title: C42_shNCOR2_A_DHT_C [RNA-seq]

value: PCa cell line

value: male

value: 10nm DHT


title: LNCaP_shNCOR2_B_DHT_B

status: Public on Nov 17 2021

type: genomic

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

country: USA

institute: Roswell Park Comprehensive Cancer Center

hyb_protocol: DNA methylation profiles were obtained using the Infinium MethylationEPIC BeadChip (EPIC array) platform, performed in the RP Genomics Shared Resource.

data_processing: Data Importing and subsequent processing was accomplished using ChAMP. Detectible beta values for all probed CpG sites were initially compiled and filtered to remove those associated with multiple alignments and known SNPs. To adjust for probe design bias (Infinium Type-I, Type-II), a beta-mixture quantile normalization method (BMIQ) was employed. Additionally, cross-array batch effect was corrected using ComBat.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: genomic DNA from cell line

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from all samples using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen), following manufacturer’s protocol.

tag: gender

value: Male

tag: sample type

value: Cell line

tag: cell line

value: LNCaP

tag: shRNA


title: C42_shNCOR2_A_DHT_B [RNA-seq]

type: SRA

library_source: transcriptomic

data_processing:
Base-calling was performed using Illumina Real Time Analysis RTA.2.7.7.0 with default parameters
Raw sequencing reads were aligned to the human genome using the splice junction aligner TopHat2.
Gene expression counts per gene were extracted from aligned reads using featureCounts.
Genome_build: GRCh37
Supplementary_files_format_and_content: processed data is in supplementary file, which is a comma-separated text file containing a matrix of read counts for each gene accession number and sample

molecule: total RNA

source_name: PCa cell line

growth_protocol: Cells were maintained at 37oC and 5.0% CO2 using a cell culture incubator with UV contamination control. LNCaP and LNCaP-C4-2 cells were regularly maintained in RPMI 1640 Medium containing 10% FBS. All media was supplemented with 100 U/mL Penicillin-Streptomycin.

extract_protocol:
Total RNA was extracted from all samples using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen), following manufacturer’s protocol.
Sequencing was performed at the Roswell Park Genomics Shared Resource core facility, and sequencing libraries prepared with the TruSeq Stranded Total RNA kit (Illumina Inc), from 1ug total RNA

treatment_protocol: Cells were treated with indicated concentration of DHT or EtOH for 6 hr.

tag: cell type

tag: cell line source gender

tag: treatment


title: 3m-CT-3

city: Nashville

first: Yinqiu

last: Wang

state: TN

address: 313 Harpeth view circle

department: medicine

institute: vumc

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt v1.16
GENCODE vM16 gene annotations were provided to STAR to improve the accuracy of mapping
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC
Feature Counts v1.15.2 was used to count the number of mapped reads to each gene
Fragments per kilobase of transcript per million mapped reads (FPKM) values for all genes in each sample were calculated based on gene length in GENCODE vM16 gene annotations.
Genome_build: mm9
Supplementary_files_format_and_content: Fragments per kilobase of transcript per million mapped reads (FPKM)
Supplementary_files_format_and_content: raw counts

molecule: polyA RNA

organism: Mus musculus

source_name: Kidney

extract_protocol:
TRAP RNA isolation
Ovation RNA-Seq Systems 1-16 for Model Organisms – Mouse (NuGEN Technologies, Redwood City, CA).
Library preparation was performed according to the manufacturer’s instructions. RNA underwent DNase treatment and cDNA was fragmented (200bp) on a Covaris LE220.

value: podocyte

tag: strain

tag: disease

value: normal

tag: genotype

value: eNOS-/-

tag: age

value: 3 months

tag: molecule subtype

value: TRAP RNA


title: SC10_35

city: Macau

first: Heng

last: Sun

address: Avendia da Universidade, Taipa

department: Faculty of Health Sciences

country: Macau

institute: University of Macau

description: total RNA

data_processing:
sickle was used for data quality control.
trim_galore-v0.4.1 was used for data trimming.
STAR-2.5.3a was used for alignment with default parameter for pair-end sequencing.
subread-1.5.3 was used for generation of read_count.
Genome_build: mm10
Supplementary_files_format_and_content: Gene read_count value for each sample were summarized in text file.

source_name: vBrL

extract_protocol:
The sorted mammary luminal cells or tumor cells re-suspended in FACS buffer (300-500 cells/µL) were mixed (3:2 ratio) with C1 Cell Suspension Reagent (Fluidigm) before loading onto a  10 to 17-μm-diameter C1 Integrated Fluidic Circuit (IFC; Fluidigm). Each capture site was carefully examined and recorded under a ZEISS microscope in bright field channel for cell doublets. Cell lysing, reverse transcription and cDNA amplification were performed on the C1 Single-Cell Auto Prep IFC, as specified by the manufacturer (protocol 100-7168 E1). The SMARTer Ultra Low RNA Kit (Clontech) was used for cDNA synthesis from the single cells.
Illumina NGS library was constructed with Nextera XT DNA Sample Prep kit (Illumina), according to the manufacturer’s recommendations (protocol 100-7168 E1).

treatment_protocol: Three-to-four month-old female virgin or pregnant at day 12.5 mice were sacrificed to isolate the fourth pair of mammary glands for single-cell preparation as previously described. In brief, the mammary glands were minced, washed in PBS and digested in DMEM/F12 containing 300 U/ml collagenase Ⅲ (S4M7602S, Worthington, Lakewood, NJ), 100 U/ml hyaluronidase (H3506; Sigma-Aldrich), 5% FBS (Gibco), 5 µg/ml insulin (350-020; Biosource, Rockville, MD), 10 ng/ml EGF (13247-051, Invitrogen), and 500 ng/ml hydrocortisone (H0888; Sigma-Aldrich) for about 1 hour at 37℃, 5% CO2. The resultant organoid suspension was sequentially re-suspended in DMEM/F12 supplemented with 5 mg/ml dispase II (825-001; Roche Diagnostics, Indianapolis, IN) and 0.1 mg/ml DNase I (58C10349; Worthington) for 5 min at 37℃, and then digested with 0.25% trypsin-EDTA for 1–2 min, and treated with RBC lysis buffer (00433-57; eBioscience, San Diego, CA) for 3 min to remove the red blood cells before filtration through a 40-µm cell strainer (352340, BD Falcon) to obtain single-cell suspension. Enrichment of Lin- epithelial cells was achieved through selective depletion of hematopoietic and endothelial cells by using the EasySeq mouse epithelial cell enrichment kit according to the manufacturer (19758; Stemcell). When the mammary tumors grew to around 1 cm in diameter, they were removed from the Brca1-defeicient mice for single-cell preparation as per the same method. The enriched Lin- mouse mammary epithelial cells and tumor cells were stained at a concentration of 1x106 cells per 100 μl of FACS buffer (HBSS with 0.5% BSA and 2 mM EDTA). Antibodies against mouse CD24 (anti CD24-PE-Cy™7, 560536, BD), and CD29 (anti CD29-APC, 102216, Biolegend) were used to stain the cells. DAPI (1 µg/ml) was also used as an indicator for cell viability. Antibody incubations were performed at 4℃ for 30 min. Then the cells were washed with PBS for twice before sorting by using FACSAria III Cell Sorter (Becton Dickinson). DAPI-CD24HiCD29LomGFP+ mammary luminal cells and CD24+ tumor cells were sorted out for following single cell RNA sequencing.

value: C57BL/6 and 129/Sv mixed

tag: tissue

value: Mammary luminal

tag: Sex

value: female


title: SC10_34

description: total RNA


title: C42_shNCOR2_A_DHT_A [RNA-seq]


title: 3m-CT-2


title: C42_shNCOR2_B_ETOH_B [RNA-seq]

value: EtOH


title: 3m-D2-2

value: Type 2 Diabetes

value: eNOS-/- db/db


title: CWR22_shCTL_PRE_PC1

scan_protocol: DNA methylation profiles were obtained using the Infinium MethylationEPIC BeadChip (EPIC array) platform, performed in the RP Genomics Shared Resource.

source_name: genomic DNA from xenograft tissue

value: PCa xenograft

tag: disease stage

value: PRE-ADT

value: shCTL


title: LNCaP_shNCOR2_B_DHT_A

value: Male


title: 3m-CT-1


title: LNCaP_shNCOR2_B_EtOH_B

value: Cell line


title: 3m-D2-1


title: SC10_33

description: total RNA


title: LNCaP_shNCOR2_B_EtOH_C

value: LNCaP


title: 3m-CT-Kidney

value: renal cells

value: total RNA


title: SC10_32

description: total RNA


title: SC10_38

description: total RNA


title: C42_shNCOR2_A_ETOH_C [RNA-seq]

value: PCa cell line

value: male


title: LNCaP_shNCOR2_B_EtOH_A


title: C42_shNCOR2_A_ETOH_B [RNA-seq]


title: SC10_29

description: total RNA


title: LNCaP_shNCOR2_A_DHT_B


title: SC10_28

description: total RNA


title: LNCaP_shNCOR2_A_DHT_C


title: SC10_27

description: total RNA


title: LNCaP_shNCOR2_A_DHT_A


title: C42_shCTL_DHT_B [RNA-seq]

value: 10nm DHT


title: LNCaP_shNCOR2_A_EtOH_C


title: LNCaP_shNCOR2_A_EtOH_B


title: C42_shCTL_DHT_A [RNA-seq]


title: SC10_26

description: total RNA

value: C57BL/6 and 129/Sv mixed


title: SC10_24

description: total RNA

value: Mammary luminal


title: C42_shCTL_ETOH_C [RNA-seq]


title: C42_shNCOR2_A_ETOH_A [RNA-seq]


title: LNCaP_shCTL_DHT_B


title: C42_shCTL_ETOH_B [RNA-seq]


title: SC10_25

description: total RNA

value: female


title: LNCaP_shNCOR2_A_EtOH_A


title: C42_shCTL_ETOH_A [RNA-seq]

value: EtOH


title: SC10_23

description: total RNA


title: LNCaP_shNCOR2_B_EtOH_C [RNA-seq]


title: SC10_30

description: total RNA


title: 24w-D1-4

value: podocyte

value: Type 1 Diabetes

tag: treatment stz

value: 8 months

value: TRAP RNA


title: LNCaP_shNCOR2_B_DHT_C [RNA-seq]


title: mouse esophageal organoid

city: Houston

first: Jae-Il

last: Park

state: Texas

address: 6565 MD Anderson BLVD

department: Dept. of Experimental Radiation Oncology

institute: M.D. Anderson Cancer Center

description: single cell RNA

data_processing:
raw base call file (BCL) was generated from Illumina software
Cellranger pipeline was used for generating FASTQ files
STAR software was used align the read files to reference genome (GRCm38/mm10)
Data analysis was conducted by R software
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: gzipped tsv file with feature and barcode sequence.
Supplementary_files_format_and_content: gzipped MEX format file with feature-barcode matrix

source_name: mouse esophageal cell

growth_protocol: Esophageal organoids were grown with Matrigel in E-MEOM medium. They were incubated with Y27632 for 3 days from seeding, and Medium was replaced every 2 days.

extract_protocol:
Organoids were isolated from Matrigel with ice-cold medium and washed with ice-cold PBS. Single cells were collected using 0.05 % Trypsin-EDTA. Single cells were used for library preparation.
RNA libraries were prepared for sequencing using 10x Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1

value: Mouse esopahgus-derived organoid

value: epithelia cells

tag: day

value: Day 8


title: LNCaP_shNCOR2_B_EtOH_B [RNA-seq]

value: LNCaP


title: SC10_17

description: total RNA


title: LNCaP_shCTL_DHT_C

tag: gender

value: Male

value: Cell line

value: shCTL


title: LNCaP_shNCOR2_B_DHT_B [RNA-seq]

value: PCa cell line

value: male


title: SC10_21

description: total RNA

value: C57BL/6 and 129/Sv mixed


title: LNCaP_shCTL_DHT_A

tag: sample type


title: LNCaP_shNCOR2_B_DHT_A [RNA-seq]

tag: cell line

value: 10nm DHT


title: SC10_18

description: total RNA

value: Mammary luminal

value: female


title: LNCaP_shCTL_EtOH_C

tag: shRNA


title: LNCaP_shNCOR2_A_DHT_B [RNA-seq]

tag: cell type


title: C42_shNCOR2_B_DHT_B


title: SC10_12

description: total RNA


title: LNCaP_shCTL_EtOH_B


title: LNCaP_shCTL_EtOH_A


title: BMSC+EC-3D-rep2

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

country: China

institute: Life Sciences Institute, Zhejiang University

data_processing:
Adaptor sequences were cut using CutAdapt and trimmed reads shorter than 30bp were discarded. Trimmed data were aligned to mouse reference genome mm10 using STAR (79), with uniquely mapping rates greater than 80%.
HTseq-count  was used to count the number of reads mapped to each gene. Then data were loaded into the R platform where further statistical analyses occurred.
Counts of genes were normalized and differentially expressed genes (p-value < 0.05, fold-change > 1.35) was determined in the DESeq2 package . Relationship among samples was assessed by principal component analysis (PCA) of DESeq2 normalized counts.
Genome_build: mm10

source_name: 3D co-cultured BMSCs

growth_protocol: All mice were kept in an SPF facility operated in a 12-hour light/dark cycle.

extract_protocol:
Total RNA was extracted by RNAiso Plus.
Smart-seq2 (Nature, 533:487, 2016)

treatment_protocol: BMSCs 3D co-cultured with bone marrow endothelial cells in EGM2 medium for 5 days.

