title: SNC46

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software v3.8

source_name: NKSCC

label_protocol: RNA from each sample was labeled according to the manufacturer's recommendations.

extract_protocol: RNA was extracted with QIAGEN FFPE RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: cohort

value: non keratinizing squamous cell cancer


title: 8095AS_2wk

status: Public on Dec 26 2019

type: SRA

city: Philadelphia

first: Daniel

last: Zhang

address: 3400 Civic Center Boulevard

country: USA

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
Raw sequencing data was demultiplexed with bcl2fastq2 v.2.19.0.316 (Illumina) with adapter trimming turned off.
Alignment was performed using STAR v.2.6.1d (Dobin et al., 2012) with the following additional parameters: --outFilterMatchNminOverLread 0.33 --outFilterScoreMinOverLread 0.33 --twopassMode Basic --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 1 --alignMatesGapMax 100000 --alignIntronMax 200000 --chimSegmentReadGapMax 3 --alignSJstitchMismatchNmax 5 -1 5 5 --outSAMstrandField intronMotif --chimOutJunctionFormat 1. GRCh38 (gencode) was used as the reference genome, and gencode v.28 GTF was used as the annotation file.
Multimapping and chimeric alignments were discarded, and uniquely mapping reads were quantified at the exon level and summarized to gene counts using Rsubread (Liao et al., 2019).
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene counts matrix

molecule: total RNA

organism: Homo sapiens

source_name: Glioblastoma organoid

growth_protocol: Glioblastoma organoids were generated by mincing fresh tumor tissue and cultured on an orbital shaker

extract_protocol:
Samples were homogenized in TRIzol using a disposable pestle and handheld motor. RNA clean-up was performed using a Zymo Research Clean & Concentrator kit after TRIzol phase separation according to the manufacturers’ protocol. RNA concentration and quality were assessed using a Nanodrop 2000.
Library preparation was performed as previously described with some minor modifications (Weng et al., 2017). About 100 ng RNA in 3.2 µL was combined with 0.25 µL RNase inhibitor (NEB) and 1 µL CDS primer (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’) in an 8-well PCR tube strip, heated to 70 ºC, and immediately placed on ice. 5.55 µL RT mix, containing 2 µL of 5X SMARTScribe RT buffer (Takara), 0.5 µL of 100 mM DTT (Millipore Sigma), 0.3 µL of 200 mM MgCl2 (Thermo Fisher Scientific), 1 µL of 10 mM dNTPs (Takara), 1 µL of 10 µM TSO primer (5’-AAGCAGTGGTATCAACGCAGAGTACATrGrGrG-3’), 0.25 µL of RNase inhibitor (NEB), and 0.5 µL SMARTScribe reverse transcriptase (Takara) was added to the reaction. RT was performed under the following conditions: 42 ºC for 90 minutes, 10 cycles of 50 ºC for 2 minutes and 42 ºC for 2 minutes, 70 ºC for 15 minutes, and 4 ºC indefinitely. For cDNA amplification, 2 µL of the RT reaction was combined with 2.5 µL of 10X Advantage 2 buffer (Takara), 0.5 µL of 10 mM dNTPs (Takara), 0.25 µL of 10 mM IS PCR primer (5’-AAGCAGTGGTATCAACGCAGAGT-3’), 19.25 µL nuclease free water (ThermoFisher), and 0.5 µL Advantage 2 DNA Polymerase (Takara). Thermocycling conditions were as follows: 94 ºC for 3 minutes, 8 cycles of 94 ºC for 15 s, 65 ºC for 30 s, and 68 ºC for 6 minutes, 72 ºC for 10 minutes, and 4 ºC indefinitely. Amplified cDNA was purified using 0.8X SPRI beads (Beckman Coulter), eluted in 10 µL nuclease-free water, and quantified using Qubit dsDNA HS assay kit (Thermo Fisher Scientific). cDNA was fragmented by combining 100 pg cDNA in 1 µL with 1 µL nuclease free water, 2X TD buffer (20 mM Tris, pH 8.0 (Thermo Fisher Scientific), 10 mM MgCl2, and 16% PEG 8000 (MilliporeSigma), and 0.5 µL Tn5 (Lucigen). The mixture was heated to 55 ºC for 10 minutes, and the reaction was terminated upon the addition of 1.25 µL of 0.2% SDS (Fisher) and incubation at room temperature for 10 minutes. Fragments were amplified by adding 27.75 µL nuclease free water (Thermo Fisher Scientific), 10 µL of 5X KAPA HiFi Fidelity Buffer (Roche), 10 mM dNTPs (Roche), 1 µL of 10 mM Nextera i7 primer, 1 µL of 10 mM Nextera i5 primer, and 2 µL KAPA HiFi Polymerase (Roche). Thermocycling conditions were as follows: 72 ºC for 5 minutes, 95 ºC for 1 minute, 14 cycles of 95 ºC for 30 s, 55 ºC for 30 s, and 72 ºC for 30 s, 72 ºC for 1 minute, and 4 ºC indefinitely. DNA was purified twice with 0.8X SPRI beads (Beckman Coulter) and eluted in 10 µL of 10 mM Tris, pH 8 (Thermo Fisher Scientific). Samples were quantified by qPCR (KAPA) and pooled at equal molar amounts. Final sequencing library fragment sizes were quantified by bioanalyzer (Agilent) with an average size of ~350 bp, and concentrations were determined by qPCR (KAPA).

treatment_protocol: In an effort to minimize variability due to sampling, we pooled 5-10 pieces of parental tumor tissue or GBOs into one sample for analyses. They were snap-frozen on dry ice, and stored at -80 ºC until processing.

tag: culture duration

value: 2 weeks


title: Single cells UP-8165PV Tumor

data_processing:
Raw sequencing data was demultiplexed with bcl2fastq2 with adapter trimming turned off. Additional processing was performed using drop-seq tools v.2.1.0 with GRCh38 as the reference genome, and gencode v.28 GTF was used as the annotation file.
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene counts matrix was constructed using drop-seq tools v2.1.0

source_name: Glioblastoma

extract_protocol: Drop-seq was performed as previously described with minor modifications (Macosko et al., 2015). Microfluidic chips were obtained from FlowJEM with plasma bonding and aquapel treatment using the same design as previously published. Each droplet co-encapsulation run was performed with 50% additional reagent volume to account for syringe and tubing dead volume as well as occasional microfluidic channel clogging and re-starts. Each sample was loaded onto 2-4 droplet generation runs, and cell suspensions and droplets were kept on ice prior to droplet encapsulation and droplet breakage. In the cDNA PCR amplification stage, between 4,000-8,000 beads were combined in a single PCR tube reaction and purified individually using 0.6x SPRI beads. cDNA across multiple runs of the same sample were pooled together and used as input for tagmentation, where the tagment reaction time was increased to 8 minutes. Final samples were purified once with 0.6x SPRI beads and a second time with 1.0x SPRI beads. Sequencing library fragment sizes were quantified by bioanalyzer, and concentrations were quantified by qPCR.

treatment_protocol: Multiple tumor pieces and GBOs were dissociated using a papain-based neural tissue dissociation kit (Miltenyi Biotech). Crude dissociates from parental tumor samples were treated with ammonium chloride based RBC lysis buffer for 5 minutes. All samples were washed three times by centrifugation at 200 g for 5 minutes and resuspension in 10 mL of calcium-free, magnesium-free DPBS. Cells were strained through a 70 µm filter (Miltenyi Biotech), analyzed for viability by trypan blue staining, and counted using an automatic cell counter.

value: 0 weeks


title: SNC44

type: RNA

label: biotin

source_name: SNEC

value: sinonasal neuroendocrine cancer


title: SNC45

source_name: SNUC

value: sinonasal undifferentiated cancer


title: SNC40


title: SNC47


title: SNC42


title: SNC39


title: SNC43


title: SNC41


title: 8095AS_Tumor


title: SNC38


title: SNC37


title: SNC34


title: 8080_Tumor


title: 8080_2wk


title: SNC36


title: SNC35


title: SNC32


title: 8036_2wk


title: 8036_1wk

value: 1 week


title: 8036_12wk

value: 12 weeks


title: 8036_Tumor


title: Single cells UP-8165PV 2wk


title: 8032_12wk


title: SNC30


title: 8032_2wk


title: 8032_1wk


title: SNC29


title: SNC31


title: SNC33


title: SNC27


title: 8017_2wk


title: 8017_12wk


title: 8017_Tumor


title: SNC28


title: 8017_1wk


title: SNC26


title: SNC25


title: SNC22


title: SNC19


title: 8010_1wk


title: 8032_Tumor


title: H1975_Control_12h_1

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

hyb_protocol: 15 µg labelled cRNA were hybridized onto Human HuGene20-st  arrays (Affymetrix, CA, USA) for 16h at 45°C using Hybridization Wash and Stain Kit (Affymetrix)

scan_protocol: Arrays were washed and stained with GeneChip Fluidics Station 450 and scanned with GeneChip Scanner 3000 using the GeneChip Operating Software (Affymetrix).

data_processing: R/Bioconductor using RMA as implemented in the R/Bioconductor package 'oligo'

label: Biotin

source_name: Lung

label_protocol: Biotinylated cRNA was generated from 1.5 µg total RNA using the One-Cycle Target Labeling Assay (Affymetrix).

growth_protocol: The human lung adenocarcinoma cell line H1975 was purchased from ATCC and cultivated in Dulbecco's modified Eagle's Medium (DMEM, Lonza) supplemented with 10% FCS (Gibco) and 1% penicillin/streptomycin (Gibco).

extract_protocol: RNeasy Mini Plus Kit (Qiagen, Hilden, Germany)

treatment_protocol: Cells were starved over night before treatment and then supplemented with 2 ng/ml of human TGFβ1 (R&D Systems #240-B-010) and 80 ng/ul of human HGF (R&D Systems) was used for stimulation and RNA was extacted at the indicated time points.

tag: gender

value: female

tag: cell line

tag: time

tag: tissue

value: Lung

tag: stimulus

value: Control


title: 7966_12wk


title: 8010_12wk


title: 7966_4wk

value: 4 weeks


title: SNC24


title: SNC21


title: SNC16


title: SNC15


title: 8010_4wk


title: 7966_2wk


title: SNC20


title: SNC14


title: SNC18


title: 7966_Tumor


title: SNC23


title: 8010_Tumor


title: SNC17


title: 7966_1wk


title: 7955_12wk


title: SNC13


title: SNC12


title: KW93

city: Islamabad

first: Muhammad Yasir

last: Abdur Rehman

state: ICT

department: Environmental Sciences

country: Pakistan

institute: Quaid-i-Azam University

description:
Peripheral Blood Stored in RNA later
Gene expression analysis of rural subjects exposed to elevated Arsenic levels in drinking water

hyb_protocol: 600ng of Cy3 Labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1X Agilent Fragmentation Buffer, 10X Blocking Agent followed by 25µl of 2X Hi-RPM Hybridization buffer to stop the fragmentation reaction as per manufacturer guidelines for Agilent Sureprint G3 Human GE Kit 8 x 60K V2 G4851B Microarrays. Hybridization Assembly wase made as per guidelines of Agilent microarrays Hybridization Chamber User guide (G2534-90001). 40µl of Hybridized sample was loaded on slide in Chamber and Incubated for 17 hours in Hybridization oven at 65°C. Gene expression wash buffers containg 10% Triton-X102 were used for washing. Microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation

scan_protocol: Immediately after washing, slides were scanned on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides. Pixel intensities were extracted as raw data from the scan images using Agilent Feature Extraction Software (Agilent) using default parameters

data_processing: All arrays were checked for their quality using ArrayQC (https://github.com/BiGCAT-UM/arrayQC_Module/), a quality control pipeline in R (version 2.10.1; The R Foundation for Statistical Computing, Vienna, Austria). For each spot the following steps were taken: local background correction, flagging of bad spots, controls and spots with too low intensity, log2 transformation, and quantile normalization. We filtered out control probes and low expressed probes. To get an idea of how bright expression probes should be, we computed the 95% percentile of the negative control probes on each array. We kept probes that are at least 10% brighter than the negative controls on at least 18 arrays (i.e. smallest number of subjects per exposure group). Next the avereps function was used to average replicate spots.

