


title: Section A 3 hpf rep 2

description: Library name: zebrafish_1000_cells_A_2


title: Gene expression, sample 5

description:
Library name: Sample5_GEX
10x Genomics


title: Section A 3 hpf rep 1

description: Library name: zebrafish_1000_cells_A_1


title: MSC, bovine 23, clone 14, adipogenic

description:
NovaSeq 2x150 bp sequencing
Bo23C14


title: Gene expression, sample 2

description:
Library name: Sample2_GEX
10x Genomics


title: MSC, bovine 23, clone 68, adipogenic

description:
NovaSeq 2x150 bp sequencing
Bo23C68


title: Section E 2 hpf rep 3

description: Library name: zebrafish_64_cells_E_3

source_name: 64 cells

value: 2 hpf (~64-cell)


title: MSC, bovine 23, clone 62, adipogenic

description:
NovaSeq 2x150 bp sequencing
Bo23C62


title: Section B 3 hpf rep 1

description: Library name: zebrafish_1000_cells_B_1


title: COTC022-0628-M-F-Brain

value: Brain


title: Section C 3 hpf rep 1

description: Library name: zebrafish_1000_cells_C_1


title: COTC022-0620-M-F-Abd Mass

value: Abdominal Mass


title: COTC022-0318-T-F-B


title: Gene expression, sample 3

description:
Library name: Sample3_GEX
10x Genomics


title: MSC, bovine 22, clone 11, adipogenic

description:
NovaSeq 2x150 bp sequencing
Bo22C11


title: Section D 2 hpf rep 3

description: Library name: zebrafish_64_cells_D_3

value: Section D


title: Section C 2 hpf rep 3

description: Library name: zebrafish_64_cells_C_3


title: MSC, bovine 20, clone 106, adipogenic

description:
NovaSeq 2x150 bp sequencing
Bo20C106


title: COTC022-0312-M-F-Lung

value: Lung


title: COTC022-0318-M-F-Lung


title: MSC, bovine 22, clone 27, adipogenic

description:
NovaSeq 2x150 bp sequencing
Bo22C27


title: COTC022-0627-M-F-Lung


title: COTC022-0312-M-F-Kidney


title: Section D 2 hpf rep 2

description: Library name: zebrafish_64_cells_D_2


title: MSC, bovine 22, clone 16, adipogenic

description:
NovaSeq 2x150 bp sequencing
Bo22C16


title: MSC, bovine 23, clone 74, non-adipogenic

description:
NovaSeq 2x150 bp sequencing
Bo23C74

value: non-adipogenic


title: MSC, bovine 17, clone 57, adipogenic

description:
NovaSeq 2x150 bp sequencing
Bo17C57


title: Section A 2 hpf rep 3

description: Library name: zebrafish_64_cells_A_3


title: MSC, bovine 22, clone 18, non-adipogenic

description:
NovaSeq 2x150 bp sequencing
Bo22C18


title: MSC, bovine 22, clone 17, non-adipogenic

description:
NovaSeq 2x150 bp sequencing
Bo22C17


title: MSC, bovine 23, clone 10, non-adipogenic

description:
NovaSeq 2x150 bp sequencing
Bo23C10


title: Section E 2 hpf rep 2

description: Library name: zebrafish_64_cells_E_2

value: Section E


title: Section C 2 hpf rep 2

description: Library name: zebrafish_64_cells_C_2

value: Section C


title: Section B 2 hpf rep 2

description: Library name: zebrafish_64_cells_B_2

value: Section B


title: COTC022-0304-T

value: Bone


title: MSC, bovine 22, clone 9, non-adipogenic

description:
NovaSeq 2x150 bp sequencing
Bo22C9


title: MSC, bovine 22, clone 5, non-adipogenic

description:
NovaSeq 2x150 bp sequencing
Bo22C5


title: Section B 2 hpf rep 3

description: Library name: zebrafish_64_cells_B_3


title: MSC, bovine 17, clone 23, non-adipogenic

description:
NovaSeq 2x150 bp sequencing
Bo17C23


title: MSC, bovine 23, clone 23, non-adipogenic

description:
NovaSeq 2x150 bp sequencing
Bo23C23


title: MSC, bovine 20, clone 15, non-adipogenic

description:
NovaSeq 2x150 bp sequencing
Bo20C15


title: COTC022-0310-T-F-B

value: Primary Malignant Tumor Tissue


title: COTC022-0310-M-F-Rib

value: Rib


title: COTC022-0304-M-S-Lung


title: MSC, bovine 23, clone 22, non-adipogenic

description:
NovaSeq 2x150 bp sequencing
Bo23C22


title: T. aestivum Fritz Heat Rep1

city: Valdivia

first: Javier

last: Canales

state: Los Ríos

address: Campus Isla Teja s/n

department: Instituto de Bioquimica y Microbiologia

country: Chile

institute: Universidad Austral de Chile

description: Library name: TA2FRIT

data_processing:
Raw sequencing reads were pseudo-aligned and quantified using Kallisto (v0.50.1) with a k-mer size of 31. The following reference transcriptomes were used: Triticum aestivum (IWGSC RefSeq v2.1) , Triticum turgidum (Svevo v1) , and Triticum monococcum (TA10622 v1.1). Differential expression analysis was performed using DESeq2 v1.42 in R.
Assembly: IWGSC RefSeq v2.1 for T.aestivum, Svevo v1 for T.turgidum, TA10622 v1.1 for T.monococcum
Supplementary files format and content: tsv files includes raw counts and tpm

organism: Triticum aestivum

source_name: Wheat grain

growth_protocol: Field experiments were conducted at the Experimental Station of the Universidad Austral de Chile (UACh) in Valdivia (39° 47' S, 73° 14' W), Chile. The crops were grown under typical temperate conditions with supplemental irrigation to prevent water stress. Plots were fertilized with 150 kg/ha N and 300 kg/ha P2O5 at sowing, with an additional 150 kg/ha N during mid-tillering.

extract_protocol:
Total RNA was isolated from complete caryopses (harvested from central spikelets) using a modified CTAB-based protocol. RNA quality was assessed using a Nanoquant Infinite M200 spectrophotometer(A260/A280 ratios between 1.8-2.0)
Illumina RNA-seq libraries were constructed using the Illumina TruSeq Stranded Total RNA Sample Prep Kit following the manufacturer's protocol. Unique barcodes were incorporated for multiplexing.

treatment_protocol: Thermal treatments were applied during the early grain-filling period (10-14 days after anthesis) using temperature-controlled polyethylene chambers. The experiment compared a Control (ambient temperature) against a severe Heat Stress treatment (TT2, up to 32°C mean temperature). Grain samples for RNA-seq were collected 3 hours after imposing the heat stress treatment on day 10 after anthesis.

value: Wheat grain

value: Hexaploid

value: 10 DAA (3h post-stress)

value: Fritz

value: Heat (TT2)

tag: batch

value: replicate 1


title: Section A 2 hpf rep 2

description: Library name: zebrafish_64_cells_A_2

value: 2 hpf (~64-cell)

value: Section A


title: T. aestivum Fritz Control Rep2

description: Library name: CBFRIT

value: Control

value: replicate 2


title: Section D 2 hpf rep 1

description: Library name: zebrafish_64_cells_D_1

value: Section D


title: COTC022-0227-M-F-T5

value: T5 Vertebra

value: Metastatic Tumor Tissue


title: Section E 2 hpf rep 1

description: Library name: zebrafish_64_cells_E_1

value: Section E


title: T. aestivum Fritz Control Rep3

description: Library name: CCFRIT

value: replicate 3


title: T. aestivum Fritz Heat Rep3

description: Library name: TC2FRIT


title: COTC022-0227-M-F-Liver

value: Liver


title: MCF7 cells, APOBEC3H_I1 (Rep2)

city: Saskatoon

first: Franco

middle: J

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

country: Canada

institute: University of Saskatchewan

description:
Replicate 2
R2300160

data_processing:
Sequence adaptor and low-quality bases were trimmed usin fastp (version 0.23.4)
Reads were aligned using STAR aligner (version 2.7.9a)
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw count for each sample

source_name: Breast

growth_protocol: Growth protocol was performed as explained in Rodriguez et al

extract_protocol:
Extract protocol was performed as explained in Rodriguez et al
Library construction protocol was performed as explained in Rodriguez et al

treatment_protocol: Treatment protocol was performed as explained in Rodriguez et al

value: Breast

value: epithelial cells

value: Induced

value: doxycyline/APOBEC3H Haplotype I


title: MCF7 cells, APOBEC3H_U2 (Rep1)

description:
Replicate 1
R2300157

value: Uninduced


title: T. aestivum Fritz Heat Rep2

description: Library name: TB2FRIT

value: Wheat grain

value: Hexaploid

value: 10 DAA (3h post-stress)

value: Fritz

value: Heat (TT2)


title: COTC021-2317-M-F-Spine

value: Spine


title: T. aestivum Fritz Control Rep1

description: Library name: CAFRIT

value: Control

value: replicate 1


title: MCF7 cells, APOBEC3H_I1 (Rep1)

description:
Replicate 1
R2300158


title: Section C 2 hpf rep 1

description: Library name: zebrafish_64_cells_C_1

value: 2 hpf (~64-cell)

value: Section C


title: MCF7 cells, APOBEC3H_I4 (Rep2)

description:
Replicate 2
R2200137


title: COTC021-2312-M-S-Rib

value: Rib

value: Metastatic Tumor Tissue


title: COTC021-2312-M-S-Kidney

value: Kidney


title: Section B 2 hpf rep 1

description: Library name: zebrafish_64_cells_B_1

value: Section B


title: Section A 2 hpf rep 1

description: Library name: zebrafish_64_cells_A_1

value: Section A


title: MCF7 cells, APOBEC3H_I4 (Rep1)

description:
Replicate 1
R2300167

value: Breast

value: epithelial cells

value: Induced

value: doxycyline/APOBEC3H Haplotype I


title: MCF7 cells, APOBEC3H_U2 (Rep2)

description:
Replicate 2
R2300159

value: Uninduced


title: COTC021-2205-M-F-Pancreas

value: Pancreas


title: COTC021-2312-M-F-Thoracic wall

value: Thoracic wall


title: MCF7 cells, APOBEC3H_U1 (Rep2)

description:
Replicate 2
R2200136


title: MCF7 cells, APOBEC3H_U1 (Rep1)

description:
Replicate 1
R2300147


title: MCF7 cells, APOBEC3B_I5 (Rep2)

description:
Replicate 2
R2200135


title: Section E 1 hpf rep 3

description: Library name: zebrafish_4_cells_E_3

source_name: 4 cells

value: 1 hpf (~4-cell)

value: Section E


title: Section D 1 hpf rep 3

description: Library name: zebrafish_4_cells_D_3

value: Section D


title: COTC021-2205-M-F-Lung

value: Lung


title: COTC021-2312-T

value: Bone

value: Primary Malignant Tumor Tissue


title: MCF7 cells, APOBEC3B_U2 (Rep2)

