title: MSTO 211H AGS treated_biological rep 2

type: RNA

city: Napoli

first: Stefania

last: Crispi

address: Via Pietro Castellino,111

department: DISBA

hyb_protocol: Total RNA was converted in labelled ssDNA and used to hybridize microarrays. All the procedures including wash and staining of array were performed following the manufacturer's instructions. Hybridization was performed by incubation with rotation at 60 rpm for 16 hours at 45°C.

scan_protocol: Clariom S arrays were scanned using the GeneChip™ Scanner 3000 7G using AGCC ( Affymetrix® GeneChip® Command Console®) software

data_processing: Samples data registration and primary analisys was performed using AGCC. After laser scanning .CEL files from array were used for data analysis. Primary data analysis was performed with the Transcriptome Analysis Console software (Thermofisher version 4.0) including the Robust Multiarray Average module for normalization. Differentially expressed genes were selected applying as cut-off criteria log2-fold change ≥+/−2 and a P-value≤0.05 comparing AGS treated cells to CTRL untreated cells.

label: Biotin

source_name: MSTO-211H cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Applied Biosystem protocol from 100 ng total RNA (Whole Transcript Expression Array User Guide).

growth_protocol: Cells were grown in RPMI 1640 at 37°C with 5% CO2

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

treatment_protocol: Cells were treated with AGS (350 micrograms/ml) or with vehicle (0.1% DMSO) for 48 hours with a double administration at 24 and 48 hours. After cells were detached collected and placed in Trizol for RNA extreaction

value: mesothelioma cells

tag: agent

value: AGS (350 micrograms/ml)


title: Torpor+radiation 1

status: Public on Jan 25 2023

type: SRA

city: Belfast

first: Thomas

last: Cahill

address: 19 Chlorine Gardens

country: United Kingdom

institute: Queens university Belfast

library_source: transcriptomic

data_processing:
Sequence quality was assessed with FastQC to identify over-represented sequences and low quality reads
Low quality reads and over-represented sequences were removed with Cutadapt
The STAR aligner was utilised to align the RNA-Seq reads to the zebrafish genome (GRCz11)
HTSeq was used to determine the number of reads per transcript
DESeq2 was used for determination of differentially expressed genes
Assembly: zebrafish genome (GRCz11)
Supplementary files format and content: TXT file

molecule: total RNA

organism: Danio rerio

source_name: Liver

extract_protocol:
Total mRNA was extracted from liver tissue of the zebrafish using Qiagen’s miRNeasy Mini kit (Qiagen, Hilden, Germany).
To prepare mRNA-Seq libraries the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA) was utilized; 100ng of total input Liver RNA was used in accordance with the manufacturer’s protocol.
High through-put RNA sequencing (RNAseq) was performed at the Queens University Belfast, Genomics Core Technology Unit on an Illumina Next SEQ 500 instruments with the mRNA library sequenced to a minimum depth of 50 million reads.

treatment_protocol: A melatonin group (28.5- melatonin) received melatonin daily for 10 days at a concentration of 24 µM for 10 days to reduce locomotion and arousal. A reduced temperature group (18.5-Ctrl) received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group (18.5-mel) was established with a 10°C reduction in ambient temperature and the addition of 24 µM melatonin. A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.

tag: radiation (cgy)

tag: temperature (c)

tag: melatonin (um)


title: Control 2


title: WT-3

city: Seoul

first: Zeeshan

last: Nasim

address: Anam-ro 145, Seongbuk-Gu

department: School of Life Sciences and Biotechnology

country: South Korea

institute: Korea University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and differentially expressed genes were identified using TopHat2-Cufflinks pipeline
Genome_build: TAIR 10
Supplementary_files_format_and_content: TPM values for each sample, in excel file

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Plant were grown  at 16°C under long day conditions on 1/2 strength MS

extract_protocol:
Total RNA was extracted using trizol reagent
Library were prepared by BGI for DNA nanoball (DNB) sequencing

treatment_protocol: Growth temperature of 16°C

tag: developmenta stage

tag: ecotype

tag: genotype

value: WT

tag: protocol

value: 16°C grown

tag: tag


title: 48hrAPF_Female_rep 1

city: Tallahassee

first: Michelle

middle: N

last: Arbeitman

state: Florida

address: 1115 W. Call Street

department: Department of Biomedical Sciences

country: USA

institute: Florida State University

data_processing:
Raw reads were processed using the CellRanger software pipeline (v.3.0.2) “cellranger count” command to align reads to the Drosophila melanogaster (BDGP6.92) STAR reference genome, customized to contain the sequence for the mCD8-GFP cDNA and generate a multidimensional feature-barcode matrix for each replicate.
Genome_build: Drosophila melanogaster (BDGP6.92)
Supplementary_files_format_and_content: feature-barcode matrix

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Central nervous system

growth_protocol: Pupae were sex-sorted at white pre-pupal stage and aged to 48hr after Puparium formation (APF) on Bromophenol blue agar plates at 25˚C on a 12 hour light and 12 hour dark cycle.

extract_protocol:
The tissue was dissected and dissociated as previously described in Brovero et al. 2020. GFP positive cells (fru P1-expressing cells) were separated using fluorescent activated cell sorting (FACS) with a FACSAria SORP with BD FACSDiva software.
Libraries were prepared following the 10x Chromium Single Cell 3’ Reagent Kits v3 User Guide using 12 PCR cycles for cDNA amplification and 16 PCR cycles for sample indexing.

treatment_protocol: Twenty 48hr after pupal formation (APF, +/- 1hr) sex-sorted flies were collected for fru P1 single cell experiments for each replicate Flies were collected and sex sorted at the white prepupal stage for appropriate aging to 48hr APF.

tag: Sex

value: Female


title: WT-1


title: Radiation 1


title: Torpor+radiation 2


title: smk7a_12D_bio rep1

city: beijing

first: xiaojiao

last: Hu

address: No.12 Zhongguancun South Main Street, Haidian District

country: China

institute: Institute of crop science, Chinese academy of agricultural science

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and   the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the maize reference genome RefGen_V4 (ftp://ftp.ensemblgenomes.org/pub/plants/release-32/gff3/zea_mays/) using HISAT2
The gene expression levels were estimated using the fragments per kilobase of the transcript per million fragments (FPKM) mapped
Supplementary files format and content: FPKM value of expressed genes for all samples

organism: Zea mays

source_name: maize kernels

extract_protocol:
The total ribonucleic acid (RNA) was isolated from the kernels of WT and smk7a collected at 12 and 20 DAP using a RNA Easy Fast Extraction Kit (DP452, Tiangen, Beijing, China)
RNA libraries for RNA-seq were prepared using a TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions

tag: tissue

value: maize kernels

tag: development stages

value: kernels 12 days after polination

tag: time

value: 12 DAP


title: smk7a_12D_bio rep2


title: WT_12D_bio rep1


title: D10_355: D10 TTNtv/+ AMG3360355 treated CMW

city: SOUTH SAN FRANCISCO

first: Tracy

last: Yamawaki

state: California

address: 1120 VETERANS BLVD.

institute: AMGEN, INC.

data_processing:
reads were aligned and count tables generated using cellranger v 4.0.0
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: barcode tsv files include cellbarcodes, features tsv files include gene identifiers, matrix files are the cell by gene count table encoded as a sparse matrix in the Market Exchange Format (MEX)

organism: Homo sapiens

source_name: cardiac microwire culture

growth_protocol: 300  μl  of  CMW  maintenance mediumcontaining DMEM/F12, 2% fetal bovine serum, 10 μg/ml insulin and 1xantibiotic/antimycotic (all from ThermoFisher)was gently added to each well for continuous culturing. Medium is changed every 2-3 days by very slowly removing halfof medium from the side of the well at half-way heightand through the drop-wise addition of halfof fresh CMW maintenance medium.

extract_protocol:
cardiac microwires were dissociated into a single cell suspension and encapsulated with the 10x Chromium
Samples were processed using the 10x Genomics 3'v3 kit

treatment_protocol: 14 days

value: cardiac microwire culture

tag: treatment

value: TTNtv/+


title: D8_355: D8 TTNtv/+ AMG3360355 treated CMW


title: anthraquinone rep3

status: Public on Jan 24 2023

city: Barcelona

first: Sara Nienke

last: Jiménez Volkerink

address: Av Diagonal 643

department: Genetics, Microbiology and Statistics

country: Spain

institute: University of Barcelona

data_processing:
read quality checking with FastQC v.0.11.8
read trimming with Trimmomatic v.0.38
mapping to reference genome with bwa-mem v.0.7.17
quality of mapping with flagstat command of samtools v.1.9
quantification of mapped reads with featureCounts of the Subread package v.2.0.1
generation of normalized abundance measurements with DESeq2
Assembly: Sphingobium sp. AntQ-1 genome
Supplementary files format and content: tab-delimited tabular file with normalized gene counts for every gene and every sample
Supplementary files format and content: tab-delimited tabular file with differential gene expression analysis between both growth conditions

organism: Sphingobium sp. AntQ-1

source_name: bacterial cells

growth_protocol: Cells were grown in liquid mineral medium supplemented with vitamin B12 containing either anthraquinone or acetate as sole carbon sources until mid exponential phase, at 150 rpm and 25ºC.

extract_protocol:
Cells were harvested by centrifugation and snap-frozen. Total RNA was extracted combining the Trizol  reagent (Invitrogen) and the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene.

value: Anthraquinone


title: anthraquinone rep1


title: acetate rep2

value: Acetate


title: D8_2: D8 TTNtv/+ CMW


title: smk7a_20D_bio rep3

value: kernels 20 days after polination

value: 20 DAP


title: smk7a_12D_bio rep3


title: HMCP_DNMT_WT_EpiLC_D2_rep2

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

institute: The Babraham Institute

library_source: genomic

data_processing:
HMCP-seq libraries were sequenced as 75 base single-end runs on an Illumina NextSeq500 instrument. Quality and adapter trimming were performed using Trim Galore v0.6.5 (using Cutadapt v2.3). Mapping to the mouse reference genome (GRCm38) was performed using Bowtie2 v2.4.1.
Assembly: GRCm38
Supplementary files format and content: HMCP_2kb.tiles_log2RPKM.txt: rows are 2 kb tiles across the genome, columns are quantitated samples as log2 RPKM
Library strategy: HMCP (5hmC pulldown and sequencing)

molecule: genomic DNA

organism: Mus musculus

source_name: EpiLC

extract_protocol:
10 ng of genomic DNA was fragmented to an average length of 150 bp using a Covaris E220 sonicator.
HMCP-seq was performed using a kit (provided by Cambridge Epigenetix) according to manufacturer's instructions.

tag: cell type

value: EpiLC


title: HMCP_DNMT_WT_EpiLC_D2_rep3


title: MSTO 211H AGS treated_biological rep 3

country: Italy

institute: CNR


title: HMCP_TET_WT_EpiLC_D1_rep3


title: anthraquinone rep2


title: HMCP_TET_WT_EpiLC_D2_rep1


title: HMCP_TET_WT_EpiLC_D1_rep2


title: HMCP_TET_WT_ESC_D0_rep2

source_name: ESC

value: ESC


title: acetate rep3


title: D10: D10 TTNtv/+ CMW


title: MSTO 211H AGS treated_biological rep 1


title: Tempo-iMG™ microglia cells, scRNAseq

city: Cleveland

first: Konstantin

last: Leskov

state: OHIO

address: 2109 Adelbert Rd, Wood W200

department: Molecular Biology and Microbiology

institute: Case Western Reserve University School of Medicine

description:
Tempo-iMG™ microglia cells
BD Rhapsody

library_source: transcriptomic single cell

data_processing:
The merging of scRNAseq and scABseq fastq files, barcoded processing, mapping, gene counting and aggregation were made using the BD Rhapsody bioinformatics pipeline at www.sevenbridges.com
Assembly: GRCh38
Supplementary files format and content: Comma-separated values (csv) tables, gene expression matrices
Supplementary files format and content: uninfectedMglia_iPSC_pseudobulk.csv: this file contains the sums of all counts for each gene in the scRNA-seq raw data from the file Un_DBEC_MolsPerCell_Unfiltered.csv.gz

source_name: Brain

extract_protocol:
Single cell capturing was performed according to the manufacter’s instructions (BD Rhapsody). Briefly, cells were captured in microwells (~0.5 million cells) were pre-treated with Human Fc block (BD, Catalog # 564219) for 10 min at room temperature, then incubated on ice for 40 min with a cocktail of oligo-indexed antibodies to 41 surface marker proteins. The cocktail included 30 antibodies from the BD ABseq Immune Discovery panel (BD,Catalog # 625970) supplemented with 11 antibodies to microglia-specific antigens as prescribed by the manufacturer (see table below). After a total of three washes with BD Stain buffer (Catalog # 554656), cells were applied to the cartridge of the BD Rhapsody system for single-cells RNAseq/ABseq and captured with barcoded beads.
Library preparation was performed according to the manufacter’s instructions (WTA and ABseq protocols, BD Rhapsody). After single cell capturing with barcoded beads, we performed reverse transcription, library indexing PCR and generated Whole Transcriptome and ABseq libraries. Sequencing was performed at Medgenome, Inc. using the Illumina HiSeq X system, PE150.