tag: stain

value: Cultured BMSCs

value: CD45-Ter119-Pdgfra+ BMSCs


title: C42_shNCOR2_B_DHT_C


title: SC10_15

description: total RNA


title: SC10_22

description: total RNA


title: LNCaP_shNCOR2_B_EtOH_A [RNA-seq]

tag: cell line source gender

tag: treatment

value: EtOH


title: SC10_16

description: total RNA

tag: strain


title: LNCaP_shNCOR2_A_EtOH_C [RNA-seq]


title: LNCaP_shNCOR2_A_DHT_C [RNA-seq]


title: LNCaP_shNCOR2_A_EtOH_B [RNA-seq]


title: SC10_10

description: total RNA


title: SC10_13

description: total RNA


title: BMSC+EC-3D-rep3

value: BMSCs 3D co-cultured with bone marrow endothelial cells in EGM2 medium for 5 days


title: C42_shNCOR2_B_DHT_A


title: LNCaP_shNCOR2_A_DHT_A [RNA-seq]


title: BMSC-3D-rep1

source_name: 3D cultured BMSCs

treatment_protocol: BMSCs 3D cultured in EGM2 medium for 5 days


title: SC10_11

description: total RNA


title: BMSC+EC-3D-rep1


title: SC10_08

description: total RNA


title: SC10_07

description: total RNA


title: C42_shNCOR2_B_ETOH_B


title: C42_shNCOR2_B_ETOH_C


title: SC10_09

description: total RNA


title: C42_shNCOR2_A_ETOH_C


title: SC10_03

description: total RNA


title: LNCaP_shNCOR2_A_EtOH_A [RNA-seq]


title: BMSC-3D-rep3

value: BMSCs 3D cultured in EGM2 medium for 5 days


title: LNCaP_shCTL_EtOH_C [RNA-seq]


title: BMSC-3D-rep2


title: C42_shNCOR2_A_DHT_C


title: LNCaP_shCTL_DHT_C [RNA-seq]


title: LNCaP_shCTL_EtOH_B [RNA-seq]


title: C42_shNCOR2_A_DHT_B


title: UT-SCC12A_C1r siRNA

city: Turku

first: Liisa

last: Nissinen

address: Medisiina D, 5th floor; Kiinamyllynkatu 10

department: Dermatology

country: Finland

institute: University of Turku

description: RNA sequencing data from cSCC

data_processing:
The samples were sequenced with the HiSeq3000 instrument using single-end sequencing with 50 bp read length.
The reads obtained from the instrument were base called using the instrument manufacturer’s base calling software and aligned against the human reference genome (GRCh38) using Star version 2.5.2b assembly.
The reads were then associated with known genes and the number of reads associated with each gene was counted using subreads package (v. 1.5.1).
The counts were normalized using the TMM normalization method of the edgeR R/Bioconductor package (R version 3.0.1, Bioconductor version 2.12).
Genome_build: GRCh38
Supplementary_files_format_and_content: For statistical testing the data were further log transformed using the voom approach in the limma package. For the visualizations and result files the TMM normalized counts are represented as RPKM values.

source_name: Cutaneous squamous cell carcinoma 12A

growth_protocol: cSCC cells were cultured and incubated at 37C.

extract_protocol:
Total RNAs were extracted according to the manufacturer's instruction and eluted in sterile water (miRNAeasy Mini Kit, Qiagen GmbH, Hilden, Germany).
mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cSCC cell lysates were harvested 72 hours after siRNA-treatment and serum-starved 24 hours before harvesting.

tag: source

value: Cutaneous SCC

value: Derived from cSCC tumors

value: Primary cSCC cells

value: C1r siRNA


title: SC1_47

description: total RNA

value: Mammary tumor


title: LNCaP_shCTL_DHT_B [RNA-seq]

value: LNCaP

value: shCTL


title: UT-SCC59A_C1r siRNA

description: RNA sequencing data from cSCC

source_name: Cutaneous squamous cell carcinoma 118

value: Metastatic cSCC cells


title: HAEC_H3K27ac_HiChIP_rep3

city: Stanford

first: Shining

last: Ma

state: CA

address: 318 Campus Drive

department: Statistics

institute: Stanford University

description: HAEC H3K27ac HiChIP replicate3

library_source: genomic

data_processing:
Library strategy: HiCHIP
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908).
FitHiChiP (PMID: 31530818) was applied to perform DNA loop calling (i.e., identification of significant contacts), where we used the bias-corrected peaks defined from hichipper (PMID: 29489746) as input, set the length of fixed-size genomic windows/bins as 5kb and selected the stringent model for inferring the background model.
Finally, the loops with q value less than 0.01 were obtained for HiChIP analysis.
Genome_build: hg19
Supplementary_files_format_and_content: allValidPairs: text file for all Valid Pairs of HiChiP
Supplementary_files_format_and_content: bed: Loops called from FitHiChIP

source_name: aortic endothelial cells

growth_protocol: Both HAEC and AoSMC were grown by following the manufacturer's instructions (Lonza, Catalog No. CC-2535 and CC-2571). Cells were cultured at 37°C  with 5% CO2 incubator and the medium was changed according to the manufacturer’s instructions.

extract_protocol:
HiChIP libraries were generated as described previously (PMID: 27643841).
Cells between passage 5 and 7 were used for HiChIP experiment. For each cell line, we collected total 3 vials. There are 5 million cells per vial.

treatment_protocol: The cells were crosslinked with freshly prepared 1% formaldehyde and quenched with a final concentration of 125 mM Glycine.

value: HAEC

value: untreated

tag: hichip target


title: SC10_06

description: total RNA

value: C57BL/6 and 129/Sv mixed

value: Mammary luminal


title: C42_shCTL_DHT_A

value: Male

value: Cell line


title: SC1_46

description: total RNA

value: female


title: C42_shCTL_DHT_B


title: HAEC_H3K27ac_HiChIP_rep1

description: HAEC H3K27ac HiChIP replicate1


title: HAEC_H3K27ac_HiChIP_rep2

description: HAEC H3K27ac HiChIP replicate2


title: C42_shCTL_DHT_C


title: UT-SCC59A_negative_control siRNA

description: RNA sequencing data from cSCC

value: Negative control siRNA


title: UT-SCC12A_negative_control siRNA

description: RNA sequencing data from cSCC


title: C42_shCTL_DHT_C [RNA-seq]

value: PCa cell line

value: male

value: 10nm DHT


title: C42_shNCOR2_A_DHT_A


title: SC1_45

description: total RNA


title: AoSMC_H3K27ac_HiChIP_rep3

description: AoSMC H3K27ac HiChIP replicate3

source_name: aortic smooth muscle cells

value: AoSMC


title: SC10_02

description: total RNA


title: C42_shNCOR2_A_ETOH_B


title: UT-SCC91_negative_control siRNA

description: RNA sequencing data from cSCC

source_name: Cutaneous squamous cell carcinoma 59A

value: Cutaneous SCC

value: Derived from cSCC tumors

value: Primary cSCC cells


title: C42_shNCOR2_A_ETOH_A


title: SC1_48

description: total RNA

value: Mammary tumor


title: LNCaP_shCTL_EtOH_A [RNA-seq]

value: LNCaP

value: shCTL

value: EtOH


title: AoSMC_H3K27ac_HiChIP_rep2

description: AoSMC H3K27ac HiChIP replicate2

value: untreated


title: Calu3 BACH1 KD rep2

city: Cleveland

first: Ann

last: Harris

state: Ohio

address: 2109 Adelbert Rd Building

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Sequences were mapped to the hg19 human genome with STAR 2.6 (https://github.com/alexdobin/STAR)
Aligned reads were assigned to genomic features with featureCounts version 1.6.3 in the Subread package (http://subread.sourceforge.net/) to estimate expression levels for each transcript.
Differential gene expression was analyzed using DEseq2 version 1.22.1 (https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html). Samples were normalized and expressed as DESEQ2 normalized counts and both a test statistic (P-value) and an adjusted P-value (q-value) were calculated.
Normalized counts were subjected to principal component analysis
Gene ontology analysis was performed using gProfiler.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include normalized count values for each Sample

growth_protocol: Cells were grown in indicated media using standard methods

extract_protocol:
Confluent Calu-3 cells were harvested for RNA extraction using TRIzol. RNA quality was confirmed by Nanodrop measurement of OD 260/280 and 260/230 ratios and stored at -80oC under ethanol. 1ug RNA was used for RNA-seq library preparation.
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit v2 (Low-Throughput protocol, Illumina).

treatment_protocol: Samples were treated with negative control siRNA Ambion Negative control #2 siRNA (Catalog #: 4390846)  or siRNA targeting BACH1 Ambion Silencer®Select (Catalog #  4392420 each at 20 nmol using RNAiMax transfection reagent (Life Technologies)

value: Human lung adenocarcinoma cell line

tag: knockdown


title: C42_shCTL_ETOH_A

value: Male


title: D4_D4_Ty2_exposed Enriched

city: Oxford

first: Alison

last: Simmons

address: John Radcliffe Hospital/Headley Way

department: The MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
intracellular_enriched_TY2.txt
WTCHG_788347_72885264

data_processing:
Reads were quality trimmed and adapters were removed using Cutadapt software
Reads were aligned to joint Salmonella-Human reference genome using STAR and cross-species multi-mappers were filtered out
Expression was quantified using Subread featureCounts, with multi-mappers counted as fractions
Data normalisation and differential expression analyses were performed using DESeq2
Genome_build: hg38, NC_003197.2, NC_016854.1 and NC_004631.1
Supplementary_files_format_and_content: Raw expression counts matrices per sample

organism:
Homo sapiens
Salmonella enterica

source_name: Monocyte-derived dendritic cells + Bacteria

growth_protocol: Leukocyte Reduction System cones were obtained from the UK National Blood Centre with informed consent following local ethical guidelines. Blood was diluted in Phosphate-Buffered Saline (PBS) and layered on a standard density gradient (LymphoprepTM). Peripheral Blood Mononuclear Cells (PBMC) were collected from the interface and washed in PBS at 4 C. Monocytes were obtained by magnetic positive selection, using the human anti-CD14+ MicroBeads (Miltenyi Biotec, Germany) according to the manufacturer’s protocol.  Freshly isolated monocytes were differentiated into Dendritic Cells (MoDCs)  in the presence of 40 ng/mL of recombinant human (rh) Granulocyte Macrophage-Colony-Stimulating Factor (GM-CSF; Peprotech) and 40 ng/mL rh Interleukin-4 (IL-4; Peprotech).

extract_protocol:
20'000 cells were sorted in PBS and spun down and the pellet resuspended in Monarch RNA lysis buffer supplemented with 2mg/mL of Lysozime (thermoFisher). Total RNA extraction was performed with the Monarch® Total RNA Miniprep Kit (New England BioLabs) according to the manufacturers.
Libraries were prepared by using the SMARTer® stranded total RNA seq v2 pico input Mammalian (Takara) with minor technical adaptations. PCR1 was carried on for 5 cycles and PCR2 for 11 cycles (for the bacterial libraries) or 12 cycles (for the host-pathogen libraries). After cDNA synthesis, the human ribosomal cDNA was removed by using probes specific to mammalian rRNA.

treatment_protocol: DCs were infected with S. Tyhpimurium strain LT2 or D23580 or S. Typhi strain Ty2 at a MOI of 10 or left uninfected for 6h before sorting.

tag: infection

tag: status

value: Bystander

tag: bacterial probe enrichment

value: Enriched


title: LNCaP_shCTL_DHT_A [RNA-seq]


title: 200-E14-H3K4me3-r2

data_processing:
Total reads were trimmed using Trim Galore (v0.4.4) with default parameters and aligned against the mouse genome build mm9 using Bowtie2 (v2.3.4.1) with default parameters. All unmapped reads and PCR duplicates were removed. Peaks were analyzed using MACS2 (v2.1.1.20160309) with the parameters “-q 0.1 --broad-cutoff 0.1 --nomodel --nolambda --broad --extsize 300 -B --SPMR -g mm”. Signal tracks for each sample were generated using “wigToBigWig” utility of UCSC.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: mouse embryonic stem cell

growth_protocol:
Female mice were injected with 5 IU of PMSG and humanely euthanized 44 h later. Fully grown oocytes were harvested from ovary in M2 medium. Female mice were injected with 5 IU of PMSG followed by hCG 44 h later. Superovulated females were crossed with fertile WT males and we could get zygotes the next day and then zygotes were cultured in KSOM (Millipore) at 37°C with 5% CO2. 2-cell, 4-cell, 8-cell, and blastocyst stage embryos were obtained at 16 h, 30 h, 48 h, and 72 h after culture, respectively.
Mature sperm were isolated from the caudal epididymis using a swim-up procedure. About 2 million sperm were used for ChIP experiment.
Mouse ES cells were cultured on 0.1% gelatin-coated plates with standard LIF/serum medium containing 15% FBS (VS500T, Ausbian), 1,000 U/ ml mouse LIF (ESG1107, Millipore), 0.1 mM non-essential amino acids (11140, Gibco), 0.055 mM β-mercaptoethanol (21985023, Gibco), 2 mM GlutaMAX (35050, Gibco), 1 mM sodium pyruvate (11360, Gibco), and 100 U/ml penicillin/streptomycin (15140, Gibco).