description:
Replicate 2
R2200134


title: COTC021-2205-M-F-Liver

value: Liver

value: Metastatic Tumor Tissue


title: MCF7 cells, APOBEC3B_U2 (Rep1)

description:
Replicate 1
R2300145


title: Section C 1 hpf rep 3

description: Library name: zebrafish_4_cells_C_3

value: Section C


title: COTC021-1912-M-F-Lung


title: Section B 1 hpf rep 3

description: Library name: zebrafish_4_cells_B_3

value: Section B


title: Section A 1 hpf rep 3

description: Library name: zebrafish_4_cells_A_3

value: Section A


title: Section D 1 hpf rep 2

description: Library name: zebrafish_4_cells_D_2


title: MCF7 cells, APOBEC3A_I4 (Rep2)

description:
Replicate 2
R2300152

value: Breast

value: epithelial cells


title: MCF7 cells, APOBEC3A_I4 (Rep1)

description:
Replicate 1
R2300150

value: Induced


title: MCF7 cells, APOBEC3A_U1 (Rep2)

description:
Replicate 2
R2300151

value: Uninduced


title: COTC021-1915-M-F-Bone


title: MCF7 cells, APOBEC3B_U1 (Rep1)

description:
Replicate 1
R2300153


title: COTC021-1417-M-F-Spine 7R

value: Spinal Cord


title: COTC021-1904-M-F-Lung


title: MCF7 cells, APOBEC3A_U1 (Rep1)

description:
Replicate 1
R2300149


title: MCF7 cells, APOBEC3B_U1 (Rep2)

description:
Replicate 2
R2300168


title: COTC021-1417-T-F-B


title: MCF7 cells, APOBEC3B_I2 (Rep1)

description:
Replicate 1
R2300154


title: MCF7 cells, APOBEC3A_I5 (Rep2)

description:
Replicate 2
R2200133


title: Section C 1 hpf rep 2

description: Library name: zebrafish_4_cells_C_2


title: MCF7 cells, APOBEC3B_I5 (Rep1)

description:
Replicate 1
R2300146


title: MCF7 cells, APOBEC3A_I5 (Rep1)

description:
Replicate 1
R2300144


title: MCF7 cells, APOBEC3A_U6 (Rep1)

description:
Replicate 1
R2300143


title: MCF7 cells, APOBEC3B_I2 (Rep2)

description:
Replicate 2
R2300156


title: MCF7 cells, APOBEC3A_U6 (Rep2)

description:
Replicate 2
R2200132


title: Section B 1 hpf rep 2

description: Library name: zebrafish_4_cells_B_2


title: p1_rep3

city: South San Francisco

first: Robert

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

description: Library name: SAM24509036

data_processing:
ATAC-seq results were analyzed using the ENCODE ATAC-seq pipeline (v2.2.2). In brief, adaptors were trimmed using cutadapt (v2.5), ATAC-seq reads were aligned to the mouse genome (mm10) using Bowtie2 (v2.3.4.3). Aligned reads were then filtered for quality and duplicates using samtools (1.9) and Picard (2.20.7). Peaks were called using MACS2 (v2.2.4). Specifically, 5’ ends of reads were shifted in a strand-specific manner to account for the Tn5 shift and identify the precise cut-sites. The shifted read-start coverage was aggregated over both strands and smoothed using a 150 bp window for peak calling in MACS2. The called peaks were filtered using exclusion lists that contain genomic regions resulting in anomalous, unstructured, or experiment independent high signal. The Irreproducible Discovery Rate (IDR 2.0.4.2) framework was used to estimate reproducibility and stringent peak calls. To assess data quality, we measured read mapping statistics, enrichment QC metrics, library complexity, reproducibility ratio and focused on the Transcription Start Site enrichment score, and the total number of peaks identified.
Normalization and PCA analysis on the reads was performed using the “DiffBind” R package (Stark et al., 2011).
Assembly: mouse genome (GRCm38)
Supplementary files format and content: MACS2 processed peak call data for each sample
Supplementary files format and content: tab-delimited text file; TMM normalized peak values for each sample

source_name: Colon tumor

growth_protocol: Organoids were cultured in basal medium containing advanced DMEM/F12 (Gibco 126340-010), 2 mM GlutaMAX™ (Gibco 35050-061), Penicillin/ Streptomycin (10,000 U/mL, Gibco 15140-122), 100 mM HEPES (pH 7.2 Genentech, Inc), N2 (Gibco 17502-048), B27 (Gibco 17504-044), 1 mM N-acetyl-L-cysteine (Sigma-Aldrich A7250) in a 1:1 media:matrigel plug (Growth factor reduced, phenol red free, Corning 356231).

extract_protocol:
Organoids were harvested using cold media on ice and treated with 300ul of ice-cold ATAC lysis buffer (Active Motif, 53150). Samples were then homogenized by pipetting and incubated on ice for 2 minutes to release nuclei. A target of 100,000 nuclei per sample was collected, as counted on a Countess 3.
Bulk ATAC-seq library preparation was performed on 100,000 nuclei using the ATAC-Seq Kit (Active Motif, 53150) according to the manufacturer's instructions. The resulting ATAC-seq libraries were quantified using a Qubit dsDNA Quantitation kit (Thermo Fisher, Q32851) and a High Sensitivity D1000 ScreenTape (Agilent, 5067-5582 and 5067-5583). Sequencing was performed on an Illumina NextSeq2000 platform, generating 35 million reads per sample.

treatment_protocol: Organoids treated with different epigenetic inhibitors as specified in the SAMPLES section at 10 µM with the exception for Panobinostat (50nM) for a total of 8 days.

value: Colon tumor

value: Epithelial cell

value: no treatment


title: COTC021-1417-M-F-Spine 6


title: COTC021-1417-M-F-Spine 7L


title: Section E 1 hpf rep 1

description: Library name: zebrafish_4_cells_E_1

value: 1 hpf (~4-cell)

value: Section E


title: Panobinostat_rep3

description: Library name: SAM24509033

value: HDAC inhibitor Panobinostat (50nM)


title: COTC021-1020-M-F-Kidney

value: Kidney


title: Panobinostat_rep2

description: Library name: SAM24509032


title: Section C 1 hpf rep 1

description: Library name: zebrafish_4_cells_C_1


title: RG108_rep3

description: Library name: SAM24509030

value: DMNT inhibitor RG-108 (10uM)


title: Panobinostat_rep1

description: Library name: SAM24509031


title: RG108_rep2

description: Library name: SAM24509029


title: Section E 1 hpf rep 2

description: Library name: zebrafish_4_cells_E_2


title: Section A 1 hpf rep 1

description: Library name: zebrafish_4_cells_A_1


title: p1_rep2

description: Library name: SAM24509035


title: COTC021-1015-M-F-Spleen 3

value: Spleen

value: Metastatic Tumor Tissue


title: COTC021-1015-M-F-Spleen 2


title: COTC021-1015-M-F-Spleen 1


title: EPZ004777_rep2

description: Library name: SAM24509026

value: DOT1L inhibitor EPZ004777 (10uM)


title: Section D 1 hpf rep 1

description: Library name: zebrafish_4_cells_D_1

value: Section D


title: HUVECs, shSWAP70_3, TNFα

description:
Library name: TKO_3
fpkm_TKO_3

data_processing:
Differential gene expression analysis was performed using DESeq2/DEGSeq (Fold Change ≥ 1.5, adjusted P ≤ 0.05) and PoissonDis (Fold Change ≥ 1.5, FDR ≤ 0.05). Functional enrichment of differentially expressed genes was conducted based on GO and KEGG annotations, using TermFinder and KEGG (phyper in R), with significant terms defined by Q ≤ 0.05.
Assembly: GRCh38
Supplementary files format and content: processed data.txt

source_name: HUVECs

extract_protocol:
Total RNA was extracted from tissues using TRIzol (Invitrogen, Carlsbad, California, USA) according to manual instruction.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China).

value: primary

value: Human umbilical vein endothelial cells

value: SWAP70 knockdown

value: TNFalpha stimulation


title: COTC021-1015-M-F-Skin

value: Skin


title: EPZ004777_rep3

description: Library name: SAM24509027

value: Colon tumor


title: COTC021-1015-M-F-Lung 3

value: Lung


title: p5_rep1

description: Library name: SAM24509019

value: Epithelial cell

value: no treatment


title: A485_rep1

description: Library name: SAM24509022

value: EP300 inhibitor A485 (10uM)


title: COTC021-1015-M-F-Lung 2


title: HUVECs, shSWAP70_2, TNFα

description:
Library name: TKO_2
fpkm_TKO_2


title: HUVECs, shSWAP70_1, TNFα

description:
Library name: TKO_1
fpkm_TKO_1


title: HUVECs, shControl_3, TNFα

description:
Library name: TKOC_3
fpkm_TKOC_3

value: WT


title: p1_rep1

description: Library name: SAM24509034


title: NPp53T castrated biol rep 4

city: Washington

first: Maho

last: Shibata

state: DC

address: 800 22nd Street, NW SEH 8430

institute: The George Washington University

description:
Library name: MS21
column name in 20221213.cast.raw.counts.csv: MS21

data_processing:
FASTQ files were assessed with FastQC. Reads were trimmed and adapter sequences were removed using cutadapt.trim.2 with -q 20 and –minimum-length 1. The adapter sequences were -a CTGTCTCTTATACACATCT and -A CTGTCTCTTATACACATCT.
Trimmed reads were aligned to the mouse GENCODE GrCm39 primary assembly (GCA_000001635.9) using STAR with annotation GTF files from GENCODE. Alignment was run with the –sjdbOverhand 100 –winAnchorMultimapNmax 100 –outFilterMultimapNmax 100 flags.
Raw read count matrices were generated for genes and TE subfamilies using TETranscripts.
Assembly: GrCm39
Supplementary files format and content: csv files, contains raw counts for each sample

source_name: prostate

extract_protocol:
Single prostates were dissected in cold 1X PBS and split into halves containing single anterior, dorsal, lateral and ventral prostate lobes. A FastPrep 24 5G bead grinder (MP Biomedicals) with stainless steel beads were used to homogenenize tissues for RNA extraction using the MagMax96 for Microarrays Total RNA Isolation kit following the Spin procedure. For castrated tissues, extracted RNA was treated with DNase.
Total RNA samples were quantified and qualified using an Agilent Bioanalyzer RNA Nano kit.  Samples were prepared for sequencing using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus.  Inputs for hormonally intact samples were normalized to 100 ng; inputs for castrated samples were normalized to 500 ng.  Indexed adapters from IDT for Illumina RNA UD Indexes Set A were used for both projects.   Libraries for hormonally intact samples were sequenced using an Illumina NextSeq 500, with 2x76 bp reads; libraries for castrated samples were sequenced using an Illumina NextSeq 2000, with 2x100 bp reads, at a read depth of 10-15M paired-end reads/sample.

treatment_protocol: 2-month-old mice were administered tamoxifen (200 mg/kg body weight) by oral gavage over four consecutive days to activate CreERT2-mediated gene recombination. For analysis of prostates from hormonally intact mice, prostates were collected 1 month after tamoxifen administration. For analysis of prostates from castrated mice, mice were surgically castrated 1 month after tamoxifen treatment. Prostates were collected 1 month after castration.