value: iPSC-derived microglia cells

value: Brain


title: acetate rep1


title: Control 1


title: HMCP_TET_WT_ESC_D0_rep1


title: Spinal Cord, T-Cell Transferred, Infected, Rep3

city: Los Angeles

first: Shaohui

last: Wang

state: CA

address: 8700 Beverly BLVD

department: Surgery

institute: Cedars Sinai Medical Center

data_processing:
Raw sequencing data was demultiplexed and converted to fastq format by using bcl2fastq v2.20
Reads were aligned to the transcriptome using STAR (version 2.6.1) [44] and RSEM (version 1.2.28) [45] with default parameters
Customed mouse GRCm38 transcriptome reference was based on mouse GENCODE version 24 annotation and HSV gene (MN136524)
Assembly: mm10
Supplementary files format and content: CSV files include counts values for each Sample

source_name: Spinal Cord

extract_protocol:
Total RNA from brain and spinal cord of infected mice were isolated using   Rneasy mini plus kit (Qiagen).
library was prepared using the Nextera XT Library Preparation kit

treatment_protocol: Mice were infected by HSV-1 VIL2, tissue were harvested at day14 PI

value: Spinal Cord

value: T Cell Transferred and HSV-1 VIL2 infected


title: MSTO 211H untreated_biological rep 1

value: mesothelioma cells

value: vehicle


title: HMCP_DNMT_WT_EpiLC_D2_rep1


title: HMCP_TET_WT_EpiLC_D2_rep2


title: HMCP_TET_WT_ESC_D0_rep3


title: Spinal Cord, T-Cell Transferred, Infected, Rep1


title: MSTO 211H untreated_biological rep 3


title: Tempo-iMG™ microglia cells, scABseq

description:
Tempo-iMG™ microglia cells
BD Rhapsody

library_source: other

data_processing:
The merging of scRNAseq and scABseq fastq files, barcoded processing, mapping, gene counting and aggregation were made using the BD Rhapsody bioinformatics pipeline at www.sevenbridges.com
Assembly: GRCh38
Supplementary files format and content: Comma-separated values (csv) tables, gene expression matrices
Supplementary files format and content: uninfectedMglia_iPSC_pseudobulk.csv: this file contains the sums of all counts for each gene in the scRNA-seq raw data from the file Un_DBEC_MolsPerCell_Unfiltered.csv.gz
Library strategy: scAB-seq

molecule: other


title: Spinal Cord, Infected, Rep2

value: HSV-1 VIL2 infected


title: MSTO 211H untreated_biological rep 2


title: Conjunctiva_B6J_normal

city: La Jolla

first: Tomoaki

last: Ando

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

hyb_protocol: The biotinylated cRNA was hybridized to arrays at 45℃ for 16 hours.

scan_protocol: The arrays were washed and stained using wash and stain kit on the Affymetrix Fluidics Station 450 (Affymetrix).

data_processing: The data were normalized with the SST-RMA algorism using a Transcriptome analyses console (Affymetrix) software.

label: biotin

source_name: B6J naïve conjunctiva

label_protocol: The total RNA (330 ng) was used to synthesize cRNA with a GeneChip WT Amplification Kit. The cDNA was fragmentated and labeled with a GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: The mice were raised in the same animal room until 6 weeks old.

extract_protocol: Total RNA was extracted from conjunctival tissue using TRI reagent (Molecular Research Center, Inc.) and RNeasy Mini Kit (Qiagen). Three samples for each strain were pooled at the equal RNA amount. The quality of total RNA was analyzed using a TapeStation (Agilent).

treatment_protocol: No treatment was performed.

value: Conjunctiva

tag: strain

value: female

tag: age

value: 6 weeks


title: Spinal Cord, Control, Rep3

value: Mock treated


title: HMCP_TET_WT_EpiLC_D2_rep3


title: Conjunctiva_Balbc_normal

source_name: Balb/c naïve conjunctiva

value: Balb/c


title: Brain, Infected, Rep1


title: Brain, T-Cell Transferred, Infected, Rep3


title: Spinal Cord, Control, Rep2


title: Brain, Control, Rep2


title: Brain, Control, Rep1


title: Spinal Cord, T-Cell Transferred, Infected, Rep2


title: Spinal Cord, Control, Rep1


title: Brain, T-Cell Transferred, Infected, Rep2


title: Spinal Cord, Infected, Rep3


title: Brain, Infected, Rep3


title: Brain, Infected, Rep2


title: Brain, T-Cell Transferred, Infected, Rep1


title: Spinal Cord, Infected, Rep1


title: Sost_cre, scRNAseq

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

description:
Sost-CreERT2-Cre+ mice (8 weeks).
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Long bone (femurs, tibiae, and humeri)

extract_protocol:
Bone extracted cells were then centrifuged at 600 rpm for 15 minutes at 4°C, washed 3 times and the pellet resuspended in αMEM supplemented with 10% FBS. TdTomato+ cells were then sorted using Fluorescence-activated cell sorting (FACS) Aria Fusion (BD Biosciences). TdTomato- cells were used as negative control for the sorting procedure.
Library was performed according to the manufacturer’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriate sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Long bone (femurs, tibiae, and humeri)

value: TdTomato positive cells


title: HSPC from myelodysplastic syndrome patient 3

city: Dublin

first: Marina

last: Ainciburu

state: Dublin

address: Foster Avenue

department: Bioinformatics

country: Ireland

institute: NIBRT

data_processing:
Demultiplexing, alignment to the hg38 genome and quantification was carried out with Cellranger (v2.1 and v3.1)
Posterior analysis (quality control, clustering, integration and differential expression) was performed with Seurat v3
Assembly: hg38
Supplementary files format and content: HDF5 Feature Barcode matrices

source_name: HSPC

extract_protocol:
Cells were sorted from bone marrow aspirates.
Single cell 3' RNA sequencing libraries were prepared using the chromiun controller from 10X Genomics. NEXTGEM Single Cell 3' Reagent Kits v2 and v3.1  were used.

value: Bone marrow

tag: condition

value: Patient with MDS

tag: facs gating

tag: reagent kit version

tag: cellranger version


title: Btg1 Q36H and CREneg Germinal Center B cells (mixed samples), scRNA-seq

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

description:
Pooled Data:
CREneg GCB Comp 1
CREneg GCB Comp 2
CREneg GCB Comp 3
Q36H GCB Comp 1
Q36H GCB Comp 2
Q36H GCB Comp 3
Please note that the raw files for this set of samples includes data for additional samples unused in this study.

data_processing:
Seven Bridges Rhapsody Analysis Pipeline version 1.0 (revision 5)
Seven Bridges Rhapsody pipeline trimmed adaptor sequences and identified UMI and cellular barcodes. R1 contains the cell barcode. Please see the file "barcode_location.txt" for an explanation of the barcode composition.
Seven Bridges Rhapsody pipeline aligned sequences to a reference file containing the sequences of targeted genes
Seven Bridges Rhapsody pipleine filtered reads based on RSEC UMI adjustment
Further analysis done in R 3.6.0 with Seurat 3.0.2 and slingshot 1.20
Genome_build: Seven Bridges Rhapsody pipleine filtered reads based on DBEC UMI adjustment
Supplementary_files_format_and_content: Matrix of gene counts per cell in csv format

source_name: GC B Cells

extract_protocol:
Cells were sorted into BD stain buffer. An average of 20K cells per mouse, with a Q36H:CREneg ratio of 70:30 was subjected to single cell RNA-seq using the BDRhapsody platform.  Library preparation for single cell, sequencing and post-processing of the raw data was performed at Weill Cornell Medicine. Libraries were prepared according to BD Rhapsody specifications.
BD Rhapsody pooled single cell RNA-seq

treatment_protocol: a 50:50 mixture of Btg1Q36H and CREneg control resting B cells were transferred into WT recipient mice and immunized the next day with NP-OVA in alum. 10 days after immunization, GCB B cells were sorted from draining lymph nodes

value: GC B Cells

value: mixed sample (non-demultiplexed) representing CREneg Control and Btg1 Q36H; CD19Cre


title: HSPC from myelodysplastic syndrome patient 1


title: HSPC from myelodysplastic syndrome patient 2


title: HSPC from myelodysplastic syndrome patient 4


title: Calu3-Onv

city: San Diego

first: Peter

last: Croucher

address: 11055 Flintkote Avenue

institute: Cardiff Oncology Inc

data_processing:
Raw fastq files were pseudo-mapped to GRCh38.p12 (Gencode v29) using Salmon v0.14
Salmon transcript counts were converted to genes using tximport (v1.18)
Genes were library size factor normalized using DESeq2 (v1.30)
Assembly: hg38
Supplementary files format and content: Comma delimited text file containing size factor normalized gene counts for each sample

source_name: Lung

growth_protocol: C4-2, LNCaP, 22Rv1, PSN-1, AU565, HCC1954, and NCIH661 were grown in RPMI-1640 with 10% fetal bovine serum (FBS). LNCaP95 was grown RPMI without phenol red and with 10% charcoal-stripped FBS. Panc 10.05 was grown in RPMI-1640 with 15% FBS, and 10 IU/ml human recombinant insulin. OAW28 was grown in Advanced DMEM with 10% FBS and supplemented with insulin. Cal33 cells were grown in DMEM media with 10% FBS. SK-OV-3 cells were grown in McCoy’s 5A with 10% FBS. MV-4-11 cells were grown in IMDM with 10% FBS. Calu3 cells were grown in MEM with 10%FBS. OCI-AML-3 cells were grown in MEM with 20% FBS. KYSE450 cells were grown in 1:1 RPMI:Ham’s F12 with 2% FBS.

extract_protocol:
Total RNA was isolated using the NucleoSpin RNA Plus Mini Kit (Macherey-Nagel) according to the manufacturer's recommendations.
RNA sequencing libraries were prepared using 400 ng of total RNA using the Kapa mRNA Hyperprep kit (Roche) according to the manufacturer’s recommendations and at 1/3rd reaction volume using 14 cycles of PCR. Libraries were analyzed using the Fragment Analyzer and quantified by qPCR prior to pooling and sequencing with the Illumina NextSeq 500 System generating 75 nt single end reads.

treatment_protocol: Cells were plated in 6-well plates and the indicated drugs were added the following day. After 16 hours drug treatment, cells were collected for isolation of total RNA.

value: Lung

tag: cell line

value: Lung Cancer

value: 75 nM onvansertib

value: 16 hours


title: NCIH661-Onv

value: 20 nM onvansertib


title: Calu3-Abi

value: 2.5 uM abiraterone acetate


title: Brain, Control, Rep3

value: Brain


title: NCIH661-AbiOnv

value: 5 uM abiraterone acetate and 20 nM onvansertib


title: Calu3-AbiOnv

value: 2.5 uM abiraterone acetate and 75 nM onvansertib


title: Control 53 [C53]

type: genomic

city: Glostrup

first: Mathis

last: Hildonen

state: Denmark

address: Gamle Landevej 7

department: Department of Clinical Genetics

country: Denmark

institute: Rigshospitalet

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Human Methylation Beadchip using the standard Illumina protocol.

scan_protocol: Arrays were imaged using an iScan instrument with standard settings.

data_processing:
Methylation data (internal cohort 1, IC1) was imported to R together with methylation data from two other datasets: 19 Kabuki samples and 57 controls from GSE97362 (public cohort, PC) and 12 Kabuki samples and 13 controls from an internal dataset for which data could not be made public due to ethical constraints (internal cohort 2, IC2).  The data was combined to 450k data using the combineArrays function and quantile normalized using minfi (v.1.38.0). M-values were generated, and a machine learning classifier for Kabuki syndrome was constructed using the m-values from 153 CpG-sites constituting an episignature for Kabuki syndrome (Aref-Eshghi et al. 2020). Data from GSE97362 and IC2 was used for training the classifier, and the classifier was verified using the data from internal cohort 1 (IC1).
Beta values and detection P-values

label: Cy3 and Cy5

source_name: Whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from whole blood using standard procedures

value: Whole blood

tag: disease state

value: Control


title: Control 52 [C52]


title: Calu3-DMSO

value: DMSO


title: Control 55 [C55]


title: Control 51 [C51]


title: Control 54 [C54]


title: NCIH661-Abi

value: 5 uM abiraterone acetate


title: NCIH661-DMSO


title: Control 50 [C50]


title: Control 48 [C48]


title: PSN1-Onv

source_name: Pancreas

value: Pancreas

value: Pancreatic Cancer


title: Control 49 [C49]


title: Panc1005-Onv

value: 30 nM onvansertib


title: Panc1005-DMSO


title: HCC1954-Abi

source_name: Breast

value: Breast

value: Her2+ Breast Cancer


title: Control 46 [C46]


title: PSN1-DMSO


title: PSN1-AbiOnv

value: 10 uM abiraterone acetate and 20 nM onvansertib


title: Panc1005-Abi

value: 10 uM abiraterone acetate


title: HCC1954-DMSO

value: 16 hours


title: Control 44 [C44]


title: Control 47 [C47]


title: AU565-AbiOnv

value: 10 uM abiraterone acetate and 15 nM onvansertib


title: PSN1-Abi


title: Panc1005-AbiOnv

value: 10 uM abiraterone acetate and 30 nM onvansertib


title: HCC1954-AbiOnv

value: 5 uM abiraterone acetate and 15 nM onvansertib


title: Control 40 [C40]


title: Control 45 [C45]


title: Control 39 [C39]


title: Control 37 [C37]


title: Control 43 [C43]


title: AU565-Onv

value: 15 nM onvansertib


title: Control 42 [C42]


title: Control 38 [C38]


title: Control 36 [C36]


title: AU565-DMSO


title: OAW28-AbiOnv

source_name: Ovary

value: Ovary

value: Ovarian Cancer


title: Control 35 [C35]

value: Whole blood

value: Control


title: OAW28-Onv


title: AU565-Abi


title: OAW28-Abi

value: 5 uM abiraterone acetate


title: Control 34 [C34]


title: Control 31 [C31]


title: Control 30 [C30]


title: Control 33 [C33]


title: Control 29 [C29]


title: OAW28-DMSO

value: DMSO


title: HCC1954-Onv


title: SKOV3-Abi


title: Control 27 [C27]


title: SKOV3-AbiOnv


title: Control 28 [C28]


title: Control 32 [C32]


title: SKOV3-Onv


title: Control 26 [C26]


title: KYSE450-AbiOnv

source_name: Esophagus

value: Esophagus

value: Head and neck squamous cell carcinoma

value: 5 uM abiraterone acetate and 20 nM onvansertib


title: SKOV3-DMSO


title: Control 25 [C25]


title: KYSE450-Onv

value: 20 nM onvansertib


title: Control 24 [C24]


title: Control 23 [C23]


title: Cal33-Onv

source_name: Tongue

value: Tongue


title: Control 22 [C22]


title: Control 21 [C21]


title: Cal33-Abi


title: Control 20 [C20]


title: Cal33-DMSO


title: KYSE450-Abi


title: Control 19 [C19]


title: Cal33-AbiOnv


title: Control 17 [C17]


title: Control 16 [C16]


title: Control 18 [C18]


title: Control 15 [C15]


title: OCIAML3-AbiOnv

source_name: Myeoloblast

value: Myeoloblast

value: Acute myeloid leukemia

value: 10 uM abiraterone acetate and 20 nM onvansertib


title: MV411-Abi

value: 10 uM abiraterone acetate

value: 16 hours


title: MV411-Onv


title: OCIAML3-DMSO


title: Control 13 [C13]


title: OCIAML3-Abi


title: MV411-AbiOnv


title: MV411-DMSO


title: LNCaP95-EnzOnv-3

source_name: Prostate

value: Prostate

value: AR-v7+ castrate-resistant prostate cancer

value: 20 uM enzalutamide and 15 nM onvansertib


title: cord blood sampling 3 (E3732)

city: Fuzhou

first: Hailong

last: Huang

state: Fujian

address: No.18 Daoshan Road, Gulou District

institute: Fujian Maternity and Child Health Hospital

description: Hybridized to CytoScan 750K

hyb_protocol: DNA was processed as follows. Restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer`s instructions.