extract_protocol:
The H3K4me3 and H2AK119ub1 CATCH-seq procedure was performed as previously described (Brind’Amour, J. et al., 2015) with some modifications. Counted cells were pelleted and re-suspended in nuclear isolation buffer (10 mM Tris-HCl, pH8.0, 140 mM NaCl, 5 mM MgCl2, 0.6% NP-40, 0.1% Triton X-100, 0.1% deoxycholate, 1 x EDTA-free proteinase inhibitor cocktail and 1 mM PMSF). Chromatin was fragmented for 7.5 or 10 min using 2 or 8 U/μl MNase at 21/25/37 °C (2 U/μl MNase at 21 °C 7.5 min for cultured cells, 2 U/μl MNase at 37 °C 7.5 min for fully grown oocytes and embryos, and 8 U/ul MNase at 25°C 10 min for sperm), and diluted in NChIP immunoprecipitation buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% Triton X-100, 1 × EDTA-free protease inhibitor cocktail and 0.1 mM PMSF). In difference to ULI-NChIP, 30 ng modified double-stranded DNAs that can be digested by I-SceI were added into the fragmented chromatin to facilitate the IP process. Chromatin with modified double-stranded DNAs was pre-cleared with 5 of 1:1 protein A:protein G Dynabeads (Life Technologies) and IPed with 700 ng of histone H3K4me3 (15410003, Digagenode) and 650 ng (mESCs, oocytes, and embryos) or 1.95 μg (sperm) H2AK119ub1 (8240, Cell Signaling Technology) antibody–bead complexes overnight at 4 °C. IPed complexes were washed twice with 200 μl of low salt wash buffer (20 mM Tris-HCl, pH 8.0, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 1 x EDTA-free proteinase inhibitor cocktail, 0.1 mM PMSF and 30 ng modified double-stranded DNAs) and twice with 200 μl of high salt wash buffer (20 mM Tris-HCl, pH 8.0, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl, 1 x EDTA-free proteinase inhibitor cocktail, 0.1 mM PMSF and 30 ng modified double-stranded DNAs). Protein–DNA complexes were eluted in 100 μl of ChIP elution buffer (100 mM NaHCO3 and 1% SDS) for 2 h at 65 °C. IPed material was purified by phenol chloroform, ethanol-precipitated and raw ChIP material was re-suspended in 10 mM Tris-HCl pH 8.0.
The sequence libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, New England Biolabs) following the manufacturer's instructions, with the exception that we adapted a two-run strategy in the DNA amplification step. The modified double-stranded DNAs were wiped off by I-SceI digestion (5 U/μl I-SceI at 37 °C for 2 h, followed by 20 min heat inactivation at 65 °C) after the first 9 cycles of PCR amplification. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform to generate 150 bp paired-end reads.

treatment_protocol: Samples were collected in 0.2% BSA in DPBS and then stored at -80℃.

value: 129/Ola, XY

tag: tissue

value: mouse embryonic stem cell

tag: antibody

value: H3K4me3 (15410003, Digagenode)


title: 200-E14-H3K4me3-r1


title: WT-ICM-H2AK119ub1

description: Blastocyst

source_name: mouse embryo (Blastocyst)

value: C57 x PWK

value: mouse embryo

value: H2AK119ub1 (8240, Cell Signaling Technology)


title: UT-SCC91_C1r siRNA

description: RNA sequencing data from cSCC

value: Cutaneous SCC

value: Derived from cSCC tumors

value: C1r siRNA


title: C4_D3_LT2_infected Enriched

description:
intracellular_enriched_LT2.txt
WTCHG_788347_72875263

value: Infected


title: Calu3 BACH1 KD rep1


title: SC1_44

description: total RNA

value: C57BL/6 and 129/Sv mixed

value: Mammary tumor

tag: Sex

value: female


title: C42_shCTL_ETOH_C

tag: gender

tag: sample type

value: Cell line

value: shCTL


title: C42_shCTL_ETOH_B

value: Male

tag: cell line

tag: shRNA


title: 20-E14-H3K4me3-r2


title: SC1_39

description: total RNA


title: SC1_43

description: total RNA


title: 20-E14-H3K4me3-r1


title: Calu3 Negative Control rep1

value: Human lung adenocarcinoma cell line

value: siNC (negative control)


title: SC1_42

description: total RNA


title: SC1_37

description: total RNA


title: SC1_41

description: total RNA


title: SC1_36

description: total RNA


title: 16HBE14o- BACH1 rep2

description:
16HBE14o-_BACH1_IDR.bw
16HBE14o-_BACH1_idr.optimal_peak.regionPeak

data_processing:
Data was analyzed using ENCODE (phase-3) transcription factor and histone ChIP-seq pipeline https://github.com/ENCODE-DCC/chip-seq-pipeline2
Genome_build: hg19
Supplementary_files_format_and_content: bigWig and narrowPeak

extract_protocol:
Cells were lysed in lysis buffer (5mM PIPES pH 8.0, 85mM KCL, 0.5% NP-40, 1x Protease Inhibitor Cocktail (Roche)). Nuclei were isolated by centrifugation, lysed in RIPA buffer (1x PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, Protease Inhibitor Cocktail), and sonicated. Protein-DNA complexes were isolated with antibody Rabbit anti-BACH1 (Bethyl Laboratories A303-057A).
DNA ends were blunted using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. Next, DNA was incubated with Klenow exo- to add 5’ adenine overhangs. Multiplex adaptors were then ligated to the ends and converted to dsDNA using 5 cycles of PCR. DNA was size-selected to contain fragments between 200 and 300bp and PCR amplified for 5 cycles. DNA was purified with 1.2x AMPure XP beads. Sequencing was performed on an Illumina Hi-Seq.

tag: cell type

value: Human bronchial epithelial cells

tag: chip antibody

tag: growth media

value: DMEM + 10% FBS


title: SC1_40

description: total RNA

tag: strain


title: WT-8Cell-H2AK119ub1-r1

source_name: mouse embryo

value: C57 x PWK


title: WT-4Cell-H2AK119ub1-r2

value: mouse embryo


title: AoSMC_H3K27ac_HiChIP_rep1

description: AoSMC H3K27ac HiChIP replicate1

value: AoSMC

tag: treatment

value: untreated


title: E14-H2AK119ub1-r2

value: 129/Ola, XY

value: mouse embryonic stem cell

value: H2AK119ub1 (8240, Cell Signaling Technology)


title: B4_D2_LT2_exposed Enriched

description:
intracellular_enriched_LT2.txt
WTCHG_788347_72865262

value: Bystander

value: Enriched


title: Calu3 BACH1 rep2

description:
Calu3_BACH1_IDR.bw
Calu3_BACH1_idr.optimal_peak.narrowPeak

value: Rabbit anti-BACH1 (Bethyl Laboratories A303-057A)


title: Calu3 Negative Control rep2


title: E3_D3_LT2_exposed Enriched

description:
intracellular_enriched_LT2.txt
WTCHG_788347_72135285


title: E14-H2AK119ub1-r1


title: SC1_38

description: total RNA

value: C57BL/6 and 129/Sv mixed

value: Mammary tumor

value: female


title: A4_D4_D23_exposed Enriched

description:
intracellular_enriched_D23580.txt
WTCHG_788347_72855261


title: H3_D2_LT2_infected Enriched

description:
intracellular_enriched_LT2.txt
WTCHG_788347_72165288

value: Infected


title: 16HBE14o- BACH1 rep1


title: SC1_35

description: total RNA


title: F3_D1_Ty2_exposed Enriched

description:
intracellular_enriched_TY2.txt
WTCHG_788347_72145286


title: G3_D4_LT2_exposed Enriched

description:
intracellular_enriched_LT2.txt
WTCHG_788347_72155287


title: WT-2Cell-H2AK119ub1-r1


title: SC1_34

description: total RNA


title: SC1_31

description: total RNA


title: A3_D1_D23580_inf Enriched

description:
intracellular_enriched_D23580.txt
WTCHG_788347_72095281


title: WT-8Cell-H2AK119ub1-r2


title: Calu3 BACH1 rep1

value: Human lung adenocarcinoma cell line


title: AH1146_Calu3_BACH1 siRNA_CFTR -80.1 kb

description:
4C-seq library with the CFTR +48.9 kb region as the viewpoint
AH1146

data_processing:
Library strategy: 4C-seq
Libraries ( AH1052, AH1054, AH1144, AH1147, AH1143, AH1146)  were sequenced on Illumina HiSeq4000 machine and others (AH1214, AH1215)  were sequenced on Illumina NextSeq550 machine.
Data were analyzed using 4cseq pipeline http://compgenomics.weizmann.ac.il/tanay/?page_id=367
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are a dataframe for each genomic fragment, together with its measured interaction frequency with the viewpoint of interest. The processed data can be used to plot a domainogram to visualize these interaction frequencies.

source_name: Human lung

extract_protocol:
Nuclei were made as per the above Methods papers with corresponding samples as listed in the treatment protocol section.
All libraries were constructed as per the above papers  PMID: 22609568 or PMID: 31351925 with the samples corresponding to the Methods papers as listed in the treatment protocol section.
4C-seq Barcoded libraries with Illumina sequencing adapters were made as per above papers  PMID: 22609568 or PMID: 31351925 for corresponding samples as listed in the tratement protocol section.

tag: genotype

value: WT_BACH1 siRNA Knockdown


title: WT-2Cell-H2AK119ub1-r2


title: WT-1Cell-H2AK119ub1-r2


title: WT-4Cell-H2AK119ub1-r1


title: C3_D3_Ty2_infected Enriched

description:
intracellular_enriched_TY2.txt
WTCHG_788347_72115283


title: G2_D1_Ty2_infected Enriched

description:
intracellular_enriched_TY2.txt
WTCHG_788347_72075279


title: AH1147_Calu3_BACH1 siRNA_CFTR -20.9 kb

description:
4C-seq library with the CFTR -80.1 kb region as the viewpoint
AH1147

value: DMEM + 10% FBS


title: AH1054_Calu3_BACH1 siRNA_CFTR -80.1 kb

description:
4C-seq library with the CFTR -80.1 kb region as the viewpoint
AH1054


title: SC1_32

description: total RNA


title: B3_D2_Ty2_infected Enriched

description:
intracellular_enriched_TY2.txt
WTCHG_788347_72105282


title: SC1_30

description: total RNA


title: H2_D1_D23580_exposed Enriched

description:
intracellular_enriched_D23580.txt
WTCHG_788347_72085280


title: WT-GV-H2AK119ub1-r1

source_name: mouse oocyte

value: mouse oocyte


title: F2_D3_D23580_exposed Enriched

description:
intracellular_enriched_D23580.txt
WTCHG_788347_72065278


title: SC1_33

description: total RNA


title: sperm-H2AK119ub1-r2

source_name: mouse sperm

value: ICR

value: mouse sperm


title: AH1143_Calu3_NC siRNA_CFTR -80.1 kb

description:
4C-seq library with the CFTR -20.9 kb region as the viewpoint
AH1143

value: WT_NC siRNA Knockdown


title: WT-GV-H2AK119ub1-r2


title: D2_Uninfected Unenriched

source_name: Monocyte-derived dendritic cells

value: Mock

value: Uninfected

value: Unenriched


title: C2_D1_LT2_infected Enriched

description:
intracellular_enriched_LT2.txt
WTCHG_788347_72035275


title: D1_Uninfected Unenriched


title: E2_D4_D23580_infected Enriched

description:
intracellular_enriched_D23580.txt
WTCHG_788347_72055277


title: SC1_26

description: total RNA


title: sperm-H2AK119ub1-r1

value: H2AK119ub1 (8240, Cell Signaling Technology)


title: AH1052_Calu3_NC siRNA_CFTR -80.1 kb

description:
4C-seq library with the CFTR promoter as the viewpoint
AH1052


title: WT-1Cell-H2AK119ub1-r1

value: C57 x PWK

value: mouse embryo


title: SC1_28

description: total RNA

value: C57BL/6 and 129/Sv mixed


title: SC1_29

description: total RNA

value: Mammary tumor


title: H1_D4_Ty2_infected Enriched

description:
intracellular_enriched_TY2.txt
WTCHG_788347_72005272

value: Enriched


title: E2_Ty2_1 Enriched

description:
Enriched_TY2.txt
WTCHG_774525_73095285

organism: Salmonella enterica subsp. enterica serovar Typhi str. Ty2

source_name: Bacteria

value: Bacterial liquid culture


title: AH1144_Calu3_NC siRNA_CFTR -20.9 kb

description:
4C-seq library with the CFTR promoter as the viewpoint
AH1144

value: Human lung adenocarcinoma cell line


title: SC1_25

description: total RNA

value: female


title: C42_shNCOR2_B_ETOH_A

source_name: genomic DNA from cell line

value: Male

value: Cell line


title: Xu738_MT3

description: total RNA

data_processing:
Drop-seq datasets were processed with Dropseq tools v.1.13. Cell and molecular barcode tagging, primer and poly-A trimming, read alignment, barcode recovering, gene/exon annotations and barcode repairs were sequentially accomplished according to the online protocol (https://github.com/broadinstitute/Drop-seq/files/2425535/Drop-seqAlignmentCookbookv1.2Jan2016.pdf).
Read alignment was done using STAR aligner against Ensembl Mus musculus GRCm38.p6 assembly.
Genome_build: Ensembl Mus musculus GRCm38.p6
Supplementary_files_format_and_content: Gene read_count value for each sample were summarized in text file.