value: prostate

tag: strain

value: C57BL/6 mixed

value: tissue

tag: age

value: 5 months

value: Tamoxifen at 2 months of age


title: COTC021-1015-T-F-B

value: Bone

value: Primary Malignant Tumor Tissue


title: Section A 1 hpf rep 2

description: Library name: zebrafish_4_cells_A_2

value: 1 hpf (~4-cell)

value: Section A


title: Section B 1 hpf rep 1

description: Library name: zebrafish_4_cells_B_1

value: Section B


title: RG108_rep1

description: Library name: SAM24509028

value: DMNT inhibitor RG-108 (10uM)


title: A485_rep3

description: Library name: SAM24509024

value: Colon tumor


title: EPZ004777_rep1

description: Library name: SAM24509025

value: DOT1L inhibitor EPZ004777 (10uM)


title: NPp53Tcastrated biol rep 2

description:
Library name: MS19
column name in 20221213.cast.raw.counts.csv: MS19


title: p5_rep3

description: Library name: SAM24509021

value: Epithelial cell


title: NPp53 castrated biol rep 5

description:
Library name: MS17
column name in 20221213.cast.raw.counts.csv: MS17


title: A485_rep2

description: Library name: SAM24509023


title: COTC021-0908-T-F-B


title: HUVECs, shControl_2, TNFα

description:
Library name: TKOC_2
fpkm_TKOC_2

value: primary

value: Human umbilical vein endothelial cells

value: TNFalpha stimulation


title: NPp53T castrated biol rep 1

description:
Library name: MS18
column name in 20221213.cast.raw.counts.csv: MS18

value: prostate


title: p5_rep2

description: Library name: SAM24509020

value: no treatment


title: NPp53 castrated biol rep 4

description:
Library name: MS16
column name in 20221213.cast.raw.counts.csv: MS16

value: C57BL/6 mixed

value: tissue


title: COTC021-0908-M-F-L4

value: L4 Vertebra

value: Metastatic Tumor Tissue


title: HUVECs, shControl_3

description:
Library name: KOC_3
fpkm_KOC_3

value: WT


title: SC_10X_3

city: Leuven

first: Sandrine

last: Da Cruz

address: Herestraat 49 |

country: Belgium

institute: VIB-KUL Center for Brain & Disease Research

description: Fresh frozen tissue, each area contains one WT section and one FUSH R521H section

data_processing:
FASTQ files were processed to generate the feature barcode (FB) matrices by using Spaceranger (version 1.1.0)
SpaceRanger output files were then further processed with SCANPY v1.8.1 for subsequent analysis
Assembly: mm10
Supplementary files format and content: processed AnnData h5ad object containing processed data from all samples
Supplementary files format and content: .tif.giz TIF original image files
Supplementary files format and content: barcodes.tsv.gz list of spatial barcodes
Supplementary files format and content: features.tsv.gz list of gene IDs
Supplementary files format and content: matrix.mtx.gz gene expression count data
Supplementary files format and content: tissue_position_list.csv Tissue position list in CSV format
Supplementary files format and content: scale_factors_json.json Scale factor JSON files
Supplementary files format and content: tissue_lowres_image.png Tissue image at low resolution in PNG format
Supplementary files format and content: tissue_hires_image.png Tissue image at high resolution in PNG format
Supplementary files format and content: aligned_fiducials.jpg Aligned images in JPG format
Supplementary files format and content: detected_tissue_image.jpg Detected tissue image in JPEG format
Library strategy: Spatial transcriptomics

source_name: mouse spinal cord

extract_protocol: Protocol available from manufacturer (10x Genomics protocol CG000239)

value: mouse spinal cord

value: spinal cord tissue

value: non-transgenic and FUS R521H


title: NPp53 castrated biol rep 2

description:
Library name: MS14
column name in 20221213.cast.raw.counts.csv: MS14

value: 5 months

value: Tamoxifen at 2 months of age


title: COTC021-0817-M-S-Lung

value: Lung


title: COTC021-0817-T-F-B

value: Bone

value: Primary Malignant Tumor Tissue


title: COTC021-0817-T


title: SC_10X_4


title: NPp53T castrated biol rep 3

description:
Library name: MS20
column name in 20221213.cast.raw.counts.csv: MS20


title: COTC021-1015-M-F-Heart

value: Heart


title: HUVECs, shControl_1

description:
Library name: KOC_1
fpkm_KOC_1

value: primary

value: Human umbilical vein endothelial cells


title: NPp53T homonally intact biol rep 5

description:
Library name: MS12
column name in 20220308.intact.raw.counts.csv: MS12

value: prostate

value: 3 months


title: Nnk_persimilis_rep2

city: Bunkyo-ku

first: Raku

last: Saito

state: Tokyo-to

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

description:
Library name: Sample84
Nnk.per.subtract.bw

data_processing:
Raw sequence reads were trimmed by fastp.
Trimmed reads were mapped to drosophila dm6 (BDGP6) genome by bowtie2.
Uniquely mapped reads were extracted by samtools.
Matrix bigwig files were produced by deeptools.
Assembly: dm6
Supplementary files format and content: general bigwig, mcool file format (generated from both replicates, linked to the corresponding rep1 sample records)

organism: Drosophila melanogaster

source_name: embryo

extract_protocol:
nc14 (2h10min-2h40min) early embryo for ChIP and MicroC
Prepared by manufacturer's protocol of NEBNext Ultra II DNA Library Prep Kit for Illumina

value: embryo

value: nc14 embryo


title: HUVECs, shControl_2

description:
Library name: KOC_2
fpkm_KOC_2


title: NPp53 castrated biol rep 3

description:
Library name: MS15
column name in 20221213.cast.raw.counts.csv: MS15

value: C57BL/6 mixed

value: tissue


title: COTC021-0817-M-F-Lung

value: Metastatic Tumor Tissue


title: Nnk_persimilis_rep1

description:
Library name: Sample83
Nnk.per.subtract.bw


title: SC_10X_1

value: mouse spinal cord

value: spinal cord tissue


title: SC_10X_2

value: non-transgenic and FUS R521H


title: NPp53T homonally intact biol rep 4

description:
Library name: MS11
column name in 20220308.intact.raw.counts.csv: MS11

value: Tamoxifen at 2 months of age


title: COTC021-0814-T-F-A


title: COTC021-0814-M-S-Spine

value: Spinal Cord


title: HUVECs, shControl_1, TNFα

description:
Library name: TKOC_1
fpkm_TKOC_1

value: WT

value: TNFalpha stimulation


title: NPp53 castrated biol rep 1

description:
Library name: MS13
column name in 20221213.cast.raw.counts.csv: MS13

value: 5 months


title: Nnk_ficusphila_rep2

description:
Library name: Sample82
Nnk.fic.subtract.bw


title: NPp53 homonally intact biol rep 4

description:
Library name: MS06
column name in 20220308.intact.raw.counts.csv: MS06


title: Nnk_suzukii_rep2

description:
Library name: Sample80
Nnk.suz.subtract.bw


title: NPp53T homonally intact biol rep 2

description:
Library name: MS09
column name in 20220308.intact.raw.counts.csv: MS09


title: Wt_ade_14d_3

city: Los Angeles

first: Lianjiu

last: Su

address: 500 Landfair Ave.

institute: University of California, Los Angeles

description: Library name: Wt_ade_14d_3

data_processing:
The quality of sequencing reads was evaluated by FastQC. The transcript quantification was performed by Salmon using mouse reference transcriptome (GRCm39). The transcript-level quantification of estimated counts, length, and abundance from Salmon were imported into DESeq2 using tximport package. DESeq2 uses a negative binomial model to model the variability of raw counts and Wald test to estimate differences between the conditions. DEseq function was performed with default setting. The transformed count data were used for PCA visualization. Using the results function, we selected genes with a adjusted p value < 0.05 and logFC > 1 or <-1 as differentially expressed genes (DEG). The p-values attained by the Wald test are corrected for multiple testing using Benjamini and Hochberg method by default. The cluster Profiler was used for GO pathway, GSEA analysis and visualization.
Assembly: GRCm39
Supplementary files format and content: quant.tar.gz file of each sample generated by Salmon stores the gene expression in quant.sf, and other information.

source_name: kidney

extract_protocol:
Total RNA was extracted with the RNeasy Mini kit (QIAGEN)
Strand-specific libraries were generated using 400 ng of total RNA using the TruSeq stranded RNA Sample Preparation Kit (Illumina).

value: kidney

value: Wild type

value: Adenine diet for 14 days


title: Nnk_suzukii_rep1

description:
Library name: Sample79
Nnk.suz.subtract.bw


title: NPp53T homonally intact biol rep 3

description:
Library name: MS10
column name in 20220308.intact.raw.counts.csv: MS10

value: prostate

value: 3 months


title: NPp53 homonally intact biol rep 3

description:
Library name: MS05
column name in 20220308.intact.raw.counts.csv: MS05


title: COTC021-0814-M-F-Rib

description: RNA was profiled using the Canine IO Panel

value: Rib


title: Wt_ade_14d_1

description: Library name: Wt_ade_14d_1


title: NPp53 homonally intact biol rep 5

description:
Library name: MS07
column name in 20220308.intact.raw.counts.csv: MS07

value: C57BL/6 mixed


title: Wt_ade_14d_2

description: Library name: Wt_ade_14d_2


title: Nnk_yakuba_rep1

description:
Library name: Sample77
Nnk.yak.subtract.bw

value: embryo

value: nc14 embryo


title: GAL3_ade_14d_3

description: Library name: GAL3_ade_14d_3

value: Gal3 KO


title: COTC021-0809-T

value: Bone

value: Primary Malignant Tumor Tissue


title: GAL3_ade_14d_1

description: Library name: GAL3_ade_14d_1


title: COTC021-0809-M-F-Oral

value: Lip

value: Metastatic Tumor Tissue


title: Hi-C, RAD21-Halo cells, untreated, rep1

city: San Francisco

first: Elphege

last: Nora

address: 555 Mission Bay Boulevard South

department: Cardiovascular Research Institute

institute: University of California San Francisco

description: Illumina NextSeq 500, Illumina HiSeq or Illumina Nova-seq

data_processing:
Reads were trimmed to 75bp (if sequenced beyond that) using cutadapt (Martin, 2011). Data was mapped to mm10 using the distiller-nf pipeline (https://github.com/open2c/distiller-nf), iteratively corrected and converted into .cool format with cooler (Abdennur and Mirny, n.d.), only considering read pairs with both sides mapping with high confidence (mapq ≥ 30). After ascertaining the overall similarity of each replicate using either cooltools (Open2C et al., 2024a) or Genova(van der Weide et al., 2021) (P(s) curves and aggregate peak analysis), the independent Hi-C replicates (up to two) were merged for each condition. Multiresolution coolers (.mcool) were then generated with cooler and balanced using iterative correction.
Assembly: mm10
Supplementary files format and content: .mcool for merged replicates provided as supplementary files - .mcool for samples with single replicates (e.g. degron titrations) are available on the corresponding  sample accession pages

growth_protocol: E14 mESCs are of XY karyotype and 129P2/Ola genetic background. mESCs were cultured in DMEM+Glutamax (ThermoFisher 10569044) supplemented with 15% Fetal Bovine Serum (ThermoFisher 10437028), 550µM b-mercaptoethanol (ThermoFisher 21985-023), 1X non-essential amino-acids (ThermoFisher 11140050), 104U of Leukemia inhibitory factor (Millipore ESG1107), PD0325901 (APExBIO A3013), CHIR-99021 (APExBIO A3011). Cells were maintained at a density of 0.2-1.5x105 cells/cm2 by passaging using TrypLE (ThermoFisher 12605010) every 24-48h on 0.1% gelatin-coated dishes at 37°C and 5% CO2. 0.1% gelatin was prepared in 1X PBS using Gelatin powder (Sigma Aldrich G1890). Medium was changed daily when cells were not passaged. Cells were checked for mycoplasma infection and tested negative.

