title: MERVLi_8C_RNA_rep1

data_processing:
Basecalls performed using bcl2fastq version 2.20.0.
Raw paired-end RNA-seq reads were aligned to the indexed mouse genome (GRCm38/mm10) using STAR aligner (version 2.5.3a). with following options, --twopassMode Basic; --outSAMtype BAM SortedByCoordinate; --outFilterType BySJout; --outFilterMultimapNmax 1; --winAnchorMultimapNmax 50; --chimSegmentMin 12; --chimJunctionOverhangMin 8; --alignSJoverhangMin 8; --alignSJDBoverhangMin 10; --outFilterMismatchNmax 999; --outFilterMismatchNoverReadLmax 0.04; --alignSJstitchMismatchNmax 5 -1 5 5; --outSAMattrRGline ID:GRPundef; --alignIntronMin 20; --alignIntronMax 1000000; --alignMatesGapMax 1000000 for unique alignments.
Aligned RNA-seq output file (.bam) was input to the featureCounts function, a part of the Subread package, to quantify uniquely aligned reads on respective annotated transcript loci (GENCODE vM25). Read count output file (.txt) was input to the DESeq2 package version 1.16.1, to detect differentially expressed genes between two biological samples.
To visualize enrichment of RNA-seq reads over representative genomic loci, bigWig files (.bw) were created from sorted BAM files using the bamCoverage function as implemented in deepTools (version 3.1.3). Figures for continuous tag counts over selected genomic intervals were created in the IGV browser (Broad Institute).
Assembly: mm10
Supplementary files format and content: Read count data (.txt) and read coverage data (.bw) from RNA-seq analysis.

source_name: MERVLi 8-cell stage embryo

extract_protocol:
Acidic Tyrode’s solution (Sigma) containing 0.2% PVA was used to remove the zona pellucida (ZP) from embryos before sample collection.
For preparation of RNA-seq library, 30 each ZP-free embryos were lysed in 1x Lysis Buffer containing RNase inhibitor (0.2 IU/µl, from SMART-Seq Stranded Kit, Clontech), directly. RNAs were randomly sheared by heating at 85℃ for 8 min and supplied to reverse transcription with random hexamers and PCR amplification. Ribosomal fragments were depleted from each cDNA sample with scZapR and scR-Probes. Indexed total RNA-seq libraries were enriched by second PCR amplification.

treatment_protocol: The CBh-dCas9-KRAB-MeCP2 fusion construct was constructed using the pX330 (#42230, Addgene) plasmid backbone. dCas9-KRAB-MeCP2 sequence was obtained from a PB-TRE-dCas9-KRAB-MeCP2 (gifted from Dr. Andrea Califana, #122267, Addgene) plasmid and subcloned into pX330 using NEBuilder HiFi DNA Assembly Cloning Kit (New England Biolabs). Constructed pX330 plasmid in which hSpCas9 site had been replaced with dCas9-KRAB-MeCP2 (hereafter referred as pX330-CRISPRi), was then subjected to subcloning of sgRNA sequences. Individual annealed sgRNA spacer with four overhangs (Sense: 5’-CACC, Antisense: 5’-AAAC) was subcloned into the BbsI site of the pX330 plasmid. Subsequently, a transcriptional unit of each gRNA vector (consisting of a human U6 promoter, gRNA spacer and scaffold sequences) was inserted into SacII-to-XbaI sites of pX330-CRISPRi plasmid. The constructed MERVL-targeting pX330-CRISPRi plasmid was microinjected into the male pronucleus of zygotes at a final concentration of 15 ng µl-1.

value: 2.5 dpc

tag: experimental conditions

value: MERVLi

tag: background strain


title: MERVLi_8C_RNA_rep2

status: Public on Feb 12 2023

type: SRA

city: Shinjuku-ku

first: Akihiko

last: Sakashita

state: Tokyo

address: 35 Shinanomachi

department: Department of Molecular Biology,

country: Japan

institute: Keio University School of Medicine

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

growth_protocol: Eight-weeks old female and male B6D2F1 (BDF1) mice were purchased from the Japan SLC, Inc. All animal experiments were reviewed and approved by the Institutional Animal Care and Use Committee (protocol no. 09105-(10) and 11045-(6)) at Keio University, where mice were maintained and fed ad libitum with standard diet and water in a temperature- and light-controlled room (23℃±3℃, 14 light/10 dark cycle).