extract_protocol:
The single cell suspension dissociated from mouse mammary glands or mammary tumors (after epithelia enrichment) were loaded to the microfluidic droplet generator for drop-seq as per the protocol described by McCarroll’s lab.
Illumina NGS library was constructed with Nextera XT DNA Sample Prep kit (Illumina), according to the protocol described by McCarroll’s lab..

treatment_protocol: Brca1-deficient (MMTV-Cre; Brca1flox/flox) mice with mammary tumor were sacrificed to isolate the fourth pair of mammary glands and the tumor for single-cell preparation as previously described. In brief, the mammary glands and tumor tissue were minced, washed in PBS and digested in DMEM/F12 containing 300 U/ml collagenase Ⅲ (S4M7602S, Worthington, Lakewood, NJ), 100 U/ml hyaluronidase (H3506; Sigma-Aldrich), 5% FBS (Gibco), 5 µg/ml insulin (350-020; Biosource, Rockville, MD), 10 ng/ml EGF (13247-051, Invitrogen), and 500 ng/ml hydrocortisone (H0888; Sigma-Aldrich) for about 1 hour at 37℃, 5% CO2. The resultant organoid suspension was sequentially re-suspended in DMEM/F12 supplemented with 5 mg/ml dispase II (825-001; Roche Diagnostics, Indianapolis, IN) and 0.1 mg/ml DNase I (58C10349; Worthington) for 5 min at 37℃, and then digested with 0.25% trypsin-EDTA for 1–2 min, and treated with RBC lysis buffer (00433-57; eBioscience, San Diego, CA) for 3 min to remove the red blood cells before filtration through a 40-µm cell strainer (352340, BD Falcon) to obtain single-cell suspension. Enrichment of Lin- epithelial cells was achieved through selective depletion of hematopoietic and endothelial cells by using the EasySeq mouse epithelial cell enrichment kit according to the manufacturer (19758; Stemcell).


title: E1_D2_D23580_exposed Enriched

description:
intracellular_enriched_D23580.txt
WTCHG_788347_71975269

value: Bystander


title: G1_D3_Ty2_exposed Enriched

description:
intracellular_enriched_TY2.txt
WTCHG_788347_71995271


title: Xu738_MT2

description: total RNA


title: SC1_24

description: total RNA


title: H1_Ty2_2 Enriched

description:
Enriched_TY2.txt
WTCHG_774525_73045280


title: SC1_22

description: total RNA


title: SC1_27

description: total RNA


title: D1_D3_D23580_infected Enriched

description:
intracellular_enriched_D23580.txt
WTCHG_788347_71965268

value: Infected


title: SC1_23

description: total RNA


title: Xu738_MT1

description: total RNA


title: SC1_21

description: total RNA


title: C1_Ty2_3 Enriched

description:
Enriched_TY2.txt
WTCHG_774525_72995275


title: S11

description: total RNA


title: Xu738_MG2

description: total RNA

value: Mammary gland


title: C1_D1_LT2_exposed Enriched

description:
intracellular_enriched_LT2.txt
WTCHG_788347_71955267


title: SC1_20

description: total RNA


title: F1_TY2 Enriched

description:
Enriched_TY2.txt
WTCHG_774525_73025278

value: Bacterial liquid culture + DFO


title: B1_D4_LT2_infected Enriched

description:
intracellular_enriched_LT2.txt
WTCHG_788347_71945266


title: S10

description: total RNA


title: S9

description: total RNA


title: C4_D3_LT2_infected Unenriched

description:
intracellular_unenriched_LT2.txt
WTCHG_766509_72875263


title: B3_TY2 Enriched

description:
Enriched_TY2.txt
WTCHG_774525_72975273


title: SC1_19

description: total RNA


title: Xu738_MG3

description: total RNA


title: SC1_17

description: total RNA


title: D4_D4_Ty2_exposed Unenriched

description:
intracellular_unenriched_TY2.txt
WTCHG_766509_72885264


title: S7

description: total RNA


title: SC1_16

description: total RNA


title: B2_TY2 Enriched

description:
Enriched_TY2.txt
WTCHG_774525_73065282


title: C1_Ty2_3 Unenriched

description:
Unenriched_TY2.txt
WTCHG_790509_72995275


title: A4_D4_D23_exposed Unenriched

description:
intracellular_unenriched_D23580.txt
WTCHG_766509_72855261


title: SC1_18

description: total RNA


title: G3_D4_LT2_exposed Unenriched

description:
intracellular_unenriched_LT2.txt
WTCHG_766509_72155287


title: SC1_15

description: total RNA


title: S6

description: total RNA


title: S2

description: total RNA


title: smd3_path_rep1

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

data_processing:
The quality of the data was assessed using fastqc.
The reads for each sample were aligned to the TAIR10 A. thaliana genome from ensembl (release v29) and reference annotation AtRTD2 (release 19.04.2016) using STAR (2.5.0a) with the following command-line parameters: STAR --runMode alignReads --sjdbOverhang 149 --sjdbGTFfile --readFilesCommand --sjdbInsertSave All --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 10 --outFilterMismatchNmax 10 --alignIntronMax 100000 --alignMatesGapMax 100000 --outSAMattrIHstart 0 --outMultimapperOrder Random --outSJfilterIntronMaxVsReadN 5000 10000 15000 20000 --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outSAMunmapped Within --sjdbFileChrStartEnd
RNA-seq alignments were split to separate read-pairs that originate from transcription on the forward and reverse strands using samtools (v1.1). Coverage graphs were calculated with genomeCoverageBed from bedtools (v2.17.0; ) with normalization to 1e7 reads and were converted to bigwig format with bedGraphToBigWig (v4).
Counts of reads for genes were generated using STAR during mapping. Table consist of four columns: name of genes, counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA and counts for the 2nd read strand aligned with RNA. Last column (i.e., 4th column) was used for differential expression analysis with DESeq2.
Genome_build: TAIR10
Supplementary_files_format_and_content: counts, bigwig

organism: Arabidopsis thaliana

source_name: smd3_path, leaves from six week old plants

growth_protocol: Plants were grown in soil under an 8 h light/16 h dark (short-day) photoperiod at 22/19°C.

extract_protocol:
Total plant RNA was isolated using Trizol reagent (Sigma) according to manufacturer’s instructions. RNA quality was verified with the Bioanalyzer (2100 Agilent).
Illumina TruSeq Stranded Total RNA with Ribo-Zero Plant rRNA Removal (Plant Leaf)

treatment_protocol: Bacteria for inoculation were cultivated overnight on LB (lysogeny broth) medium with rifampicin (50 mg/ml) at 28°C with vigorous shaking and centrifuged at 3500g for 7 min in room temperature. The bacterial pellet was washed once and resuspended in 10 mM MgCl2 and adjusted to 106 cfu/ml (OD600nm = 0.003). Plants were inoculated by spraying Pst or 10 mM MgCl2 (as a control) containing 0.05% Silwet L-77 (Chemtura) then boxes with plants were covered with plastic lids overnight. Leaves were harvested 48 h post infection.

tag: age

value: six week old plants

value: Pst

value: leaves


title: E3_D3_LT2_exposed Unenriched

description:
intracellular_unenriched_LT2.txt
WTCHG_766509_72135285

tag: infection

value: Unenriched


title: smd3_con_rep3

source_name: smd3_con, leaves from six week old plants

value: control


title: ST-Ty2 Unenriched

description:
Unenriched_TY2.txt
WTCHG_545174_271123

tag: status


title: smd3_path_rep2


title: smd3_path_rep3


title: smd3_con_rep2


title: SC1_13

description: total RNA

value: C57BL/6 and 129/Sv mixed


title: S8

description: total RNA


title: SC1_11

description: total RNA

value: Mammary tumor


title: X738T

data_processing:
trimmomatic-0.35 was used for data trimming.
tophat-2.0.13 was used for alignment with default parameter for pair-end sequencin
cufflinks-2.2.1 was used with default parameter to get gene FPKM value
Genome_build: mm10
Supplementary_files_format_and_content: gene FPKM value for each sample were summarized in text file

source_name: Mouse mammary tumor

extract_protocol:
Mammary tumors were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (Cat#E7530L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (Cat#E7530L) according to the protocols of the manufacturer.

value: Mixed

value: Mammary primary tumor


title: H3_D2_LT2_infected Unenriched

description:
intracellular_unenriched_LT2.txt
WTCHG_766509_72165288

tag: bacterial probe enrichment


title: B4_D2_LT2_exposed Unenriched

description:
intracellular_unenriched_LT2.txt
WTCHG_766509_72865262


title: smd3_con_rep1

tag: tissue


title: C3_D3_Ty2_infected Unenriched

description:
intracellular_unenriched_TY2.txt
WTCHG_766509_72115283


title: X606T


title: Col0_path_rep3

source_name: Col0_path, leaves from six week old plants

value: wild type


title: SC1_10

description: total RNA

value: female


title: B3_D2_Ty2_infected Unenriched

description:
intracellular_unenriched_TY2.txt
WTCHG_766509_72105282


title: X9387T


title: Col0_path_rep2


title: X520T


title: SC1_12

description: total RNA


title: X493T2


title: SC1_09

description: total RNA


title: A3_D1_D23580_inf Unenriched

description:
intracellular_unenriched_D23580.txt
WTCHG_766509_72095281


title: X493T1


title: Col0_path_rep1


title: H2_D1_D23580_exposed Unenriched

description:
intracellular_unenriched_D23580.txt
WTCHG_766509_72085280


title: G2_D1_Ty2_infected Unenriched

description:
intracellular_unenriched_TY2.txt
WTCHG_766509_72075279


title: X4351T


title: SC1_07

description: total RNA


title: X2265T


title: SC1_08

description: total RNA


title: Col0_con_rep3

source_name: Col0_con, leaves from six week old plants


title: F2_D3_D23580_exposed Unenriched

description:
intracellular_unenriched_D23580.txt
WTCHG_766509_72065278


title: Col0_con_rep2


title: SC1_05

description: total RNA


title: E2_D4_D23580_infected Unenriched

description:
intracellular_unenriched_D23580.txt
WTCHG_766509_72055277


title: Col0_con_rep1


title: Prx1_BM

data_processing:
scRNA-Seq data were processed using the Cell Ranger pipelines (version 3.0.1, 10x Genomics) for sample demultiplexing, read mapping (mm10/GRCm38), barcode processing and single-cell transcript counting. We excluded low-quality cells with fewer than 500 detected genes (each gene must have at least one UMI aligned) and contaminating cells. Gene expression in each cell was represented as transcripts per 10k transcripts (TP10K), representing the fraction of each gene's UMI count with respect to total UMIs in the cell and multiplied by 10,000.
Genome_build: mm10
Supplementary_files_format_and_content: gene-barcode matrices

source_name: Long bones

extract_protocol:
Chromium Controller (10x Genomics) with the Single Cell 3’ v2 kit
Chromium Single cell 3' Reagent Kits v2

treatment_protocol: Nomal feeding

tag: stain

value: Bone marrows and bone fragments

value: Nomal feeding

value: 8 weeks


title: SC1_04

description: total RNA

tag: Sex


title: SC1_03

description: total RNA


title: H1_D4_Ty2_infected Unenriched

description:
intracellular_unenriched_TY2.txt
WTCHG_766509_72005272

value: Infected


title: SC1_02

description: total RNA


title: MCY_Irradiation

growth_protocol: Normal feeding

treatment_protocol: All mice were kept in an SPF facility operated in a 12-hour light/dark cycle.

value: CD45-Ter119-Tie2-Lepr-Cre+ cells

value: Sub-lethally irradiated (5 Gy) at 7 weeks old, analyzed after one week


title: MCY_Fracture

treatment_protocol: Normal feeding

value: Femur fractured at 7 weeks old, analyzed after one week


title: MCY_Rosiglitazone

growth_protocol: Nomal feeding, then fed with 20 g/kg rosiglitazone-containing chow at 5 weeks old, analyzed after 5 weeks.

value: Fed with 20 g/kg rosiglitazone-containing chow at 5 weeks old, analyzed after 5 weeks


title: G1_D3_Ty2_exposed Unenriched

description:
intracellular_unenriched_TY2.txt
WTCHG_766509_71995271

value: Bystander


title: Virus #2 replicate #2 IFNB1-depleted mRNA

city: San Diego

first: Alistair

middle: Brian

last: Russell

address: 9500 Gilman Dr,

department: Biological Sciences

institute: University of California, San Diego

description: mRNA

data_processing:
Data were processed with a custom pipeline described at https://github.com/a5russell/Defective_Library_Mendes_Russell
grch38
Supplementary_files_format_and_content: tab-delineated files with raw count data for transcripts or barcodes

organism: Influenza A virus (A/WSN/1933(H1N1))

source_name: A549 cells

extract_protocol:
RNA was extracted using column-based miniprep kits, either from Qiagen or NEB.
SMART-Seq for mRNA samples, amplicon sequencing for others

tag: library treatment

value: IFNB1 MACS-depleted

tag: library identity

value: natural diversity


title: SC1_01

description: total RNA

value: C57BL/6 and 129/Sv mixed


title: E1_D2_D23580_exposed Unenriched

description:
intracellular_unenriched_D23580.txt
WTCHG_766509_71975269

source_name: Monocyte-derived dendritic cells + Bacteria

value: Unenriched


title: MCY_Aging


title: Virus #1 replicate #2 IFNB1-depleted mRNA

description: mRNA


title: X437T

value: Mixed


title: Virus #1 replicate #1 IFNB1-depleted mRNA

description: mRNA


title: X731T

value: Mammary primary tumor


title: D1_D3_D23580_infected Unenriched

description:
intracellular_unenriched_D23580.txt
WTCHG_766509_71965268


title: C2_D1_LT2_infected Unenriched

description:
intracellular_unenriched_LT2.txt
WTCHG_766509_72035275


title: SC1_14

description: total RNA

value: Mammary tumor


title: B1_D4_LT2_infected Unenriched

description:
intracellular_unenriched_LT2.txt
WTCHG_766509_71945266


title: X370T


title: Virus #1 replicate #2 IFNB1-enriched mRNA

description: mRNA

value: IFNB1 MACS-enriched


title: X153T


title: G2_D23 Enriched

description:
Enriched_D23580.txt
WTCHG_774525_73115287

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. D23580

value: Bacterial liquid culture

value: Bacterial liquid culture + DFO

value: Enriched


title: Virus #2 replicate #1 IFNB1-depleted mRNA

description: mRNA


title: X92T


title: TGF-β2 treated (TGF beta #3)

type: RNA

city: Kumamoto

first: Junji

last: Saruwatari

state: Select One...

address: 5-1 Oe-honmachi, Chuo-ku

department: Department of Pharmacology and Therapeutics

country: Japan

institute: Kumamoto University

description: microRNA expression data in exosome derived from monkey trabecular meshwork cells treated with TGF-β2.

hyb_protocol: Following fragmentation, 21.5 μL of biotin-labeled cRNA were hybridized for 16-18 hr at 48°C on Affymetrix GeneChip® miRNA 4.0 Array in conjugate with the FlashTag® Biotin HSR RNA Labeling Kit.  GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: GeneChips were scanned using the the GeneChip® Scanner 3000 (Thermo Fisher Scientific).