extract_protocol:
kit manufacturer protocol
Arima Hi-C cat#A510008. Hi-C was performed using the kit from Arima Genomics as per manufacturer’s instructions (202103-1577). Briefly, mESCs were dissociated using TrypLE, resuspended in culture medium and counted. 5-10 million cells were spun down at 100g for 5 minutes at RT. Supernatant was discarded and the cell pellets were resuspended in 5 ml of 1X PBS. Cells were crosslinked using 2% formaldehyde (diluted from 37% formaldehyde - Electron Microscopy Sciences 15686), mixed by inverting the tubes 10 times and incubated at RT for 10 minutes. Quenching was done using the Stop solution 1 provided with the kit, mixed by inverting the tubes 10 times and incubated at RT for 5 minutes. Samples were then incubated on ice for 15 minutes, spun down at 100g for 5 minutes at 4°C. After discarding the supernatant, cells were resuspended in cold 1X PBS, counted, aliquoted at a density of 1x106 cells/tube and spun down at 100g for 5 minutes at 4°C. Supernatant was discarded, cell pellets were snap frozen on dry ice and stored at -70°C.

treatment_protocol: Degradation of proteins tagged with the Auxin-Inducible Degron (44 amino-acid AID* truncation with residues 71–114) was induced by adding Indole-3-acetic acid sodium (IAA, Sigma Cat #I5148-2G) to a final concentration of 500μM. Degradation of proteins tagged with the FKBP12F36V degron was induced by adding dTAG-13 (abbreviated dTAG - Sigma Cat, SML2601).

value: Mouse Embryonic Stem Cells


title: COTC021-0809-M-S-Kidney

value: Kidney


title: Nnk_simulans_rep2

description:
Library name: Sample76
Nnk.sim.subtract.bw


title: COTC021-0809-M-F-Lung

value: Lung


title: Hi-C, RAD21-FKBP cells, dTAG-45nM-6h, rep1


title: Nnk_simulans_rep1

description:
Library name: Sample75
Nnk.sim.subtract.bw


title: COTC021-0811-M-F-Lung


title: COTC021-0709-M-F-Lung


title: COTC021-0731-M-F-Liver

value: Liver


title: NPp53 homonally intact biol rep 2

description:
Library name: MS04
column name in 20220308.intact.raw.counts.csv: MS04

value: tissue

value: Tamoxifen at 2 months of age


title: Nnk_yakuba_rep2

description:
Library name: Sample78
Nnk.yak.subtract.bw


title: NPp53T homonally intact biol rep 1

description:
Library name: MS08
column name in 20220308.intact.raw.counts.csv: MS08

value: prostate


title: NPp53 homonally intact biol rep 1

description:
Library name: MS03
column name in 20220308.intact.raw.counts.csv: MS03

value: 3 months


title: GAL3_ade_14d_2

description: Library name: GAL3_ade_14d_2

value: kidney

value: Adenine diet for 14 days


title: COTC021-0709-M-F-Bone


title: lung metastasis rep1

description: Library name: LIB5420042_SAM24363626

data_processing:
Sample demultiplexing, barcode processing and single cell 3' gene counting were performed using 10X Cell Ranger. Reads were aligned to GRCm38 mouse reference assembly. Low quality cells with a percentage of mitochondrial reads above 25% or the number of detected genes below 200 were excluded for further analysis. Per-gene UMI counts were normalized by the total number of transcripts per cell, scaled by the median number of transcripts across all cells and log-transformed for downstream analysis.
Dataset cell clustering and visualization were performed as described in the OSCA book (https://osca.bioconductor.org) (Amezquita et al. 2020; PMID: 31792435). Dimensionality reduction and clustering were performed to obtain a common UMAP coordinate space and grouping for all cells. Clustering and visualization were based on the top 20 principal components. We used the 50 nearest neighbors (k=50) and a resolution of 0.3 for graph-based clustering. Gene signatures were scored using the UCell R package (Andreatta 2021; PMID: 34285779)
Assembly: GRCm38/mm10
Supplementary files format and content: .rds format - SingleCellExperiment objects for the GeneExpressionMatrix

source_name: lung

growth_protocol: NSG mice were implanted orthotopically with AKVPSL organoids and developed primary colon tumors as well as liver and lung metastases.

extract_protocol:
At humane endpoint, liver and lung metastases were isolated, tissues digested as described above and live RFP⁺ tumor epithelial cells sorted from each metastatic site and subjected to single-cell RNA sequencing, profiling ~10,000 cells per tissue.
Sample processing for single-cell RNA-seq was done using Chromium Single Cell 3’ Library reagent kit v2 following manufacturer’s guide (10x Genomics). Cell density and viability of single-cell suspension were determined by Vi-CELL XR cell counter (Beckman Coulter) or by manual counting using a hemocytometer. We loaded ~10,000 cells on each chip. cDNAs and libraries were prepared following the manufacturer’s user guide (10x Genomics). Libraries were profiled by Tapestation D1000 kit (Agilent) and quantified using IQubit HS dsDNA kit (Invitrogen). Each library was sequenced in one lane of HiSeq4000 (Illumina) following the manufacturer’s sequencing specification (10x Genomics).

value: lung

value: Tumor epithelial cells


title: deltaCG4282_MicroC_rep2

description:
Library name: Sample72
deltaCG4282_100bp.mcool

value: embryo

value: nc14 embryo


title: Nnk_ficusphila_rep1

description:
Library name: Sample81
Nnk.fic.subtract.bw


title: Hi-C, PDS5AB-AID cells, RAD21-FKBP_auxin_dTAG-25nM-6h , rep1

value: PDS5A-AID, PDS5B-AID, Tir1, RAD21-FKBP-Halotag

value: dTAG_25nM_6h, auxin_6h


title: deltaCG4282_MicroC_rep1

description:
Library name: Sample71
deltaCG4282_100bp.mcool


title: Hi-C, PDS5AB-AID cells, RAD21-FKBP_auxin_dTAG-10nM-6h, rep1

value: dTAG_10nM_6h, auxin_6h


title: COTC021-0621-M-F-Lymph Node

data_processing: Normalization was accomplished using the nanostringr platform using the positive control normalization approach. Sample-specific correlation within each sample lane was also performed using CodeSet context (housekeeping gene) normalization

source_name: FFPE

value: Lymph Node

value: Metastatic Tumor Tissue


title: sis2∆ mutant grown in7.35 mM potassium, biol rep 3

first: Adam

middle: James

last: Waite

address: 1170 Veterans Blvd

institute: Calico Life Sciences LLC

description: Library name: CGY4134.735.C

data_processing:
Raw sequencing reads were demultiplexed with bcl2fastq
Reads were trimmed with cutadapt v2.6 with parameters -j 8 -e 0.1 -q 20 -O 1.
Trimmed reads were aligned to build R64-1-1 of the S. cerevisiae genome using STAR v2.7.6a with extra parameters --twopassMode Basic --outSAMunmapped Within --outSAMattributes NH HI AS NM MD --outSAMstrandField intronMotif.
Alignments were quantified using all features with featureCounts from subread version 1.6.2 in paired end mode with options -O --fraction.
Genes were then filtered down to those with at least 20 total counts across all samples across experiments.
Assembly: R64-1-1
Supplementary files format and content: comma-delimited text file with raw read counts for each sample

organism: Saccharomyces cerevisiae

source_name: culture

growth_protocol: Strains were struck from a -80 °C freezer onto 2% agar plates containing YEPD (1% yeast extract, 2% peptone, 2% glucose) and grown until colonies were visible (typically 2-3 days). Cells were inoculated into synthetic complete (SC) media (2 g 10X SC mix [Sunrise], 6.7 g YNB+NH4 [Sunrise], 20 g glucose per liter, buffered to pH 4.5, filter sterilized), and grown for 16-24 hours to saturation. These “overnight” cultures were then diluted into the experimental media and grown for 24 hours in exponential phase, diluting as necessary so that the cell culture never exceeded an OD of 0.1.

extract_protocol:
0.5 OD of cells was collected onto a 0.45 µm nylon filter (HNWP02500, Millipore Sigma) using a vacuum filtration system. Cell were resuspended in 200 µL of Lysis buffer (10 mM Tris [pH 8.0], 0.5% SDS, 10 mM EDTA). After adding of 200 µL acid phenol (pH 4.3), samples were vortexed for 30 s. Samples were then incubated at 65°C for 30 min in a thermomixer with intermittent shaking (2,000 rpm for 1 min every 15 min). Finally, a total of 400 µL of ethanol was added and the RNA was purified using the Direct-zol RNA Miniprep Plus kit (R2071; Zymo Research) according to the manufacturer’s instructions, including the optional DNase digestion step. RNA integrity was confirmed using an Agilent Bioanalyzer.
The Poly A selection + NEB Ultra II Directional RNA Library Prep Kit (New England BioLabs Inc., Massachusetts, USA) was used to generate cDNA and libraries according to the manufacturer’s protocol. The libraries were indexed using Admera's in-house index primers and cleaned up using AFTMag NGS DNA Clean Beads (Abclonal science, RK20257). The indexed libraries were pooled and sequenced on the Illumina NovaSeq X plus platform with a read length of 2x150bp.

treatment_protocol: Strains were grown to saturation overnight in media containing standard (7.35 mM) potassium. From these overnight cultures, strains were diluted into media containing the appropriate potassium concentration in biological triplicate and grown for an additional 24 hours, ensuring that the OD600 did not go above ~0.1.

value: culture

value: MATa sis2d0::kanMX

value: regular potassium


title: deltaCG17361_MicroC_rep2

description:
Library name: Sample70
deltaCG17361_100bp.mcool


title: Hi-C, NIPBL-FKBP cells, dTAG-24h, rep2

value: Mouse Embryonic Stem Cells

value: NIPBL-FKBP


title: COTC021-0621-M-F-Kidney

extract_protocol: RNA was extracted using RNeasy Mini reagents and protocol. RNA quality was determined by Agilent 2100 Bioanalyzer’s DV200 analysis.