scan_protocol: The arrays were then washed using Affymetrix Fluidics Stations, and scanned using the GeneChip Scanner 750K

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console (AGCC version 4.0.0.1567). Data processing and analysis (CEL file generation, smoothing and segmentation) were used Chromosome Analysis Suite (version 3.3).
Copy number variation status (CNV)

source_name: cord blood sampling 3

label_protocol: As per manufacturer (Affymetrix) protocol

extract_protocol: Genomic DNA of fetal cells in amniotic fluid or cord blood sampling was extracted with using the QIAamp DNA extraction kit (Qiagen, Dusseldorf, Germany)

value: cord blood sampling

tag: diagnosis


title: Control 14 [C14]

value: Whole blood

value: Control


title: liver, starved, 72 days, C6

city: Shanghai

first: Xiaozhao

last: Han

address: 999 Huchengring Road

institute: Shanghai Ocean University

data_processing:
Raw data (raw reads) of fastq format were firstly processed to filter out low quality reads and obtain the clean reads using Trimmomatic
The clean reads were mapped to the Korean rockfish genome using HISAT2.
FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeq count.
An adjusted p-value (q-value < 0.05) and fold change (FC) ratio (|log2FC| ≥ 1) were used to determine the differentially expressed genes.
Assembly: the reference genome has been deposited at CNSA(CNGB Nucleotide Sequence Archive) under the accession ID CNP0000222. The assembled genome can be obtained by assembly ID CNA0000824.
Supplementary files format and content: tab-delimited text files include clean_data_summary
Supplementary files format and content: tab-delimited text files include counts_anno
Supplementary files format and content: tab-delimited text files include DEG_combinded_nofiltered
Supplementary files format and content: tab-delimited text files include FPKM_anno
Supplementary files format and content: tab-delimited text files include genome_mapping_stat

organism: Sebastes schlegelii

source_name: liver

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The libraries were sequenced on an Illumina HiSeq X Ten platform and paired-end reads were generated.

value: liver

value: starved, 72 days


title: cord blood sampling (20201012)

description: Hybridized to CytoScan 750K

source_name: amniotic fluid fetal cells


title: liver, starved, 72 days, E6


title: Control 12 [C12]


title: KYSE450-DMSO

value: Esophagus

value: Head and neck squamous cell carcinoma

value: DMSO


title: LNCaP95-Enz-3

value: 20 uM enzalutamide


title: LNCaP95-EnzOnv-2


title: liver, feeding, 72 days, E1

value: feeding, 72 days


title: cord blood sampling 3 (20200902)

description: Hybridized to CytoScan 750K


title: Control 10 [C10]


title: LNCaP95-Enz-1


title: Control 8 [C8]


title: liver, feeding, 72 days, B1


title: LNCaP95-EnzOnv-1


title: LNCaP95-AbiOnv-2

value: 10 uM abiraterone acetate and 15 nM onvansertib


title: LNCaP95-AbiOnv-3


title: amniotic fluid fetal cells (20201207)

description: Hybridized to CytoScan 750K

value: amniotic fluid fetal cells


title: LNCaP95-Enz-2


title: amniotic fluid fetal cells 14 (20201224)

description: Hybridized to CytoScan 750K


title: liver, starved, 72 days, A6


title: LNCaP95-Onv-3

value: 15 nM onvansertib


title: LNCaP95-AbiOnv-1

value: 16 hours


title: liver, feeding, 72 days, D1


title: LNCaP95-Onv-2

value: Prostate


title: ME49_IAA3

city: Indianapolis

first: Michael

middle: James

last: Holmes

state: IN

address: 635 Barnhill Drive

department: Pharmacology & Toxicology

institute: Indiana University School of Medicine

data_processing:
paired end reads were aligned to Toxoplasma gondii genome (ME49 v52) with hisat2 using default settings
counts against protein coding genes were obtained with htseq-count using default settings
differential gene expression was assessed by DESeq2 using default settings
Assembly: Toxoplasma gondii ME49 v52 (toxodb.org)
Supplementary files format and content: RH_counts (tab delimited)
Supplementary files format and content: ME49_counts (tab delimited)

organism: Toxoplasma gondii

growth_protocol: Freshly lysed tachyzoites were innoculated on confluent HFFs, grown for 24 hourst

extract_protocol:
parasites were syringe lysed, filtered through 3um membrane, rinsed in PBS and total RNA was collected with TRIZOL
Libraries were constructed from polyA-enriched RNA using standard Illumina protocols

treatment_protocol: parasites were treated with 500uM IAA or equivalent volume ethanol vehicle for 24 hours

value: tachyzoite

tag: genotype

value: Me49[delta]hxgprt::TUB1:Firefly Luciferase; [delta]ku80::SAG1:CAT,TUB1:TIR1-3FLAG, AP2XII-2^HA-AID

value: 500uM indole-3-acetic acid, 24h


title: LNCaP95-Abi-3

value: AR-v7+ castrate-resistant prostate cancer

value: 10 uM abiraterone acetate


title: ME49_IAA2


title: Control 11 [C11]

value: Whole blood

value: Control


title: LNCaP95-Abi-2


title: Control 9 [C9]


title: LNCaP95-Onv-1


title: Control 6 [C6]


title: ME49_IAA1


title: LNCaP95-DMSO-3


title: Control 5 [C5]


title: Control 41 [C41]


title: ME49_control3

value: ethanol vehicle control


title: LNCaP95-Abi-1


title: LNCaP95-DMSO-2


title: ME49_control2


title: Control 4 [C4]


title: Control 3 [C3]


title: LNCaP95-DMSO-1


title: Control 7 [C7]


title: 22Rv1-EnzOnv-3

value: 10 uM enzalutamide and 20 nM onvansertib


title: 22Rv1-EnzOnv-2


title: ME49_control1


title: 22Rv1-Enz-2

value: 10 uM enzalutamide


title: 22Rv1-EnzOnv-1


title: Control 1 [C1]


title: Control 2 [C2]


title: Kabuki patient 5 [P5]

value: Kabuki syndrome


title: 22Rv1-Enz-3


title: RH_control2


title: 22Rv1-Onv-1

value: 20 nM onvansertib


title: Kabuki patient 7 [P7]


title: RH_IAA2


title: RH_control1


title: 22Rv1-AbiOnv-1

value: 5 uM abiraterone acetate and 20 nM onvansertib


title: 22Rv1-Onv-3


title: 22Rv1-DMSO-1

value: DMSO


title: 22Rv1-DMSO-2


title: Kabuki patient 3 [P3]


title: AP2XII-2_rep3

description:
AP2XII-2_CUTnTAG_peaks.bed
AP2XII-2.bigwig

data_processing:
map to Toxoplasma genome (ME49 v52) with bowtie2 allowing for mate pair dovetailing
call peaks with MACS2 using default settings (without control)
Assembly: ME49 v52 (toxodb.org)
Supplementary files format and content: AP2XII-2 peak file (BED)
Supplementary files format and content: AP2XII-2 binding sites (bigiwig)
Library strategy: CUT&TAG

growth_protocol: Freshly lysed tachyzoites were innoculated on confluent HFFs, grown for 24 hours

extract_protocol:
monolayers were syringe lysed and filtered, cell pellets rinsed with PBS twice
As per manufacturer: CUT&TAG-IT Assay kit, Anti-Rabbit, Active motif, Cat no. 53160


title: 22Rv1-Enz-1


title: Kabuki patient 6 [P6]


title: 22Rv1-AbiOnv-2


title: RH_control3


title: Kabuki patient 4 [P4]


title: AP2XII-2_rep2


title: Kabuki patient 2 [P2]


title: LNCaP-EnzOnv-2

value: LNCaP

value: Androgen-dependent prostate cancer

value: 10 uM enzalutamide and 30 nM onvansertib


title: 22Rv1-Abi-1

value: Prostate

value: 5 uM abiraterone acetate

value: 16 hours


title: RH_IAA1

value: tachyzoite

value: 500uM indole-3-acetic acid, 24h


title: 22Rv1-DMSO-3

value: AR-v7+ castrate-resistant prostate cancer


title: LNCaP-Enz-3


title: RH_IAA3


title: 22Rv1-Onv-2


title: LNCaP-AbiOnv-3

value: 5 uM abiraterone acetate and 30 nM onvansertib


title: 22Rv1-AbiOnv-3


title: 22Rv1-Abi-3


title: LNCaP-AbiOnv-1


title: LNCaP-Onv-2

value: 30 nM onvansertib


title: LNCaP-EnzOnv-3


title: AP2XII-2_rep1


title: untagged_control1

description:
AP2XII-2_CUTnTAG_peaks.bed
control.bigwig


title: Kabuki patient 1 [P1]

value: Whole blood


title: LNCaP-Enz-2

value: 10 uM enzalutamide


title: LNCaP-EnzOnv-1


title: OCIAML3-Onv

value: Myeoloblast

value: Acute myeloid leukemia


title: LNCaP-Onv-1


title: Combination-3

city: Osaka

first: Yosuke

last: Ota

state: Osaka

address: 3-1-98 Kasugade-naka konohanaku

department: Cancer Research Unit

country: Japan

institute: Sumitomo Pharma

hyb_protocol: RNA was lebeled / hybridized with gene specific fluorescent probe using nCounter PanCancer Mouse Immune Profiling kit as descrived in protocol by vendor

scan_protocol: Fluorescent signal was scanned by using nCounter MAX Analysis system as described in protocol by vendor

data_processing: Raw data was normalized by normalization module within nCounter Advanced Analysis 2.0. Probes for normalization were selected based on algolizum within normalization module

source_name: CT26 tumor

growth_protocol: 1x10^6 cells of CT26 were inoculated into dorsal frank in Balb/c mouse. When tumor volume reached 130-170mm^3, mice were assigned to each group.

extract_protocol: total RNA from in vivo CT26 tumors were extracted by using Maxwell RSC simply RNA tissue kit.

treatment_protocol: DSP-0509 was dosed with 5 mg/kg i.v. and anti PD-1 antibody was dosed with 200ug/mouse. Tumors were resected 4 days after dosing.

value: CT26 tumor

value: DSP-0509 + PD-1 antibody


title: 22Rv1-Abi-2


title: LNCaP-Enz-1

value: LNCaP


title: LNCaP-AbiOnv-2

value: Androgen-dependent prostate cancer


title: PD-1-3

label_protocol: RNA was lebeled / hybridized with gene specific fluorescent probe using nCounter PanCancer Mouse Immune Profiling kit as descrived in protocol by vendor

value: PD-1 antibody


title: LNCaP-Onv-3

value: Prostate


title: DSP-0509-1


title: C42-Enz-1

value: Castrate-resistant prostate cancer


title: LNCaP-Abi-2

value: 5 uM abiraterone acetate

value: 16 hours


title: C42-AbiOnv-2

value: 5 uM abiraterone acetate and 15 nM onvansertib


title: PD-1-1


title: C42-AbiOnv-1


title: LNCaP-DMSO-2

value: DMSO


title: Combination-2


title: DSP-0509-2


title: vehicle-1

value: vehicle


title: LNCaP-Abi-3


title: LNCaP-Abi-1


title: C42-EnzOnv-2

value: 10 uM enzalutamide and 15 nM onvansertib


title: C42-EnzOnv-3


title: LNCaP-DMSO-3


title: C42-Enz-3


title: C42-DMSO-1


title: C42-DMSO-2


title: Eschierichia coli K-12 MG1655,water control, replicate 3

city: Qingdao

first: Mingyu

address: 72 Haibin Rd.