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) 4.0 using Affymetrix default analysis settings and the Robust Multiarray Average (RMA) algorithm was used for normalization of the data to generate single expression value for each probe set.

label: biotin

organism: Macaca mulatta

source_name: Exosome derived from trabecular meshwork cells treated with TGF-β2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 130-1000 ng total RNA.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: eye


title: D2_D23 Enriched

description:
Enriched_D23580.txt
WTCHG_774525_73085284


title: Virus #2 replicate #2 IFNB1-depleted vRNA

description: vRNA


title: X149T2


title: X1515T


title: C1_D1_LT2_exposed Unenriched

description:
intracellular_unenriched_LT2.txt
WTCHG_766509_71955267


title: A2_D23_3 Enriched

description:
Enriched_D23580.txt
WTCHG_774525_73055281


title: TGF-β2 treated (TGF beta #2)

value: Exosome derived from trabecular meshwork cells treated with TGF-β2


title: X149T1


title: Virus #2 replicate #2 IFNB1-enriched mRNA

description: mRNA


title: G1_D23_1 Enriched

description:
Enriched_D23580.txt
WTCHG_774525_73035279


title: JJN3 HMCL control cells replicate 2

city: Milan

first: Antonino

last: Neri

state: Milan

address: Via Francesco Sforza, 35

country: Italy

institute: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip® Human Gene 2.0 ST arrays (Thermo Fisher Scientific,Affymetrix, Waltham, MA, USA), according to the standard protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning of the arrays was performed using the GeneChip Scanner 7G

data_processing: Normalized expression values were obtained using Robust Multi Array Average (RMA) procedure. A custom annotation pipeline was applied that combined GENCODE v25 (Ensembl v87) annotations with the CDF (Chip Definition File) version 21 for gene annotations freely available at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/21.0.0/genecodeg.asp, in order to withdraw probes that map to regions where ambiguous detection due to transcript (Ronchetti D., et al. SciRep 2018)  overlap might occur.

label_protocol: RNA samples were processed using WT PLUS Reagent Kit, according to manifacturer’s protocol (Thermo Fisher Scientific, Waltham, MA, USA)

growth_protocol: HMCLs were cultured in RPMI-1640 media containing 10% FBS (GIBCO; Life Technologies, Carlsbad, CA), 2 μmol/L glutamine, 100 U/mL penicillin, and 100 μg/mL streptomycin (GIBCO; Life Technologies, Carlsbad, CA) and tested for mycoplasma contamination.

extract_protocol: Total RNA was purified from duplicate samples by resuspending in TRI Reagent (Sigma-Aldrich) and freezing at –80°C before processing.

treatment_protocol: JJN3 cells were treated with 5.0 µM HTOL for 24h

value: control


title: Virus #1 replicate #1 IFNB1-enriched mRNA

description: mRNA


title: TGF-β2 treated (TGF beta #1)


title: Virus #2 replicate #1 IFNB1-enriched mRNA

description: mRNA


title: JJN3 HMCL HTOL treated cells replicate 2

value: HTOL


title: Virus #2 replicate #1 IFNB1-depleted vRNA

description: vRNA


title: E1_D23 Enriched

description:
Enriched_D23580.txt
WTCHG_774525_73015277


title: JJN3 HMCL HTOL treated cells replicate 1


title: JJN3 HMCL control cells replicate 1


title: Collagen type 1 treated (collagen #2)

description: microRNA expression data in exosome derived from monkey trabecular meshwork cells treated with collagen type 1.

source_name: Exosome derived from trabecular meshwork cells treated with collagen type 1


title: Collagen type 1 treated (collagen #3)

value: Exosome derived from trabecular meshwork cells treated with collagen type 1


title: X147T


title: Collagen type 1 treated (collagen #1)


title: Virus #1 replicate #1 IFNB1-depleted vRNA

description: vRNA


title: Virus #2 replicate #1 IFNB1-enriched vRNA

description: vRNA


title: X1418T


title: D23_G2 Unenriched

description:
Unenriched_D23580.txt
WTCHG_790509_73115287


title: X154T


title: Virus #2 replicate #2 IFNB1-enriched vRNA

description: vRNA


title: Control #2

description: microRNA expression data in exosome derived from monkey trabecular meshwork cells.

source_name: Exosome derived from trabecular meshwork cells


title: B1_D23_2 Enriched

description:
Enriched_D23580.txt
WTCHG_774525_72985274


title: Control #3

value: Exosome derived from trabecular meshwork cells


title: D23_D2 Unenriched

description:
Unenriched_D23580.txt
WTCHG_790509_73085284


title: Virus #1 replicate #2 IFNB1-depleted vRNA

description: vRNA

value: IFNB1 MACS-depleted


title: A2_D23_3 Unenriched

description:
Unenriched_D23580.txt
WTCHG_790509_73055281


title: D23_E1 Unenriched

description:
Unenriched_D23580.txt
WTCHG_790509_73015277


title: Virus #1 replicate #1 IFNB1-enriched vRNA

description: vRNA

value: natural diversity


title: X1310T2


title: Virus #1 replicate #2 IFNB1-enriched vRNA

description: vRNA


title: X1463T1


title: X1463T2


title: X1310T1


title: Control #1


title: eds1 pbl19/pPBL19:PBL19C3A-GFP-HA transgenic plants#1 [EC-1-28D]

status: Public on Nov 16 2021

city: Guangzhou

first: yujia

last: Li

address: No. 132, Huan East Road, Panyu District, Guangzhou City

department: School of life science

institute: sun yet-sen university

data_processing:
libraries were sequenced using  Illumina platform
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.clean data were aligned to the Arabidopsis TAIR10 genome by HISAT2(2.0.4)with parameters --dta -p 6 --max-intronlen 5000000
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: TAIR10 genome
Supplementary_files_format_and_content: FPKM; raw counts

source_name: rosette of Arabidopsis thaliana

extract_protocol:
Total RNA was extracted from 28- day-old WT, pbl19/pPBL19-PBL19C3A-GFP-HA, sid2 pbl19/pPBL19-PBL19C3A-GFP-HA, and eds1 pbl19/pPBL19-PBL19C3A-GFP-HA with using the RNAiso Plus reagent (Takara Bio, Japan).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ecotype

tag: genotype/variation

value: Rosettes

value: Four-week-old

tag: phenotype

value: untreated


title: eds1 pbl19/pPBL19:PBL19C3A-GFP-HA transgenic plants#2 [EC-2-28D]


title: STM-D23580 Unenriched

description:
Unenriched_D23580.txt
WTCHG_545174_270135

value: Unenriched


title: pbl19/pPBL19C3A-GFP-HA transgenic plants#2 [C3A-2-28D]

value: pbl19/pPBL19C3A-GFP-HA transgenic

value: constitutive immunity


title: sid2 pbl19/pPBL19:PBL19C3A-GFP-HA transgenic plants#1 [SC-1-28D]


title: pbl19/pPBL19C3A-GFP-HA transgenic plants#1 [C3A-1-28D]


title: WT#1 [WT-1-28D]

value: WT


title: sid2 pbl19/pPBL19:PBL19C3A-GFP-HA transgenic plants#2 [SC-2-28D]


title: HAVSMCs, LINC02015 CHIRPinput

city: Shanghai

first: Qiang

last: Ji

address: 180 Fenglin Rd.

institute: Zhongshan Hospital Fudan University

description:
mapping.info
LINC02015_macs2_peaks

data_processing:
Library strategy: ChIRP-seq
Chromatin isolation by RNA purification (ChIRP) sequencing was applied to explore the interaction relationship among LncRNA, RNA-binding protein and DNA.
Localization of the active binding sites was specified by high-throughput sequencing. Clean data were compared with STAR2.
Peak calling analysis was applied to spot enriched gene peaks using MACS.
Genome_build: hg38
Supplementary_files_format_and_content: enriched peaks *.txt

source_name: Vascular smooth muscle cells

growth_protocol: Human aortic VSMCs (HAVSMCs) were cultured with Ham’s F-12K medium (Gibco, NY, USA) containing 10% fetal bovine serum (Gibco, Australia). Cells were cultured in a humidified 37°C incubator with 5% CO2.

extract_protocol:
Cells were washed with PBS and incubated in lysis buffer. The genomic DNA was extracted through lysis, ultrasonication, probe hybridization, magnetic beads purification and separation.
ChIRP-Seq libraries were prepared using TELP developed by PengXu et al. (PMID: 25223787) with slightly modification.

treatment_protocol: The cells were plated in 6-well plates and treated with different agents when they became 70%–80% confluent.

tag: cell type

value: Human aortic vascular smooth muscle cells (HAVSMCs)

tag: fraction

value: input


title: HAVSMCs, LINC02015 CHIRPpositive

description:
mapping.info
LINC02015_macs2_peaks


title: Mouse tumor xenographt visium data from mice GP024_dKDCD36_Palm_Diet

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

description:
Human Xenographt tumor in mouse model
Visium fresh-frozen protocol
No sorting
Visium

data_processing:
alignment, filtering, barcode counting, and UMI counting: scRNAseq: Cell Ranger v4.0.0; Visium: Space Ranger 1.1.0
scRNAseq: Cell Ranger v4.0.0; Visium: Space Ranger 1.1.0
Genome_build: mouse: mm10; human-mouse: GRCh38-3.0.0-mm10
Supplementary_files_format_and_content: barcodes.tsv: cell barcodes
Supplementary_files_format_and_content: features.tsv: gene names
Supplementary_files_format_and_content: matrix.mtx: count matrix
Supplementary_files_format_and_content: spatial.zip: spatial data

source_name: Tumor xenographt slides

extract_protocol:
scRNAseq: As described in the v3.0 single-cell 3’ mRNA kit (10x Genomics) protocol (CGO00183 Rev C), after GEMs generation and reverse transcription, the cDNA was extracted by Dynabeads MyOne SILANE clean up following manufacturer’s instructions. The obtained cDNA was then used for amplification.    Visium: Tissues were permeabilized with a proprietary enzyme (10 min), and reverse-transcription and second-strand synthesis were performed on the slide, with cDNA quantification via qRT-PCR using KAPA SYBR FAST-qPCR kit (KAPA Biosystems), and analyzed on the LightCycler®480 Real-Time PCR System (Roche). qRT-PCR results (Cq value at 25% of peak fluorescence) revealed cDNA amplification. The Visium slide serial number was V19S23-040.
scRNAseq: Cell concentration and viability of the single-cell suspension were verified by counting with a TC20™ Automated Cell Counter (Biorad). Cells were partitioned into Gel Bead-In-Emulsions (GEMs) using the Chromium Controller system (10´ Genomics) with the aim of a target cell recovery of 5,000 cells. Single-cell Gene Expression (GEX) libraries were prepared using Chromium™ Single Cell 3¢ Library & Gel Bead Kit v2 (10´ Genomics, Cat. N. 120237) following manufacturer's instructions. Briefly after GEM-RT clean up, cDNA was amplified using 12 cycles. cDNA QC and quantification were performed on an Agilent Bioanalyzer High Sensitivity chip (Agilent Technologies). Libraries were indexed by PCR using the PN-220103 Chromiumi7 Sample Index Plate (10´ Genomics). Size distribution and concentration of 3¢ GEX libraries were verified on an Agilent Bioanalyzer High Sensitivity chip (Agilent Technologies). Sequencing was carried out on an Illumina Hiseq4000 sequencer to obtain approximately 40,000 reads/cell.    Visium: Libraries were constructed as per manufacturer’s instructions; ST libraries were then quantified by High-Sensitivity DNA Assay 2100 Agilent. Libraries were sequenced on a NovaSeq6000 platform (Illumina, US) using 100 bp paired-end dual-indexed set up. Around 200 million paired-end reads were obtained for each tissue section. Read 1 was sequenced with 28 cycles; i7 index, 10 cycles; i5 index, 10 cycles; and read 2, 82 cycles.