value: Kidney


title: sis2∆ mutant grown in 7.35 mM potassium, biol rep 2

description: Library name: CGY4134.735.B


title: yw_MicroC_rep2

description:
Library name: Sample74
yw_100bp.mcool


title: liver metastasis rep2

description: Library name: LIB5420044_SAM24363628

source_name: liver

value: liver


title: Hi-C, RAD21-FKBP cells, dTAG-20nM-6h, rep1


title: deltaKipferl_MicroC_rep2

description:
Library name: Sample66
deltaKipferl_100bp.mcool


title: Hi-C, WAPL-AID cells, auxin-6h, rep2

value: WAPL-AID, Tir1


title: deltaD19A_MicroC_rep1

description:
Library name: Sample67
deltaD19A_100bp.mcool


title: yw_MicroC_rep1

description:
Library name: Sample73
yw_100bp.mcool


title: Hi-C, WAPL-AID cells, RAD21-FKBP_auxin_dTAG-25nM-6h, rep1

value: WAPL-AID, Tir1, RAD21-FKBP-Halotag


title: liver metastasis rep1

description: Library name: LIB5420041_SAM24363625

value: Tumor epithelial cells


title: COTC021-0601-M-F-Kidney 8


title: Hi-C, WAPL-AID cells, RAD21-FKBP_auxin_dTAG-8nM-6h, rep1

value: dTAG_8nM_6h, auxin_6h


title: COTC021-0601-M-F-Kidney 7


title: lung metastasis rep2

description: Library name: LIB5420045_SAM24363629

value: lung


title: WT grown in7.35 mM potassium, biol rep 3

description: Library name: CGY4130.735.C

value: MATa


title: COTC021-0621-M-F-Lung

value: Lung


title: COTC021-0621-M-F-Liver

value: Liver


title: COTC021-0327-T

value: Bone

value: Primary Malignant Tumor Tissue


title: Hi-C, PDS5AB-AID_NIPBL-FKBP cells, auxin-6h_dTAG-6h, rep2

value: PDS5A-AID, PDS5B-AID, Tir1, NIPBL-FKBP, RAD21-Halotag

value: dTAG_6h, auxin_6h


title: sis2∆ mutant grown in 0.5 mM potassium, biol rep 2

description: Library name: CGY4134.05.B

value: culture

value: MATa sis2d0::kanMX

value: low potassium


title: deltaCG17361_MicroC_rep1

description:
Library name: Sample69
deltaCG17361_100bp.mcool

value: embryo

value: nc14 embryo


title: deltaD19A_MicroC_rep2

description:
Library name: Sample68
deltaD19A_100bp.mcool


title: Hi-C, NIPBL-FKBP cells, dTAG-24h, rep1

value: Mouse Embryonic Stem Cells

value: NIPBL-FKBP


title: WT grown in 7.35 mM potassium, biol rep 2

description: Library name: CGY4130.735.B

value: regular potassium


title: COTC021-0327-M-S-Kidney

description: RNA was profiled using the Canine IO Panel

source_name: Snap Frozen

value: Kidney

value: Metastatic Tumor Tissue


title: COTC021-0621-M-F-Heart

value: Heart


title: sis2∆ mutant grown in 7.35 mM potassium, biol rep 1

description: Library name: CGY4134.735.A


title: Hi-C, PDS5AB-AID_NIPBL-FKBP cells, auxin-6h_dTAG-6h, rep1


title: Zw5_FLAG-ChIP_rep2

description: Library name: Sample58

data_processing:
Raw sequence reads were trimmed by fastp.
Trimmed reads were mapped to drosophila dm6 (BDGP6) genome by bowtie2.
Uniquely mapped reads were extracted by samtools.
Matrix bigwig files were produced by deeptools.
Peak calling were performed by MACS2.
Assembly: dm6
Supplementary files format and content: general bigwig, narrowPeak file format

extract_protocol:
nc14 (2h10min-2h40min) early embryo for ChIP and adult ovary for RNA-seq
Prepared by manufacturer's protocol of NEBNext Ultra II DNA Library Prep Kit for Illumina


title: sis2∆ mutant grown in 0.5 mM potassium, biol rep 3

description: Library name: CGY4134.05.C


title: Hi-C, WAPL-AID_NIPBL-FKBP cells, auxin-6h_dTAG-6h, rep2

value: WAPL-AID, Tir1, NIPBL-FKBP, RAD21-Halotag


title: Hi-C, RAD21-AID cells, auxin-3h30, rep2

value: RAD21-AID, Tir1


title: WT grown in 0.5 mM potassium, biol rep 2

description: Library name: CGY4130.05.B

value: MATa


title: control_Pol2-ChIP_rep2

description: Library name: Sample60

value: yw (used for Pol II-ChIP)


title: COTC021-0327-M-F-Lymph Node 1

value: Lymph Node


title: WT grown in 0.5 mM potassium, biol rep 1

description: Library name: CGY4130.05.A


title: COTC021-0301-M-F-SubLumbar

value: Sub Lumbar


title: deltaKipferl_MicroC_rep1

description:
Library name: Sample65
deltaKipferl_100bp.mcool


title: aged 24hrs, biol rep 3

description: Library name: WT 24h 3

extract_protocol:
Bulk RNA-seq was performed by Admera Health. Total RNA was extracted and then purified using RNeasy Plant Mini- Yeast (Qiagen Cat no. / ID.  74904). according to the manufacturer’s protocols. Quality and quantity of RNA were assessed on a TapeStation (Agilent), and samples with an RNA integrity number (RIN) > 6 were used for subsequent library preparation.
The Poly A selection + NEB Ultra II Directional RNA Library Prep Kit (New England BioLabs Inc., Massachusetts, USA) was used to generate cDNA and libraries according to the manufacturer’s protocol. The libraries were indexed using Admera's in-house index primers and cleaned up using AFTMag NGS DNA Clean Beads (Abclonal science, RK20257). The indexed libraries were pooled and sequenced on the Illumina NovaSeq X plus platform with a read length of 2x150bp.

treatment_protocol: Aged samples were aged in ministat aging devices according to Hendrickson et al. (2018). A new experimental platform facilitates assessment of the transcriptional and chromatin landscapes of aging yeast. eLife. 7:e39911. https://doi.org/10.7554/eLife.39911

value: culture

value: aged


title: COTC021-0301-T-F-B

value: Bone

value: Primary Malignant Tumor Tissue


title: Zif_FLAG-ChIP_rep2

description: Library name: Sample56

value: embryo

value: nc14 embryo


title: Hi-C, PDS5B-AID cells, auxin-6h, rep1

description: Illumina NextSeq 500, Illumina HiSeq or Illumina Nova-seq

value: Mouse Embryonic Stem Cells

value: PDS5B-AID, Tir1


title: aged 24hrs, biol rep 2

description: Library name: WT 24h 2


title: Hi-C, NIPBL-FKBP cells, untreated, rep2

value: NIPBL-FKBP


title: sis2∆ mutant grown in 0.5 mM potassium, biol rep 1

description: Library name: CGY4134.05.A

value: MATa sis2d0::kanMX

value: low potassium


title: Hi-C, WAPL-AID_NIPBL-FKBP cells, auxin-6h_dTAG-6h, rep1

value: WAPL-AID, Tir1, NIPBL-FKBP, RAD21-Halotag

value: dTAG_6h, auxin_6h


title: Zelda_FLAG-ChIP_rep2

description: Library name: Sample54


title: COTC021-0301-M-F-Lung

value: Lung

value: Metastatic Tumor Tissue


title: aged 24hrs, biol rep 1

description: Library name: WT 24h 1


title: control_Pol2-ChIP_rep1

description: Library name: Sample59

value: yw (used for Pol II-ChIP)


title: young, biol rep 3

description: Library name: WT log 3

value: young


title: COTC021-0301-M-F-Liver

value: Liver


title: COTC021-0327-M-F-Lymph Node 3

value: Lymph Node


title: WT grown in 7.35 mM potassium, biol rep 1

description: Library name: CGY4130.735.A

value: culture

value: MATa

value: regular potassium


title: Hi-C, NIPBL-FKBP cells, dTAG-6h, rep2


title: WT grown in 0.5 mM potassium, biol rep 3

description: Library name: CGY4130.05.C


title: Hi-C, WAPL-AID cells, auxin-6h, rep1

value: WAPL-AID, Tir1


title: Zw5_FLAG-ChIP_rep1

description: Library name: Sample57

value: embryo

value: nc14 embryo


title: Hi-C, PDS5AB-AID cells, untreated, rep2

value: Mouse Embryonic Stem Cells

value: PDS5A-AID, PDS5B-AID, Tir1


title: young, biol rep 2

description: Library name: WT log 2


title: Hi-C, RAD21-AID cells, untreated, rep2

value: RAD21-AID, Tir1


title: Wek_FLAG-ChIP_rep1

description: Library name: Sample49


title: Hi-C, RAD21-AID cells, auxin-3h30, rep1


title: COTC021-0213-M-S-Abd Mass-2

value: Abdominal Mass


title: young, biol rep 1

description: Library name: WT log 1


title: Zif_FLAG-ChIP_rep1

description: Library name: Sample55


title: COTC021-0301-M-F-Mesentary

value: Mesentery


title: CCN1-A4

first: Joshua

middle: Evan

last: Burda

address: 127 S San Vicente Blvd

department: Biomedical Sciences, Center for Neural Science and Medicine

institute: Cedars Sinai Medical Center

description:
Library name: Sample 7
cultured microglia treated with CCN1

data_processing:
Data quality was assessed using Illumina SAV and demultiplexing was performed using Illumina Bcl2fastq2. Alignment by STAR aligner (v.2.7.11b). Data normalization and differential expression by EdgeR (v.3.28.0). Read counting by EdgeR (v.3.28.0).
Assembly: mm39
Supplementary files format and content: .tab, .xlsx

source_name: brain

growth_protocol: A 50uL spot drop containing 50,000 microglia cells was seeded into 24 well plates coated with poly-L-lysine(0.01%). Cells were cultured for 7 days in microglia media, with a full media change given on day 1 followed by a half media change on day 4. Microglia media contained 10% fetal bovine serum, 1x penicillin-streptomycin, 10ng/mL mouse GM-CSF, 10ng/mL mouse M-CSF, and 10ng/mL TGFB1.

extract_protocol:
Mice were perfused with ice-cold PBS with heparin and the brain was freshly dissected. Brains were dissociated with the Miltenyi Neural Tissue Dissociation Kit (P) and the GentleMACS dissociator with heaters per manufacturer instructions. Microglia were isolated via magnetic purification with CD11b beads. RNA was isolated using RNeasy Plus Micro Kit (Qiagen, Cat. 74034)
RNA integrity was analyzed using the 2100 Bioanalyzer (Agilent) with the RNA Pico chip, with RIN ≥ 9.6 for all samples. RNA concentration was determined using the RiboGreen RNA Assay.