department: State Key Laboratory of Microbial Technology

institute: Shandong University

data_processing:
Base calling was performed with the Illumina CASAVA 1.8 software to generate raw reads.
Raw data (raw reads) of fastq format were processed through in-house perl scripts from Novogene Technology Co. Ltd. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Both building index of reference genome and aligning clean reads to reference genome used Bowtie2-2.2.3.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Genome assembly used was E. coli K12 MG1655 genome from Genbank (Genome assembly GCA_000005845.2 ASM584v2. Nucleotide accession No. NC_000913.3)
Supplementary files format and content: tab-delimited text files including gene ids (in b-numbers), read counts, and RPKM values for each Sample

organism: Escherichia coli

growth_protocol: E. coli K12 strain MG1655 was cultivated in LB broth at 37 °C and grown to mid-logarithmic phase. Then the culture was inoculated in MHB medium (1% inoculant) containing IC50 concentrations of antibiotics and grown to mid-logarithmic phase with shaking

extract_protocol:
RNA was extracted using the Bacterial RNA Kit (Omega Bio-Tek, USA) according to the manufacturer’s instructions.
Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

value: water


title: vehicle-3


title: PD-1-2


title: C42-EnzOnv-1


title: Combination-1


title: Eschierichia coli K-12 MG1655, ethanol control, replicate 2

value: ethanol


title: LNCaP-DMSO-1


title: Pt_4

city: Birmingham

first: Paul

last: Moss

state: West Midlands

address: Vincent Drive

department: Immunology and Immunotherapy

institute: University of Birmingham

description: single cell

data_processing:
Raw reads were processed using CellRanger (10X Genomics, v3) functions mkfastq and count. Raw bcl files were converted to fastq and aligned to the human reference genome GRCh38
Assembly: hg38
Supplementary files format and content: Counts matrix with raw feature counts for each cell

source_name: PDAC tissue

growth_protocol: Single cell suspensions of digested tumor tissue were surface stained with anti-CD45 BV785 (2D1, Biolegend), anti-EpCAM APC (9C4, Biolegend) and anti-Podoplanin AF488 (NC-08, Biolegend) to confirm the presence of immune cells, epithelial cells and fibroblasts, respectively. PI was added prior to sorting to exclude non-viable cells. Live CD45+ and CD45- populations were sorted and adjusted to 1 x 103/ml

extract_protocol:
PI was added prior to sorting to exclude non-viable cells. Live CD45+ and CD45- populations were sorted and adjusted to 1 x 103/ml.
Samples with >85% cell viability were processed at the Genomics Birmingham Sequencing Facility (University of Birmingham, UK) for gene expression profiling using the 10X Genomics platform. Around 1.7 x 104 cells per sample were processed using the Chromium Controller for a recovery of 1 x 104 cells per sample, and library preparation was performed using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 according to manufacturer’s instructions. Library quantification was performed using TapeStation (Agilent). Samples were sequenced on an Illumina NextSeq 500 (150 bps, paired-end) at a sequencing depth of >50,000 raw reads/cell.
(150 bps, paired-end) at a sequencing depth of >50,000 raw reads/cell.

value: Mixed


title: C42-Enz-2

value: 10 uM enzalutamide


title: vehicle-2

value: CT26 tumor


title: AM_pi_8

city: Jacksonville

first: Tushar

last: Patel

state: FL

address: 4500 San Pablo Road

institute: Mayo Clinic

description: Extracellular vesicle RNA

data_processing:
Intensity correction and base calling and assigning of Q-score greater than 30
Adapter trimming
Reads mapped to miRBase
Reads mapped to smallRNA database
Genome_build: homo sapiens, GRCh37, miRbase 20
Supplementary_files_format_and_content: .xlsx file containing raw counts

growth_protocol: HepG2 or LX2 cells in individual wells

extract_protocol:
Total cellular RNA isolated by TRIzol, Extracellular vesicle-RNA isolated by ExoQuick-TC and SeraMir Kit from SBI (System Biosciences)
NEBNext Small RNA Library Preparation kit

treatment_protocol: Co-Culture of HepG2 or LX2 cells in transwell inserts

tag: co-culture


title: DSP-0509-3


title: Eschierichia coli K-12 MG1655, treated with tetracycline, replicate 3

value: tetracycline


title: AM_pi_4

description: Extracellular vesicle RNA

value: No


title: AM_pi_3

description: Total Cell RNA


title: C42-Abi-3


title: C42-Onv-3

value: 15 nM onvansertib


title: Eschierichia coli K-12 MG1655, ethanol control, replicate 1


title: C42-AbiOnv-3


title: AM_pi_1

description: Total Cell RNA


title: C42-Abi-2


title: C42-DMSO-3


title: C42-Onv-1


title: Eschierichia coli K-12 MG1655, ethanol control, replicate 3


title: Eschierichia coli K-12 MG1655, treated with polymyxin E, replicate 2

value: polymyxin E


title: C42-Abi-1

value: Prostate


title: Eschierichia coli K-12 MG1655, water control, replicate 2


title: SNU-1079_YC1_6hr_1

city: Chapel Hill

first: William

last: Kim

state: NC

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

institute: UNC Chapel Hill

description: High SULT1A1 expressing, IDH1 mutant

data_processing:
75b paired-end reads were sequenced on a NextSeq 500 Desktop Sequencer using a high output flow cell kit (Illumina), yielding an average of over 28M reads per sample.
QC-passed reads were aligned to the human reference genome using STAR
Transcript abundance estimates for each sample were performed using SALMON
Raw SALMON read counts for all RNAseq samples were normalized by DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: DESeq2_YC1_Bardeesy_normalized_counts.txt

source_name: cholangiocarcinoma cell line

extract_protocol:
RNA was extracted with Qiagen RNeasy Plus Mini kit
Libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina)

tag: treatment time

value: 6 hours


title: SNU-1079_YC1_16hr_3

description: High SULT1A1 expressing, IDH1 mutant


title: Pt_3

description: single cell


title: Eschierichia coli K-12 MG1655, water control, replicate 1


title: C42-Onv-2

tag: tissue

value: Castrate-resistant prostate cancer


title: SNU-1079_YC1_16hr_2

description: High SULT1A1 expressing, IDH1 mutant


title: SNU-1079_DMSO_6hr_3

description: High SULT1A1 expressing, IDH1 mutant

value: 16 hours


title: AM_pi_5

description: Total Cell RNA


title: AM_pi_7

description: Total Cell RNA


title: SNU-1079_YC1_6hr_3

description: High SULT1A1 expressing, IDH1 mutant


title: Eschierichia coli K-12 MG1655, treated with polymyxin E, replicate 3


title: Pt_1

description: single cell


title: Eschierichia coli K-12 MG1655, treated with tetracycline, replicate 1


title: SNU-1079_YC1_6hr_2

description: High SULT1A1 expressing, IDH1 mutant


title: AM_pi_2

description: Extracellular vesicle RNA


title: SNU-1079_DMSO_6hr_1

description: High SULT1A1 expressing, IDH1 mutant


title: Eschierichia coli K-12 MG1655, treated with tetracycline, replicate 2


title: AM_pi_6

description: Extracellular vesicle RNA


title: SNU-1079_DMSO_16hr_1

description: High SULT1A1 expressing, IDH1 mutant


title: Eschierichia coli K-12 MG1655, treated with kanamycin, replicate 3

value: kanamycin


title: Eschierichia coli K-12 MG1655, treated with polymyxin E, replicate 1


title: RBE_YC1_6hr_3

description: High SULT1A1 expressing, IDH1 mutant

value: RBE


title: SNU-1079_YC1_16hr_1

description: High SULT1A1 expressing, IDH1 mutant


title: Eschierichia coli K-12 MG1655, treated with mitomycin C, replicate 3

value: mitomycin C


title: Eschierichia coli K-12 MG1655, treated with mitomycin C, replicate 1


title: SNU-1079_DMSO_16hr_3

description: High SULT1A1 expressing, IDH1 mutant

value: DMSO


title: RBE_YC1_6hr_2

description: High SULT1A1 expressing, IDH1 mutant


title: Eschierichia coli K-12 MG1655, treated with mitomycin C, replicate 2


title: SNU-1079_DMSO_16hr_2

description: High SULT1A1 expressing, IDH1 mutant


title: Eschierichia coli K-12 MG1655, treated with kanamycin, replicate 2


title: RBE_YC1_16hr_1

description: High SULT1A1 expressing, IDH1 mutant


title: RBE_YC1_16hr_3

description: High SULT1A1 expressing, IDH1 mutant


title: RBE_YC1_16hr_2

description: High SULT1A1 expressing, IDH1 mutant


title: SNU-1079_DMSO_6hr_2

description: High SULT1A1 expressing, IDH1 mutant


title: RBE_DMSO_6hr_3

description: High SULT1A1 expressing, IDH1 mutant


title: RBE_DMSO_6hr_2

description: High SULT1A1 expressing, IDH1 mutant


title: RBE_DMSO_16hr_3

description: High SULT1A1 expressing, IDH1 mutant


title: Eschierichia coli K-12 MG1655, treated with imipenem, replicate 2

value: imipenem


title: RBE_DMSO_16hr_2

description: High SULT1A1 expressing, IDH1 mutant


title: Eschierichia coli K-12 MG1655, treated with imipenem, replicate 1


title: Eschierichia coli K-12 MG1655, treated with erythromycin, replicate 1

value: erythromycin


title: PCHiC_TET_KO_EpiLC_D2_rep2

city: Cambridge

first: Simon

address: Babraham Research Campus

institute: The Babraham Institute

data_processing:
PCHiC-seq libraries were sequenced as 75 base paired-end runs on an Illumina HiSeq2500 instrument. Quality and adapter trimming were performed using Trim Galore v0.6.5 (using Cutadapt v2.3). Mapping to the mouse reference genome (GRCm38) was performed using the HiCUP pipeline v0.7.2. CHiCAGO (version 1.10.1) (Cairns et al. 2016) was used to define significant Promoter-PIR interactions above expected background. Two biological replicates for each of the conditions were combined and normalised as part of the CHiCAGO pipeline and used to score interactions, which correspond to -log transformed weighted P-values for each promoter-PIR pair. We included interactions with a CHiCAGO interaction score of >5 in at least one condition.
Assembly: GRCm38
Supplementary files format and content: PCHiC_peak.matrix_chicago.scores.txt: rows are significant interactions in any of the conditions, columns are Chicago scores for each of the conditions and information on bait and other end regions. Replicates are handled by Chicago resulting in  only one value for each conditions.

source_name: EpiLC

extract_protocol:
30 million cells were fixed in 2% formaldehyde for 10 minutes and quenched in 0.125M glycine before washing in ice cold phosphate-buffered-saline, scraping and flash freezing. Cells were permeabilized and digested using HindIII (NEB). Restriction sites were filled using Klenow (NEB) in the presence of dCTP, dCGP, dTTP and biotin-14-dATP (Life Technologies). In solution ligation was carried out as described in Nagano et. al, 2015, and DNA was reverse-crosslinked, proteinase K and RNase A treated before purification using phenol/chloroform and ethanol precipitation. Biotin-marked ligation products were isolated with MyOne Streptavidin C1 dynabeads (Life Technologies). Promoter capture (PC) was performed as detailed in Schoenfelder et al., 2015. Briefly, 500 ng of Hi-C DNA was lyophilized using a vacuum concentrator. Pulldown and cleanups were performed as described in the manufacturer’s instructions (SureSelect Target Enrichment, Agilent Technologies). The bait system used was as described in Schoenfelder et al., 2015, and included 39,021 biotinylated RNA complementary to the fragment ends of 22,225 mouse gene promoters, consisting of either 1 or 2 RNA baits per promoter overlapping HindIII fragment depending on the complexity of the DNA sequence.
Paired-end (PE) adapters were ligated using T4 DNA ligase (NEB) before amplification using PE PCR 1.0 and PE PCR 2.0 primers (Illumina).
HiC (promoter capture HiC)

value: EpiLC


title: PCHiC_TET_WT_EpiLC_D2_rep1


title: PCHiC_TET_WT_EpiLC_D2_rep2


title: PCHiC_TET_KO_EpiLC_D2_rep1


title: Eschierichia coli K-12 MG1655, treated with kanamycin, replicate 1


title: PCHiC_TET_KO_ESC_D0_rep2

source_name: ESC

value: ESC


title: PCHiC_TET_WT_ESC_D0_rep1


title: RBE_DMSO_6hr_1

description: High SULT1A1 expressing, IDH1 mutant


title: Eschierichia coli K-12 MG1655, treated with ciprofloxacin, replicate 2

value: ciprofloxacin


title: PCHiC_DNMT_WT_EpiLC_D2_rep2


title: PCHiC_TET_KO_ESC_D0_rep1


title: PCHiC_DNMT_KO_EpiLC_D2_rep1


title: PCHiC_DNMT_WT_EpiLC_D2_rep1


title: Eschierichia coli K-12 MG1655, treated with ciprofloxacin, replicate 1


title: Eschierichia coli K-12 MG1655, treated with ciprofloxacin, replicate 3


title: PCHiC_DNMT_KO_ESC_D0_rep1


title: RBE_DMSO_16hr_1

description: High SULT1A1 expressing, IDH1 mutant


title: Eschierichia coli K-12 MG1655, treated with chloramphenicol, replicate 3

value: chloramphenicol


title: PCHiC_DNMT_KO_EpiLC_D2_rep2


title: RBE_YC1_6hr_1

description: High SULT1A1 expressing, IDH1 mutant


title: Eschierichia coli K-12 MG1655, treated with erythromycin, replicate 2


title: PCHiC_DNMT_WT_ESC_D0_rep2


title: Eschierichia coli K-12 MG1655, treated with chloramphenicol, replicate 2


title: Eschierichia coli K-12 MG1655, treated with erythromycin, replicate 3


title: RCC4/VA Nx/FICZ INPUT rep2

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

institute: University of Oxford

data_processing:
Illumina adaptor sequences were trimmed using Trimgalore (0.3.3) and reads were aligned to Genome Reference Consortium GRCh37 (hg19) using BWA (0.7.5a-r405). Low quality mapping was removed (MapQ < 15) using SAMtools (0.1.19)
Low quality mapping was removed (MapQ < 15) using SAMtools (0.1.19) and reads mapping to Duke Encode black list regions (http://hgwdev.cse.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeMapability) were excluded using BEDTools (2.17.0)
Duplicate reads were marked for exclusion using Picard tools (2.0.1) (http://picard.sourceforge.net/).
ChIP-seq peaks were identified using T-PIC (Tree shape Peak Identification for ChIP-Seq) and MACS (Model-based analysis of ChIP-Seq) in control mode
Peaks detected by both peak callers were filtered quantitatively using the total count under the peak to include only peaks that were above the 99.99th percentile of random background regions selected from the ENCODE DNASE II cluster (p-value < 0.0001).
Assembly: GRCh37 (hg19)
Supplementary files format and content: bigwig and bed files of called peaks

source_name: RCC4+VA (empty vector) renal cell carcinoma cell line

growth_protocol: DMEM culture medium was supplemented with 10% FBS, L-glutamine and penicillin-streptomycin. Cells were plated on 15 cm plates, allowed to grow in phenol red–free DMEM supplemented with 10% dextran-coated charcoal-treated foetal calf serum, L-glutamine and penicillin-streptomycin for approximately 48 hours before treatments. Cells were harvested at approximately 80% confluency.