source_name: High Arsenic exposed subjects (Mean Urinary As. 196.48±46.80 µg/g.creat)

label_protocol: Cyanine-3 (Cy3) labelled cRNA was prepared from 200ng Total RNA using Agilent one colour Quick Amp Labeling kit according to manufacturer protocol followed by Qiagen RNAeasy Column Purification. Purified cRNA yeild was measured through Nanodrop-1000 Spectrophotometer

extract_protocol: RNA from the samples taken in RNA later was isolated using Ambion Ribopure-Blood RNA Kit (Cat#AM1928) as per manufacturer guidelines. Extracted RNA was quantified using Nanodrop-1000 Spectrophotomer and RNA quality was checked through Agilent 2100 Bioanalyzer

treatment_protocol: Freshly taken blood samples were taken RNA later and within two hours of samples collection, samples were stored at -80C

value: Whole Blood

value: Female

tag: age group

value: 40 or Above

tag: smoking status

value: Non smokers

tag: residence type

value: Rural


title: KW89


title: KW81


title: 7955_2wk


title: 7955_1wk


title: 7955_4wk


title: SNC10


title: 7955_Tumor


title: Dnmt3ab_DKO_E65_ExE_B6DBAxPWK_RRBS_embryo6

city: Cincinnati

first: Zhiyuan

last: Chen

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

description:
Sample 18
Acute depletion of Dnmt3a/3b by 1-cell CRIPSR/Cas9 injection.
5mC

library_source: genomic

data_processing:
RNA-seq datasets:
Low quality bases and sequencing adaptors of raw RNA-seq reads were trimmed using Trim Galore (version 0.4.5) with parameters “-q 20 –length 20bp”. Reads after trimming were then aligned to the mm9 reference genome using HISAT2 (version 2.1.0) with parameters “--sp 1000,1000 --dta-cufflinks --no-unal”.
Following reads mapping, uniquely aligned reads were retrieved by selecting the alignment records with “NH:i:1” tag and mapping quality greater than 30.
SNPsplit (version 0.3.2) was used separate parental-allele-specific reads and bamCoverage from deepTools (version 3.0.2) was used to generate bigwig tracks with parameters “--skipNonCoveredRegions --binSize 10 --scaleFactor 1”.
Raw read counts for each gene were generated using TEtranscripts (version 1.5.1) and statistical significance [i.e. false discovery rate (FDR)] was computed using the DESeq R package (version 1.34.1) . Only genes with RPKM > 1 in either group, FDR < 0.05 and fold change (FC > 2) were considered as differentially expressed. RPKM values were generated using Cufflinks (version 2.2.1) with default parameters.
WGBS datasets:
WGBS raw reads were trimmed using Trim Galore (version 0.4.5) with parameters “-q 20 –length 35bp -clip-R1 9 –three_prime_clip_R1 9”. Following reads trimming, Bismark (version 0.17.0) was used to align the reads to the mm9 reference genome.
Only uniquely aligned and non-PCR duplicate reads were used for downstream analyses. PCR-duplicates were identified using “MarkDuplicates” from Picard Tools (version 2.8.0). The DNA methylation level for each CpGs was computed as “reads containing methylated C / (reads containing methylated C + reads containing unmethylated C).
Parental-origins of the WGBS reads were determined using SNPsplit (version 0.3.2) and “bedGraphToBigWig” was used to convert bedGraph format to bigwig tracks. The minimum reads coverage for non-allelic and allelic DNA methylation tracks are five and three, respectively.
RRBS datasets:
RRBS reads were trimmed using Trim Galore (version 0.4.5) with parameters “--rrbs --paired -q 20 –length 35bp”. Bismark (version 0.17.0) was used to align the trimmed reads to the mm9 reference genome with default parameters. B6/DBA and PWK SNPs were masked as “N” for the reference assembly.
Uniquely aligned reads were used to compute methylation levels of each CpGs similar to the WGBS datasets. Generation of allelic DNA methylation tracks are the same as the WGBS datasets except that only CpGs with >5 reads coverage were used.
CUT&RUN datasets:
After quality trimming using Trim Galore version (0.4.5), the CUT&RUN reads were aligned to a custom mm9 reference genome (B6/129 and PWK SNPs masked as “N” for H3K4me3 and B6/DBA and PWK SNPs marked as "N" for H3K27me3) using Bowtie2 (version 2.2.9) with the following parameter: “-t -q -N 1 -L 25 --no-unal -I 150 -X 800 --no-mixed --no-discordant”.
After removing non-uniquely mapped reads and PCR duplicates, MACS2 (version 2.1.1) was used to call H3K4me3 and H3K27me3 peaks.
The CUT&RUN bigwig tracks were generated using BamCoverage in deepTools (version 3.0.2).
For allelic H3K27me3 and H3K4me3 enrichment analyses, the parental origins of the reads were determined using SNPsplit (version 0.3.2).
Genome_build: For datasets involved with Dnmt3l and Eed transgenic mouse lines, reference genome was the mm9 (MGSCv37) build with B6/129 and PWK SNPs masked as "N". For Dnmt3a/3b acute depletion experiments, mm9 (MGSCv37) build with B6/DBA and PWK SNPs masked as "N" was used.
Supplementary_files_format_and_content: *.bw: BigWig files that can be uploaded on a genome browser to view methylated cytosine, H3K27me3, H3K4me3, and RNA levels at different genomic locations.

molecule: genomic DNA

organism: Mus musculus

source_name: E6.5 extraembryonic ectoderm

extract_protocol:
As all libraries generated in this study involved low-input techniques, samples collected were directly put into lysis buffer for further library construction.
RNA-seq (Sample 1-13):
For low-input RNA-seq libraries, SMARTer Ultra Low Input RNA cDNA preparation kit (Clontech, 643890) was used for reverse transcription and cDNA amplification. cDNA were then fragmented, adaptor-ligated and amplified using Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s instructions. Single-end 100bp sequencing was performed on a HiSeq 2500 sequencer (Illumina).
Bisulfite-seq (Sample 24-25):
For low-input whole genome bisulfite sequencing (WGBS), the libraries were constructed using the PBAT method (Clark SJ et al., Nature Protocol. 2017 Mar; 12(3):534-547, PMID:28182018).
Bisulfite-seq (reduced representation) (Sample 14-19):
For low-input RRBS, the libraries were prepared as previously described (Shen L et al., Cell Stem Cell. 2014 Oct 2; 15(4):459-471. PMID:25280220).
H3K27me3 and H3K4me3 profiling using CUT&RUN (Sample 20-23, 26-31):
Eed CTR and matKO embryos H3K4me3 and H3K27me3 CUT&RUN libraries were constructed as previously described (Skene and Henikoff, 2017 eLife. 2017; 6: e21856, PMID: 28079019).

tag: strain/background

value: B6/DBA x PWK

tag: parental genotype

value: WT x WT

value: E6.5 extraembryonic ectoderm


title: SNC09


title: KP169

value: Male


title: SNC11

value: non keratinizing squamous cell cancer


title: KW80


title: SNC08

value: sinonasal neuroendocrine cancer


title: KP148

value: 26-39 years


title: BD176


title: 7930_12wk

value: 12 weeks


title: SNC06

value: sinonasal undifferentiated cancer


title: KP158


title: KM43

value: 16-25 years


title: KW84


title: SC39


title: SNC07


title: 7930_4wk


title: KW87


title: SNC05


title: SC34


title: 7930_2wk

value: 2 weeks


title: 7930_1wk

value: 1 week


title: KW85

value: Whole Blood


title: GR134


title: 7930_Tumor

value: 0 weeks


title: BD191


title: 7884T_12wk


title: GR132


title: SNC02


title: GR115


title: SNC03


title: SNC04


title: GR126


title: SM12


title: BD178

source_name: Medium Arsenic exposed subjects (Mean Urinary As. 84.77±9.36 µg/g.creat)

value: Female


title: 7884T_8wk

value: 8 weeks


title: KP173

value: 40 or Above

value: Non smokers

value: Rural


title: 7884T_2wk


title: 7884T_1wk


title: KP156


title: 7884T_Tumor


title: 7884F_12wk


title: KW83


title: KP151


title: GR112


title: 7884F_8wk


title: KW78


title: 7884F_2wk


title: Oa_CTR_T40_4

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

description: Blood samples were aseptically collected in Paxgene blood collection tubes, allowed to rest for 2 hours at room temperature, then stored at –20 °C till the extraction process.

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized using R2.15.0 statistical software.

organism: Ovis aries

source_name: Sheep, Ovis aries, female, 3-4 y old, control

label_protocol: Amplification and labelling was done according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

extract_protocol: RNA from blood samples was isolated using Paxgene RNA extraction kit, according to manufacturer's instruction. Isolated RNA was purified using Qiagen RNeasy Mini Kit protocol.

value: female

tag: age

value: 3-4 y old

value: Blood sample


title: KP160

value: Male


title: SNC01

value: sinonasal neuroendocrine cancer


title: Oa_CTR_T40_5


title: KW76


title: Oa_CTR_T40_2


title: GR135


title: Oa_CTR_T40_1


title: KM59


title: KM54


title: SM20

value: 26-39 years


title: Oa_CTR_T0_3


title: KM46


title: CF74


title: Oa_CTR_T40_3


title: SM17


title: SM8


title: Oa_CTR_T0_5


title: SC33


title: 7867_4wk

value: 4 weeks


title: 7867_12wk

value: 12 weeks


title: 7884F_1wk


title: 7867_2wk

value: 2 weeks


title: SM7

value: 16-25 years


title: Oa_CTR_T0_2


title: 7884F_Tumor


title: BD174

source_name: Low Arsenic exposed subjects (Mean Urinary As. 36.28±10.13 µg/g.creat)

value: Whole Blood


title: GR140


title: Oa_CTR_T0_4


title: BD193


title: Oa_CTR_T0_1


title: Oa_IOD_T40_10

source_name: Sheep, Ovis aries, female, 3-4 y old, supplemented (IOD 28 mg/animal/day)


title: BD190


title: KM47


title: SC26


title: SC29


title: Oa_IOD_T40_8


title: AK201


title: 7867_Tumor

value: 0 weeks


title: BD195

value: Female


title: Oa_IOD_T40_9


title: Oa_IOD_T40_7


title: KP161


title: 7803_12wk


title: 7803_4wk


title: 7867_1wk

value: 1 week


title: BD187


title: Oa_IOD_T40_6


title: 7803_2wk


title: 7803_1wk


title: 7803_Tumor


title: KM52


title: BD192


title: Oa_IOD_T40_5


title: 7790_12wk


title: SM16


title: GR124


title: SM19


title: 7790_4wk


title: Eed-ETA-rep2

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

institute: European Institute of Oncology

data_processing:
Paired-end reads were aligned to the mouse reference genome mm10, or mm10 and dm6 for histone ChIP-Rx, using Bowtie v1.2.2 (Langmead et al., 2009) without allowing for multi-mapping (–m 1) and parameters -I 10 -X 1000. PCR duplicates were removed using samblaster (Faust and Hall, 2014). Ambiguous reads mapping to both mm10 and dm6 were discarded. Peaks were called using MACS2 v2.1.1 (Zhang et al., 2008) with parameters -f BAMPE --keep-dup all -m 10 30 -p 1e-10.
Reads were aligned to the mouse reference genome mm10 using STAR v2.7 without allowing multimapping reads (--outFilterMultimapNmax 1). PCR duplicates were removed using samblaster (Faust and Hall, 2014). Gene counts were calculated using featureCounts (Liao et al., 2014) with parameters -s 0 -t exon -g gene_name using Gencode M21 (GRCm38) annotation downloaded from (https://www.gencodegenes.org/mouse/). Differential expression analyses were performed using the R package DESeq2 v1.20 (Love et al., 2014) using default parameters. Log2FoldChanges and adjusted p-values were corrected using the apeglm (Zhu et al., 2019) and IHW (Ignatiadis et al., 2016) packages, respectively.  Genes with an absolute log2 fold change of 1.5 and FDR < 0.05 were considered as differentially expressed
Genome_build: mm10
Supplementary_files_format_and_content: counts.tsv : raw counts, Normalized_counts.tsv : normalized counts (DESeq2), Eed_OHT-vs-Eed_ETA_diffexp_log2fc1.5_pval0.05.tsv : differential expression results

source_name: mESC

growth_protocol: mESCs were grown on 0.1% gelatin-coated dishes in 2i/LIF-containing GMEM medium (Euroclone) supplemented with 20% fetal calf serum (Euroclone), 2 mM glutamine (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Gibco), 0.1 mM non-essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), 50 µM ß-mercaptoethanol phosphate buffered saline (PBS; Gibco), 1000 U/ml leukemia inhibitory factor (LIF; produced in-house), and GSK3β and MEK 1/2 inhibitors (ABCR GmbH) to a final concentration of 3 mM and 1 mM, respectively