treatment_protocol: On day 7, cells were either left untreated or treated with CCN1 (Peprotech: 120-25) at 50ng/mL or vehicle (BSA) for 24 hours. Each condition was carried out in triplicate for each experiment. Cells were then removed using a cell scraper, replicates pooled, and then processed for RNA isolation

value: brain

value: primary adult microglia

value: 50ng/mL recombinant CCN4


title: CCN1-A3

description:
Library name: Sample 6
cultured microglia treated with CCN1

value: 50ng/mL recombinant CCN3


title: control_FLAG-ChIP_rep2

description: Library name: Sample52

value: yw (used for FLAG-ChIP)


title: Hi-C, PDS5AB-AID cells, auxin-6h, rep2


title: Trem_FLAG-ChIP_rep2

description: Library name: Sample48


title: COTC021-0213-M-F-Kidney

value: Kidney

value: Metastatic Tumor Tissue


title: Hi-C, NIPBL-FKBP cells, dTAG-6h, rep1

value: NIPBL-FKBP


title: Zelda_FLAG-ChIP_rep1

description: Library name: Sample53


title: COTC021-0201-T-F-B

value: Bone

value: Primary Malignant Tumor Tissue


title: Hi-C, PDS5B-AID cells, untreated, rep1

value: PDS5B-AID, Tir1


title: Hi-C, NIPBL-FKBP cells, untreated, rep1


title: CCN1-A2

description:
Library name: Sample 5
cultured microglia treated with CCN1

value: 50ng/mL recombinant CCN2


title: Trem_FLAG-ChIP_rep1

description: Library name: Sample47

value: embryo

value: nc14 embryo


title: SuHw_FLAG-ChIP_rep2

description: Library name: Sample46


title: COTC021-0201-M-F-Lung

value: Lung


title: CCN1-A1

description:
Library name: Sample 4
cultured microglia treated with CCN1

value: 50ng/mL recombinant CCN1


title: COTC021-0213-T

source_name: RNAlater


title: COTC021-0301-M-F-Kidney


title: control_FLAG-ChIP_rep1

description: Library name: Sample51


title: COTC021-0103-M-F-Skin

value: Skin


title: Hi-C, RAD21-AID cells, untreated, rep1

value: Mouse Embryonic Stem Cells

value: RAD21-AID, Tir1


title: Wek_FLAG-ChIP_rep2

description: Library name: Sample50


title: BSA-A3

description:
Library name: Sample 3
cultured microglia treated with BSA

value: brain

value: primary adult microglia

value: 50ng/mL BSA (vehicle)


title: COTC021-0213-M-F-Abd Mass 1

value: Abdominal Mass


title: NnkWT_FLAG-ChIP_rep2

description: Library name: Sample42


title: Odj_FLAG-ChIP_rep1

description: Library name: Sample43


title: SuHw_FLAG-ChIP_rep1

description: Library name: Sample45


title: NnkdeltaZAD_FLAG-ChIP_rep2

description: Library name: Sample40


title: Hi-C, PDS5AB-AID cells, auxin-6h, rep1

value: PDS5A-AID, PDS5B-AID, Tir1


title: NnkWT_FLAG-ChIP_rep1

description: Library name: Sample41


title: CYSP-1

city: Suzhou

first: Hu

last: ya'nan

state: Jiangsu

address: 199 Ren-Ai Road, Suzhou Industrial Park

department: Department of Cell Biology

institute: Medical College of Soochow University

description: Library name: Sample 4

data_processing:
Sequence reads were trimmed for adapters sequence/low-quality sequence using fastp (version 0.18.0)
Trimmed sequence reads were mapped to Ensembl_release106 using HISAT2. 2.4
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach
Read count extraction and normalization were performed using RSEM software
Assembly: Ensembl_release106
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: marrow

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen) according to the user guide for RNA-seq analysis.
Total RNA was extracted, and the eukaryotic mRNA was enriched by Oligo (dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversely transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs).

value: marrow

value: MSCs

value: Mesenchymal stem cell

value: WT

value: CYSP in neural differentiation media for 7d


title: Hi-C, PDS5AB-AID cells, untreated, rep1


title: COTC021-0103-M-F-Liver

first: Christina

last: Mazcko

address: 10 Center Drive Room 1B58

institute: NCI

value: Liver

value: Metastatic Tumor Tissue


title: COTC021-0103-M-F-Kidney

value: Kidney


title: Odj_FLAG-ChIP_rep2

description: Library name: Sample44

value: embryo

value: nc14 embryo


title: Hi-C, PDS5A-AID cells, auxin-6h, rep1

value: Mouse Embryonic Stem Cells

value: PDS5A-AID, Tir1


title: COTC021-0103-M-F-Lung-3

value: Lung


title: BSA-A2

description:
Library name: Sample 2
cultured microglia treated with BSA

value: brain

value: primary adult microglia


title: NnkdeltaZAD_FLAG-ChIP_rep1

description: Library name: Sample39


title: COTC021-0103-M-F-Lung-2


title: CYSP-3

description: Library name: Sample 6


title: BSA-A1

description:
Library name: Sample 1
cultured microglia treated with BSA

value: 50ng/mL BSA (vehicle)


title: Hi-C, untagged cells, untreated, rep2


title: Hi-C, PDS5A-AID cells, untreated, rep1


title: Hi-C, untagged cells, untreated,  rep1


title: CYSP-2

description: Library name: Sample 5


title: AKPS P5 mouse #817_rep3

description:
Library name: SAM24419318
EpCam+ cells sorted from AKPS P5 colon tumor _mouse #817

data_processing:
ATAC-seq results were analyzed using the ENCODE ATAC-seq pipeline (v2.2.2). In brief, adaptors were trimmed using cutadapt (v2.5), ATAC-seq reads were aligned to the mouse genome (mm10) using Bowtie2 (v2.3.4.3). Aligned reads were then filtered for quality and duplicates using samtools (1.9) and Picard (2.20.7). Peaks were called using MACS2 (v2.2.4). Specifically, 5’ ends of reads were shifted in a strand-specific manner to account for the Tn5 shift and identify the precise cut-sites. The shifted read-start coverage was aggregated over both strands and smoothed using a 150 bp window for peak calling in MACS2. The called peaks were filtered using exclusion lists that contain genomic regions resulting in anomalous, unstructured, or experiment independent high signal. The Irreproducible Discovery Rate (IDR 2.0.4.2) framework was used to estimate reproducibility and stringent peak calls. To assess data quality, we measured read mapping statistics, enrichment QC metrics, library complexity, reproducibility ratio and focused on the Transcription Start Site enrichment score, and the total number of peaks identified.
Normalization and differential binding analysis on the reads was performed using the “DiffBind” R package (Stark et al., 2011) by contrasting P5 samples with P1 samples.
Assembly: mouse genome (GRCm38)
Supplementary files format and content: MACS2 processed peak call data for each sample
Supplementary files format and content: bigwig file for normalized group average density
Supplementary files format and content: tab-delimited text file; TMM normalized peak values for each sample

growth_protocol: 1x10^4 AKPS P1 (m4) organoids and or AKPS P5 (m484) organoids were orthotopically injected into the colon of C57BL/6N mice. 5 weeks post orthotopic injection colon tumors were harvested and digested into single cells.

extract_protocol:
Sorted cells were spun at 500g for 5 min at 4°C, lysed in ice-cold ATAC resuspension buffer [10 mM tris-HCl (pH 7.4), 10 mM NaCl, and 3 mM MgCl2] containing 0.1% NP-40 (Sigma-Aldrich), 0.1% Tween 20 (Sigma-Aldrich), and 0.01% digitonin (Promega), pipetted up and down three times, and incubated on ice for 3 min. Cells were then washed in the ATAC resuspension buffer containing 0.1% Tween 20. Cell pellets were resuspended and DNA was tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina, FC-121-1031). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen, 28004).
ATAC-seq libraries were generated using the ATAC-Seq Kit (Active Motif, 53150). Libraries were quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and profiled using the D5000 ScreenTape on TapeStation 4200 (Agilent Technologies). Libraries were pooled and sequenced on an Illumina sequencer to generate 25 million paired-end 50-base pair reads per library

value: Colon tumor

value: Epithelial cell

value: no treatment


title: AKPS P5 mouse #816_rep2

description:
Library name: SAM24419317
EpCam+ cells sorted from AKPS P5 colon tumor _mouse #816


title: Nnk_FLAG-ChIP_rep1

description: Library name: Sample37


title: CK-1

description: Library name: Sample 1

value: marrow

value: MSCs

value: Mesenchymal stem cell

value: DMSO in neural differentiation media for 7 days


title: M1BP_FLAG-ChIP_rep2

description: Library name: Sample36


title: AKPS P1 mouse #804_rep4

description:
Library name: SAM24419315
EpCam+ cells sorted from AKPS P1 colon tumor _mouse #804


title: MSC, pig 35, clone 34, low adipogenic

description: NovaSeq 2x150 bp sequencing

data_processing:
Raw sequence data converted to fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software
Trimming for adapters and poor quality reads was performed using Trimmomatic v0.36
Mapping performed using STAR aligner v2.5.2b
Gene hit counts calculated using feature Counts from the Subread package v1.5.2
Differential expression analysis performed using DESeq2 v1.16.1, including another Pig16 low adipogenic sample (C14) where the raw files were lost
Assembly: Sscrofa10.2
Supplementary files format and content: raw_counts_clonal.csv: comma separated values containing raw reads and associated hgnc symbols for each mapped gene and each sample

organism: Sus scrofa

source_name: mesenchymal stem cell

growth_protocol: MSC cultures were generated by enzymatic digestion of porcine adipose tissues followed by in vitro expansion of MSCs and clones generated by single cell sorting in media containing 10% FBS and bFGF (5 ng/ml). To determine adipogenic capacity, clones underwent standard adipogenic differentiation then were stained with Oil Red O and quantified. "High" clones were the highest scoring clones, "low" clones had lower scores but still had adipocytes present.

extract_protocol:
RNA was extracted using TRIzol and further purified using QIAGEN RNeasy columns
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufaturer's instructions

value: mesenchymal stem cell

value: low adipogenic


title: CK-3

description: Library name: Sample 3

value: WT


title: M1BP_FLAG-ChIP_rep1

description: Library name: Sample35

value: embryo

value: nc14 embryo


title: DMSO repeat3

city: Hangzhou,

first: Guangyue

last: Li

state: Zhejiang

address: No.600 Dunyu Rd., Xihu District

institute: westlake university

description: Library name: C3

data_processing:
Sequence data quality was assessed using the Phred+33 quality scoring system to ensure high fidelity across all datasets.
Clean reads were aligned with the reference genome using HISAT (v2.2.1)
Gene expression levels were measured using RSEM (v1.3.1)
Assembly: GRCh38
Supplementary files format and content: csv files include raw count for each sample

source_name: Liver

growth_protocol: HepG2 cells were cultured in 10 cm plates comprising three control and three treatment replicates.