extract_protocol:
Chromatin immunoprecipitation (ChIP) experiments were performed using antibodies directed against HIF-1a (rabbit polyclonal, PM14), HIF-2a (rabbit polyclonal, PM9), HIF-1b (rabbit polyclonal, Novus Biologicals) or AHR (Cell Signaling 83200).
Automated library preparation was performed using the Apollo prep system (Takara, PrepX Comp ILMN 32i DNA Lib 96).

treatment_protocol: Hypoxic incubations were performed at 0.5% oxygen for 6 hours in a hypoxia chamber (InvivO2 400 workstation, Ruskinn Technology). Treatments with AHR ligands (ITE 100nM, FICZ 10nM or DMSO vehicle 0.1%) were performed for 30 minutes  prior to harvest.

tag: ambient o2 concentration

tag: duration of hypoxia

value: FICZ 10nM

tag: duration of treatment

value: 0.5 hours

tag: chip antibody

value: renal cell carcinoma cell line


title: PCHiC_TET_WT_ESC_D0_rep2

last: Andrews

tag: cell type

tag: time


title: RCC4/VA Nx/ITE INPUT rep2

tag: treatment

value: ITE 100nM


title: RCC4/VA Nx/ITE INPUT rep3


title: Input_DNMT_KO_EpiLC_D2_rep1

data_processing:
ChIP-seq libraries were sequenced as 50 base paired-end runs on an Illumina NovaSeq instrument. Quality and adapter trimming were performed using Trim Galore v0.6.5 (using Cutadapt v2.3). Mapping to the mouse reference genome (GRCm38) was performed using Bowtie2 v2.4.1.
Assembly: GRCm38
Supplementary files format and content: ChIP_2kb.tiles_log2RPKM.txt: rows are 2 kb tiles across the genome, columns are quantitated samples as log2 RPKM

extract_protocol:
Chromatin from 10 million cells was sonicated to between 200-600 bp using a Bioruptor Plus (Diagenode). 100µL of Dynabeads Protein G (Invitrogen, 10003D) were used per immunoprecipitation. The following antibodies were used: H3K4me3 (Abcam, ab8580), H3K27me3 (Millipore, 07-449), H3K4me1 (Active Motif, 39297), H3K27ac (Abcam, ab4729), CTCF (Millipore, 07-729).
Libraries were prepared using the NEBNext Ultra II Library Prep Kit for Illumina (New England Biolabs, E7645) following the manufacturer’s instructions. Libraries were size selected after amplification using Agencourt Ampure XP beads (Fisher Scientific, 10136224) prior to pooling and sequencing.


title: Eschierichia coli K-12 MG1655, treated with chloramphenicol, replicate 1

tag: strain


title: Input_DNMT_KO_ESC_D0_rep3


title: Eschierichia coli K-12 MG1655, treated with imipenem, replicate 3


title: RCC4/VA Nx/DMSO INPUT rep2


title: PCHiC_DNMT_WT_ESC_D0_rep1


title: Input_DNMT_KO_EpiLC_D2_rep2


title: Input_DNMT_KO_ESC_D0_rep1


title: Input_DNMT_KO_EpiLC_D2_rep3


title: PCHiC_DNMT_KO_ESC_D0_rep2


title: Input_DNMT_WT_EpiLC_D2_rep3


title: Eschierichia coli K-12 MG1655, treated with ceftazidime, replicate 3

value: ceftazidime


title: Input_DNMT_WT_ESC_D0_rep3


title: WGBS_TET_KO_EpiLC_D2_rep3

data_processing:
WGBS-seq libraries were sequenced as 150 base paired-end runs on an Illumina HiSeq2500 instrument. Quality and adapter trimming were performed using Trim Galore v0.6.6 (using Cutadapt v2.3). Bismark v0.23.0 was used to align DNA reads to the bisulfite converted GRCm38 mouse genome then perform methylation calling.
Assembly: GRCm38
Supplementary files format and content: methylation_100CpGwindows_percent.txt: WGBS data was quantitated across 100 CpG using the Seqmonk methylation quantitation pipeline (min count per position = 1, min number of observations = 20) and is expressed in percent.

extract_protocol:
As an input for WGBS 400 ng of genomic DNA was fragmented to between 300 and 400 bp using a Covaris E220 water bath sonicator following manufacturer’s instructions. The DNA ends were repaired using NEBNext Ultra II Library Prep (New England Biolabs, E7645) reagents and methylated adapters were annealed according to the manufacturer’s instructions. Fragments were purified using Agencourt Ampure XP beads (Fisher Scientific, 10136224) and bisulfite converted using a Zymo EZ Methylation Gold kit (Zymo, D5005) according to the manufacturer’s instructions and eluting the converted DNA in 15µL of provided elution buffer.
Bisulfite treated DNA was amplified using NEBNext index primers (NEB, E7335) and KAPA HiFi Uracil+ mastermix (Roche, KK2801/2) using the following protocol: 1 minute at 98ºC, 10 cycles of 15 seconds at 98ºC, 30 seconds at 65ºC, 30 seconds at 72ºC followed by a final extension for 1 minute at 72ºC. Libraries purified using 0.8x volumes of Agencourt Ampure XP beads (Fisher Scientific, 10136224) to remove contaminating adapters.


title: Eschierichia coli K-12 MG1655, treated with ceftazidime, replicate 2


title: H3K27me3_DNMT_KO_EpiLC_D2_rep3


title: RCC4/VA Nx/FICZ AHR ChIP rep2

value: AHR (Cell Signaling, 83200)


title: Input_DNMT_KO_ESC_D0_rep2


title: Eschierichia coli K-12 MG1655, treated with ceftazidime, replicate 1


title: RCC4/VA Nx/ITE HIF-1b ChIP rep2


title: Input_DNMT_WT_ESC_D0_rep1


title: RCC4/VA Nx/FICZ HIF-1b ChIP rep2


title: RCC4/VA Nx/ITE HIF-2a ChIP rep2

value: HIF-2a (rabbit polyclonal, PM9)


title: H3K27me3_DNMT_KO_ESC_D0_rep2


title: RCC4/VA Nx/ITE HIF-1a ChIP rep2

value: HIF-1a (rabbit polyclonal, PM14)


title: RCC4/VA Nx/FICZ HIF-2a ChIP rep2


title: H3K27me3_TET_KO_EpiLC_D2_rep3


title: H3K27me3_DNMT_KO_EpiLC_D2_rep1


title: Input_DNMT_WT_EpiLC_D2_rep2


title: RCC4/VA Nx/ITE AHR ChIP rep2


title: H3K27me3_TET_KO_EpiLC_D2_rep1


title: RCC4/VA Nx/DMSO AHR ChIP rep2


title: Input_DNMT_WT_EpiLC_D2_rep1


title: Input_DNMT_WT_ESC_D0_rep2


title: RCC4/VA Nx/FICZ HIF-1a ChIP rep2


title: WGBS_TET_KO_EpiLC_D2_rep1


title: H3K27me3_DNMT_KO_ESC_D0_rep3


title: H3K27me3_DNMT_KO_EpiLC_D2_rep2


title: WGBS_TET_KO_ESC_D0_rep2


title: WGBS_TET_KO_EpiLC_D1_rep3


title: H3K27me3_TET_KO_EpiLC_D2_rep2


title: WGBS_TET_KO_ESC_D0_rep1


title: RCC4/VA Nx/DMSO HIF-1a ChIP rep2


title: WGBS_DNMT_WT_EpiLC_D2_rep3


title: RCC4/VA Nx/FICZ INPUT rep1


title: H3K27me3_DNMT_KO_ESC_D0_rep1


title: H3K27me3_DNMT_WT_ESC_D0_rep2


title: H3K27me3_TET_WT_EpiLC_D2_rep3


title: RCC4/VA Nx/DMSO HIF-2a ChIP rep2


title: WGBS_TET_KO_EpiLC_D1_rep2


title: H3K27me3_TET_KO_ESC_D0_rep3


title: H3K27me3_TET_KO_ESC_D0_rep2


title: WGBS_TET_KO_EpiLC_D2_rep2


title: H3K27me3_TET_WT_ESC_D0_rep3


title: RCC4/VA Nx/FICZ AHR ChIP rep1


title: RCC4/VA Nx/DMSO HIF-1b ChIP rep2


title: H3K27me3_DNMT_WT_EpiLC_D2_rep3


title: WGBS_TET_KO_EpiLC_D1_rep1


title: WGBS_TET_KO_ESC_D0_rep3


title: H3K27ac_DNMT_KO_EpiLC_D2_rep3


title: RCC4/VA Nx/FICZ HIF-1b ChIP rep1


title: H3K27me3_DNMT_WT_ESC_D0_rep3


title: H3K27me3_TET_WT_ESC_D0_rep1


title: WGBS_DNMT_WT_EpiLC_D1_rep1


title: H3K27me3_TET_KO_ESC_D0_rep1


title: H3K27me3_DNMT_WT_EpiLC_D2_rep1


title: H3K27me3_DNMT_WT_EpiLC_D2_rep2


title: WGBS_DNMT_WT_EpiLC_D2_rep1


title: WGBS_DNMT_WT_EpiLC_D2_rep2


title: H3K27me3_DNMT_WT_ESC_D0_rep1


title: RCC4/VA Nx/FICZ HIF-1a ChIP rep1


title: H3K27ac_DNMT_KO_ESC_D0_rep1


title: H3K27me3_TET_WT_EpiLC_D2_rep2


title: RCC4/VA Nx/ITE AHR ChIP rep3


title: H3K27ac_TET_KO_EpiLC_D2_rep1


title: WGBS_DNMT_WT_ESC_D0_rep1


title: H3K27ac_TET_KO_ESC_D0_rep2


title: RCC4/VA Nx/DMSO INPUT rep1


title: RCC4/VA Nx/ITE INPUT rep1


title: WGBS_TET_WT_EpiLC_D2_rep3


title: H3K27me3_TET_WT_EpiLC_D2_rep1


title: H3K27ac_DNMT_KO_ESC_D0_rep2


title: H3K27ac_DNMT_WT_EpiLC_D2_rep3


title: WGBS_DNMT_WT_EpiLC_D1_rep3


title: H3K27ac_DNMT_KO_EpiLC_D2_rep2


title: H3K27ac_DNMT_KO_EpiLC_D2_rep1


title: WGBS_DNMT_WT_ESC_D0_rep2


title: H3K27ac_DNMT_WT_EpiLC_D2_rep1


title: H3K27ac_TET_KO_ESC_D0_rep3


title: WGBS_DNMT_WT_EpiLC_D1_rep2


title: RCC4/VA Nx/DMSO AHR ChIP rep1


title: RCC4/VA Nx/DMSO HIF-1b ChIP rep1


title: H3K27ac_DNMT_WT_ESC_D0_rep3


title: H3K27ac_DNMT_WT_ESC_D0_rep1


title: WGBS_TET_WT_EpiLC_D1_rep3


title: RCC4/VA Nx/ITE HIF-2a ChIP rep1


title: RCC4/VA Nx/ITE HIF-1b ChIP rep1


title: H3K27ac_DNMT_KO_ESC_D0_rep3


title: H3K27ac_TET_KO_EpiLC_D2_rep3


title: H3K27ac_TET_KO_EpiLC_D2_rep2


title: WGBS_DNMT_WT_ESC_D0_rep3


title: WGBS_TET_WT_EpiLC_D2_rep1


title: RCC4/VA Nx/ITE HIF-1a ChIP rep1


title: H3K27ac_DNMT_WT_ESC_D0_rep2


title: RCC4/VHL Hx/FICZ INPUT rep2

source_name: RCC4+VHL renal cell carcinoma cell line

value: 6 hours


title: H3K27ac_TET_WT_ESC_D0_rep2


title: H3K4me3_DNMT_KO_EpiLC_D2_rep3


title: WGBS_TET_WT_EpiLC_D1_rep1


title: WGBS_TET_WT_EpiLC_D2_rep2


title: H3K4me3_DNMT_KO_ESC_D0_rep3


title: H3K27ac_DNMT_WT_EpiLC_D2_rep2


title: RCC4/VA Nx/FICZ HIF-2a ChIP rep1


title: RCC4/VA Nx/DMSO HIF-2a ChIP rep1


title: H3K27ac_TET_KO_ESC_D0_rep1


title: H3K27ac_TET_WT_ESC_D0_rep1


title: H3K4me3_TET_KO_EpiLC_D2_rep3


title: RCC4/VHL Hx/DMSO INPUT rep2


title: RCC4/VHL Nx/ITE INPUT rep2


title: RNA_DNMT_KO_EB_D8_rep1

data_processing:
RNA-seq libraries were sequenced as 75 base paired-end runs on an Illumina HiSeq2500 instrument. Quality and adapter trimming were performed using Trim Galore v0.6.1 (using Cutadapt v1.18). Mapping to the mouse reference genome (GRCm38) was performed using Hisat2 v2.1.0 (--no-softclip) guided by known splice sites from Ensembl annotation v90.
Assembly: GRCm38
Supplementary files format and content: expression_gene_log2RPKM.txt: rows are genes and columns are individual samples quantitated as log2 RPKM

source_name: EB

extract_protocol:
RNA was isolated from cells using QIAshredder columns and RNeasy Mini kits (QIAGEN) according to the manufacturer’s instructions. Isolated RNA samples were treated with TURBO DNase (Thermo Fisher Scientific, AM2238).
stranded RNA-seq (opposing strand) with Oligo dT pulldown