extract_protocol:
Total RNA was extracted with the Quick-RNA™ MiniPrep extraction kit (Zymo Research) and retro-transcribed with ImProm-II™ Reverse Transcription System (Promega) according to the manufacturer’s instructions
RNA-seq was performed following SMART-seq2 protocol (Picelli et al., 2014)

treatment_protocol: Indicated cells were treated for 72 h with 0.5 μM 4-hydroxytamoxifen (OHT; or EtOH as vehicle) in order to delete Ring1b gene

tag: chip antibody

tag: library strategy

value: RNA-seq


title: WT72-MTF2KO-H3K27me3Inp

extract_protocol:
ChIP experiments were performed according to standard protocols as described previously (Ferrari et al., 2014)
DNA libraries were prepared with 2–10 ng of DNA using an in-house protocol (Blecher-Gonen et al., 2013) by the IEO genomic facility

value: Input

value: ChIP-seq


title: Eed-OHT-rep1


title: WTETA-MTF2


title: Eed-OHT-rep2


title: WT72-Rybp

value: Rybp


title: WTETA-JARID2


title: Oa_IOD_T40_2

value: female

value: 3-4 y old


title: Oa_IOD_T40_1

value: Blood sample


title: Eed-ETA-rep1


title: Oa_IOD_T40_4


title: Oa_IOD_T40_3


title: WT72-MTF2KO-SUZ12


title: WT72-MTF2KO-H3K27me3


title: Oa_IOD_T0_10

source_name: Sheep, Ovis aries, female, 3-4 y old, unsupplemented control


title: SM18

value: Male

value: Non smokers

value: Rural


title: WT72-MTF2


title: Oa_IOD_T0_9


title: Oa_IOD_T0_8


title: 7790_2wk


title: WT72-JARID2


title: WT72-EPOP

value: EPOP


title: 7790_1wk


title: WT72-Cbx7


title: WT72-AEBP2


title: 7790_Tumor


title: WT48-MTF2


title: PARETA-MTF2KO-H3K27me3


title: PARETA-MTF2KO-SUZ12


title: PARETA-Rybp


title: 7788PMS_4wk

value: 4 weeks


title: Oa_IOD_T0_7


title: 7788PMS_1wk


title: 7788PMS_12wk

value: 12 weeks


title: PARETA-MTF2KO-H3K27me3Inp


title: WT48-JARID2


title: Oa_IOD_T0_6


title: PARETA-MTF2


title: PARETA-EPOP


title: 7788PMS_2wk

value: 2 weeks


title: PARETA-Cbx7


title: PARETA-AEBP2


title: Oa_IOD_T0_2


title: Oa_IOD_T0_4


title: PARE72-Rybp


title: Oa_IOD_T0_3


title: 7788POS_12wk


title: PAR72-MTF2KO-SUZ12


title: 7788PMS_Tumor

value: 0 weeks


title: Oa_IOD_T0_5


title: CHMP2Bintron5 E rep 6

city: Strasbourg

first: Frédérique

last: René

address: 11 rue Humann

department: U1118 INSERM

country: France

institute: INSERM  - University of Strasbourg

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were mapped onto mm10 assembly of mouse genome using Tophat v2.0.14 (Kim et al., 2013) and bowtie2 v2.1.0 aligner.
Quantification of gene expression was performed using HTSeq v0.6.1 (Anders et al., 2015) using gene annotations from Ensembl release 81.
Genome_build: mm10
Supplementary_files_format_and_content: Tabulated text file containing raw read counts in each sample.

source_name: spinal cord

extract_protocol:
Total RNA was prepared following standard protocols. Briefly, each frozen sample was placed into a tube containing a 5-mm stainless steel bead. Working on ice, 1 mL Trizol reagent (Invitrogen, Groningen, The Netherlands) was added, and homogenization was performed twice in a TissueLyser (Qiagen) at 30 Hz for 3 minutes. Samples for RNA-sequencing analysis were then processed using the RNeasy Mini Kit (Qiagen, 74104) according to manufacturer instructions.
Libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA Sample Preparation kit according to Illumina user guide (PN 15031047) with the following modifications: 2 minutes mRNA fragmentation and 12 cycles library PCR amplification.

tag: strain

value: FVB/N x C57BL/6 x DBA/2

tag: genotype

value: CHMP2Bintron5; 12 copies

value: 10-12 months


title: 7788POS_4wk


title: PARETA-JARID2


title: CHMP2Bintron5 E rep 5


title: PAR72-MTF2KO-H3K27me3Inp

value: Input


title: Oa_IOD_T0_1


title: PAR72-MTF2KO-H3K27me3

value: ChIP-seq


title: 7788POS_1wk

value: 1 week


title: PAR72-MTF2


title: 7788POS_2wk


title: CHMP2Bintron5 E rep 4


title: PAR72-JARID2


title: CHMP2Bintron5 E rep 2


title: PAR72-EPOP


title: CHMP2Bintron5 E rep 3


title: 7788POS_Tumor


title: PAR72-AEBP2


title: PAR48-MTF2


title: CHMP2Bintron5 E rep 1


title: PAR72-Cbx7


title: PAR48-JARID2


title: I53SETA-MTF2


title: I53SETA-JARID2


title: 7788LAT_4wk


title: WT E rep 6

value: non transgenic control


title: I53S72-Rybp

value: Rybp


title: WT E rep 5


title: I53S72-MTF2KO-H3K27me3


title: WT E rep 4


title: I53S72-MTF2KO-H3K27me3Inp


title: I53S72-MTF2


title: 7788LAT_1wk


title: WT E rep 3


title: I53S72-JARID2


title: 7788LAT_Tumor


title: I53S72-EPOP


title: I53S72-Cbx7


title: 7788MED_12wk


title: WT E rep 2


title: 7788LAT_12wk


title: 7788MED_4wk


title: I53S48-MTF2


title: 7788MED_2wk


title: 7788MED_1wk


title: WT-ETA-rep2

data_processing:
Paired-end reads were aligned to the mouse reference genome mm10, or mm10 and dm6 for histone ChIP-Rx, using Bowtie v1.2.2 (Langmead et al., 2009) without allowing for multi-mapping (–m 1) and parameters -I 10 -X 1000. PCR duplicates were removed using samblaster (Faust and Hall, 2014). Ambiguous reads mapping to both mm10 and dm6 were discarded. Peaks were called using MACS2 v2.1.1 (Zhang et al., 2008) with parameters -f BAMPE --keep-dup all -m 10 30 -p 1e-10.
Reads were aligned to the mouse reference genome mm10 using STAR v2.7 without allowing multimapping reads (--outFilterMultimapNmax 1). PCR duplicates were removed using samblaster (Faust and Hall, 2014). Gene counts were calculated using featureCounts (Liao et al., 2014) with parameters -s 0 -t exon -g gene_name using Gencode M21 (GRCm38) annotation downloaded from (https://www.gencodegenes.org/mouse/). Differential expression analyses were performed using the R package DESeq2 v1.20 (Love et al., 2014) using default parameters. Log2FoldChanges and adjusted p-values were corrected using the apeglm (Zhu et al., 2019) and IHW (Ignatiadis et al., 2016) packages, respectively.  Genes with an absolute log2 fold change of 1.5 and FDR < 0.05 were considered as differentially expressed
Genome_build: mm10
Supplementary_files_format_and_content: Ring1_ETA-vs-WT_ETA_diffexp_log2fc1.5_pval0.05.tsv: Differential Expression Analysis, I53S_ETA-vs-WT_ETA_diffexp_log2fc1.5_pval0.05.tsv: Differential Expression Analysis, Ring1_ETA-vs-I53S_ETA_diffexp_log2fc1.5_pval0.05.tsv: Differential Expression Analysis, Ring1_OHT-vs-WT_OHT_diffexp_log2fc1.5_pval0.05.tsv: Differential Expression Analysis, I53S_OHT-vs-WT_OHT_diffexp_log2fc1.5_pval0.05.tsv: Differential Expression Analysis, Ring1_OHT-vs-I53S_OHT_diffexp_log2fc1.5_pval0.05.tsv: Differential Expression Analysis, Ring1_OHT-vs-Ring1_ETA_diffexp_log2fc1.5_pval0.05.tsv: Differential Expression Analysis, I53S_OHT-vs-I53S_ETA_diffexp_log2fc1.5_pval0.05.tsv: Differential Expression Analysis, WT_OHT-vs-WT_ETA_diffexp_log2fc1.5_pval0.05.tsv: Differential Expression Analysis, Normalized_counts.tsv: Normalized counts, Raw_counts.tsv: Raw counts


title: I53S48-JARID2


title: WT E rep 1


title: I53S72-MTF2KO-SUZ12


title: CHMP2Bintron5 S rep 4

value: 6 months


title: E14_input


title: 7788LAT_2wk


title: Ring1-ETA-rep2


title: CHMP2Bintron5 S rep 2


title: WT-OHT-rep2


title: CHMP2Bintron5 S rep 3


title: 7788MED_Tumor


title: Ring1-ETA-rep1


title: Ring1-OHT-rep1


title: I53S72-AEBP2


title: I53S-OHT-rep2


title: 7788ANT_12wk


title: I53S-ETA-rep2


title: WT S rep5


title: Ring1-OHT-rep2


title: WT-ETA-rep1


title: 7788ANT_4wk


title: I53S-ETA-rep1


title: I53S-OHT-rep1


title: WT S rep3


title: PAROHT-PCGF6


title: 7788ANT_2wk


title: WTOHT-JARID2


title: WTOHT-H2A119Ub


title: 7788ANT_1wk


title: PAROHT-PCGF2


title: 7788ANT_Tumor


title: WT S rep2


title: WT S rep1


title: UP-8095AS GBO

data_processing:
Raw sequencing data was demultiplexed with bcl2fastq2 with adapter trimming turned off.
Alignment was performed using BWA-MEM with default parameters and a GRCh38 reference genome kindly provided by the Broad Institute on a public GATK resource FTP server (Li and Durbin, 2009). Pre-processing according to GATK best practices, including marking PCR duplicates and base quality recalibration, were performed using Picard tools v.1.141 and GATK v.4.1.0.0. (DePristo et al., 2011; McKenna et al., 2010; Van der Auwera et al., 2013). A database of known polymorphic sites was used from the GATK resource bundle based on dbSNP build 146.
Somatic variants were identified using four different variant calling tools: Mutect2, Varscan2, Freebayes, and Manta/Strelka2. Mutect2 was run with a panel of normals composed of the 11 samples used in this study, a population germline variant resource from gnomAD (Broad Institute), and allele frequencies of variants not included in the germline resource set to 0.0000025 (Cibulskis et al., 2013). GATK contamination detection was performed using a small ExAC reference provided by the GATK resource bundle, and filtering was performed using default parameters. Varscan2 was run using default parameters, and somatic variants were filtered for a p-value < 0.05 and alternate allele frequency > 0.05 (Koboldt et al., 2012; Li et al., 2009). Freebayes was run in somatic mode with the following additional parameters (Garrison and Math, 2012): -F 0.05 --pooled-continuous --pooled-discrete. Variants were filtered using vcflib by breaking multiallelic records into separate lines, identifying putative somatic variants by comparison with the paired whole blood sample, filtering for variant calls where the QUAL field >20, and filtering for variant calls where the coverage was > 20. Prior to running Strelka2, Manta was used to call candidate somatic indels in exome mode across only the primary GRCh38 contigs (Chen et al., 2016). Then, Strelka2 was run in exome mode using identified candidate indels also across the primary GRCh38 contigs to identify somatic variants (Kim et al., 2018). Somatic variants were filtered using default settings. VCFtools was used for variant manipulations throughout these analyses (Danecek et al., 2011).
Identified somatic variants in the individual samples were called if identified by two or more variant calling tools using the above described workflow. Variants identified in the parental tumor and corresponding GBOs were pooled to yield a final variant list. Allele frequencies were queried at these sites in the parental tumors and corresponding GBOs using bcftools mpileup accepting anomalous read pairs and disabling probabilistic realignment for base alignment quality calculation (Li, 2011). This approach of “recovering” variants is inspired by previous work in cancer organoids (Kopper et al., 2019). Annovar was used to annotate variants with the following databases (Wang et al., 2010): RefGene (2017), dbNSFP35a (Liu et al., 2011; Liu et al., 2016), COSMIC v88 (Forbes et al., 2017), ClinVar (Landrum et al., 2016), and avsnp (based on dbsnp 150). Variants highlighted in in Figure 3C come from a list of significantly mutated genes from work by Brennan and coworkers (Brennan et al., 2013).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tables of somatic variants in the glioblastoma tumor and corresponding glioblastoma organoids

extract_protocol:
DNA was extracted using the Zymo Quick-DNA Microprep Kit. DNA quality were assessed using a Nanodrop 2000 (Thermo Fisher Scientific) and quantified using the Qubit high sensitivity dsDNA assay (Thermo Fisher Scientific).
Exome-seq libraries were prepared using the Nextera Flex for Enrichment kit (Illumina), Illumina exome panel oligos (Illumina), and IDT for Illumina DNA UD set A index primers (Illumina) according to the manufacturer’s instructions. Genomic DNA inputs varied from 25 to 300 µg, and pre-enrichment samples were combined at equal amounts by mass in 9 or 10 plex pools for enrichment. Sequencing library fragment sizes were quantified by bioanalyzer (Agilent), and concentrations were quantified by qPCR (KAPA). Samples were combined 18- or 19-plex equimolar pools with whole blood, corresponding parental tumor, and corresponding GBO combined in the same sequencing run

treatment_protocol: At least 5-10 pieces of parent tumor or GBOs at 2 weeks were combined into one sample, snap-frozen on dry ice, and stored at -80 ºC until processing. A 50 µL aliquot of whole blood obtained at the time of surgery was also snap-frozen on dry ice and stored at -80 ºC until processing.