extract_protocol:
total RNA was isolated using the TRIzol reagent (Cat# 15596026; Invitrogen, USA). RNA quality and concentration were assessed by agarose gel electrophoresis and an Eppendorf BioSpectrometer.
For all six samples (including controls and DAP treatments), sequencing libraries were prepared using the DNBSEQ platform. The sequencing was performed by BGI Genomics Co., Ltd. (Shenzhen, China), generating 150 bp paired-end reads (PE150) .

treatment_protocol: Cells were treated with DMSO (control) or 160 µM DAP for 24 h

value: Liver

value: DMSO


title: AKPS P5 mouse #811_814_rep4

description:
Library name: SAM24419319
EpCam+ cells sorted from AKPS P5 colon tumor _mouse #811 and 814 (pooled)


title: DAP repeat2

description: Library name: T2

value: DAP

value: Daphnetin (DAP)


title: COTC021-0103-M-F-Brain

value: Brain

value: Metastatic Tumor Tissue


title: DMSO repeat2

description: Library name: C2


title: Nnk_FLAG-ChIP_rep2

description: Library name: Sample38


title: AKPS P5 mouse #815_rep1

description:
Library name: SAM24419316
EpCam+ cells sorted from AKPS P5 colon tumor _mouse #815

value: Colon tumor

value: Epithelial cell


title: CK-2

description: Library name: Sample 2

value: marrow


title: MSC, pig 35, clone 39, high adipogenic

description: NovaSeq 2x150 bp sequencing

value: high adipogenic


title: GAF_FLAG-ChIP_rep2

description: Library name: Sample32


title: MSC, pig 35, clone 15, low adipogenic

description: NovaSeq 2x150 bp sequencing


title: DAP repeat3

description: Library name: T3


title: DAP repeat1

description: Library name: T1


title: AKPS P1 mouse #803_rep3

description:
Library name: SAM24419314
EpCam+ cells sorted from AKPS P1 colon tumor _mouse #803

value: no treatment


title: E13.5, PGC, male, replicate 2, Hi-C

city: London

first: Tien-Chi

last: Huang

address: Du Cane Road, Hammersmith Hospital Campus

department: Epigenetics

institute: MRC Laboratory of Medical Sciences

description:
Hi-C male PGC rep 2
merged_reps_male_PGC_whole_genome_norm_chr1to19_chrXY_1mb.cool

data_processing:
Hi-C reads were trimmed using Trim Galore v0.6.6 (https://github.com/FelixKrueger/TrimGalore). In order to get data as homogeneous as possible, and given that male reads were 100bp and female reads were 50bp long, male reads were initially hard-trimmed 50bp from their 3’ end in order to get 50bp reads for both the male and female samples. Then, quality trimming and adapter removal was done to all reads using trim_galore with default parameters.
Hi-C matrices were obtained using FANC v 0.9.23 (Kruse et al., 2020) using the fanc auto command establishing the restriction enzyme with -r DpnII and adding a ligation error filter with --le-inward-cutoff and --le-outward-cutoff set to 10kb. Reads were aligned to the mm39 genome. Normalization of Hi-C matrices was done using Knight-Ruiz balancing method per chromosome.
Additional, whole-genome normalized Hi-C matrices were obtained to make plots displaying multiple or all chromosomes. For these, reads from female samples were realigned to the mm39 genome excluding the Y chromosome. Then, matrices were normalised with fanc hic --bin-size 1mb --normalise --whole-matrix and --subset, this last parameter followed by the list of all autosome, chrX, and, in male, chrY.
Assembly: mm39
Supplementary files format and content: Hi-C matrices in .cool format

source_name: PGC

extract_protocol:
GFP-positive cells (PGC) and GFP-negative cells (Somatic) were isolated by fluorescence-activated cell sorting (FACS) using Aria IIu (BD Bioscience) or Aria III (BD Bioscience) flow cytometer.
Hi-C library generation was performed as described previously (Nagano et al., 2017), with some modifications. Per replicate, 10,000 cells were fixed in 2% PFA for 10 minutes, lysed in lysis buffer (30 minutes on ice), and digested with DpnII (NEB) overnight at 37C rotating (950rpm). Restriction overhangs were filled-in with Klenow (NEB) using biotin-14-dATP (Jena Bioscience), and ligation was performed in ligation buffer for 4 hours at 16C (T4 DNA ligase; Life Technologies). After overnight decrosslinking at 65C, the ligated DNA was tagmented to produce fragments of 300-700 bp range. Ligation products were isolated using MyOne C1 streptavidin beads (Life Technologies), followed by washing with Wash&Binding buffer and nuclease-free water. Isolated Hi-C ligation products on the beads were then used directly for PCR amplification (total of 5 PCR cycles), and the final Hi-C library was purified with AMPure XP beads (Beckman Coulter). The libraries were paired-end sequenced on HiSeq 2500 with ~500mln paired reads per replicate.

tag: Sex

value: male

value: PGC


title: CUT&Tag of HU-HSA-3 using Kla Ab with glucose for 4 h

city: Sapporo

first: Suzuki

last: Tamami

state: Hokkaido

address: Kita-18-jo, Nishi-9-chome, Kita-ku

department: Department of Clinical Sciences, Faculty of Veterinary

institute: Hokkaido University

description: Library name: CT_Kla_H2_25mM_4h

data_processing:
Sequencing reads that qualified with Fastp v0.26.0 were mapped to the CanFam3.1 canine reference genome from Ensembl using Bowtie2 v2.5.4.
For sample normalization, sum of fragments coverage was determined by calculating the number of fragments which were ranged from 1 to 1,000 bp in bedpe formats converted from mapped bam files using bedtools v2.31.1
Assembly: CanFam3.1
Supplementary files format and content: bedgraph files
Library strategy: CUT&Tag

growth_protocol: DMEM witth indicated glucose concentration, 10% fetal bovine serum and penicillin–streptomycin at 37°C with 5% CO2.

extract_protocol:
DNA from canine hemangiosarcoma cell line was digested by pAG-Tn5.
For DNA amplification, PCR was performed for purified DNA fragments with index primers using PCR Master Mix. The process consists of 72°C for 5 min for 1 cycle, 98°C for 40 sec and 63°C for 10 sec for 13 cycles, and 72°C for 1 min for 1 cycle. Amplified DNA was purified with AMpure. DNA concentration was measured with Qubit using a dsDNA high sensitivity kit. DNA quality was checked with TapeStation using a D5000 High sensitivity kit.

treatment_protocol: with or without 25 mM glucose for 4 or 48 hours

value: canine hemangiosarcoma

value: Glucose 25 mM for 48 h

tag: antibody

value: Kla


title: GAF_FLAG-ChIP_rep1

description: Library name: Sample31

value: embryo

value: nc14 embryo


title: DMSO repeat1

description: Library name: C1

value: Liver

value: WT

value: DMSO


title: L3mbt_FLAG-ChIP_rep2

description: Library name: Sample34


title: AKPS P1 mouse #802_rep2

description:
Library name: SAM24419313
EpCam+ cells sorted from AKPS P1 colon tumor _mouse #802

source_name: Colon tumor


title: MSC, pig 35, clone 28, high adipogenic

description: NovaSeq 2x150 bp sequencing

value: mesenchymal stem cell


title: CUT&Tag of HU-HSA-3 using RNAPII-Ser5 Ab with glucose for 48 h

description: Library name: CT_RNAPII_H3_25mM_48h


title: E13.5, Soma, male, replicate 2, Hi-C

description:
Hi-C male soma rep 2
merged_reps_male_soma_whole_genome_norm_chr1to19_chrXY_1mb.cool

source_name: somatic

value: somatic


title: AKPS P1 mouse #801_rep1

description:
Library name: SAM24419312
EpCam+ cells sorted from AKPS P1 colon tumor _mouse #801

value: Colon tumor


title: MSC, pig 35, clone 8, low adipogenic

description: NovaSeq 2x150 bp sequencing

value: low adipogenic


title: CUT&Tag of HU-HSA-3 using Kla Ab without glucose for 4 h

description: Library name: CT_Kla_H2_0mM_4h

value: Glucose 0 mM for 48 h


title: CUT&Tag of HU-HSA-3 using H3K4me3 Ab without glucose for 4 h

description: Library name: CT_H3K4me3_H2_0mM_4h


title: E13.5, PGC, male, replicate 1, Hi-C

description:
Hi-C male PGC rep 1
merged_reps_male_PGC_whole_genome_norm_chr1to19_chrXY_1mb.cool


title: MSC, pig 34, clone 21, low adipogenic

description: NovaSeq 2x150 bp sequencing


title: MSC, pig 34, clone 20, high adipogenic

description: NovaSeq 2x150 bp sequencing

value: high adipogenic


title: CUT&Tag of HU-HSA-3 using H3K4me3 Ab with glucose for 4 h

description: Library name: CT_H3K4me3_H2_25mM_4h


title: D19BdeltaZADindeltaD19B_FLAG-ChIP_rep2

description: Library name: Sample28

value: D19BdeltaZAD-GFP-3xFLAG in deltaD19B


title: L3mbt_FLAG-ChIP_rep1

description: Library name: Sample33


title: fs1hL_FLAG-ChIP_rep2

description: Library name: Sample30


title: E13.5, Soma, male, replicate 1, Hi-C

description:
Hi-C male soma rep 1
merged_reps_male_soma_whole_genome_norm_chr1to19_chrXY_1mb.cool

value: male


title: CUT&Tag of HU-HSA-3 using RNAPII-Ser5 Ab without glucose for 48 h

description: Library name: CT_RNAPII_H3_0mM_48h


title: MSC, pig 34, clone 16, low adipogenic

description: NovaSeq 2x150 bp sequencing


title: E13.5, PGC, female, replicate 2, Hi-C

description:
Hi-C female PGC rep 2
merged_reps_female_PGC_whole_genome_norm_chr1to19_chrX_1mb.cool

value: female

value: PGC


title: CUT&Tag of HU-HSA-3 using H3K4me3 Ab with glucose for 48 h

description: Library name: CT_H3K4me3_H3_25mM_48h

value: canine hemangiosarcoma

value: Glucose 25 mM for 48 h


title: MSC, pig 35, clone 9, high adipogenic

description: NovaSeq 2x150 bp sequencing


title: D19BdeltaZADindeltaD19B_FLAG-ChIP_rep1

description: Library name: Sample27

value: embryo


title: D19BWTindeltaD19B_FLAG-ChIP_rep2

description: Library name: Sample26

value: nc14 embryo

value: D19BWT-GFP-3xFLAG in deltaD19B


title: MSC, pig 34, clone 7, high adipogenic

description: NovaSeq 2x150 bp sequencing


title: fs1hL_FLAG-ChIP_rep1

description: Library name: Sample29


title: CUT&Tag of HU-HSA-3 using H3K4me3 Ab without glucose for 48 h

description: Library name: CT_H3K4me3_H3_0mM_48h


title: MSC, pig 34, clone 2, high adipogenic

description: NovaSeq 2x150 bp sequencing


title: MSC, pig 34, clone 1, low adipogenic

description: NovaSeq 2x150 bp sequencing


title: E13.5, PGC, female, replicate 1, Hi-C

description:
Hi-C female PGC rep 1
merged_reps_female_PGC_whole_genome_norm_chr1to19_chrX_1mb.cool