treatment_protocol: scRNAseq: cells were selected on the basis of their Forward and Side scatter excluding cellular debris. Doublets and dead cells were eliminated by DAPI. GFP-positive cells were gated excluding lineage-BV–positive cells. This population was selected for further CD36 human expression analysis. Tumour-associated stromal cells were gated excluding endothelial (CD31+), macrophages (CD45+) and human (GFP+) cells. This population was selected for further mouse stromal gene expression analysis.    Visium: Xenografted tumours were dissected from mice, embedded in Tissue-Tek O.C.T. compound (Ref. 4583 Sakura) within biopsy 10105 mm cryomolds (Ref 62534-10 Sakura) and quickly snap-frozen in an isopentane bath chilled with liquid nitrogen (LN2).

tag: diet

value: Palm oil rich

tag: knock out

value: Inducible lentiviral shCD36

tag: strain

value: NOD scid gamma (NSG) (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ)


title: Mouse tumor xenographt visium data from mice GP027_PKLO_Palm_Diet

value: empty pLKO.1-TRC lentiviral vector


title: Mouse tumor xenographt visium data from mice GP20004_dKDCD36_CT_Diet

value: Control diet


title: mESCs, shEV_HiC

city: Singapore

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
HiC reads were aligned to mm9 genome assembly using BWA with runHiC pipeline using the default settings (https://pypi.org/project/runHiC/)
Genome_build: mm9
Supplementary_files_format_and_content: The cool and hic file were the matrix of Hi-C for each Sample.

growth_protocol: E14 mouse embryonic stem cells (mESCs) were cultured using mouse ES medium prepared in DMEM high glucose (Hyclone) supplemented with 15 percent ES cell FBS (Gibco), 2mM L-glutamine (Gibco), 1X Pen-Strep (Gibco), 100 micromolar MEM non-essential amino acids (Gibco), 100 micromolar 2-mercaptoethanol (Gibco), and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore). The mouse ES line was cultured on plates pre-coated with 0.1 percent gelatine (porcine).

extract_protocol:
Freshly sorted cells were kept on ice and typically aliquoted to 1M cell pellets and the input levels of chromatin required for Hi-C were determined per million. The cells were immediately crosslinked with 2% formaldehyde for 10 min, quenching with 0.25M glycine for 5 min at room temperature and 5 min on ice, followed by lysis, digestion with a restriction enzyme cocktail, filling the 5′-overhangs while incorporating biotin-14-dATP (a biotinylated nucleotide), followed by ligating the resulting blunt-end fragments, shearing the DNA to a 400–700-bp fragment size using a Covaris ME220 focused ultra-sonicator, capturing the biotinylated ligation junctions with streptavidin beads. The reagents for all reactions were obtained from Arima Hi-C kits.
Libraries were prepared according to Illumina's instructions with optimised rounds of PCR amplification, and finally analyzed the resulting fragments with paired-end sequencing.

treatment_protocol: E14 cells were harvested using trypsinization and were re-seeded into 6-well plates which were pre-coated with gelatine. The seeding density was 300,000 cells per well of the plates. These cells were cultured at 37 degree Celsius for 20-24 hours and the cells were replenished with fresh medium at least 2 hours prior to transfection. The cells were then transfected with 3 microgram of the plasmid constructs (shControl, shSetdb1, shSmc1a) using 4.5 microliters of Lipofectamine 2000 (Thermofisher), as per the manufacturer’s protocol. Puromycin (1 microgram/millliter) containing mESC medium was added to the cells 24 hours after transfection to select for the transfected plasmids. This process of selection was repeated once more 48 hours after transfection. The cells were finally harvested 72 hours after transfection.

tag: cell line

value: mouse embryonic stem cells (mESCs)

tag: transfection

value: shEV

tag: genotype

value: control


title: Mouse tumor xenographt visium data from mice GP029_PLKO_CT_Diet


title: mESCs, shSetdb1_HiC

value: Setdb1 KD


title: mESCs, shSmc1a_HiC

value: Smc1a KD


title: Mouse tumor microenvironment cells from mice 25_shcD36_PALM_diet

description:
10X Chromium 3' RNA-seq
GFP-positive cells were gated excluding lineage-BV–positive cells. This population was selected for further CD36 human expression analysis. Tumour-associated stromal cells were gated excluding endothelial (CD31+), macrophages (CD45+) and human (GFP+) cells
single-cell RNA-seq

source_name: Tumor microenvironment cells


title: Mouse tumor microenvironment cells from mice 25_shcD36_ctdiet


title: LowNras2

city: Chicago

first: Megan

middle: E.

last: McNerney

state: Illinois

address: 900 East 57th Street, KCBD 5128

department: Pathology

institute: The University of Chicago

data_processing:
RNA-seq reads were aligned to hg19 with Tophat using default parameters. Reads with quality scores >30 were counted using HTseq-tools and analyzed with EdgeR
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq text file contains EdgeR results for Gene name, log fold change, log counts per million, p value and q values for Cux1-low versus Cux1-low;NrasG12D.

source_name: Cux1-low;Nras12D HSPC

growth_protocol: Mice were treated with pI:C and doxycycline for four weeks.

extract_protocol:
RNA was isolated using Trizol.
Barcoded RNA-seq libraries were generated using the standard Illumina TruSEQ v2 kit.

treatment_protocol: Lineage-/KIT+/SCA1+/CD135- HSPCs were sorted by flow cytometry.

value: HSPCs


title: Low2

source_name: Cux1-low HSPC


title: Mouse tumor microenvironment cells from mice 25_Plko_ct_diet


title: WT#2 [WT-2-28D]

value: Rosettes

tag: age

value: Four-week-old

tag: treatment

value: untreated


title: LowNras3


title: LowNras1


title: Low1


title: RR-DLBCL: 1689010

city: Philadelphia

first: Daniel

middle: J

last: Landsburg

state: PA

address: 3400 Civic Center Boulevard, #12-182

department: Perelman School of Medicine

institute: University of Pennsylvania

data_processing:
Sequencing was performed in a Hi-Seq 2500 sequencer (Illumina) and base calling was performed with Illumina HCS software.
Reads were mapped to human reference genome HG38 and counted using the STAR aligner with default parameters.
Ensembl gene identifiers were converted to known Entrez gene IDs based on gene2ensembl (https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2ensembl.gz)

source_name: RR-DLBCL

extract_protocol:
Samples consisted of (up to) four FFPE tumor tissue slides per subject.  The tissue was removed from slides and pooled for extraction.  DNA and RNA extraction was performed according to manufacturers protocol using the Qiagen AllPrep FFPE kit (https://www.qiagen.com/us/products/discovery-and-translational-research/dna-rna-purification/multianalyte-and-virus/allprep-dnarna-ffpe-kit/).  Resulting RNA was assessed for concentration using the RiboGreen Assay.
Sequencing libraries were prepared via the Illumina TruSeq RNA Acces (TruSeq RNA Exome) kit (https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-rna-access.html).

tag: disease state

value: relapsed-refractory diffuse large B-cell lymphoma (RR DLBCL)

tag: tissue

value: FFPE tumor


title: RR-DLBCL: 1689750


title: RR-DLBCL: 1686895


title: RR-DLBCL: 1686915


title: RR-DLBCL: 1686999


title: RR-DLBCL: 1686903


title: RR-DLBCL: 1686914


title: RR-DLBCL: 1686920


title: RR-DLBCL: 1686902


title: RR-DLBCL: 1686896


title: RR-DLBCL: 1686892


title: RR-DLBCL: 1686888


title: RR-DLBCL: 1686883


title: F3_D1_Ty2_exposed Unenriched

description:
intracellular_unenriched_TY2.txt
WTCHG_766509_72145286

data_processing:
Reads were quality trimmed and adapters were removed using Cutadapt software
Reads were aligned to joint Salmonella-Human reference genome using STAR and cross-species multi-mappers were filtered out
Expression was quantified using Subread featureCounts, with multi-mappers counted as fractions
Data normalisation and differential expression analyses were performed using DESeq2
Genome_build: hg38, NC_003197.2, NC_016854.1 and NC_004631.1
Supplementary_files_format_and_content: Raw expression counts matrices per sample

extract_protocol:
20'000 cells were sorted in PBS and spun down and the pellet resuspended in Monarch RNA lysis buffer supplemented with 2mg/mL of Lysozime (thermoFisher). Total RNA extraction was performed with the Monarch® Total RNA Miniprep Kit (New England BioLabs) according to the manufacturers.
Libraries were prepared by using the SMARTer® stranded total RNA seq v2 pico input Mammalian (Takara) with minor technical adaptations. PCR1 was carried on for 5 cycles and PCR2 for 11 cycles (for the bacterial libraries) or 12 cycles (for the host-pathogen libraries). After cDNA synthesis, the human ribosomal cDNA was removed by using probes specific to mammalian rRNA.

tag: infection

tag: status

value: Bystander

tag: bacterial probe enrichment

value: Unenriched


title: RR-DLBCL: 1686884


title: RR-DLBCL: 1686868


title: RR-DLBCL: 1686880


title: RR-DLBCL: 1686876


title: RR-DLBCL: 1686875


title: RR-DLBCL: 1689741


title: RR-DLBCL: 1686923


title: RR-DLBCL: 1686869


title: RR-DLBCL: 1686873


title: RR-DLBCL: 1686860


title: Mouse tumor microenvironment cells from mice 25_Plko_Palmdiet

value: Palm oil rich


title: RR-DLBCL: 1686838


title: RR-DLBCL: 1686857


title: RR-DLBCL: 1686851


title: RR-DLBCL: 1686853


title: RR-DLBCL: 1686885


title: RR-DLBCL: 1686846


title: RR-DLBCL: 1686874


title: Untreated_14Days_rep2

data_processing:
Sequenced reads were trimmed for adaptor sequence using Trimmomatic (version 0.36)
Reads were aligned to the hg19 genome (Ensembl GRCh37.75) using TopHat Aligner (version 2.1.1)
For differentially expressed genes (DEGs), read count was performed using featureCounts (version 1.6.0) and DEGs were called using DESeq2 (version 1.26.0).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each sample.

source_name: OSCC cells

extract_protocol:
RNA was extracted following the manufacturer´s recommendations and treated with TURBO DNA-free Kit (AM1907, Thermo Fisher)
Libraries were prepared with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat Kit (RS-122-2201/2202, Illumina). Samples were sequenced on a HiSeq2500 sequencer (Illumina) using V4 chemistry, generating 125-bp single reads.

value: Untreated 14D


title: Untreated_14Days_rep1


title: RR-DLBCL: 1686882


title: Treated4_14Days_rep3

value: post-PA 14D


title: Treated4_14Days_rep2


title: Untreated_14Days_rep3


title: RR-DLBCL: 1686872


title: Untreated_NotSorted_rep3

value: Untreated 4D


title: RR-DLBCL: 1686865


title: Treated4_14Days_rep1


title: Untreated_NotSorted_rep2


title: Untreated_NotSorted_rep1


title: Treated4_NotSorted_rep3

value: post-PA 4D


title: Treated4_NotSorted_rep2


title: K9_PC_H3K9me3

data_processing:
Samples were sequenced on a HiSeq2500 sequencer (Illumina) using V4 chemistry, generating 50-bp paired-end reads.
After adapter-cleaning and quality correction using Trimmomatic (version 0.36), paired-end reads were aligned to the hg19 genome (UCSC) using Bowtie 2 Aligner (version 0.3.3.1). Duplicate reads were removed using SAMtools (version 1.3.1).
Peaks were called using MACS2 (version 2.0.10) and an FDR < 0.05. Differential peaks were determined using the DiffBind package (version 2.4.8) in R (version 3.5.2) and an FDR < 0.05.   The distribution of the differential regions within genomic features was conducted with HOMER (version 2015-03-22).
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using bedGraphToBigWig tool from ENCODE

growth_protocol: SCC-25 (ATCCR CRL-168TM) were grown in keratinocyte serum-free media (KSFM, Gibco) supplemented with 5 μg ml–1 penicillin/streptomycin, 0.025 mg ml–1 bovine pituitary extract and 0.2 μg ml–1 hEGF.

extract_protocol:
Lysates were obtained, nuclei sonicated and histone-DNA complexes  isolated with antibody according to the ChIP-IT High Sensitivity kit® from Active Motif (ref. 53040).
Libraries were prepared according to Illumina's instructions accompanying the NEBNext Ultra DNA Library Prep kit (Ref.:#7370).

treatment_protocol: SCC cells growing in serum–free media were treated in vitro with 300 μM palmitic acid for 96 h (4 days) and after palmitic acid withdrawal cells were passaged normally (when reaching 80% confluence) for 14 days and collected for chromatin fixation.