tag: tumor vs. normal

value: Tumor


title: CHMP2Bintron5 S rep 1


title: I53SOHT-H2A119UbInp


title: I53SOHT-SUZ12


title: CHMP2Bintron5 A rep5

value: 1.5 month


title: CHMP2Bintron5 A rep4


title: UP-8095AS Tumor

tag: culture duration


title: WT-OHT-rep1


title: WT S rep4


title: WTOHT-H2A119UbInp


title: PARETA-PCGF6


title: WTOHT-PCGF6


title: UP-8080 GBO


title: PAROHT-SUZ12


title: CHMP2Bintron5 A rep2


title: WTOHT-SUZ12


title: UP-8080 Blood

source_name: Whole Blood

value: Normal


title: I53SOHT-PCGF6


title: PARETA-H2A119Ub


title: CHMP2Bintron5 A rep1


title: UP-8036 GBO


title: WTA rep6


title: PAROHT-H3K27me3Inp


title: PARETA-H3K27me3Inp


title: UP-8095 Blood


title: PAROHT-RING1B


title: WTA rep4


title: CHMP2Bintron5 A rep3


title: WTA rep5


title: I53SOHT-RING1B


title: PARETA-RING1B


title: PARETA-SUZ12


title: UP-8036 Blood


title: WTA rep3


title: PARETA-H3K27me3


title: UP-8080 Tumor


title: I53SOHT-MTF2


title: KM51

value: Whole Blood

tag: gender

value: Male

value: 26-39 years

value: Non smokers

value: Rural


title: UP-8017 Tumor

value: 0 weeks


title: WTA rep2

value: FVB/N x C57BL/6 x DBA/2


title: I53SOHT-H3K27me3


title: WTA rep1


title: UP-8036 Tumor


title: I53SOHT-H2A119Ub


title: NaIO3 3 [s6]

city: Shanghai

first: zhimin

last: Tang

address: 833 Zhizaoju Road

country: China

institute: Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Solexa pipeline v1.8 software used for basecalling.
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The differentially expressed genes and transcripts were filtered using R package Ballgown
Genome_build: hg19
Supplementary_files_format_and_content: The Fastq format file contains the sequence of reads and the sequencing quality of base.

source_name: NaIO3-treated human ARPE-19 cells

growth_protocol: Human ARPE-19 cells were cultured in DMEM/F12 medium supplemented with penicillin/streptomycin and 10% FBS at 37 °C with 5% CO2 in incubator.

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

treatment_protocol: NaIO3 treatment for 24 h in human ARPE-19 cells

tag: cell line

tag: cell type

value: Retinal pigment epithelial (RPE) cells

tag: passages

tag: treatment

value: NaIO3 for 24 h


title: NaIO3 2 [s5]


title: UP-8017 Blood


title: WTOHT-PCGF2


title: PAROHT-H2A119UbInp

value: Input


title: UP-8010 Blood


title: UP-8010 Tumor


title: UP-8017 GBO

value: 2 weeks


title: WTOHT-MTF2


title: NaIO3 1 [s4]


title: I53SOHT-JARID2


title: Con 2 [s2]

source_name: Human ARPE-19 cells

value: none (control)


title: UP-7930 GBO

source_name: Glioblastoma organoid


title: WTOHT-H3K27me3Inp


title: PAROHT-H3K27me3


title: UP-7930 Tumor

source_name: Glioblastoma


title: UP-7930 Blood


title: UP-8010 GBO


title: WTOHT-RING1B


title: I53SOHT-PCGF2


title: Rooster rep4

city: Fuchu-shi

first: Tsuyoshi

last: Shimmura

state: Tokyo

address: 3-8-1 Harumi-cho

country: Japan

institute: Tokyo University of Agriculture and Technology

description:
E
The same sample was dividely sequenced twice and therefore the two csfasta and qual files exist. These files were conbinedly aligned at analysis.
DE_DvsE.xlsx

data_processing:
RNA-seq reads were aligned to chicken reference genome and annotation (Ensemble WASHUC2 (14 May2012), iGenomes index and annotation packages) using Tophat (version 1.3.2) with the options for SOLiD color space.
The aligned short reads were counted using Cufflinks (version 2.0.2).
The normalization and differential analysis was performed using edge R.
The transcripts with inverted fold-change between the two comparisons (chicks versus T chicks, and rooster versus hens) and without annotation were filtered out.
Genome_build: Ensemble WASHUC2
Supplementary_files_format_and_content: Excel file include FC and FDR for each group.

organism: Gallus gallus

source_name: ICo of midbrain

extract_protocol:
The brains were removed, and punches of ICo were flash-frozen on dry ice. The ribosomal-RNA-minus RNAs (–rRNA) were prepared by removing DNA with TURBO DNA-free Kit (Ambion) from isolated RNA and then removing the ribosomal RNA with RiboMinus Eukaryote Kit for RNA-Seq (Invitrogen).
According to SOLiD RNA-seq kit protocol (Applied Biosystems), the cDNA libraries were prepared from –rRNAs.

tag: line

value: GSP, a highly inbred line

tag: tissue

value: ICo of midbrain

value: > 20 weeks of age


title: UP-7884T GBO

value: Tumor


title: Rooster rep3


title: PARETA-H2A119UbInp


title: Con 3 [s3]


title: UP-7884T Tumor


title: UP-7884F GBO


title: I53SOHT-H3K27me3Inp


title: E15.5_PGC_Female_rep1

city: Kashihara

first: Hisato

last: Kobayashi

state: Nara

address: 840 Shijo-Cho

department: Department of Embryology

institute: Nara Medical University

data_processing:
Basecalls were performed using NextSeq 500/550 RTA software, v. 2.4.11
FASTQ files were generated using bcl2fastq, v. 2.18.0.12
The first 3 bases were trimmed out from raw reads using FASTX-Toolkit 0.0.13.2
Trimmed reads were further quality-trimmed using Cutadapt v. 1.14 program with the following configurations: trimming of the primer sequence "Clontech SMART CDS Primer II A: AAGCAGTGGTATCAACGCAGAGTAC", minimal base quality is 20, minimal read length after trimming is 35 nt
RNA-seq reads were aligned to the rn6 Rat genome assembly using TopHat2, v. 2.1.0
Cufflinks v. 2.2.1 program and Ensembl gene annotation (rn6, 32545 genes) were used to calculate RPKM values
Genome_build: rn6
Supplementary_files_format_and_content: RPKMs

organism: Rattus norvegicus

source_name: Primordial germ cell

extract_protocol:
Total RNA was extracted using PicoPure RNA Isolation Kit (Thermo Fisher Scientific) according to manufacturer’s protocols.
RNA-seq libraries were prepared using using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio).

value: Primordial germ cell

value: Embryonic day 15.5

value: Female


title: Con 1 [s1]


title: Hen rep4

description:
D
The same sample was dividely sequenced twice and therefore the two csfasta and qual files exist. These files were conbinedly aligned at analysis.
DE_DvsE.xlsx


title: UP-7884F Tumor


title: UP-7884 Blood

value: Normal


title: PARETA-PCGF2


title: E15.5_PGC_Male_rep2

value: Male


title: E15.5_PGC_Male_rep1


title: Rooster rep1


title: Hen rep3


title: UP-7805 GBO


title: HepG2 treated with cinobufagin for 24 h-2

city: Tianjin

first: Zhongwei

last: Xu

state: Tianjin

address: No.1 Huizhi Huan Road , DongLi district, Tianjin City, China, Shuguang Zhou

institute: Logistics University of Chinese People’s Armed Police Force

data_processing:
Basecalls performed using BGISEQ-500
SOAPnuke was used to get the "clean reads".
Mapping clean reads to hg19 whole genome using HISAT
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: UCSC Hg19
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample ...

source_name: liver cancer HepG2 cells

growth_protocol: According to previous description, analysis of transcriptome was carried out using the RNAs extracted from HepG2 and Huh-7 cells treated 5 μmol/L for 0, 12 and 24 h. RNA-Seq technology (Illumina HiSeq 2000) was performed to acquire the transcriptome data. The expression levels of each gene were obtained from RNA-Seq data based on the RPKM (reads per kilobase per million) value. When compared samples from group, RNA-Seq and raw intensity values were divided by the median value in each sample for normalization. Details of the quantitative analysis of transcriptome data was supplied in Supporting Information. All experiments were performed in triplicate.

extract_protocol:
Add 0.2ml chloroform to 1ml TRIzol, vibrate violently for 15 seconds, leave at room temperature for 3 minutes, and centrifuge at 10000×g for 15 minutes. The aqueous phase is transferred to the new tube, and the organic phase can be retained if DNA and protein are separated. The RNA in the aqueous phase was precipitated with isopropanol. Add 0.5ml isopropanol to 1ml TRIzol and leave at room temperature for 10 minutes. After centrifugation at 2 -- 8℃10000×g for 10 minutes, no RNA precipitation was observed before centrifugation, and gelatinous precipitation appeared on the side and bottom of the tube after centrifugation. Remove the supernatant. The RNA precipitate was washed with 75% ethanol. Add at least 1ml 75% ethanol to 1ml TRIzol. Centrifuge at 2-8℃ for 5 min at no more than 7500×g, discard supernatant. Leave to dry or vacuum dry the RNA precipitate at room temperature for about 5-10 minutes. Do not vacuum centrifuge dry, too dry will lead to the dissolution of RNA greatly reduced. Add 25-200 l of RNase free water, smack it several times with the nozzle, and place it at 55-60 ° c for 10 minutes to dissolve the RNA.
RNA libraries were prepared for sequencing using  oligo -dT beads

value: cinobufagin for 24 h


title: HepG2 treated with cinobufagin for 24 h-3

treatment_protocol: According to previous description, analysis of transcriptome was carried out using the RNAs extracted from HepG2 and Huh-7 cells treated 5 μmol/L for 0, 12 and 24 h


title: E12.5_PGC_rep2

value: Embryonic day 12.5


title: Hen rep2


title: E15.5_PGC_Female_rep2


title: Rooster rep2


title: UP-7805 Tumor

value: 0 weeks


title: E12.5_PGC_rep1


title: HepG2 treated with cinobufagin for 12 h-3

value: cinobufagin for 12 h


title: Hen rep1


title: E11.5_PGC_rep2

value: Embryonic day 11.5


title: UP-7805 Blood


title: HepG2 treated with cinobufagin for 12 h-2


title: HepG2 treated with cinobufagin for 24 h-1


title: UP-7803 GBO


title: E11.5_PGC_rep1


title: Capon rep3

description:
C
The same sample was dividely sequenced twice and therefore the two csfasta and qual files exist. These files were conbinedly aligned at analysis.
DE_CvsE.xlsx