value: EB


title: RCC4/VHL Hx/ITE INPUT rep2


title: WGBS_TET_WT_ESC_D0_rep1


title: H3K4me3_DNMT_KO_EpiLC_D2_rep1


title: H3K4me3_DNMT_KO_EpiLC_D2_rep2


title: WGBS_TET_WT_EpiLC_D1_rep2


title: WGBS_TET_WT_ESC_D0_rep2


title: RCC4/VA Nx/DMSO HIF-1a ChIP rep1

value: DMSO


title: H3K27ac_TET_WT_EpiLC_D2_rep2


title: H3K27ac_TET_WT_EpiLC_D2_rep3


title: H3K4me3_DNMT_KO_ESC_D0_rep1


title: H3K27ac_TET_WT_EpiLC_D2_rep1


title: RNA_DNMT_KO_EB_D6_rep3


title: H3K4me3_TET_KO_ESC_D0_rep3


title: RCC4/VHL Nx/FICZ INPUT rep2


title: H3K4me3_DNMT_KO_ESC_D0_rep2


title: RNA_DNMT_KO_EB_D8_rep3


title: H3K27ac_TET_WT_ESC_D0_rep3


title: WGBS_TET_WT_ESC_D0_rep3


title: RNA_DNMT_KO_EB_D6_rep2


title: H3K4me3_TET_KO_EpiLC_D2_rep1


title: RCC4/VHL Nx/DMSO INPUT rep2


title: H3K4me3_TET_KO_ESC_D0_rep1


title: RNA_DNMT_KO_EB_D6_rep1


title: H3K4me3_DNMT_WT_EpiLC_D2_rep2


title: H3K4me3_TET_KO_EpiLC_D2_rep2


title: RNA_DNMT_KO_EB_D8_rep2


title: H3K4me3_DNMT_WT_EpiLC_D2_rep1


title: RCC4/VHL Hx/FICZ HIF-1b ChIP rep2


title: H3K4me3_DNMT_WT_ESC_D0_rep2


title: RCC4/VHL Hx/FICZ HIF-2a ChIP rep2


title: H3K4me3_TET_WT_EpiLC_D2_rep3


title: RNA_DNMT_KO_EB_D4_rep3


title: H3K4me3_TET_WT_EpiLC_D2_rep1


title: RCC4/VHL Hx/FICZ AHR ChIP rep2


title: H3K4me3_TET_WT_ESC_D0_rep3


title: H3K4me3_TET_WT_EpiLC_D2_rep2


title: H3K4me3_DNMT_WT_ESC_D0_rep1


title: H3K4me3_DNMT_WT_ESC_D0_rep3


title: H3K4me3_DNMT_WT_EpiLC_D2_rep3


title: H3K4me3_TET_KO_ESC_D0_rep2


title: RNA_DNMT_KO_EB_D4_rep2


title: RCC4/VHL Hx/ITE AHR ChIP rep2


title: RNA_DNMT_KO_EB_D2_rep2


title: RCC4/VHL Hx/ITE HIF-2a ChIP rep2


title: H3K4me1_DNMT_KO_EpiLC_D2_rep3


title: RNA_DNMT_KO_EB_D2_rep3


title: H3K4me3_TET_WT_ESC_D0_rep2


title: H3K4me3_TET_WT_ESC_D0_rep1


title: RNA_DNMT_KO_EB_D4_rep1


title: RCC4/VHL Hx/FICZ HIF-1a ChIP rep2


title: H3K4me1_DNMT_KO_EpiLC_D2_rep2


title: RNA_DNMT_KO_EpiLC_D2_rep3


title: RCC4/VHL Hx/ITE HIF-1b ChIP rep2


title: RCC4/VHL Hx/DMSO AHR ChIP rep2


title: RCC4/VHL Hx/ITE HIF-1a ChIP rep2


title: H3K4me1_DNMT_KO_ESC_D0_rep3


title: H3K4me1_TET_KO_EpiLC_D2_rep2


title: H3K4me1_DNMT_KO_ESC_D0_rep2


title: RNA_DNMT_KO_EpiLC_D2_rep2


title: RNA_DNMT_KO_ESC_D0_rep3


title: H3K4me1_TET_KO_EpiLC_D2_rep1


title: RNA_DNMT_KO_EpiLC_D2_rep1


title: RNA_DNMT_KO_EpiLC_D1_rep1


title: H3K4me1_DNMT_KO_ESC_D0_rep1


title: RCC4/VHL Hx/DMSO HIF-1b ChIP rep2


title: RNA_DNMT_KO_EpiLC_D1_rep3


title: H3K4me1_DNMT_WT_EpiLC_D2_rep2


title: H3K4me1_DNMT_WT_EpiLC_D2_rep3


title: RNA_DNMT_KO_EpiLC_D1_rep2


title: H3K4me1_DNMT_WT_ESC_D0_rep2


title: RNA_DNMT_KO_ESC_D0_rep2


title: RCC4/VHL Hx/DMSO HIF-2a ChIP rep2


title: H3K4me1_TET_KO_ESC_D0_rep2


title: H3K4me1_DNMT_WT_EpiLC_D2_rep1


title: H3K4me1_TET_KO_EpiLC_D2_rep3


title: H3K4me1_DNMT_KO_EpiLC_D2_rep1


title: RCC4/VHL Nx/FICZ HIF-2a ChIP rep2


title: H3K4me1_TET_KO_ESC_D0_rep3


title: H3K4me1_DNMT_WT_ESC_D0_rep3


title: RCC4/VHL Nx/FICZ HIF-1b ChIP rep2


title: RCC4/VHL Hx/DMSO HIF-1a ChIP rep2


title: H3K4me1_TET_KO_ESC_D0_rep1


title: RNA_DNMT_KO_ESC_D0_rep1


title: RCC4/VHL Nx/FICZ AHR ChIP rep2


title: RCC4/VHL Nx/FICZ HIF-1a ChIP rep2


title: RNA_TET_KO_EB_D8_rep3


title: H3K4me1_TET_WT_EpiLC_D2_rep2


title: H3K4me1_DNMT_WT_ESC_D0_rep1


title: H3K4me1_TET_WT_ESC_D0_rep2


title: CTCF_DNMT_KO_EpiLC_D2_rep2

value: CTCF


title: RCC4/VHL Nx/ITE HIF-1b ChIP rep2


title: CTCF_DNMT_KO_ESC_D0_rep3


title: RNA_TET_KO_EB_D8_rep2


title: CTCF_DNMT_KO_EpiLC_D2_rep1


title: RNA_TET_KO_EB_D6_rep3


title: CTCF_DNMT_KO_ESC_D0_rep1


title: RNA_TET_KO_EB_D6_rep2


title: RCC4/VHL Nx/ITE HIF-1a ChIP rep2


title: RNA_TET_KO_EB_D4_rep3


title: CTCF_TET_KO_EpiLC_D2_rep3


title: RCC4/VHL Nx/DMSO HIF-1b ChIP rep2


title: RCC4/VHL Nx/DMSO HIF-2a ChIP rep2


title: RCC4/VHL Nx/DMSO AHR ChIP rep2


title: RCC4/VHL Nx/ITE AHR ChIP rep2


title: CTCF_TET_KO_EpiLC_D2_rep2


title: H3K4me1_TET_WT_EpiLC_D2_rep1


title: CTCF_DNMT_KO_EpiLC_D2_rep3


title: H3K4me1_TET_WT_ESC_D0_rep3


title: H3K4me1_TET_WT_EpiLC_D2_rep3


title: CTCF_TET_KO_EpiLC_D2_rep1


title: H3K4me1_TET_WT_ESC_D0_rep1


title: RNA_TET_KO_EB_D8_rep1


title: RNA_TET_KO_EB_D6_rep1


title: RCC4/VHL Nx/DMSO HIF-1a ChIP rep2


title: RNA_TET_KO_EB_D4_rep2


title: CTCF_DNMT_KO_ESC_D0_rep2


title: RCC4/VHL Nx/ITE HIF-2a ChIP rep2


title: RCC4/VHL Hx/FICZ INPUT rep1


title: CTCF_TET_KO_ESC_D0_rep2


title: RNA_TET_KO_EB_D4_rep1


title: CTCF_DNMT_WT_EpiLC_D2_rep1


title: CTCF_DNMT_WT_EpiLC_D2_rep3


title: RNA_TET_KO_EB_D2_rep1


title: RNA_TET_KO_EpiLC_D2_rep3


title: CTCF_DNMT_WT_ESC_D0_rep2


title: CTCF_DNMT_WT_EpiLC_D2_rep2


title: CTCF_TET_WT_EpiLC_D2_rep3


title: RCC4/VHL Nx/FICZ INPUT rep1


title: CTCF_TET_WT_EpiLC_D2_rep2


title: CTCF_TET_KO_ESC_D0_rep3


title: RCC4/VHL Nx/ITE INPUT rep1


title: CTCF_TET_KO_ESC_D0_rep1


title: RCC4/VHL Hx/DMSO INPUT rep1


title: RCC4/VHL Hx/ITE INPUT rep1


title: RNA_TET_KO_EpiLC_D2_rep2


title: CTCF_TET_WT_ESC_D0_rep3


title: CTCF_DNMT_WT_ESC_D0_rep3


title: RCC4/VHL Hx/FICZ AHR ChIP rep1


title: RCC4/VHL Hx/FICZ HIF-2a ChIP rep1


title: RNA_TET_KO_EpiLC_D1_rep2


title: RCC4/VHL Nx/DMSO INPUT rep1


title: CTCF_TET_WT_ESC_D0_rep2


title: CTCF_DNMT_WT_ESC_D0_rep1


title: RNA_TET_KO_EpiLC_D2_rep1


title: RNA_TET_KO_EpiLC_D1_rep1


title: CTCF_TET_WT_ESC_D0_rep1


title: RNA_TET_KO_EpiLC_D1_rep3


title: CTCF_TET_WT_EpiLC_D2_rep1


title: RCC4/VHL Hx/FICZ HIF-1b ChIP rep1


title: RNA_TET_KO_ESC_D0_rep2


title: Wt_AI_tot03_SC_SP_CTACAC [3]

city: Geneve

first: George

last: Allen

state: Geneve

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

data_processing:
Library strategy: 5PSeq
Demultiplexing using bcl2fastq v2.20.0.422 at default settings, allowing one mismatch and minimum read length of 35nt
Quality control with FASTQC and MultiQC v1.9 at default parameters
Adapter trimming using cutadapt 2.3 with Python 3.7.2, options: --minimum-length 28; -e 0.2; -o 9; --nextseq-trim 20 , Adapter 1 AGATCGGAAGAGCAC
Extraction of barcodes and UMI using umitools and options --bc-pattern CCCCCCNNNNNNNN, whitelist.txt file of barcodes was provided and fastq files where spitted according to barcode
Mapping of reads using STAR and options: --alignEndsType Extend5pOfRead1; --outFilterMatchNminOverLread 0.9; --outFilterMultimapNmax 3; --limitBAMsortRAM 100000000000; alignIntronMax 2500
Deduplication using UMIs was done with umitools
Count statistics on species and RNA composition were determined using bedtools intersect (aka intersectBed) Version: v2.29.2, bedtools intersect [OPTIONS] -a <bed/gff/vcf/bam> -b <bed/gff/vcf/bam>
Genome_build: Saccharomyces cerevisiae R64-1-1, Schizosaccharomyces pombe (ASM294v2)  and Schizosaccharomyces pombe: GCF_000002945.1_ASM294v2_genomic.fna; GCF_000002945.1_ASM294v2_genomic.gff was created and files were mapped using STAR
Supplementary_files_format_and_content: Bedgraphs of forward (fwd) and reverse (rev) 5P read positions were created using BEDTools genomecov program with options {-bg -strand [+/-] -5} of concatenated Saccharomyces cerevisiae and Schizosaccharomyces pombe genome

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in glucose rich medium (YPD) to exponential phase and for

extract_protocol:
Total RNA was prepared by adding acid phenol (200 ul) on the cell pellet together with 200 ul of TES (Tris/EDTA/SDS) (Current Protocols in Molecular Biology (1993)), soluble RNA was prepared by lysing the cell pellet as for polysome profiling (Panasenko and Collart, 2012, doi:10.1111/j.1365-2958.2011.07957.x), and addition of an equal volume of hot acid phenol to the lysis buffer.
HT-5PSeq libraries were generated as reported (Zhang and Pelechano, doi: https://doi.org/10.1101/2020.06.22.165134) with minor modifications.   In brief, 15µg total RNA, containing 5% total RNA from Schizosaccharomyces pombe as spike-in, was used. Each sample was spited in two. One part was used for preparing conventional HT-5PSeq libraries and the other part for was random fragmented prior to the preparation of HT-5PSeq libraries (negative control).  For random fragmented samples: 7.5ug RNA was fragmentation at 80 ̊C for five minutes in fragmentation buffer (40mM Tris Acetate pH 8.1, 100mM KOAc and 30mM MgOAc). Samples were purified using 1.8x volumes of RNACleanXP beads (Beckman Coulter) following re-phosphorylation of 5’OH sites at 37 ̊C for 60 minutes with 5 Units of T4 Polynucleotide kinase (PNK, NEB). Subsequent, reaction was purified using Phenol:Chloroform: Isoamyl Alcohol (24:25:1), followed by sodium acetate-ethanol precipitation. From this step forward, experimental pipelines for random fragmented and HT-5PSeq library preparation merge.   For HT-5PSeq Libraries: 7.5 µg RNA was ligated over night at 16˚C to r5P_RNA_MPX oligo (CrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU rXrXrXrXrXrX rNrNrNrNrNrNrNrN) carrying a sample barcode (rX) and unique molecular identifiers (rN). Ligase was deactivated using 5mM EDTA and heat at 65˚C for 10 minutes (up to X individual barcoded RNA ligations were pooled) and subsequent purified using 1.8x volumes of RNAClean XP beads (Beckman Coulter). Ligated RNA was then reverse transcribed using random hexamer (5Pseq-RT, GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNN, 20µM) and oligo-dT (5Pseq-dT, GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTTTTTTTTTT at 0.05µM) oligos to prime. After, remaining RNA was degraded using NaOH. Ribosomal RNA was removed using previously descrived rRNA DNA oligo depletion mixes, following a duplex-specific nuclease (DSN, Evrogen) digestion. rRNA depleted cDNA was amplified by PCR (17 cycles) and final product was enriched for fragments with the range of 300-500nt using Ampure XP.   Size selected HT-5P Libraries were quantified by fluorescence (Qubit, Thermo Fisher), size estimated using an Agilent Bioanalyzer and sequenced using a NextSeq500 Illumina sequencer (75cycles High output kit).  Sequencing files were demultiplexed using bcl2fastq v2.20.0.422 (one mismatch, minimum length 35nt), and adapters were trimmed using cutadapt 2.3.  at default settings, allowing one mismatch and minimum read length of 35nt. In addition to standard illumine dual index (i5, i7), the inline sample and UMI barcode was analyzed using Umitools. Reads were mapped to the concatenated genome of S. cervisiae (R64-1-1) and S. pombe (ASM294v2) using STAR.  Second read enables to splits reads between oligo-dT or random primer. That information was not used in the current analysis.