title: CUT&Tag of HU-HSA-3 using Kla Ab with glucose for 48 h

description: Library name: CT_Kla_H3_25mM_48h

value: Kla


title: D19BWTindeltaD19B_FLAG-ChIP_rep1

description: Library name: Sample25


title: E13.5, Soma, female, replicate 2, Hi-C

description:
Hi-C female soma rep 2
merged_reps_female_soma_whole_genome_norm_chr1to19_chrX_1mb.cool


title: CUT&Tag of HU-HSA-3 using Kla Ab without glucose for 48 h

description: Library name: CT_Kla_H3_0mM_48h


title: CUT&Tag of HU-HSA-2 using H3K27ac Ab with glucose for 48 h

description: Library name: CT_H3K27ac_H2_25mM_48h


title: D19B_FLAG-ChIP_rep1

description: Library name: Sample23


title: D19B_FLAG-ChIP_rep2

description: Library name: Sample24


title: MSC, pig 19, clone 37, high adipogenic

description: NovaSeq 2x150 bp sequencing


title: Plasmax_3

city: Melbourne

first: Kristin

middle: K

last: Brown

state: VIC

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Library name: rna-94_S1
Column name in rawcounts_Fedropout_RNAseq.txt: Plasmax_3

data_processing:
QC, alignment, and counting were performed in Galaxy.
Sample QC was performed using FastQC (v0.72). Reads were trimmed using Cutadapt (v1.16)
Reads were mapped to human genome assembly (Ensembl hg19, GRCh37) using RNA STAR (v2.7.5b)
Counting was performed using featurecounts (v1.6.3)
Differentially expressed genes were identified using Degust (Limma-Voom v3.40.6)
Assembly: Reads were mapped to human genome assembly (Ensembl hg19, GRCh37)
Supplementary files format and content: Count file generated by featureCounts

growth_protocol: HepG2 cells were maintained in EMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1mM sodium pyruvate, and 2 mM glutamine. The cells were grown in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel) as per manufacturer's instructions.
cDNA libraries were prepared using QuantSeq 3' mRNA seq kit (Lexogen).

treatment_protocol: For all experiments, 2x105 HepG2 cells were seeded in 6-well plates in EMEM containing 10% heat-inactivated FBS. 24 hours after seeding, wells were washed with PBS and the appropriate media (EMEM, Plasmax, Plasmax-TE, or Plasmax-TE+Fe) containing 10% heat-inactivated FBS was added. Media was refreshed after 48 hours and cells were harvested 96 hours after transition to the different media types.

value: Hepatic cell

value: WT

value: Plasmax


title: E13.5, Soma, female, replicate 1, Hi-C

description:
Hi-C female soma rep 1
merged_reps_female_soma_whole_genome_norm_chr1to19_chrX_1mb.cool

value: somatic


title: CUT&Tag of HU-HSA-2 using H3K27ac Ab without glucose for 48 h

description: Library name: CT_H3K27ac_H2_0mM_48h


title: MSC, pig 19, clone 29, high adipogenic

first: F. Xavier

last: Donadeu

address: Easter Bush

institute: University of edinburgh

description: NovaSeq 2x150 bp sequencing

value: mesenchymal stem cell


title: MSC, pig 19, clone 16, high adipogenic

description: NovaSeq 2x150 bp sequencing


title: D19A_FLAG-ChIP_rep1

description: Library name: Sample21


title: MSC, pig 19, clone 30, low adipogenic

description: NovaSeq 2x150 bp sequencing

value: low adipogenic


title: Plasmax-TE_3

description:
Library name: rna-95_S2
Column name in rawcounts_Fedropout_RNAseq.txt: Plasmax-TE_3

value: Plasmax-TE


title: EMEM_3

description:
Library name: rna-93_S12
Column name in rawcounts_Fedropout_RNAseq.txt: EMEM_3

value: EMEM


title: CTCF_FLAG-ChIP_rep2

description: Library name: Sample20


title: D19A_FLAG-ChIP_rep2

description: Library name: Sample22


title: Plasmax-TE+Fe_3

description:
Library name: rna-92_S11
Column name in rawcounts_Fedropout_RNAseq.txt: Plasmax-TE+Fe_3

value: Plasmax-TE+Fe


title: CUT&Tag of HU-HSA-2 using H3K4me3 Ab with glucose for 48 h

description: Library name: CT_H3K4me3_H2_25mM_48h


title: CUT&Tag of HU-HSA-2 using H3K4me3 Ab without glucose for 48 h

description: Library name: CT_H3K4me3_H2_0mM_48h

value: Glucose 0 mM for 48 h


title: MSC, pig 19, clone 21, low adipogenic

description: NovaSeq 2x150 bp sequencing


title: CUT&Tag of HU-HSA-2 using Kla Ab with glucose for 48 h

description: Library name: CT_Kla_H2_25mM_48h


title: CUT&Tag of HU-HSA-2 using Kla Ab without glucose for 48 h

description: Library name: CT_Kla_H2_0mM_48h


title: Plasmax-TE_2

description:
Library name: rna-91_S10
Column name in rawcounts_Fedropout_RNAseq.txt: Plasmax-TE_2


title: CTCF_FLAG-ChIP_rep1

description: Library name: Sample19


title: MSC, pig 19, clone 14, low adipogenic

description: NovaSeq 2x150 bp sequencing


title: EMEM_2

description:
Library name: rna-89_S8
Column name in rawcounts_Fedropout_RNAseq.txt: EMEM_2


title: CP190_FLAG-ChIP_rep1

description: Library name: Sample17


title: MSC, pig 16, clone 26, high adipogenic

description: NovaSeq 2x150 bp sequencing

value: high adipogenic


title: Plasmax-TE+Fe_2

description:
Library name: rna-88_S7
Column name in rawcounts_Fedropout_RNAseq.txt: Plasmax-TE+Fe_2


title: RNA-seq of HU-HSA-3 with glucose rep2

description:
Library name: RNA_H3_25mM_48h_2
GeneExpressionMatrixTPM_H3_48h_CF3.tsv

data_processing:
Sequencing reads were mapped to the CanFam3.1 canine reference genome using STAR.
Expression levels were estimated using RSEM. Differential expression was analyzed with edgeR 3.42.0
Assembly: CanFam3.1
Supplementary files format and content: tsv file include TPM count in each sample

growth_protocol: DMEM as indictaed glucose concentration with 10% fetal bovine serum and penicillin–streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using a NucleoSpin RNA isolation kit
mRNA-seq libraries were constructed using a NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: w/o 25 mM glucose for 4 or 48 hours

value: with glucose


title: Plasmax_2

description:
Library name: rna-90_S9
Column name in rawcounts_Fedropout_RNAseq.txt: Plasmax_2


title: RNA-seq of HU-HSA-3 with glucose rep3

description:
Library name: RNA_H3_25mM_48h_3
GeneExpressionMatrixTPM_H3_48h_CF3.tsv


title: MSC, pig 16, clone 9, high adipogenic

description: NovaSeq 2x150 bp sequencing


title: CP190_FLAG-ChIP_rep2

description: Library name: Sample18


title: MSC, pig 16, clone 22, low adipogenic

description: NovaSeq 2x150 bp sequencing


title: CG4936_FLAG-ChIP_rep1

description: Library name: Sample15


title: CG4282_FLAG-ChIP_rep1

description: Library name: Sample13


title: Plasmax-TE_1

description:
Library name: rna-87_S6
Column name in rawcounts_Fedropout_RNAseq.txt: Plasmax-TE_1


title: RNA-seq of HU-HSA-3 with glucose rep1

description:
Library name: RNA_H3_25mM_48h_1
GeneExpressionMatrixTPM_H3_48h_CF3.tsv


title: CG4282_FLAG-ChIP_rep2

description: Library name: Sample14


title: MSC, pig 16, clone 11, low adipogenic

description: NovaSeq 2x150 bp sequencing


title: RNA-seq of HU-HSA-3 without glucose rep1

description:
Library name: RNA_H3_0mM_48h_1
GeneExpressionMatrixTPM_H3_48h_CF3.tsv

value: without glucose


title: MSC, pig 16, clone 1, high adipogenic

description: NovaSeq 2x150 bp sequencing


title: T. turgidum Queule Heat Rep3

first: Javier

last: Canales

address: Campus Isla Teja s/n

institute: Universidad Austral de Chile

description: Library name: TC2QUEU

data_processing:
Raw sequencing reads were pseudo-aligned and quantified using Kallisto (v0.50.1) with a k-mer size of 31. The following reference transcriptomes were used: Triticum aestivum (IWGSC RefSeq v2.1) , Triticum turgidum (Svevo v1) , and Triticum monococcum (TA10622 v1.1). Differential expression analysis was performed using DESeq2 v1.42 in R.
Assembly: IWGSC RefSeq v2.1 for T.aestivum, Svevo v1 for T.turgidum, TA10622 v1.1 for T.monococcum
Supplementary files format and content: tsv files includes raw counts and tpm

organism: Triticum turgidum

source_name: Wheat grain

extract_protocol:
Total RNA was isolated from complete caryopses (harvested from central spikelets) using a modified CTAB-based protocol. RNA quality was assessed using a Nanoquant Infinite M200 spectrophotometer(A260/A280 ratios between 1.8-2.0)
Illumina RNA-seq libraries were constructed using the Illumina TruSeq Stranded Total RNA Sample Prep Kit following the manufacturer's protocol. Unique barcodes were incorporated for multiplexing.

value: Wheat grain

value: Tetraploid

value: 10 DAA (3h post-stress)

value: Queule

value: Heat (TT2)

value: replicate 3


title: RNA-seq of HU-HSA-3 without glucose rep3

description:
Library name: RNA_H3_0mM_48h_3
GeneExpressionMatrixTPM_H3_48h_CF3.tsv


title: EMEM_1

description:
Library name: rna-85_S4
Column name in rawcounts_Fedropout_RNAseq.txt: EMEM_1

value: Hepatic cell

value: WT


title: CG30020WT_FLAG-ChIP_rep2

description: Library name: Sample12

value: embryo

value: nc14 embryo


title: CG4936_FLAG-ChIP_rep2

description: Library name: Sample16


title: RNA-seq of HU-HSA-3 without glucose rep2

description:
Library name: RNA_H3_0mM_48h_2
GeneExpressionMatrixTPM_H3_48h_CF3.tsv


title: Plasmax-TE+Fe_1

description:
Library name: rna-96_S3
Column name in rawcounts_Fedropout_RNAseq.txt: Plasmax-TE+Fe_1


title: Plasmax_1

description:
Library name: rna-86_S5
Column name in rawcounts_Fedropout_RNAseq.txt: Plasmax_1

value: Plasmax


title: T. turgidum Queule Heat Rep2

description: Library name: TB2QUEU

value: replicate 2


title: RNA-seq of HU-HSA-2 with glucose rep3

description:
Library name: RNA_H2_25mM_48h_3
GeneExpressionMatrixTPM_H2_48h_CF3.tsv