value: SCC-25 cells

value: PA-Treated

tag: replicate


title: Treated4_NotSorted_rep1


title: K9_PB_H3K9me3


title: K9_PA_H3K9me3


title: K9_CC_H3K9me3

value: Untreated


title: K9_CB_H3K9me3


title: K9_CA_H3K9me3


title: RR-DLBCL: 1686847


title: K9_P1_H3K9me3


title: K9_P3_H3K9me3


title: K9_C2_H3K9me3


title: K9_C3_H3K9me3


title: EGR_PC_H3K4me3

value: SCC-25 EGR2_KD cells


title: K9_C1_H3K9me3


title: EGR_P2_H3K4me3


title: EGR_PA_H3K4me3


title: EGR_PB_H3K4me3


title: K9_P2_H3K9me3


title: EGR_P3_H3K4me3


title: EGR_P1_H3K4me3


title: EGR_CA_H3K4me3


title: EGR_CC_H3K4me3


title: EGR_CB_H3K4me3


title: EGR_C1_H3K4me3


title: EGR_C2_H3K4me3


title: EGR_C3_H3K4me3


title: H3K27ac_ChIPSeq_SCC_4_3

description:
H3K27ac_ChIPSeq
post-PA 14D

data_processing:
Trimmomatic  (v0.36) software (Bolger et al., 2014) was used to remove possible contaminations
Reads were aligned to the human genome build hg19 using BWA (v0.7.12) software (Li H. and Durbin R., 2009)
Aligned bam files were coordinate sorted and duplicates were removed with samtools (v1.3.1) software (Li, Handsaker et al. 2009)
Peaks were called using GeneRich (version 0.6) and an FDR < 0.05. GeneRich was also used to remove duplicate reads. Differential peaks were determined using the DiffBind package (version 2.4.8) in R (version 3.5.2) and an FDR < 0.05.   The distribution of the differential regions within genomic features was conducted with HOMER (version 2015-03-22).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig: Browser peak files. BigWig files are created from wiggle (wig) type files using the program wigToBigWig.

treatment_protocol: SCC cells growing in serum–free media were treated in vitro with 300 μM palmitic acid  for 96 h (4 days) and after palmitic acid withdrawal cells were passaged normally (when reaching 80% confluence) for 14 days and collected for chromatin fixation.


title: H3K27ac_ChIPSeq_SCC_4_2

description:
H3K27ac_ChIPSeq
post-PA 14D


title: H3K27ac_ChIPSeq_SCC_2_1

description:
H3K27ac_ChIPSeq
Untreated 14D


title: H3K27ac_ChIPSeq_SCC_3_3

description:
H3K27ac_ChIPSeq
post-PA 4D


title: H3K27ac_ChIPSeq_SCC_2_2

description:
H3K27ac_ChIPSeq
Untreated 14D


title: H3K27ac_ChIPSeq_SCC_3_1

description:
H3K27ac_ChIPSeq
post-PA 4D


title: H3K27ac_ChIPSeq_SCC_3_2

description:
H3K27ac_ChIPSeq
post-PA 4D


title: H3K27ac_ChIPSeq_SCC_4_1

description:
H3K27ac_ChIPSeq
post-PA 14D


title: H3K27ac_ChIPSeq_SCC_2_3

description:
H3K27ac_ChIPSeq
Untreated 14D


title: EGR_PB

data_processing:
Samples were sequenced on a HiSeq2500 sequencer (Illumina) using V4 chemistry, generating 50-bp paired-end reads.
After adapter-cleaning and quality correction using Trimmomatic (version 0.36), paired-end reads were aligned to the hg19 genome (UCSC) using Bowtie 2 Aligner (version 0.3.3.1). Duplicate reads were removed using SAMtools (version 1.3.1).
Peaks were called using GeneRich (version 0.6) and an FDR < 0.05. GeneRich was also used to remove duplicate reads. Differential peaks were determined using the DiffBind package (version 2.4.8) in R (version 3.5.2) and an FDR < 0.05.   The distribution of the differential regions within genomic features was conducted with HOMER (version 2015-03-22).
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using bedGraphToBigWig tool from ENCODE

extract_protocol:
Chromatin was sonicated for 15 min in a Bioruptor Pico (Diagenode), and 45 ug of chromatin and 8 ug of EGR2 antibody (ref. Ab43020) were used in the immunoprecipitation step.
EGR2 ChIPs were performed following the ChIP-IT High Sensitivity kit® recommendations.

tag: shRNA

value: control pLKO.1


title: EGR_CC

tag: cell type


title: H3K27ac_ChIPSeq_SCC_1_1

description:
H3K27ac_ChIPSeq
Untreated 4D


title: EGR_CB


title: EGR_CA


title: H3K27ac_ChIPSeq_SCC_1_2

description:
H3K27ac_ChIPSeq
Untreated 4D


title: EGR_PC


title: EGR_PA


title: EGR_P1


title: EGR_P2


title: EGR_C3


title: EGR2_PC_ChIPSeq

value: SCC-25 CD36_KD cells


title: EGR_P3


title: EGR_C2


title: EGR2_PB_ChIPSeq


title: EGR2_PA_ChIPSeq


title: EGR2_CB_ChIPSeq


title: EGR2_CA_ChIPSeq


title: EGR2_P2_ChIPSeq


title: 28357_28358_input DNA_VDH15 [re-used 3]

description:
input_1_28357_GCTAAC
input_2_28358_CTTCCA

data_processing:
Trimmomatic  (v0.36) software (Bolger et al., 2014) was used to remove possible contaminations
Reads were aligned to the human genome build hg19 using BWA (v0.7.12) software (Li H. and Durbin R., 2009)
Aligned bam files were coordinate sorted and duplicates were removed with samtools (v1.3.1) software (Li, Handsaker et al. 2009)
Peak calling to determine enrichment over the background was done with MACS (v2.1.2) callpeak (Zhang, Liu et al. 2008) with the broad flag method and q-value narrow 0.05 and broad cutoff 0.0001
Signal tracks on ChIPSeq peaks enrichment levels over whole genome were generated with MACS (v2.1.2) bdgcmp on the bedGraph files generated by MACS (v2.1.2) callpeak
Genome_build: hg19
Supplementary_files_format_and_content: bigWig: Browser peak files. BigWig files are created from wiggle (wig) type files using the program wigToBigWig.
Supplementary_files_format_and_content: xls:  tabular file which contains information about called peaks. You can open it in excel and sort/filter using excel functions. Information include: chromosome name, start position of peak, end position of peak, length of peak region, absolute peak summit position, pileup height at peak summit,-log10(pvalue) for the peak summit, fold enrichment for this peak summit against random Poisson distribution with local lambda,-log10(qvalue) at peak summit
Supplementary_files_format_and_content: bed (broadPeak): BED6+3 format which contains the peak locations together with peak summit, p-value, and q-value. You can load it into genome browser.

source_name: input DNA

growth_protocol: VDH-15 cells were grown in keratinocyte serum-free media (KSFM, Gibco) supplemented with 5 μg ml–1 penicillin/streptomycin, 0.025 mg ml–1 bovine pituitary extract and 0.2 μg ml–1 hEGF.

extract_protocol:
Lysates were obtained, nuclei sonicated and histone-DNA complexes isolated with antibody according to the ChIP-IT High Sensitivity kit® from Active Motif (ref. 53040).
Libraries were prepared according to Illumina's instructions accompanying the NEBNext Ultra DNA Library Prep kit (Ref.:#7370).

treatment_protocol: VDH-15 cells growing in serum–free media were treated in vitro with 300 μM palmitic acid  for 96 h (4 days) and after palmitic acid withdrawal cells were passaged normally (when reaching 80% confluence) for 14 days and collected for chromatin fixation

value: oral squamous cell carcinoma (OSCC) cell line

tag: chip antibody

value: none; input


title: H3K27ac_ChIPSeq_SCC_1_3

description:
H3K27ac_ChIPSeq
Untreated 4D


title: EGR2_CC_ChIPSeq


title: EGR2_P3_ChIPSeq


title: 33754_VDH-15_post-PA 14D_MLL2_ChIPSeq

source_name: VDH-15_post-PA 14D_MLL2_ChIPSeq

value: MLL2 in-house antibody


title: 33755_VDH-15_post-PA 14D_MLL2_ChIPSeq


title: EGR2_C1_ChIPSeq


title: EGR2_P1_ChIPSeq


title: EGR2_C3_ChIPSeq


title: 33752_VDH-15_Untreated 14D_MLL2_ChIPSeq

source_name: VDH-15_Untreated 14D_MLL2_ChIPSeq


title: 33753_VDH-15_post-PA 14D_MLL2_ChIPSeq


title: 33750_VDH-15_Untreated 14D_MLL2_ChIPSeq


title: EGR_C1


title: 33751_VDH-15_Untreated 14D_MLL2_ChIPSeq


title: 33747_VDH-15_post-PA 14D_MLL1_ChIPSeq

source_name: VDH-15_post-PA 14D_MLL1_ChIPSeq

value: MLL1 in-house antibody


title: 33748_VDH-15_post-PA 14D_MLL1_ChIPSeq


title: 33745_VDH-15_Untreated 14D_MLL1_ChIPSeq

source_name: VDH-15_Untreated 14D_MLL1_ChIPSeq


title: 00014AAB_VDH-15 OSCC tumor_PALM Diet 2ary PTs_H3K4me3_ChIPSeq

data_processing:
Trimmomatic  (v0.36) software (Bolger et al., 2014) was used to remove possible contaminations
Reads were aligned to the human genome build hg19 using BWA (v0.7.12) software (Li H. and Durbin R., 2009)
Aligned bam files were coordinate sorted and duplicates were removed with samtools (v1.3.1) software (Li, Handsaker et al. 2009)
Peak calling to determine enrichment over the background was done with MACS (v2.1.2) callpeak (Zhang, Liu et al. 2008) with the broad flag method and q-value narrow 0.05 and broad cutoff 0.01
Signal tracks on ChIPSeq peaks enrichment levels over whole genome were generated with MACS (v2.1.2) bdgcmp on the bedGraph files generated by MACS (v2.1.2) callpeak
Genome_build: hg19
Supplementary_files_format_and_content: bigWig: Browser peak files. BigWig files are created from wiggle (wig) type files using the program wigToBigWig.
Supplementary_files_format_and_content: xls:  tabular file which contains information about called peaks. You can open it in excel and sort/filter using excel functions. Information include: chromosome name, start position of peak, end position of peak, length of peak region, absolute peak summit position, pileup height at peak summit,-log10(pvalue) for the peak summit, fold enrichment for this peak summit against random Poisson distribution with local lambda,-log10(qvalue) at peak summit
Supplementary_files_format_and_content: bed (broadPeak): BED6+3 format which contains the peak locations together with peak summit, p-value, and q-value. You can load it into genome browser.

growth_protocol: Patient-deirved cells (VDH-15) were injected intra-tongue of primary recipient NSG mice (fed for 10 days either with CTRL or PALM diets); h2kd- GFP+ human cancer cells were sorted from primary tumors and re-injected intra-tongue of secondary recipient mice fed with standard diet.

extract_protocol:
h2kd- GFP+ VDH-15 cells were sorted from secondary recipient primary tumors for chromatin fixation and ChIP-Seq following the True MicroChIP kit from Diagenode (ref. C01010130) intructions.
Libraries were prepared according to Illumina's instructions accompanying the NEBNext Ultra DNA Library Prep kit (Ref.:#7370).

treatment_protocol: 10 days feeding of CTRL or PALM diet in primary recipient mice.

tag: cell line source

value: Technical Batch 2 PALM Diet 2ary PTs

value: H3K4me3 (Diagenode, C15410003)


title: 33749_VDH-15_post-PA 14D_MLL1_ChIPSeq


title: EGR2_C2_ChIPSeq


title: 33744_VDH-15_Untreated 14D_MLL1_ChIPSeq


title: 00008AAB_VDH-15 OSCC tumor_PALM Diet 2ary PTs_H3K4me3_ChIPSeq

value: Technical Batch 1 PALM Diet 2ary PTs


title: 00011AAB_VDH-15 OSCC tumor_CTRL Diet 2ary PTs_H3K4me3_ChIPSeq

value: Technical Batch 2 CTRL Diet 2ary PTs


title: 00006AAB_VDH-15 OSCC tumor_PALM Diet 2ary PTs_H3K4me3_ChIPSeq


title: 00012AAB_VDH-15 OSCC tumor_PALM Diet 2ary PTs_H3K4me3_ChIPSeq


title: 33746_VDH-15_Untreated 14D_MLL1_ChIPSeq

value: Untreated 14D


title: 00005AAB_VDH-15 OSCC tumor_CTRL Diet 2ary PTs_H3K4me3_ChIPSeq

value: Technical Batch 1 CTRL Diet 2ary PTs


title: 00010AAB_VDH-15 OSCC tumor_CTRL Diet 2ary PTs_H3K4me3_ChIPSeq


title: 28357_28358_input DNA_VDH15 [re-used 2]

data_processing:
Trimmomatic  (v0.36) software (Bolger et al., 2014) was used to remove possible contaminations
Reads were aligned to the human genome build hg19 using BWA (v0.7.12) software (Li H. and Durbin R., 2009)
Aligned bam files were coordinate sorted and duplicates were removed with samtools (v1.3.1) software (Li, Handsaker et al. 2009)
Peak calling to determine enrichment over the background was done with MACS (v2.1.2) callpeak (Zhang, Liu et al. 2008) with the broad flag method and q-value narrow and broad cutoff 0.05
Signal tracks on ChIPSeq peaks enrichment levels over whole genome were generated with MACS (v2.1.2) bdgcmp on the bedGraph files generated by MACS (v2.1.2) callpeak
Genome_build: hg19
Supplementary_files_format_and_content: bigWig: Browser peak files. BigWig files are created from wiggle (wig) type files using the program wigToBigWig.
Supplementary_files_format_and_content: xls:  tabular file which contains information about called peaks. You can open it in excel and sort/filter using excel functions. Information include: chromosome name, start position of peak, end position of peak, length of peak region, absolute peak summit position, pileup height at peak summit,-log10(pvalue) for the peak summit, fold enrichment for this peak summit against random Poisson distribution with local lambda,-log10(qvalue) at peak summit
Supplementary_files_format_and_content: bed (broadPeak): BED6+3 format which contains the peak locations together with peak summit, p-value, and q-value. You can load it into genome browser.