treatment_protocol: Strains with a degron were additionally treated for 15 min at 1 mM final.

value: ADH1p-TIR1::URA3 leu2 trp1 ura3

tag: culture conditions

value: YPD exponential growth, 15 min auxin 1mM final

tag: library protocol

value: HT-5PSeq Multiplexed RNA ligation

tag: molecule

value: total RNA


title: RNA_TET_KO_EB_D2_rep2


title: ATAC_DNMT_KO_EpiLC_D2_rep3

data_processing:
ATAC-seq libraries were sequenced as 50 base single-end runs on an Illumina HiSeq2500 instrument. Quality and adapter trimming were performed using Trim Galore v0.6.5 (using Cutadapt v2.3). Mapping to the mouse reference genome (GRCm38) was performed using Bowtie2 v2.4.1
Assembly: GRCm38
Supplementary files format and content: ATAC_2kb.tiles_log2RPKM.txt: rows are 2 kb tiles across the genome, columns are quantitations of samples as log2 RPKM

extract_protocol:
ATAC-seq was performed based on published protocols (Buenrostro et al., 2015) using reagents from a Nextera sequencing kit (Illumina, FC-121-1030). Cells were detached using TrypLE Express (Gibco, 12604013), counted, and 10,000 cells aliquoted into DNA LoBind tubes (Eppendorf, 0030108051). Cells were pelleted for 5 minutes at 500g and 4ºC before lysis in 10µL of cold lysis buffer (10mM Tris HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IgePal CA-630) and immediate repeated centrifugation. Supernatant was removed and the nuclear pellet was suspended in 20µL of transposition mix (1x TD buffer and 0.5µL TDE1 TN5 enzyme) before incubation at 37ºC for 30 minutes with mixing at 1000 RPM using a heated shaker. Samples were purified immediately using a MinElute DNA purification kit (QIAGEN).
Transposed DNA was amplified using the adapters described by Buenrostro et al., 2015 at 1.25µM and NEBNext High Fidelity 2x Mastermix (New England Biolabs, M0541) in a 50µL reaction (5 minutes at 72ºC, 30 seconds at 98ºC, followed by 13 cycles of 10 seconds at 98°C, 75 seconds at 65°C and 60 seconds at 72°C). Samples were purified and size selected using Agencourt Ampure XP beads(Fisher Scientific, 10136224) prior to pooling and sequencing.

value: EpiLC


title: Wt_AI_tot02_SC_SP_TAATGT [2]


title: ATAC_DNMT_KO_EpiLC_D2_rep2


title: RCC4/VHL Hx/ITE AHR ChIP rep1


title: ATAC_DNMT_KO_EpiLC_D2_rep1


title: RNA_DNMT_WT_EB_D8_rep2


title: Wt_AI_tot01_ CGTGCA

source_name: Wt_AI_tot01_ CGTGCA


title: RCC4/VHL Hx/ITE HIF-1b ChIP rep1


title: RCC4/VHL Hx/FICZ HIF-1a ChIP rep1

value: FICZ 10nM


title: ATAC_DNMT_KO_EpiLC_D1_rep3


title: Wt_AI_sol03_SC_SP_GTGATC [6]

value: soluble RNA


title: RNA_TET_KO_ESC_D0_rep1

value: ESC


title: Wt_AI_sol02_SC_SP_ACGCTG [5]


title: ATAC_DNMT_KO_EpiLC_D1_rep2


title: RCC4/VHL Hx/DMSO AHR ChIP rep1

value: 0.5 hours

value: renal cell carcinoma cell line


title: RNA_DNMT_WT_EB_D8_rep3


title: RCC4/VHL Hx/ITE HIF-2a ChIP rep1

value: ITE 100nM


title: RNA_TET_KO_ESC_D0_rep3


title: RNA_DNMT_WT_EB_D6_rep3


title: RNA_DNMT_WT_EB_D8_rep1


title: RCC4/VHL Hx/DMSO HIF-1b ChIP rep1


title: Not5p_AI_tot1_GACTAG

value: ADH1p-TIR1::URA3 leu2 trp1 ura3 not5::NOT5-AID-Myc9-NATMX4


title: ATAC_DNMT_KO_EpiLC_D1_rep1


title: RCC4/VHL Hx/DMSO HIF-2a ChIP rep1

value: HIF-2a (rabbit polyclonal, PM9)


title: ATAC_DNMT_KO_ESC_D0_rep2


title: Not5p_AI_tot03_SC_SP_GTGATC


title: ATAC_DNMT_KO_ESC_D0_rep3


title: Wt_AI_sol01_SC_SP_GACTAG [4]


title: Not5p_AI_tot02_SC_SP_ACGCTG


title: ATAC_DNMT_KO_ESC_D0_rep1


title: RCC4/VHL Hx/ITE HIF-1a ChIP rep1

value: 6 hours

value: HIF-1a (rabbit polyclonal, PM14)


title: RCC4/VHL Nx/FICZ AHR ChIP rep1

value: AHR (Cell Signaling, 83200)


title: RNA_DNMT_WT_EB_D6_rep2

value: EB


title: RNA_DNMT_WT_EB_D2_rep3


title: RCC4/VHL Nx/FICZ HIF-1b ChIP rep1


title: Not5p_AI_sol02_SC_SP_CGTGCA


title: RNA_DNMT_WT_EB_D6_rep1


title: RCC4/VHL Nx/FICZ HIF-2a ChIP rep1


title: ATAC_TET_KO_EpiLC_D1_rep3


title: ATAC_TET_KO_EpiLC_D2_rep1


title: RNA_DNMT_WT_EB_D4_rep2


title: Not5p_AI_sol01_SC_SP_ACTGGT


title: RCC4/VHL Nx/FICZ HIF-1a ChIP rep1


title: ATAC_TET_KO_EpiLC_D2_rep3


title: RNA_DNMT_WT_EB_D4_rep1


title: Not4p_AI_tot03_SC_SP_ACGCTG

value: ADH1p-TIR1::URA3 leu2 trp1 ura3 not4::NOT4-AID-Myc9-NATMX4


title: RCC4/VHL Nx/ITE AHR ChIP rep1


title: Not4p_AI_tot02_SC_SP_GACTAG

value: YPD exponential growth, 15 min auxin 1mM final


title: RNA_DNMT_WT_EB_D2_rep2


title: RCC4/VHL Hx/DMSO HIF-1a ChIP rep1

value: DMSO


title: RNA_DNMT_WT_EpiLC_D2_rep3


title: RNA_DNMT_WT_EB_D2_rep1


title: ATAC_TET_KO_ESC_D0_rep3


title: RCC4/VHL Nx/ITE HIF-1a ChIP rep1


title: Not4p_AI_sol03_SC_SP_CGTGCA

value: HT-5PSeq Multiplexed RNA ligation


title: RNA_DNMT_WT_EpiLC_D2_rep2

value: EpiLC


title: RCC4/VHL Nx/ITE HIF-1b ChIP rep1


title: ATAC_TET_KO_EpiLC_D1_rep2


title: ATAC_TET_KO_EpiLC_D1_rep1


title: RNA_DNMT_WT_EpiLC_D1_rep2


title: ATAC_TET_KO_ESC_D0_rep1


title: ATAC_DNMT_WT_EpiLC_D2_rep3


title: RNA_DNMT_WT_EpiLC_D1_rep1


title: RCC4/VHL Nx/DMSO HIF-2a ChIP rep1


title: Not1p_AI_tot03_SC_SP_GACTAG [3]

value: ADH1p-TIR1::URA3 leu2 trp1 ura3 not1::NOT1-AID-Myc9-NATMX4

value: total RNA


title: RCC4/VHL Nx/DMSO HIF-1a ChIP rep1


title: Not4p_AI_sol02_SC_SP_ACTGGT

value: soluble RNA


title: RNA_DNMT_WT_ESC_D0_rep1

value: ESC


title: Not4p_AI_tot01_CTACAC


title: RNA_DNMT_WT_EpiLC_D2_rep1


title: RCC4/VHL Hx/ITE rep6

data_processing:
Illumina adaptor sequences were trimmed using Trimgalore (0.3.3)
Reads were aligned to Genome Reference Consortium GRCh37 (hg19) using HISAT2 (2.05) (http://daehwankimlab.github.io/hisat2/) and non-uniquely mapped fragments were excluded using Picard tools (2.0.1) (http://broadinstitute.github.io/picard/)
Total read counts for each UCSC defined gene were extracted using HTSeq (0.5.4p3) with ‘intersection-strict’ mode
Significantly regulated genes were identified using DESeq2
Assembly: GRCh37 (hg19)
Supplementary files format and content: tab-delimited text files from htseq

growth_protocol: DMEM culture medium was supplemented with 10% FBS, L-glutamine and penicillin-streptomycin. Cells were plated on 6 cm plates, allowed to grow in phenol red–free DMEM supplemented with 10% dextran-coated charcoal-treated foetal calf serum, L-glutamine and penicillin-streptomycin for approximately 48 hours before treatments. Cells were harvested at approximately 80% confluency.

extract_protocol:
Cells were lysed in TRIzol and total RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo Research), with an on-column DNaseI-treatment. Poly-A mRNA was purified using NEBNext Poly-A mRNA Magnetic Isolation Module.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

treatment_protocol: Hypoxic incubations were performed at 0.5% oxygen for 6 hours in a hypoxia chamber (InvivO2 400 workstation, Ruskinn Technology). Treatments with ITE (100nM) or DMSO vehicle (0.1%) were performed for 6 hours.

value: ITE

value: renal cell carcinoma cell line


title: RCC4/VHL Nx/DMSO HIF-1b ChIP rep1

value: 0.5 hours


title: ATAC_DNMT_WT_EpiLC_D1_rep3


title: Not1p_AI_sol03_SC_SP_ACTGGT [6]


title: RCC4/VHL Hx/ITE rep5


title: RNA_TET_WT_EB_D8_rep2


title: RCC4/VHL Hx/ITE rep4


title: RNA_DNMT_WT_ESC_D0_rep2


title: ATAC_DNMT_WT_EpiLC_D1_rep1


title: Not5p_AI_sol03_SC_SP_TAATGT

value: ADH1p-TIR1::URA3 leu2 trp1 ura3 not5::NOT5-AID-Myc9-NATMX4


title: RNA_TET_WT_EB_D8_rep1


title: RCC4/VHL Hx/ITE rep3

value: 6 hours


title: Not1p_AI_sol01_SC_SP_ACGCTG [4]


title: ATAC_DNMT_WT_EpiLC_D2_rep1


title: RNA_TET_WT_EB_D6_rep3


title: frg_Wt_AI_tot03_SC_SP_CGTGCA

value: MATalpha his3 leu2 ura3 lys2

value: random fragmented HT-5PSeq Multiplexed RNA ligation


title: RNA_TET_WT_EB_D8_rep3

value: EB


title: Not1p_AI_tot02_SC_SP_CTACAC [2]


title: Not4p_AI_sol01_SC_SP_GTGATC

value: ADH1p-TIR1::URA3 leu2 trp1 ura3 not4::NOT4-AID-Myc9-NATMX4


title: RCC4/VHL Nx/DMSO AHR ChIP rep1

value: AHR (Cell Signaling, 83200)


title: ATAC_DNMT_WT_ESC_D0_rep3


title: Not1p_AI_tot01_TAATGT

value: YPD exponential growth, 15 min auxin 1mM final


title: ATAC_DNMT_WT_EpiLC_D2_rep2


title: ATAC_DNMT_WT_EpiLC_D1_rep2


title: Not1p_AI_sol02_SC_SP_GTGATC [5]

value: HT-5PSeq Multiplexed RNA ligation


title: RCC4/VHL Nx/ITE HIF-2a ChIP rep1

value: ITE 100nM

value: HIF-2a (rabbit polyclonal, PM9)