title: UP-7803 Tumor


title: E10.5_PGC_rep2

value: Embryonic day 10.5


title: Capon rep2


title: HepG2 control 1


title: E10.5_PGC_rep1


title: UP-7803 Blood


title: HepG2 treated with cinobufagin for 12 h-1


title: UP-7790 GBO

value: 2 weeks


title: Testosteron-implanted chicke rep4

description:
B
The same sample was dividely sequenced twice and therefore the two csfasta and qual files exist. These files were conbinedly aligned at analysis.
DE_AvsB.xlsx

value: 5 days after hatching


title: E9.5_PGC_rep2

value: Embryonic day 9.5


title: Huh-7 treated with cinobufagin for 24 h-2

source_name: liver cancer Huh-7 cells


title: E9.5_PGC_rep1


title: Capon rep1

value: GSP, a highly inbred line

value: ICo of midbrain


title: Huh-7 treated with cinobufagin for 24 h-3


title: Huh-7 treated with cinobufagin for 24 h-1


title: UP-7790 Blood


title: E7.75_Epiblast_Female_rep1

source_name: Epiblast

value: Epiblast

value: Embryonic day 7.75


title: Testosteron-implanted chicke rep2


title: Testosteron-implanted chicke rep3


title: Testosteron-implanted chicke rep1


title: E7.75_Epiblast_Male_rep2


title: UP-7788PMS GBO

value: Tumor


title: E7.75_Epiblast_Male_rep1


title: Huh-7 treated with cinobufagin for 12 h-2


title: Huh-7 treated with cinobufagin for 12 h-1


title: E7.25_Epiblast_Female_rep1

value: Embryonic day 7.25

value: Female


title: UP-7788ANT GBO


title: Control chick rep3

description:
A
The same sample was dividely sequenced twice and therefore the two csfasta and qual files exist. These files were conbinedly aligned at analysis.
DE_AvsB.xlsx


title: UP-7790 Tumor


title: E7.25_Epiblast_Male_rep2

value: Male


title: Huh-7 control 3


title: Control chick rep2


title: Huh-7 control 2


title: Huh-7 control 1


title: UP-7788ANT Tumor


title: E7.25_Epiblast_Male_rep1


title: UP-7788 Blood

value: Normal


title: Control chick rep1


title: UP-7788PMS Tumor


title: Huh-7 treated with cinobufagin for 12 h-3


title: Control chick rep4


title: PAROHT-H2A119Ub


title: Capon rep4

value: > 20 weeks of age


title: LLC Exosome2

status: Public on Dec 25 2019

city: Zhengzhou

first: Can

middle: can

last: Du

address: Daxue Road

institute: The First Affiliated Hospital of Zhengzhou University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: cell supernatant

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: LLC cells were maintained at 37°C in a humidified atmosphere of 5% CO2

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: LLC cell supernatant was collected for exosomes isolation

value: Lewis lung carcinoma (LLC) cell line

tag: sample type

value: LLC cell supernatant collected for exosomes isolation


title: Biotin-DDX18-Control-ChIP-seq

city: Rochester

first: jinlong

last: lu

state: NY

address: 213 Hutchinson Hall

institute: University of Rochester

description:
DNA
DDX18-ChIP-seq-peaks.xlsx

data_processing:
RNA-seq, ChIP/CLAP-seq reads were aligned to the mm9 or mm10 genome assembly using Tophat v2.0.11,allowing for uniquely mapped reads and mapping both spliced and unspliced reads.
Basecalls performed using CASAVA version
FPKM was calculated by Cufflink 2.1.1
Genome_build: mm10

source_name: BirA-mES cells

extract_protocol:
Cell culture: ESCs were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).
RNA-seq: Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
ChIP-seq: BirA- or FLAG-Biotin-ESCs were cross-linked with 1% formaldehyde for 10 min at room temperature and quenched with glycine to a final concentration of 0.125 M for another 5min. Chromatin was sonicated, cleared by centrifugation, and incubated overnight at 4℃ with Dynabeads M280 streptavidin. followed by stringent washes and elution. Eluates were reverse cross-linked overnight at 65℃ and deproteinated with proteinase K at 56℃ for 30 min. DNA was purified using DNA purification kit (Qiagen).
CLIP and TAP-seq: The CLIP method was performed as described before with the specific modifications below. TAP method was developed by our lab sharing most of the same steps with CLIP, but including tandom purification and avoiding SDS-PAGE separation. About 107 cells of FbioDDX18 ESCs grown on one 15-cm plate were harvested and resuspended with 5 ml cold PBS. The cells were plated back to the plate and crosslinked with 600 mJ/cm2 of 254 nm UV light. The nucleuses were prepared by incubated the cells in hypotonic buffer (20 mM HEPES, pH 7.5, 10 mM KCl, 1.5 mM MgCl2, 1 mM EDTA, 0.2% NP-40, 10% glycerol, 1 mM DTT, 1 mM PMSF, 1/500 proteinase inhibitor cocktail, 400 U/ml RNase Inhibitor) for 4 minutes and the cells were lysed by a 26 5/8 Gauge needle and briefly sonicated. Incubate the cells for 30mins on a rotator at 4℃. Treat the lysate with 30 µl RQ1 DNase at 37℃ for 10mins. The insoluble pellet was spun down and the supernatant was harvested. About 40 µl pre-equilibrated FLAG M2 resins (Sigma) were used for each purification. The FLAG resins were incubated with lysate overnight at 4 °C and washed twice with cold CLIP lysis buffer and two more times with high salt wash buffer (5XPBS, 0.5% NP-40, 0.5% sodium deoxycholate, 0.1% SDS). For TAP experiments, the proteins were eluted with 200 ng/ml 3xFLAG peptide dissolved in CLIP lysis buffer (sigma) for three times. The eluents were pooled together and incubated with 60 µl pre-equilibrated streptavidin (M-280, Invitrogen) beads for three hours. The samples were washed twice with SDS-urea wash buffer (50 mM Tris pH 7.4, 2% SDS, 1 M urea) and twice with SDS-high salt wash buffer (5XPBS, 0.5% NP-40, 0.5% SDS) at room temperature. The protein-RNA complex bound beads were washed four times with PNK buffer (50 mM Tris pH 7.4, 10 mM MgCl2, 0.5% NP-40). Then the RNAs were partially digested with MNase (NEB, 1:105 diluted) at 37 °C for 10 min (mixed with an Eppendorf Thermomixer at 1,200 rpm for 5 second per 30 seconds). The reaction was stopped by PNK-EGTA buffer (PNK buffer with 2 mM EGTA). Then the beads were washed twice with SDS-urea wash buffer and twice with PNK buffer. To dephosphorylate the RNA, the beads were treated with CIP (NEB) for 10 min at 37 °C (mixed with an Eppendorf Thermomixer at 1,200 rpm for 5 seconds per 30 seconds). After two more washes with PNK buffer, the pre-adenylated 3’ linker (rAppAGATCGGAAGAGCACACGTCT-NH2, Takara) was ligated with truncated T4 RNA ligase 2 (NEB) at 16 °C overnight. The non-ligated 3’ linker was washed away with two washes of CLIP lysis buffer and two washes of PNK buffer. The RNAs were then phosphorylated by T4 PNK (NEB) for 10 min at 37 °C. Then for CLIP experiments, the RNA was subjected to SDS–PAGE separation and transfer, autoradiograph, ribonucleoprotein isolation, proteinase K treatment, and overnight RNA precipitation. For TAP experiments, the samples were treated with Proteinase K (50 mM Tris, pH 7.4, 150 mM NaCl, 0.5% SDS, and 20 µg Proteinase K) for 30 min at 37 °C to elute the protein-RNA complex. Then the RNAs were purified and ligated with 5’ RNA adaptor (GUUCAGAGUUCUACAGUCCGACGAUC, TAKARA) by T4 RNA ligase (Ambion). Then the RNAs were reverse transcribed by Superscript III with RT primer (AGACGTGTGCTCTTCCGATCT, Takara) and amplified for 20 cycles with Q5 DNA polymerase (NEB)
NEBNext Ultra RNA/DNA Library Prep Kit for Illumina

value: embryonic stem cells

value: serum+LIF


title: FLAG-Biotin-DDX18-CLIP-seq-1

description:
RNA
ann.equal.DDX18-1.merge.CLIP.sort.bed.txt

source_name: FLAG-Biotin-DDX18-mES cells


title: Biotin-DDX18-ChIP-seq

description:
DNA
DDX18-ChIP-seq-peaks.xlsx


title: FLAG-Biotin-DDX18-CLIP-seq-2

description:
RNA
ann.equal.DDX18-2.merge.CLIP.sort.bed.txt


title: FLAG-Biotin-DDX18-TAP-seq-1

description:
RNA
ann.equal.DDX18-TAP-1.merge.bed.txt


title: E3.5-DDX18 KO-2

description:
messenger RNA
E3.5-RNA-seq.xlsx

source_name: DDX18 KO-2-E3.5 embryo

value: E3.5 embryo

value: Isolated from pregnant DDX18 heterozygous mice at E3.5


title: Kidney_Fcgr2b-ko, Sting-ko_rep2

city: Bangkok

first: Arthid

last: Thim-uam

address: Rama IV

department: Biomedical science

country: Thailand

institute: Chulalongkorn University

description:
103_2_Fcgr2b-ko, Sting-ko
Gene expression profiling of Sting related genes

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 40μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Mouse GE 8X60K, V2 Microarrays (Agilent®). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven. then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010).

scan_protocol: The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies, Inc.)

data_processing: Microarray results were extracted using Agilent Feature Extraction software v11.0 (Agilent Technologies)

source_name: whole Kidney of Fcgr2b-ko, Sting-ko mouse, 6 months old

label_protocol: 100ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000(NanoDrop, Wilmington, USA).

extract_protocol: A total of RNA was extracted from the kidneys by Trizol reagent (Invitrogen, CA, USA) as per manufacturer’s instructions followed by RNA purified using the RNeasy mini kit and treated with DNase I. RNA purity and integrity were evaluated by ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA), Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

tag: strain background

tag: genotype/variation

value: Fcgr2b-ko, Sting-ko

value: 6 months old

value: Kidney


title: LLC Exosome1


title: Kidney_Sting-ko_rep2

description:
73_1_Sting-ko
Gene expression profiling of Sting related genes

source_name: whole Kidney of Sting-ko mouse, 6 months old

value: Sting-ko

tag: age


title: Kidney_WT_rep1

description:
57_2_WT
Gene expression profiling of Sting related genes

source_name: whole Kidney of wildtype mouse, 6 months old

value: wild type


title: Kidney_Fcgr2b-ko_rep3

description:
89_3_Fcgr2b-ko
Gene expression profiling of Sting related genes

source_name: whole Kidney of lupus mouse, 6 months old

value: lupus mouse


title: Kidney_Sting-ko_rep1

description:
58_2_Sting-ko
Gene expression profiling of Sting related genes


title: Kidney_Fcgr2b-ko, Sting-ko_rep3

description:
88_6_Fcgr2b-ko, Sting-ko
Gene expression profiling of Sting related genes


title: E3.5-DDX18 KO-1

description:
messenger RNA
E3.5-RNA-seq.xlsx

source_name: DDX18 KO-1-E3.5 embryo


title: Kidney_Fcgr2b-ko, Sting-ko_rep1

description:
78_3_Fcgr2b-ko, Sting-ko
Gene expression profiling of Sting related genes


title: E3.5-WT-2

description:
messenger RNA
E3.5-RNA-seq.xlsx

source_name: WT-2-E3.5 embryo


title: Kidney_WT_rep3

description:
114_2_WT
Gene expression profiling of Sting related genes


title: E3.5-WT-1

description:
messenger RNA
E3.5-RNA-seq.xlsx

source_name: WT-1-E3.5 embryo


title: mESC-CHX-10-2

description:
messenger RNA
ESC-CHX-RNA-seq.xlsx

source_name: CJ9 mES cells

value: serum+LIF+10 µM CHX


title: FLAG-Biotin-DDX18-TAP-seq-2

description:
RNA
ann.equal.DDX18-TAP-2.merge.bed.txt


title: Kidney_WT_rep4

description:
114_5_WT
Gene expression profiling of Sting related genes


title: Kidney_Sting-ko_rep3

description:
161_1_Sting-ko
Gene expression profiling of Sting related genes


title: Kidney_Fcgr2b-ko_rep4

description:
88_4_Fcgr2b-ko
Gene expression profiling of Sting related genes


title: mESC-CHX-10-1

description:
messenger RNA
ESC-CHX-RNA-seq.xlsx


title: Kidney_Fcgr2b-ko_rep1

description:
67_1_Fcgr2b-ko
Gene expression profiling of Sting related genes


title: Kidney_WT_rep2

description:
71_2_WT
Gene expression profiling of Sting related genes


title: Kidney_Sting-ko_rep4

description:
154_1_Sting-ko
Gene expression profiling of Sting related genes


title: Kidney_Fcgr2b-ko, Sting-ko_rep4

description:
89_2_Fcgr2b-ko, Sting-ko
Gene expression profiling of Sting related genes