growth_protocol: Patient-derived cells (VDH-15) were grown in keratinocyte serum-free media (KSFM, Gibco) supplemented with 5 μg ml–1 penicillin/streptomycin, 0.025 mg ml–1 bovine pituitary extract and 0.2 μg ml–1 hEGF.

value: input DNA


title: 35794_VDH-15_control pLKO.1_post-PA 14D_H3K4me3_ChIPSeq

value: post-PA 14D


title: 00007AAB_VDH-15 OSCC tumor_PALM Diet 2ary PTs_H3K4me3_ChIPSeq


title: 35793_VDH-15_control pLKO.1_post-PA 14D_H3K4me3_ChIPSeq


title: 00004AAB_VDH-15 OSCC tumor_CTRL Diet 2ary PTs_H3K4me3_ChIPSeq


title: 35792_VDH-15_control pLKO.1_post-PA 14D_H3K4me3_ChIPSeq


title: 34282_input_DNA_InVivo

value: PT input DNA


title: 35797_VDH-15_control pLKO.1_Untreated 14D_H3K4me3_ChIPSeq


title: 35796_VDH-15_control pLKO.1_Untreated 14D_H3K4me3_ChIPSeq


title: 00013AAB_VDH-15 OSCC tumor_PALM Diet 2ary PTs_H3K4me3_ChIPSeq


title: 21910_21911_21912_input DNA_SCC25 [re-used 3]

description:
INPUT_1_21910_ATCACG
INPUT_2_21911_ACTTGA
INPUT_4_21912_GGCTAC


title: 21951_SCC-25_post-PA 14D_H3K4me3_ChIPSeq

description:
SCC_4_2_21951_AGTCAA
SCC_4_2_21951_ANTCAA
SCC_4_2_21951_NGTCAA

source_name: SCC-25_post-PA 14D_H3K4me3_ChIPSeq


title: 21952_SCC-25_post-PA 14D_H3K4me3_ChIPSeq

description:
SCC_4_3_21952_GAGTGG
SCC_4_3_21952_GNGTGG
SCC_4_3_21952_NAGTGG


title: 21949_SCC-25_Untreated 14D_H3K4me3_ChIPSeq

source_name: SCC-25_Untreated 14D_H3K4me3_ChIPSeq


title: 35800_VDH-15_Set1A KD cells_Untreated 14D_H3K4me3_ChIPSeq

value: Set1A #42 KD cells


title: 35799_VDH-15_Set1A KD cells_Untreated 14D_H3K4me3_ChIPSeq


title: 21950_SCC-25_post-PA 14D_H3K4me3_ChIPSeq

description:
SCC_4_1_21950_GGCTAC
SCC_4_1_21950_GNCTAC
SCC_4_1_21950_NGCTAC


title: 35802_VDH-15_Set1A KD cells_post-PA 14D_H3K4me3_ChIPSeq


title: 35795_VDH-15_control pLKO.1_Untreated 14D_H3K4me3_ChIPSeq


title: 21910_21911_21912_input DNA_SCC25 [re-used 2]

growth_protocol: SCC-25 (ATCCR CRL-168TM) and patient-derived cells (VDH-15) were grown in keratinocyte serum-free media (KSFM, Gibco) supplemented with 5 μg ml–1 penicillin/streptomycin, 0.025 mg ml–1 bovine pituitary extract and 0.2 μg ml–1 hEGF.

treatment_protocol: SCC cells growing in serum–free media were treated in vitro with 50 μM oleic acid for 96 h (4 days) and after palmitic acid withdrawal cells were passaged normally (when reaching 80% confluence) for 14 days and collected for chromatin fixation.


title: 28357_28358_input DNA_VDH15 [re-used]


title: 30892_VDH-15_Untreated 14D_H3K4me3_ChIPSeq

source_name: VDH-15_Untreated 14D_H3K4me3_ChIPSeq


title: 30895_VDH-15_post-OA 14D_H3K4me3_ChIPSeq

source_name: VDH-15_post-OA 14D_H3K4me3_ChIPSeq

value: post-OA 14D


title: 30894_VDH-15_post-OA 14D_H3K4me3_ChIPSeq

value: control pLKO.1


title: 30893_VDH-15_post-OA 14D_H3K4me3_ChIPSeq


title: 30891_VDH-15_Untreated 14D_H3K4me3_ChIPSeq


title: 30899_SCC-25_post-OA 14D_H3K4me3_ChIPSeq

source_name: SCC-25_post-OA 14D_H3K4me3_ChIPSeq


title: 30900_SCC-25_post-OA 14D_H3K4me3_ChIPSeq


title: 21947_SCC-25_Untreated 14D_H3K4me3_ChIPSeq


title: 35803_VDH-15_Set1A KD cells_post-PA 14D_H3K4me3_ChIPSeq


title: 30901_SCC-25_post-OA 14D_H3K4me3_ChIPSeq


title: 30898_SCC-25_Untreated 14D_H3K4me3_ChIPSeq


title: 30890_VDH-15_Untreated 14D_H3K4me3_ChIPSeq


title: 35801_VDH-15_Set1A KD cells_post-PA 14D_H3K4me3_ChIPSeq


title: 30897_SCC-25_Untreated 14D_H3K4me3_ChIPSeq


title: 35798_VDH-15_Set1A KD cells_Untreated 14D_H3K4me3_ChIPSeq


title: 30896_SCC-25_Untreated 14D_H3K4me3_ChIPSeq


title: 28357_28358_input DNA_VDH15


title: 21910_21911_21912_input DNA_SCC25 [re-used]


title: 28356_VDH-15_H3K4me1_ChIPSeq

source_name: VDH-15_post-PA 14D_H3K4me1_ChIPSeq

value: H3K4me1 (Abcam, ab8895)


title: 28355_VDH-15_H3K4me1_ChIPSeq

value: oral squamous cell carcinoma (OSCC) cell line


title: 28354_VDH-15_H3K4me1_ChIPSeq


title: 21948_SCC-25_Untreated 14D_H3K4me3_ChIPSeq


title: 28351_VDH-15_H3K4me1_ChIPSeq

source_name: VDH-15_Untreated 14D_H3K4me1_ChIPSeq


title: 28353_VDH-15_H3K4me1_ChIPSeq


title: 21908_SCC-25_H3K4me1_ChIPSeq

source_name: SCC-25_post-PA 14D_H3K4me1_ChIPSeq


title: 28352_VDH-15_H3K4me1_ChIPSeq


title: 21909_SCC-25_H3K4me1_ChIPSeq


title: 21907_SCC-25_H3K4me1_ChIPSeq


title: 21906_SCC-25_H3K4me1_ChIPSeq

source_name: SCC-25_Untreated 14D_H3K4me1_ChIPSeq


title: 21910_21911_21912_input DNA_SCC-25


title: 21905_SCC-25_H3K4me1_ChIPSeq


title: 30126_H3K27me3_ChIPSeq

value: H3K27me3 (Abcam,  ab6002)


title: 30125_H3K27me3_ChIPSeq


title: 30119_H3K27me3_ChIPSeq


title: 30118_H3K27me3_ChIPSeq


title: P8_PA14_P2759_N715.S507

description:
processed data file: P2759.tsv
CD2ALANXX_4_N715-S507-NX-xt

data_processing:
Reads were then demultiplexed according to the cell barcodes
Sequenced reads were filtered for low-complexity or low-quality sequence.
High quality reads were mapped according to the GEM pipeline
Genome_build: Human:  GRCh38
Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing gene expression values as read counts

extract_protocol:
Live SCC-25 sorted cells were lysed using lysis buffer (0.2% Triton-100, 1U/ul RNase inhibitor). Reverse transcription was performed using SuperScript II (ThermoFisher Scientific) in the presence of 1 μM oligo-dT30VN (IDT), 1 μM template-switching oligonucleotides (QIAGEN), and 1 M betaine.
Libraries were prepared according to the Nextera XT (Illumina) instructions.

treatment_protocol: Cells growing in serum–free media were treated in vitro with 300 μM palmitic acid for 96 h (4 days) and after palmitic acid withdrawal cells were passaged normally (when reaching 80% confluence) for 14 days and collected for sorting of live SCC-25 cells into 96 well sorting plates.

tag: protocol

value: Smart-seq2; full-length RNA-seq


title: P8_PA14_P2759_N715.S508

description:
processed data file: P2759.tsv
CD2ALANXX_4_N715-S508-NX-xt


title: P8_PA14_P2759_N715.S505

description:
processed data file: P2759.tsv
CD2ALANXX_4_N715-S505-NX-xt


title: P8_PA14_P2759_N715.S503

description:
processed data file: P2759.tsv
CD2ALANXX_4_N715-S503-NX-xt


title: P8_PA14_P2759_N715.S510

description:
processed data file: P2759.tsv
CD2ALANXX_4_N715-S510-NX-xt


title: P8_PA14_P2759_N714.S508

description:
processed data file: P2759.tsv
CD2ALANXX_4_N714-S508-NX-xt


title: P8_PA14_P2759_N714.S511

description:
processed data file: P2759.tsv
CD2ALANXX_4_N714-S511-NX-xt


title: P8_PA14_P2759_N714.S510

description:
processed data file: P2759.tsv
CD2ALANXX_4_N714-S510-NX-xt


title: P8_PA14_P2759_N715.S502

description:
processed data file: P2759.tsv
CD2ALANXX_4_N715-S502-NX-xt


title: P8_PA14_P2759_N714.S507

description:
processed data file: P2759.tsv
CD2ALANXX_4_N714-S507-NX-xt


title: P8_PA14_P2759_N714.S505

description:
processed data file: P2759.tsv
CD2ALANXX_4_N714-S505-NX-xt


title: P8_PA14_P2759_N714.S506

description:
processed data file: P2759.tsv
CD2ALANXX_4_N714-S506-NX-xt


title: P8_PA14_P2759_N714.S503

description:
processed data file: P2759.tsv
CD2ALANXX_4_N714-S503-NX-xt


title: 21904_SCC-25_H3K4me1_ChIPSeq


title: P8_PA14_P2759_N714.S502

description:
processed data file: P2759.tsv
CD2ALANXX_4_N714-S502-NX-xt


title: P8_PA14_P2759_N712.S511

description:
processed data file: P2759.tsv
CD2ALANXX_4_N712-S511-NX-xt


title: 30124_H3K27me3_ChIPSeq


title: P8_PA14_P2759_N715.S511

description:
processed data file: P2759.tsv
CD2ALANXX_4_N715-S511-NX-xt


title: P8_PA14_P2759_N712.S507

description:
processed data file: P2759.tsv
CD2ALANXX_4_N712-S507-NX-xt


title: P8_PA14_P2759_N712.S508

description:
processed data file: P2759.tsv
CD2ALANXX_4_N712-S508-NX-xt


title: P8_PA14_P2759_N712.S510

description:
processed data file: P2759.tsv
CD2ALANXX_4_N712-S510-NX-xt


title: P8_PA14_P2759_N712.S506

description:
processed data file: P2759.tsv
CD2ALANXX_4_N712-S506-NX-xt


title: P8_PA14_P2759_N715.S506

description:
processed data file: P2759.tsv
CD2ALANXX_4_N715-S506-NX-xt


title: P8_UN14_P2759_N711.S511

description:
processed data file: P2759.tsv
CD2ALANXX_4_N711-S511-NX-xt


title: Empty_P2759_N712.S502

description:
processed data file: P2759.tsv
CD2ALANXX_4_N712-S502-NX-xt

source_name: Empty


title: P8_PA14_P2759_N712.S505

description:
processed data file: P2759.tsv
CD2ALANXX_4_N712-S505-NX-xt


title: P8_PA14_P2759_N712.S503

description:
processed data file: P2759.tsv
CD2ALANXX_4_N712-S503-NX-xt


title: P8_UN14_P2759_N711.S510

description:
processed data file: P2759.tsv
CD2ALANXX_4_N711-S510-NX-xt


title: P8_UN14_P2759_N711.S508

description:
processed data file: P2759.tsv
CD2ALANXX_4_N711-S508-NX-xt


title: P8_UN14_P2759_N711.S507

description:
processed data file: P2759.tsv
CD2ALANXX_4_N711-S507-NX-xt


title: P8_UN14_P2759_N710.S511

description:
processed data file: P2759.tsv
CD2ALANXX_4_N710-S511-NX-xt


title: P8_UN14_P2759_N711.S502

description:
processed data file: P2759.tsv
CD2ALANXX_4_N711-S502-NX-xt


title: P8_UN14_P2759_N710.S506

description:
processed data file: P2759.tsv
CD2ALANXX_4_N710-S506-NX-xt


title: P8_UN14_P2759_N710.S505

description:
processed data file: P2759.tsv
CD2ALANXX_4_N710-S505-NX-xt


title: P8_UN14_P2759_N710.S508

description:
processed data file: P2759.tsv
CD2ALANXX_4_N710-S508-NX-xt


title: P8_UN14_P2759_N710.S503

description:
processed data file: P2759.tsv
CD2ALANXX_4_N710-S503-NX-xt


title: P8_UN14_P2759_N710.S510

description:
processed data file: P2759.tsv
CD2ALANXX_4_N710-S510-NX-xt


title: P8_UN14_P2759_N711.S506

description:
processed data file: P2759.tsv
CD2ALANXX_4_N711-S506-NX-xt