title: RNA_TET_WT_EB_D6_rep2


title: RCC4/VHL Hx/ITE rep2


title: ATAC_TET_KO_ESC_D0_rep2


title: RNA_TET_WT_EB_D6_rep1


title: ATAC_DNMT_WT_ESC_D0_rep1


title: RCC4/VHL Hx/DMSO rep6

value: DMSO


title: frg_Wt_AI_tot01_SC_SP_ACTGGT

value: ADH1p-TIR1::URA3 leu2 trp1 ura3

value: total RNA


title: ATAC_TET_WT_EpiLC_D2_rep3

value: EpiLC


title: ATAC_DNMT_WT_ESC_D0_rep2

value: ESC


title: RCC4/VHL Hx/ITE rep1

value: ITE

value: renal cell carcinoma cell line


title: RNA_TET_WT_EB_D4_rep2


title: ATAC_TET_WT_EpiLC_D2_rep2


title: frg_Wt_AI_sol03_SC_SP_ACGCTG

value: soluble RNA


title: frg_Wt_AI_sol02_SC_SP_GACTAG


title: RNA_TET_WT_EB_D4_rep1


title: RCC4/VHL Hx/DMSO rep5

value: 6 hours


title: RCC4/VHL Hx/DMSO rep4


title: frg_Wt_AI_tot02_SC_SP_CGTGCA

value: MATalpha his3 leu2 ura3 lys2

value: random fragmented HT-5PSeq Multiplexed RNA ligation


title: ATAC_TET_WT_EpiLC_D1_rep3


title: RCC4/VHL Hx/DMSO rep3


title: RNA_TET_WT_EB_D2_rep3

value: EB


title: ATAC_TET_WT_EpiLC_D2_rep1


title: RCC4/VHL Hx/DMSO rep1


title: RCC4/VHL Hx/DMSO rep2


title: RNA_TET_WT_EB_D2_rep2


title: frg_Wt_AI_sol01_SC_SP_CTACAC


title: RNA_TET_WT_EB_D4_rep3


title: frg_Not5p_AI_tot02_SC_SP_GACTAG

value: ADH1p-TIR1::URA3 leu2 trp1 ura3 not5::NOT5-AID-Myc9-NATMX4


title: frg_Not5p_AI_tot03_SC_SP_ACGCTG

value: YPD exponential growth, 15 min auxin 1mM final


title: RCC4/VHL Nx/ITE rep6


title: RNA_TET_WT_EB_D2_rep1


title: ATAC_TET_WT_ESC_D0_rep2


title: frg_Not5p_AI_tot01_SC_SP_CTACAC


title: ATAC_TET_WT_ESC_D0_rep3


title: RNA_TET_WT_EpiLC_D2_rep3


title: RCC4/VHL Nx/ITE rep5


title: RNA_TET_WT_EpiLC_D2_rep2


title: ATAC_TET_WT_EpiLC_D1_rep2


title: ATAC_TET_WT_EpiLC_D1_rep1


title: frg_Not5p_AI_sol02_SC_SP_ACTGGT


title: frg_Not5p_AI_sol03_SC_SP_CGTGCA


title: ATAC_TET_WT_ESC_D0_rep1


title: murineTumor_VavPBcl2_Btg1q36_het, repl5

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to mm10 using STAR with default parameters
TPM were obtained using Rsubread and RefSeq gene annotation
Genome_build: mm10
Supplementary_files_format_and_content: Transcripts per million (TPM)

source_name: Splenic B cells

extract_protocol: RNA-seq libraries were prepared using the Illumina TruSeq stranded mRNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies)

value: Splenic B cells

tag: sorting strategy

value: PNA+ enriched cells, sorted as Live B220+ FAS+ CD38neg using BD Influx cell sorter


title: RNA_TET_WT_EpiLC_D2_rep1


title: RNA_TET_WT_EpiLC_D1_rep3


title: RCC4/VHL Nx/ITE rep2


title: RCC4/VHL Nx/ITE rep3


title: murineTumor_VavPBcl2_Btg1q36_het, repl4


title: RCC4/VHL Nx/ITE rep4


title: RNA_TET_WT_ESC_D0_rep3


title: frg_Not4p_AI_tot03_SC_SP_GACTAG

value: ADH1p-TIR1::URA3 leu2 trp1 ura3 not4::NOT4-AID-Myc9-NATMX4


title: murineTumor_VavPBcl2_Btg1q36_het, repl3

value: PNA+ enriched cells, sorted as Live B220+ FAS+ CD38neg using BD FACSAria II cell sorter


title: frg_Not4p_AI_sol03_SC_SP_ACTGGT


title: murineTumor_VavPBcl2_Btg1q36_het, repl1


title: frg_Not4p_AI_tot02_SC_SP_CTACAC


title: frg_Not4p_AI_tot01_SC_SP_CGTGCA


title: RCC4/VHL Nx/ITE rep1


title: frg_Not4p_AI_sol02_SC_SP_GTGATC


title: RNA_TET_WT_EpiLC_D1_rep1


title: RCC4/VHL Nx/DMSO rep4

value: DMSO


title: frg_Not5p_AI_sol01_SC_SP_GTGATC


title: RNA_TET_WT_ESC_D0_rep1


title: RCC4/VHL Nx/DMSO rep3


title: murineTumor_VavPBcl2, repl3


title: murineTumor_VavPBcl2, repl4


title: frg_Not1p_AI_tot03_SC_SP_CTACAC

value: ADH1p-TIR1::URA3 leu2 trp1 ura3 not1::NOT1-AID-Myc9-NATMX4

value: total RNA


title: murineTumor_VavPBcl2, repl2


title: RCC4/VHL Nx/DMSO rep1


title: murineTumor_VavPBcl2, repl1


title: RNA_TET_WT_ESC_D0_rep2

value: ESC


title: frg_Not1p_AI_tot02_SC_SP_CGTGCA


title: frg_Not4p_AI_sol01_SC_SP_ACGCTG


title: frg_Not1p_AI_tot01_SC_SP_CGTGCA


title: murineGCB_Btg1q36h_het_GFPMYCpositive, repl8

data_processing:
Genome_build: mm10
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to mm10 using STAR with default parameters
RNA-seq TPM were obtained using Rsubread and RefSeq gene annotation
RIP-seq reads were aligned to merged mm10-ERCC92 using STAR with default parameters
RIP-seq read counts were obtained using Rsubread and RefSeq gene annotation.  ERCC-normalized read counts were obtained using Rsubread and RefSeq gene annotation.  Read counts were normalized using RUVg method from RUVSeq package.  TPM were calculated using ERCC-normalized read counts.
Supplementary_files_format_and_content: Transcripts per million (TPM)

source_name: Germinal center B cells transfected with heterozygous Btg1Q36H allele + GFP-Myc with expression of GFP-Myc

extract_protocol:
Takara SMART-Seq v4 Ultra Low Input RNA Kit
Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies)

value: Germinal center B cells

tag: transfection

value: Live B220+ FAS+ GL7+ GFP-Myc+ cells using BD Influx Cell Sorter


title: murineGCB_Btg1q36h_het_GFPMYCpositive, repl7

value: heterozygous Btg1Q36H allele + GFP-Myc with expression of GFP-Myc


title: RCC4/VHL Nx/DMSO rep2

value: 6 hours

value: renal cell carcinoma cell line


title: RCC4/VHL Nx/DMSO rep5


title: RNA_TET_WT_EpiLC_D1_rep2

value: EpiLC

tag: genotype


title: SUDHL4_V5-EGFP_RIPseq_IP, repl2

data_processing:
Genome_build: hg19
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to mm10 using STAR with default parameters
RNA-seq TPM were obtained using Rsubread and RefSeq gene annotation
RIP-seq reads were aligned to merged mm10-ERCC92 using STAR with default parameters
RIP-seq read counts were obtained using Rsubread and RefSeq gene annotation.  ERCC-normalized read counts were obtained using Rsubread and RefSeq gene annotation.  Read counts were normalized using RUVg method from RUVSeq package.  TPM were calculated using ERCC-normalized read counts.
Supplementary_files_format_and_content: Transcripts per million (TPM)

source_name: SUDHL4 cell line transfected with V5-EGFP allele

extract_protocol:
Illumina TruSeq stranded mRNA kit
Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies)

value: SUDHL4 cells

value: V5-EGFP allele

tag: rip antibody

value: RIPantibody


title: SUDHL4_V5-EGFP_RIPseq_input, repl4


title: murineGCB_Btg1q36h_het_GFPMYCnegative, repl7

source_name: Germinal center B cells transfected with heterozygous Btg1Q36H allele + GFP-Myc without expression of GFP-Myc

value: Live B220+ FAS+ GL7+ GFP-Myc- cells using BD Influx Cell Sorter


title: SUDHL4_EV, repl2

source_name: SUDHL4 cell line transfected with empty vector

value: empty vector


title: diff veh2

first: Kenneth

last: White

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the mouse genome using STAR (v2.7.2a) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to mm10 genes using featureCounts (from subread v1.6.2) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 2 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using likelihood ratio test method in edgeR (v3.24.3).
Assembly: mm10
Supplementary files format and content: raw count

source_name: MPC2 cells

growth_protocol: Murine progenitor cells clone 2 (MPC2), a conditionally immortalized mesenchymal stem cell line, were cultured in MEM-alpha (Invitrogen, Thermo-Fisher Scientific) supplemented with 10% fetal bovine serum (FBS; Hyclone), 25 mM L-glutamine, and 25 mM penicillin-streptomycin (Sigma-Aldrich, St. Louis, MO, USA) at 33°C and 5% CO2 to proliferate. Cells were plated at a density of 1.0x10^5 cells per well in 6- or 12-well plates and incubated overnight before being transferred to a 37°C incubator for osteogenic differentiation and cultured in maintenance media supplemented with mineralization conditions of 4 mM beta-glycerophosphate and 50 ug/mL ascorbic acid. Cells were differentiated for 3 weeks with osteogenic media changes every 2-3 days.

extract_protocol:
Total RNA was extracted (with a DNase step) using the same methods as described in “RNA preparation” section of methods. Total RNA was evaluated for its quantity and quality using Agilent Bioanalyzer 2100. For RNA quality, a RIN number of 7 or higher is desired. The RIN number for all of the samples was 10. 100 ng of total RNA was used.
cDNA library preparation includes mRNA purification/enrichment, RNA fragmentation, cDNA synthesis, ligation of index adaptors, and amplification, following the KAPA mRNA Hyper Prep Kit Technical Data Sheet, KR1352 – v4.17 (Roche Corporate). Each resulting indexed library was quantified and its quality accessed by Qubit and Agilent Bioanalyzer, and multiple libraries pooled in equal molarity. The pooled libraries were denatured and neutralized before loading to NovaSeq 6000 sequencer at 300pM final concentration for 100b paired-end sequencing (Illumina, Inc.). Approximately 30-40M reads per library were generated. A Phred quality score (Q score) was used to measure the quality of sequencing. More than 90% of the sequencing reads reached Q30 (99.9% base call accuracy).

treatment_protocol: Both cell types were treated for 48 hours with either vehicle (DMSO) or 50 uM of the HIF-PHI FG-4592 (Roxadustat)

value: Osteocyte

value: vehicle (DMSO)


title: diff FG1

value: 50 uM FG-4592 (Roxadustat)


title: frg_Not1p_AI_sol02_SC_SP_ACGCTG

value: ADH1p-TIR1::URA3 leu2 trp1 ura3 not1::NOT1-AID-Myc9-NATMX4

value: YPD exponential growth, 15 min auxin 1mM final

value: random fragmented HT-5PSeq Multiplexed RNA ligation

value: soluble RNA


title: diff FG2


title: RCC4/VHL Nx/DMSO rep6

value: DMSO


title: murineGCB_Btg1q36h_het_GFPMYCnegative, repl6

value: Germinal center B cells

value: heterozygous Btg1Q36H allele + GFP-Myc without expression of GFP-Myc


title: SUDHL4_V5-EGFP_RIPseq_input, repl2


title: SUDHL4_EV, repl1


title: murineTumor_VavPBcl2_Btg1q36_het, repl2

value: Splenic B cells

value: PNA+ enriched cells, sorted as Live B220+ FAS+ CD38neg using BD Influx cell sorter


title: SUDHL4_V5-EGFP_RIPseq_IP, repl4

value: SUDHL4 cells


title: murineGCB_Btg1q36h_het_GFPMYCpositive, repl6

value: heterozygous Btg1Q36H allele + GFP-Myc with expression of GFP-Myc

value: Live B220+ FAS+ GL7+ GFP-Myc+ cells using BD Influx Cell Sorter


title: undiff FG3

value: MSC


title: SUDHL4_EV, repl3

value: empty vector


title: diff veh3

value: Osteocyte


title: diff FG3


title: murineGCB_Btg1q36h_het_GFPMYCnegative, repl8

value: Live B220+ FAS+ GL7+ GFP-Myc- cells using BD Influx Cell Sorter


title: SUDHL4_V5-EGFP_RIPseq_IP, repl1

value: V5-EGFP allele

value: RIPantibody


title: murineGCB_cre_GFPMYCnegative, repl6

source_name: Germinal center B cells transfected with CD19-Cre control + GFP-Myc without expression of GFP-Myc


title: frg_Not1p_AI_sol01_SC_SP_GACTAG

value: ADH1p-TIR1::URA3 leu2 trp1 ura3 not1::NOT1-AID-Myc9-NATMX4

value: YPD exponential growth, 15 min auxin 1mM final


title: SUDHL4_V5-BTG1q36h_RIPseq_IP, repl4

source_name: SUDHL4 cell line transfected with V5-BTG1Q36H allele

value: V5-BTG1Q36H allele


title: undiff veh2

value: vehicle (DMSO)


title: murineGCB_Btg1q36h_het, repl5

source_name: Germinal center B cells transfected with heterozygous Btg1Q36H allele

value: Germinal center B cells

value: heterozygous Btg1Q36H allele

value: Live B220+ FAS+ GL7+ cells using BD Influx Cell Sorter


title: undiff veh3


title: SUDHL4_V5-EGFP_RIPseq_IP, repl3


title: murineGCB_Btg1q36h_het, repl4


title: frg_Not1p_AI_sol03_SC_SP_GTGATC

value: random fragmented HT-5PSeq Multiplexed RNA ligation

value: soluble RNA


title: murineGCB_cre_GFPMYCpositive, repl6

source_name: Germinal center B cells transfected with CD19-Cre control + GFP-Myc with expression of GFP-Myc


title: SUDHL4_BTG1q36h, repl1

source_name: SUDHL4 cell line transfected with BTG1Q36H allele

value: SUDHL4 cells

value: BTG1Q36H allele


title: SUDHL4_BTG1wt, repl1

source_name: SUDHL4 cell line transfected with BTG1WT allele

value: BTG1WT allele


title: undiff FG2

value: MSC

value: 50 uM FG-4592 (Roxadustat)


title: SUDHL4_V5-BTG1q36h_RIPseq_input, repl4


title: SUDHL4_V5-EGFP_RIPseq_input, repl3


title: SUDHL4_V5-EGFP_RIPseq_input, repl1


title: diff veh1

value: Osteocyte


title: SUDHL4_V5-BTG1q36h_RIPseq_input, repl3


title: murineGCB_cre_GFPMYCpositive, repl5

value: CD19-Cre control + GFP-Myc with expression of GFP-Myc

value: Live B220+ FAS+ GL7+ GFP-Myc+ cells using BD Influx Cell Sorter


title: murineGCB_Btg1q36h_het, repl1


title: SUDHL4_V5-BTG1q36h_RIPseq_IP, repl3

value: RIPantibody


title: SUDHL4_BTG1q36h, repl2