title: mESC-CHX-control-2

description:
messenger RNA
ESC-CHX-RNA-seq.xlsx

value: serum+LIF+0 µM CHX


title: mESC-CHX-control-1

description:
messenger RNA
ESC-CHX-RNA-seq.xlsx


title: p53 KO-ActD-10-1

description:
messenger RNA
p53KO-ActD-RNA-seq.xlsx

value: serum+LIF+10 ng/ml ActD


title: p53 KO-ActD-control-1

description:
messenger RNA
p53KO-ActD-RNA-seq.xlsx

value: serum+LIF+0 ng/ml ActD


title: mESC-ActD-10-2

description:
messenger RNA
ESC-ActD-RNA-seq.xlsx


title: mESC-ActD-10-1

description:
messenger RNA
ESC-ActD-RNA-seq.xlsx


title: p53 KO-ActD-control-2

description:
messenger RNA
p53KO-ActD-RNA-seq.xlsx


title: mESC-ActD-5-2

description:
messenger RNA
ESC-ActD-RNA-seq.xlsx

value: serum+LIF+5 ng/ml ActD


title: Kidney_Fcgr2b-ko_rep2

description:
76_4_Fcgr2b-ko
Gene expression profiling of Sting related genes


title: mESC-ActD-control-3

description:
messenger RNA
ESC-ActD-RNA-seq.xlsx


title: mESC-ActD-5-1

description:
messenger RNA
ESC-ActD-RNA-seq.xlsx


title: mESC-ActD-control-1

description:
messenger RNA
ESC-ActD-RNA-seq.xlsx


title: mESC-ActD-control-2

description:
messenger RNA
ESC-ActD-RNA-seq.xlsx


title: mESC-control-1

description:
messenger RNA
ESC-DDX18 KD-RNA-seq.xlsx


title: mESC-control-2

description:
messenger RNA
ESC-DDX18 KD-RNA-seq.xlsx


title: mESC-DDX18-KD1

description:
messenger RNA
ESC-DDX18 KD-RNA-seq.xlsx


title: mESC-DDX18-KD2

description:
messenger RNA
ESC-DDX18 KD-RNA-seq.xlsx


title: WTOHT-H3K27me3

source_name: mESC

tag: chip antibody


title: H3K4me3 Ankrd31 -/- adult Rep2

city: Bethesda

first: Kevin

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

description: ChIP-Seq

data_processing:
Reads were aligned to the mm10 genome assembly. H3K4me3 ChIP-Seq reads were mapped to the reference genome using bwa mem (0.7.12).The pipeline described in Khil et al. Genome Res. 2012 was used to align SSDS reads to the genome (available at https://github.com/kevbrick/SSDSpipeline).
Uniquely mapping fragments unambiguously derived from ssDNA (ssDNA type 1) and having both reads with a mapping quality score ≥ 30 were used for identifying hotspot locations (peak calling). NCIS was used to estimate the background fraction for each library. Peak calling was performed using MACS (v.2.1.0.20150420) with the following parameters : --ratio [output from NCIS] -g mm --bw 1000 --keep-dup all --slocal 5000. DSB hotspots within regions previously blacklisted were removed and hotspot strength was calculated as described previously(Smagulova et al., Genes Dev 2016).
Genome_build: mm10
Supplementary_files_format_and_content: The processed file dataTable_hotspots.tab contains calculated coverage for all samples at a merged set of DSB hotspots from all SSDS samples.
Supplementary_files_format_and_content: BED files contain the DSB hotspots identified for each SSDS sample.

source_name: Whole testis

extract_protocol:
As described in Smagulova et al., 2011, Brick et al., 2012
As described in Smagulova et al., 2011, Brick et al., 2012

value: Ankrd31 -/-

tag: Sex

value: male

value: Adult

tag: antibody

value: Anti-H3K4me3 Millipore (#07-473)


title: SSDS Prdm9-/- Adult

description:
GSM869790
ChIP-Single Stranded DNA Sequencing (SSDS)

extract_protocol: Lysates from mouse testis cells were crosslinked, sonicated and immunoprecipitated with anti-DMC1 or anti-RAD51 antibodies. Size selection of library fragments of 150 - 250 bp was performed after PCR amplification. SSDS samples were denatured and quickly renatured before adapter ligation.

tag: genotype

value: Prdm9 -/-

value: Anti-DMC1 Santa Cruz (C-20, sc 8973)


title: H3K4me3 Ankrd31 +/+ adult Rep2

description: ChIP-Seq

value: Ankrd31 +/+


title: H3K4me3 Ankrd31 -/- adult Rep1

description: ChIP-Seq


title: SSDS wild-type Adult

description:
GSM2664276
ChIP-Single Stranded DNA Sequencing (SSDS)

extract_protocol: Embryos were collected at E15.5, ovaries were dissected in cold PBS and stored at -80oC until use. 90 or 250 ovaries were fixed in 1 ml PBS with 1% paraformaldehyde for 3 min, quenched and homogenized with Dounce homogenizer.  Cells were collected by 10 minute centrifugation at 900g using a bucket rotor. The pellet was washed in 1 ml of the following buffers: 1) PBS 2) 0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH8. Cells were lysed in 0.5 ml of the lysis buffer (1% SDS, 10 mM EDTA, 50 mM TrisCl pH8 with complete protein inhibitor cocktail (Roche) and the chromatin was sheared with Misonix sonicator with the following parameters: efficiency 1, 10 s on, 20 s off, total sonication time 4 min. Chromatin was cleared by 10 min centrifugation at 12,000g at 4C. The supernatant was diluted 2-fold by ChiP buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM TrisHCl , 167 mM NaCl) and dialyzed against the same buffer for 5 hour at 4oC.     Chromatin was incubated with 6Âµg of custom made anti-DMC1 antibody and 20Âµl Dynabead beads  (10002D, Invitrogen) at 4oC overnight followed by washing with 500Âµl of the following buffers: 1) 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM TrisHCl, 150 mM NaCl; 2) 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM TrisCl pH8, 500 mM NaCl; 3) 0.25 M LiCl, 1% Igepal, 1 mM EDTA, 10 mM TrisCl, pH8, 1% Deoxycholic acid. DNA protein complexes were eluted by two consecutive 15 min incubations at 650C using elution buffer (0.1M NaHCO3, 1%SDS, 5mM  DTT). The eluates were combined and crosslinking was reversed at 650C for 5 hours. The samples were deproteinized and cleaned up with MinElute PCR purification kit (QIAGEN). The sequencing library was prepared as previously described (Brick et al. 2012).     For H3K4me3 CHiP-Seq and DMC1 SSDS protocols from testis, testicular samples were obtained frozen and were directly thawed in 1% paraformaldehyde and gently dissociated. Testis sample preparation was performed as described previously (Brick et al., 2012).  !Sample_extract_protocol_ch1 = DMC1 and H3K4Me3 ChIP were performed as described previously (Smagulova et al., 2011; Khil et al., 2012; Brick et al., 2012) with minor modifications.  Sequencing libraries for anti-H3K4Me3 samples were prepared according to manufacturer's protocol (Illumina) and anti-DMC1 libraries were prepared following the method described in (Khil et al., 2012).

value: wild-type


title: H3K4me3 Ankrd31 +/+ adult Rep1

description: ChIP-Seq


title: SSDS Ankrd31 +/- 12dpp

description: ChIP-Single Stranded DNA Sequencing (SSDS)

extract_protocol:
Brick, Pratto et al., Methods in Enzymology (2018)
Brick, Pratto et al., Methods in Enzymology (2018)

value: Ankrd31 +/-

value: 12 days post partum


title: SSDS Ankrd31 -/- Adult


title: SSDS Ankrd31 +/+ 12dpp


title: SSDS Ankrd31 -/- 12dpp


title: TB-9

city: Gainesville

first: Heather

middle: M

last: Brockway

state: FL

department: Physiology and Functional Genomics

institute: University of Florida

data_processing:
FASTQC (Galaxy v0.71) was used to examine sequence quality
TrimGalore (Galaxy v0.4.3.1) was used to trim adaptors
Bowtie2 (Galaxy v2.3.4.1) was used to map reads using end-to-end and senstive analysis preset parameters
FeatureCounts (Galaxy v 1.6.0.3) was used to generate read counts
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text files including read counds per gene for each sample

source_name: placental villous tissue

extract_protocol:
placental villous tissue was flash frozen within an hour of delivery. Frozen samples were placed in RNALater Ice and thawed for homogenization and total  RNA extraction using the RNAeasy Mini kit (Qiagen). 50-100 ug of total RNA was submitted for quality assessment and sequencing.
Long RNA libraries were generated using a RiboZero Kit (Illumina) using standard protocols.
RNA-sequencing on Illumina 2000 HiSeq  at the University of Cincinnati Genomics, Epigenomics and Sequencing Core

value: normal term placental villous tissue


title: TB-8


title: TB-5


title: TB-4


title: TB-7


title: TB-3


title: TB-2


title: isPTB-8

value: idiopathic spontaneous preterm placental villous tissue


title: TB-6


title: IgS SSDS wildtype testis Adult

value: Anti-IgG Abcam (ab46540)


title: TB-1


title: isPTB-6


title: isPTB-3


title: p53 KO-ActD-10-2

description:
messenger RNA
p53KO-ActD-RNA-seq.xlsx

value: embryonic stem cells

tag: strain


title: isPTB-1


title: isPTB-7


title: isPTB-4


title: isPTB-2


title: Input_rep2

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
Library strategy: eCLIP-seq
Basecalls performed using CASAVA
CLIP-seq reads treated with the protocol outlined in Van Nostrand et al. (2016) Briefly, reads were adapter-trimmed using cutadapt and aligned to the human hg19 genome using STAR version 2.4.2a
Mapped reads were then processed and peaks were called with scripts from the Yeo Lab
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were produced using bamCoverage in the deeptools package

source_name: Prostate

growth_protocol: LNCAP cells were maintained in in RPMI media supplemented with 10% fetal bovine serum (FBS; Lonza) 1mM sodium pyruvate (Gibco, 11360070), non-essential amino acids (Gibco; 11140050) and 50U/ml Penicillin-Streptomycin (Gibco, 15140163).

extract_protocol:
LNCAP cells were grown on 150mm dishes were UV crosslinked (150mJ), using the UV Stratalinker 2400. Cell pellets were flash frozen in liquid nitrogen. RBP complex isolation and eCLIP library preparation was performed as described by Van Nostrand et al. (2016)
eCLIP libraries were prepared using the protocol described by Van Nostrand et al. (2016)

treatment_protocol: LNCAP cells growing at steady state were UV-crosslinked in PBS and harvested for CLIP. RNA-RBP complexes were isolated using an overnight pulldown with HNRNPM antibody (SC20001; SantaCruz), and further purified by PAGE electrophoresis. eCLIP library preparation was performed as described by Van Nostrand et al. (2016)

value: Epithelial cells

value: LNCaP

value: input


title: Input_rep1


title: isPTB-5


title: Input_ES [ChIP-seq]

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 2
Peak calling was done using MACS 2.1.1 with the following configurations: -q 1e-5 --llocal=10000 --bw 300 -m 5,30 --slocal=1000 -B --keep-dup=1
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were produced using bamCoverage in the deeptools package

source_name: embryonic stem cells

growth_protocol: ESCs were cultured in Serum+Lif (SL) medium on gelatin coated plates

extract_protocol:
Lysates were clarified from sonicated cells and histone-DNA complexes were enriched using PRDM15 antibody. Antibody is an in-house produced rabbit polyclonal antibody against PRDM15.
Directional RNA library was prepared according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.

treatment_protocol: ESCs were fixed using 1% formaldehyde, collected in SDS lysis buffer and frozen for ChIP. Detailed experimental procedures can be found in the supplemental method section of the paper.

value: none (input)


title: Hnrnpm_rep1

value: HNRNPM


title: PRDM15_ES [ChIP-seq]

description:
genomic DNA enriched using PRDM15 antibody
CME825_NS001-SR-R00590-CAGATC_S8

value: PRDM15 Antibody (Guccione lab)


title: Hnrnpm_rep2


title: KO_hPRDM15_ZNmut1_B (RNA-seq)

data_processing:
Basecalls performed using CASAVA
Sequenced reads were mapped to mm9 genome using STAR version 2.4.2a with default parameters
FPKM and differential expression were calculated using the htseq package and DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file with gene level counts generated with htseq/deseq2 in R

extract_protocol:
RNA was isolated from cells using the Purelink RNA Mini Kit (Thermo Fisher Scientific; 12183018A)following the manufacturer’s protocol.
Directional RNA library was prepared according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.

treatment_protocol: OHT (50nM) was added to the medium O/N to delete endogenous mouse Prdm15 from isogenic Prdm15flf::RCM2. These lines were ectopically expressing either Wt or mutated human PRDM15, or empty vector as a control.

value: ESCs

tag: modification

value: overexpression of ZNF-domain mutant hPRDM15


title: KO_10 (RNA-seq)

description: 6.5 d.p.c emrbyo

source_name: 6.5 d.p.c embryo

growth_protocol: RNA was isolated from 6.5 d.p.c embryos resulting from intercrosses between Prdm15lacZ/+ mice

value: embryo


title: KO_hPRDM15-ZNmut1_A (RNA-seq)


title: KO_hPRDM15-PRmut2_A (RNA-seq)

value: overexpression of PR-domain mutant2 hPRDM15


title: WT_B (RNA-seq)


title: KO_hPRDM15_PRmut1_B (RNA-seq)

value: overexpression of PR-domain mutant1 hPRDM15


title: KO_hPRDM15_PRmut2_B (RNA-seq)


title: KO_hPRDM15-WT_B (RNA-seq)

value: overexpression of wildtype hPRDM15


title: WT_A (RNA-seq)


title: Input_E6.5 (ChIP-seq)

source_name: 6.5 d.p.c embryos

treatment_protocol: Embryos were fixed using 1% formaldehyde, collected in SDS lysis buffer and frozen for ChIP. Detailed experimental procedures can be found in the supplemental method section of the paper.


title: KO_9 (RNA-seq)

description: 6.5 d.p.c emrbyo


title: PRDM15_E6.5 (ChIP-seq)


title: KO_hPRDM15_WT_A (RNA-seq)


title: KO_hPRDM15_PRmut1_A (RNA-seq)


title: KO_7 (RNA-seq)

description: 6.5 d.p.c emrbyo


title: KO_A (RNA-seq)


title: KO_B (RNA-seq)


title: KO_8 (RNA-seq)

description: 6.5 d.p.c emrbyo


title: KO_6 (RNA-seq)

description: 6.5 d.p.c emrbyo


title: KO_4 (RNA-seq)

description: 6.5 d.p.c emrbyo


title: KO_5 (RNA-seq)

description: 6.5 d.p.c emrbyo


title: KO_3 (RNA-seq)

description: 6.5 d.p.c emrbyo


title: Psoriasis lesion rep5 [PS_5]

first: Zengyang

last: Yu

address: 301 Yanchang Road

institute: Shanghai Tenth People's Hospital, Tongji University School of Medicine

description:
processed data file:
mRNA_counts.txt
lncRNA_counts.txt
miRNA_counts.txt

data_processing:
Raw sequencing reads were processed and pre-qualified using Trimmomatic. Clean reads were then aligned to a human reference genome using hisat2 in order to obtain mapped locations and sequence features of clean reads. Fragments Per kb Per Million Reads (FPKM) method was used to calculate the abundance of each transcript.
For lncRNA prediction, StringTie was used to reconstruct transcripts from BLAST results for each sample based on a probability model. Several strict steps were then performed in order to screen potential lncRNAs. First, reconstructed transcripts were aligned to reference transcripts, and coding transcripts and known loci were filtered out. Second, transcripts longer than 200 bp and with more than two exons were filtered out, and CPC, CNCI, Pfam and PLEK software packages were applied to remove transcripts with coding potential. The final sequences were considered lncRNAs.
For small RNA sequencing reads, sequences with adapters or N bases were removed from raw reads, and clean reads were attained by screening out sequences of low quality (Q20 <80%) and lengths outside the range of 15-41 nt. Clean reads were then aligned to Rfam (version 10.0) and a cDNA database to annotate and filter out rRNAs, snRNAs, snoRNAs, tRNAs and mRNAs. Screened miRNAs were further aligned to Repbase to remove repeating sequences, BLAST-searched against mature sequences in mRBase, known miRNAs were annotated, and unannotated sequences were then identified by miRDeep2 and RNAfold. Sequences capable of forming microRNA hairpin precursors were considered novel miRNAs. The abundance of annotated miRNAs and novel miRNAs was determined by the transcript per million (TPM) method.
We used DESeq to standardise transcript counts for mRNAs and lncRNAs in each sample, and significant differences in each comparison (PN vs. NN, PS vs. PN, PS vs. NN) were identified by Negative Binomial Distribution tests.
Differentially expressed miRNAs were determined by the DEG algorithm in the R package with a threshold of p <0.05 and log2FC >1. The targets of differentially expressed miRNAs were predicted by miRanda, with S (single‐residue‐pair match scores) ≥150, ΔG ≤-30 kcal/mol, and strict 5’ seed pairing.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: RPKM values for each Sample.

source_name: Psoriasis lesion

extract_protocol:
Total RNA was isolated using a mirVana miRNA ISOlation Kit (Ambion), and RNA quantity and quality were assessed using a NanoDrop 2000 (Thermo Fisher Scientific).
TruSeq Stranded Total RNA kit with Ribo-Zero Gold (Illumina) was employed to construct a cDNA library.

tag: subject status

value: psoriasis patient

value: skin

tag: tissue subtype

value: Psoriatic plaque tissue (PS)


title: Psoriasis lesion rep4 [PS_4]


title: Psoriasis lesion rep1 [PS_1]


title: Psoriasis lesion rep3 [PS_3]


title: WT_8 (RNA-seq)

description: 6.5 d.p.c emrbyo

value: wild type


title: Psoriasis lesion rep2 [PS_2]


title: WT_5 (RNA-seq)

description: 6.5 d.p.c emrbyo


title: KO_2 (RNA-seq)

description: 6.5 d.p.c emrbyo


title: WT_7 (RNA-seq)

description: 6.5 d.p.c emrbyo


title: WT_6 (RNA-seq)

description: 6.5 d.p.c emrbyo


title: WT_2 (RNA-seq)

description: 6.5 d.p.c emrbyo


title: WT_3 (RNA-seq)

description: 6.5 d.p.c emrbyo


title: Psoriasis Non-lesion rep5 [PN_5]

source_name: Psoriasis Non-lesion

value: adjacent normal skin tissue (PN)


title: Psoriasis Non-lesion rep4 [PN_4]


title: Healthy rep1 [NN_1]

source_name: healthy skin control

value: healthy control

value: healthy skin control


title: Psoriasis Non-lesion rep2 [PN_2]


title: Psoriasis Non-lesion rep1 [PN_1]


title: Healthy rep3 [NN_3]


title: Healthy rep5 [NN_5]


title: Psoriasis Non-lesion rep3 [PN_3]


title: Healthy rep2 [NN_2]


title: Healthy rep4 [NN_4]


title: WT_1 (RNA-seq)

description: 6.5 d.p.c emrbyo


title: WT_4 (RNA-seq)

description: 6.5 d.p.c emrbyo


title: KO_1 (RNA-seq)

description: 6.5 d.p.c emrbyo


title: RD shSNAI2 MYOD

first: Javed

last: Khan

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

data_processing:
ChIP enriched DNA reads were mapped to reference genome using BWA version 0.7.10
The ChIP-seq peaks were called by MACS2 version 2.1.0.  Duplicates were allowed
The enhancers were identified using ROSE2 pipeline in bamliquidator 1.3
Enrichment of known and de novo motifs were found using HOMER version 4.8.2
Genome_build: Hg19
Supplementary_files_format_and_content: peak files are tab delimited text files (BED coordinates) for each sample.

source_name: RD

growth_protocol: Primary tumors were flash frozen at -80 °C until ready for use

extract_protocol:
[harvesting protocol] ChIP samples harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit).  ChIP enriched DNA was treated with Proteinase K at 55 ˚C for 30 minutes followed by reversal of crosslinks by heating to 80 ˚C for 2 hours, and DNA purification by column (MiniElute PCR purification kit, Qiagen).
DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol.
Standard Illumina barcodes were introduced during library preparation with the Illumina TruSeq ChIP Sample Prep Kit 48 Samples - Set A Cat# IP-202-1012

tag: cell line

value: RD

value: MyoD, Santa Cruz (cat sc-32758, lot I1113)

tag: enrichment target

value: MYOD

tag: mechanistic classifications of chip protein target

value: Myogenic Transcription Factor


title: RD shCtrl MYOD

tag: treatment

value: shCtrl


title: Oligo RNA Sequencing Rep 1

city: Huntsville

first: Ryne

last: Ramaker

state: AL

address: 601 Genome Way

department: Genetics

institute: University of Alabama at Birmingham

description: RawCountTable.txt

data_processing:
Library strategy: STARR-seq
FASTQ files were adapter trimmed using cutadapt 1.2.1
Trimmed FASTQ files were aligned to a custom reference in a manner that required perfect match in only the correct orientation
Aligned SAM files were converted to count tables using samtools version 1.2 indexing (RawCountTable.txt)
Genome_build: hg19
Supplementary_files_format_and_content: The RawCountTable.txt was generated using samtools version 1.2 indexing on the aligned SAM files. The file is a tab delimited text file with columns 7-13 representing a different sample and each row representing a test element described in columns 1-6.

source_name: HepG2 Cancer Cell Line

growth_protocol: Our STARR-seq library was transfected into HepG2 cells in 30cm plates with 25 million cells per plate. Cells were grown in DMEM + 10% FBS

extract_protocol:
24 hours post transfection cells were scrapped from their plates andRNA was isolated using the Norgen total RNA Purificaiton Kit using manufacturer's instructions.
Poly-A RNA was isolated for each replicate using Dynabead Oligo-dT beads (Life Technologies) with double selection. The elution was subjected to Dnase digestion with TURBO Dnase (Life Tech) at 37C for 30 min and cleaned up with the Zymo RNA Clean and Concentrate Kit. Reverse transcription was performed for each replicate with the STARR-seq Gene Specific Primer and SuperScript III Reverse Transcriptase. A subsequent junction PCR was performed on the cDNA for 15 cycles followed by addition of Illumina sequencing primers with an additional 5 cycles of PCR. The resulting ~200bp fragments were sequenced on an Illumina NextSeq with 150bp paired end sequencing using standard protocols.

treatment_protocol: HepG2 cells were transfected with 532ug of our plasmid DNA containing our oligo pool using FuGene reagents at a 4:1 ratio.

value: RNA


title: Oligo RNA Sequencing Rep 4

description: RawCountTable.txt


title: Plasmid DNA Reference Sample

description: RawCountTable.txt

value: Input DNA


title: Oligo RNA Sequencing Rep 3

description: RawCountTable.txt


title: Oligo RNA Sequencing Rep 6

description: RawCountTable.txt


title: 19-9-11 hiPSCs_CH6uM_0h

city: University park

first: Yuqian

last: Jiang

state: PA

address: W345 millennium science complex

institute: PSU

data_processing:
Data were collected with Illumina HiSeq in Rapid Run mode using 100 nt single read sequencing. Original output are Fastq files.
RNAseq library reads were mapped to the human genome (hg19) with HISAT.
RNAseq reads were then processed with samtools and bedtools, finally processed in python rpkmforgenes to generate TXT processed files.
Genome_build: hg19
Supplementary_files_format_and_content: Text files include RPKM values for each Sample.

source_name: 19-9-11 hiPSCs_treated by CHIR99021 6uM for 0 hour

growth_protocol: 19-9-11 hiPSCs were cultured in mTeSR1 medium on matrigel-coated plates.

extract_protocol:
Cells were lysed with TRI-reagent for 1min and RNA was extracted with Direct-zol RNA MiniPrep Plus kit (Zymo research), followed by RNA purification with RNA clean & concentrator kit (Zymo Research).
Samples were analyzed with Agilent Bioanalyer for quality control. mRNA libraries were generated with the TruSeq Stranded mRNA library construction kit. Data were collected with Illumina HiSeq in Rapid Run mode using 100 nt single read sequencing.

treatment_protocol: 19-9-11 hiPSCs were treated with 6uM CHIR99021 in RPMI medium for up to 21h.

tag: cell type

value: control

tag: time


title: 19-9-11 hiPSCs_CH6uM_12h

source_name: 19-9-11 hiPSCs_treated by CHIR99021 6uM for 12 hours

value: CH


title: 19-9-11 hiPSCs_CH6uM_15h

source_name: 19-9-11 hiPSCs_treated by CHIR99021 6uM for 15 hours


title: 19-9-11 hiPSCs_CH6uM_18h

source_name: 19-9-11 hiPSCs_treated by CHIR99021 6uM for 18 hours


title: 19-9-11 hiPSCs_CH6uM_21h

source_name: 19-9-11 hiPSCs_treated by CHIR99021 6uM for 21 hours


title: 19-9-11 hiPSCs_CH6uM_6h

source_name: 19-9-11 hiPSCs_treated by CHIR99021 6uM for 6 hours


title: Oligo RNA Sequencing Rep 2

description: RawCountTable.txt

tag: sample type


title: CTR shCtrl MYOD

source_name: CTR

value: CTR

value: anti-MYOD (Santa Cruz, sc-760, M-318)


title: Oligo RNA Sequencing Rep 5

description: RawCountTable.txt


title: RD shSNAI2 SNAI2

value: Slug (C19G7) Rabbit mAb,  CST 9585

value: Trancription Factor


title: RD shCtrl H3K27ac

value: anti-H3K27ac Ab4729

value: Active enhancers


title: RD shCtrl SNAI2


title: CTR shSNAI2 MYOD


title: 19-9-11 hiPSCs_CH6uM_3h

source_name: 19-9-11 hiPSCs_treated by CHIR99021 6uM for 3 hours


title: CTR D48 SNAI2

value: Transcription Factor

value: DMSO


title: CTR shCtrl input

value: input

value: shRNA control


title: WHR63_kidney_Nudt12_KO

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

data_processing:
Reads were sorted into individual libraries based on the barcodes and mapped to the mouse genome (GRCm38;Ensembl release 95) using salmon v0.12.0.  Further analysis was performed using R version 3.6.0  (R Core Team, 2017) and Bioconductor (Huber et al., 2015). The DESeq function of DESeq2 1.24.0 bioconductor package (Love et al., 2014) was used to obtain log2 fold changes of gene expression between wild-type and mutant samples and the adjusted p-values. Adjusted p-value 0.1 was used as a threshold for statistical significance. The liver and kidney tissues were analysed separately.
For quantification of circadian expression changes, one replicate of Nudt12-/- and Nudt12+/+ were analysed by RNAseq at different time points (ZT0-ZT20).  The reads were mapped by salmon and the read counts were summarized to gene levels and normalized to library sizes (rpm).
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed data files contain gene expression data.

source_name: kidney

growth_protocol: We targeted the endogenous Nudt12 locus in mouse embryos of the B6D2F1/J hybrid line (also called B6D2; The Jackson Laboratory, stock no. 100006). It is a cross between C57BL/6J (B6) and DBA/2J (D2), and heterozygous for all B6 and D2 alleles. Single-cell mouse embryos were injected with two different guide RNAs (gRNAs) that direct the DNA endonuclease Cas9 to delete a region within exon 6. Founder mice were identified by genotyping PCR and crossed with wildtype C57BL/6J (Janvier) partners to obtain germline transmission. We identified a mouse line with 58 bp deletion in the exon 6 that removes the critical catalytic residues that constitute the nudix motif. It also creates a premature termination codon that leads to the removal of the transcripts via nonsense-mediated decay (NMD).

extract_protocol:
Total RNA was isolated using the Trizol reagent (ThermoFisher Scientific; 15596026) from relevant tissues of indicated genotypes.
RNA concentration was measured with a Qubit fluorimeter (Life Technologies) and RNA integrity assessed with a Bioanalyzer (Agilent Technologies). The TruSeq Stranded Total RNA kit with Ribo-Zero Gold was used for library preparation with 500 ng of total RNA as input. Library molarity and quality was assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were diluted at 2 nM and pooled before the clustering process on a HiSeq 4000 Single Read flow cell. Reads of 100 bases were generated using the TruSeq SBS reagents on the Illumina HiSeq 4000 sequencer (iGE3 Genomics Platform, University of Geneva).

treatment_protocol: For circadian expression study, the mice were converted to standard time points in the animal house, with 12 hours light and 12 hours dark a day, and let get used to the condition for 10 days. After that, these mice were harvested every 4 hour from the start of "light on" (ZT0) to "light off" (ZT12) to "light on" (ZT0) again, resulting in collection of 6 different time points as: ZT0, ZT4, ZT8, ZT12, ZT16, ZT20.

value: 3-4 months

value: KO

tag: zeitgeber


title: WHR65_kidney_Nudt12_KO

tag: age


title: 19-9-11 hiPSCs_CH6uM_9h

source_name: 19-9-11 hiPSCs_treated by CHIR99021 6uM for 9 hours


title: CTR shSNAI2 SNAI2

tag: chip antibody

value: shRNA against SNAI2


title: WHR62_kidney_Nudt12_WT

value: WT


title: CTR T48 SNAI2

value: Trametinib 100 nM


title: WHR64_kidney_Nudt12_KO


title: CTR shSNAI2 H3K27ac

value: H3K27ac (Active Motif, 39133)


title: WHR61_kidney_Nudt12_WT


title: CTR shCtrl SNAI2


title: CTR shCtrl H3K27ac


title: JR1 shCtrl SNAI2


title: WHR59_liver_Nudt12_KO

source_name: liver


title: WHR58_liver_Nudt12_KO


title: WHR60_kidney_Nudt12_WT


title: JR1 shCtrl H3K27ac


title: WHR54_liver_Nudt12_WT


title: WHR55_liver_Nudt12_WT


title: RMS225 input

description: DNA (input control)

source_name: RMS primary tumor, PAX3-FOXO1

extract_protocol:
ChIP samples harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit) with H3K27ac pAb cat. #39133.  ChIP enriched DNA was treated with Proteinase K at 55 ˚C for 30 minutes followed by reversal of crosslinks by heating to 80 ˚C for 2 hours, and DNA purification by column (MiniElute PCR purification kit, Qiagen).
DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol.
Standard Illumina barcodes were introduced during library preparation with the Illumina TruSeq ChIP Sample Prep Kit 48 Samples - Set A Cat# IP-202-1012

tag: target function

value: control


title: WHR148_liver_Nudt12_KO_ ZT16

value: 4-6 months


title: RMS246 input

description: DNA (input control)

tag: antibody


title: RMS225 H3K27ac

description: DNA (ChIP-enriched)


title: RMS235 H3K27ac

description: DNA (ChIP-enriched)

source_name: RMS primary tumor, PAX3-NCOA1


title: RMS246 H3K27ac

description: DNA (ChIP-enriched)


title: WHR149_liver_Nudt12_KO_ ZT20

tag: genotype


title: WHR147_liver_Nudt12_KO_ ZT12


title: WHR146_liver_Nudt12_KO_ ZT8


title: RMS224 input

description: DNA (input control)


title: WHR145_liver_Nudt12_KO_ ZT4


title: RMS224 H3K27ac

description: DNA (ChIP-enriched)


title: WHR144_liver_Nudt12_KO_ ZT0


title: JR1 shCtrl input


title: LNCAP_2B9_SHRNA_3

data_processing:
Basecalls performed using CASAVA
Sequenced reads were mapped to hg19 whole genome using STAR version 2.4.2a with default parameters
FPKM and differential expression were calculated using the Cufflinks suite version 2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Prostate

extract_protocol:
RNA was isolated from shRNA treated LNCAP cells using the Purelink RNA Mini Kit (Thermo Fisher Scientific; 12183018A)in conjunction with Trizol Reagent (Invitrogen; 15596018) following the manufacturer’s protocol.
Directional RNA library was prepared according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.

treatment_protocol: LNCAP cells were infected at ~MOI1 with lentiviruses (PLKO.1) expressing control non-targetting shRNA (SCR) or HNRNPM specific shRNA (2B7 and 2B9). Virus infected cells were then selected in puromycin containing media (1ug/ml) after a 2 day infection. After selection was completed, cells were harvested for RNA isolation.

tag: shRNA

value: HNRNPM targetting shRNA (2B9)

value: Epithelial cells

value: LNCaP


title: WHR56_liver_Nudt12_WT


title: WHR143_liver_Nudt12_WT_ ZT20


title: LNCAP_2B9_SHRNA_2


title: WHR57_liver_Nudt12_KO


title: RMS235 input

description: DNA (input control)


title: WHR142_liver_Nudt12_WT_ ZT16


title: LNCAP_2B9_SHRNA_1


title: WHR141_liver_Nudt12_WT_ ZT12


title: LNCAP_2B7_SHRNA_2

value: HNRNPM targetting shRNA (2B7)


title: input Cse4-HA

city: Worcester

first: Richard

middle: E

last: Baker

state: MA

address: 55 Lake Avenue North

department: Microbiology & Physiological Systems

institute: University of Massachusetts Medical School

data_processing:
ChIP-seq reads were aligned to the sacCer3 genome assembly using Bowtie version 1.0.0 with the following parameters: -n2 -m3 --best --strata -S. Peaks were called using MACS version 2.1.1.20160226 in paired-end mode with the following settings:  -g 1.21e7 --keep-dup auto -B --SPMR. Pileups were generated during peak calling.
Genome_build: sacCer3
Supplementary_files_format_and_content: Averaged bedGraph files were generated using macs2 cmbreps; scores are reads per million total reads.

organism: Saccharomyces cerevisiae

source_name: sonicated spheroplasts

growth_protocol: Cells grown at 25 degrees C in YEPD broth

extract_protocol:
Spheroplasts were prepared, washed, and lysed in detergent containing buffer with protease inhibitors. Lysate was sonicated to obtain DNA fragments of average size 100 bp
Libraries were prepared using Illumina Nextera DNA Library Kit #FC-121-1031

tag: strain background

tag: genotype/variation


title: Cse4-HA IP

value: anti-HA agarose beads (A2220, Sigma)


title: notag IP


title: MCF7-FN

city: Monterrey

first: Victor

last: Trevino

state: Nuevo León

address: Ave. Eugenio Garza Sada 2501 Sur

department: Investigación e Innovación

country: Mexico

institute: Tecnológico de Monterrey

data_processing:
Reads trimmed by Trimmomatic in Galaxy
Trimmed reads aligned using RNA-Star
Counts obtained by feature counts
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

source_name: Breast cancer cell line MCF-7

growth_protocol: DMEM-F12 + 10%FBS

extract_protocol:
GenElute Mammalian Total RNA Miniprep Kit
TruSeq-RNA-Library-Prep-Kit

treatment_protocol: CRISPR/Cas9, PX459 plasmid

value: Control


title: LNCAP_SCR_SHRNA_3

value: non-targetting shRNA


title: WHR140_liver_Nudt12_WT_ ZT8


title: notag input


title: WHR139_liver_Nudt12_WT_ ZT4


title: LNCAP_SCR_SHRNA_2


title: LNCAP_SCR_SHRNA_1


title: LNCAP_2B7_SHRNA_3


title: IMR90.iBMEC.Day 50

city: New York

first: Tyler

last: Lu

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

data_processing:
Analyses were performed using the Seurat package in R (version 3.0.3).
UMI counts files that had been knee-filtered were downloaded from the Illumina BaseSpace Sequence Hub.
Following best practices in the package suggestions UMI counts were log-normalized and after the most highly variable genes selected the data matrices were scaled using a linear model with variation arising from UMI counts mitigated for.
Principal component analysis was subsequently performed on this matrix and after reviewing principal component heatmaps and jackstraw plots Uniform Manifold Approximation and Projection (UMAP) visualization was performed using the top 30 components and clustering resolution was set at 0.8.

source_name: hPSC-Derived

growth_protocol: Cells were grown in 10cm coated tissue culture dishes using media specific for each cell type.

extract_protocol:
A single-cell suspension was loaded into the Bio-Rad ddSEQ Single-Cell Isolator on which cells were isolated, lysed and barcoded in droplets.
Libraries were generated with direct tagmentation followed by 3’ enrichment and sample indexing using Illumina Nextera library prep kit.
ddSeq

value: hPSC-Derived cell

tag: differentiation condition

value: With Retinoic Acid


title: MCF7-F13

value: Mutant


title: LNCAP_2B7_SHRNA_1

tag: cell line


title: WHR138_liver_Nudt12_WT_ ZT0