tag: days post-coitum (dpc)


title: RNA seq data of TRB3 ZF replicate 2

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

country: USA

institute: University of California, Los Angeles

description: RNA seq data of TRB3 ZF replicate 2

data_processing:
All libraries were sequenced at a length of 50 bps with HiSeq 2500 or NovaSeq 6000 platforms following manufacturer’s instructions (Illumina). Raw reads were aligned to the Arabidopsis reference genome (TAIR10) with Bowtie2 (v2.1.0)43, allowing only uniquely mapped reads with perfect matches. Duplicated reads were removed with Samtools (v1.9)44. Peaks were called using MACS2 (v2.1.1)45.
RNA-seq analysis: Cleaned short reads were aligned to reference genome tair10 by Bowtie2 (v2.1.0), and expression abundance was calculated by RSEM with default parameters68. Heatmaps were visualized with the R package pheatmap. To reduce false positive of differential expression, transcripts with less than 5 reads of all replicates in total were regarded as lowly expressed genes and have been removed in subsequent analysis. Differential expression analysis was conducted using edgeR. A threshold of p value < 0.05 and Fold Change > 2 were used to decide whether significant expression difference exists between samples.
ChIP-seq analysis: ChIP-seq fastq reads were aligned to the TAIR10 reference genome with Bowtie (v1.1.2)70, allowing only uniquely mapping reads with 0 mismatches. Duplicated reads were removed by Samtools. ChIP-seq peaks were called by MACS2 (v2.1.1) and annotated with ChIPseeker71. Differential peaks were called by bdgdiff function in MACS2. ChIP-seq data metaplots were plotted by deeptools (v2.5.1)72. For Pol II 5’ occupancy analysis, Pol II occupancy was calculated based normalized reads count (RPKM) on a TSS +/- 200 bp region and a TSS +500 bp to TTS gene body region by bedtools.
Whole genome bisulfite sequencing (BS-seq) analysis: Trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to trim adapters after filtering low quality reads. BS-seq reads were aligned to TAIR10 reference genome by Bismark (v0.18.2)73 with default settings. Reads with three or more consecutive CHH sites were considered as unconverted reads and filtered. DNA methylation levels were defined as #C/ (#C + #T). DMRs (Differentially Methylated Regions) were called by DMRcaller with p < 0.01 for where the differences in CG, CHG, and CHH methylation were at least 0.4, 0.2, and 0.1, respectively.
BS-PCR analysis: BS-PCR data were analyzed with a previously published pipeline. BS-PCR data were trimmed with primer sequences and mapped to TAIR10 reference genome with bsmap (v2.90) allowing 2 mismatches and 1 best hit (-v 2 -w 1).
BS-sPCR reads were mapped to TAIR10 reference genome by bsmap (v2.90) with allowing 2 mismatches and 1 best hit (-v 2 -w 1)46. Reads with three or more consecutively methylated CHH sites were considered as non-converted reads and removed from the analyses. DNA methylation levels were calculated by #C/ (#C + #T). Differential Methylated Regions (DMRs) were called by methdiff function with every 100bp bin for where the difference in CG, CHG, and CHH methylation are at least 0.4, 0.2, and 0.1, respectively.
Assembly: Tair10
Supplementary files format and content: bed, bigwig, wig

organism: Arabidopsis thaliana

source_name: Arabidopsis leaf tissue

growth_protocol: Arabidopsis plants of the Columbia-0 (Col-0) ecotype were used in this study. All plants were grown under green house condition (16 h light/8 h dark, 22C). Floral tissues were collected from 5-6 week plants

extract_protocol:
ChIP seq: Libraries were prepared with Ovation Ultra Low System V2 kits following the manufacturer’s instructions. BS seq: 300 ng of DNA was sheared to 200bp with a Covaris S2 (Covaris). Libraries were prepared with the Epitect Bisulfite Conversion kit (QIAGEN) and the Ovation Ultralow Methyl-seq kit (NuGEN) following the manufacturer’s instructions. RNA seq: 1 ug of total RNA was used for library preparation with TruSeq Stranded mRNA kit (Illumina). Libraries were sequenced on HiSeq 2500 or NovaSeq 6000 (Illumina).
Plants total RNAs were extracted with TRIzol and Direct-zol RNA Miniprep kit (Zymo, R2050). Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina) following the manufacturer instructions.
RNA-seq library preparation: Plants total RNAs were extracted with TRIzol and Direct-zol RNA Miniprep kit (Zymo, R2050). Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina) following the manufacturer instructions.
ChIP-seq library preparation: 10 grams of inflorescence and meristem tissues were used for Flag, H3, H3K4me3, and H3K27me3 ChIP-seq. ChIP were performed as described previously60 with anti-FLAG M2 (Sigma), anti-H3 (Ab1791, Abcam), anti-H3K4me3 (Milipore Sigma 04-745),  andanti-H3K4me3 (Milipore Sigma 07-449) antibodies.
BS-PCR and McrBC assay for FWA tandem repeat: For BS-PCR of FWA tandem repeat, genomic DNA was extracted from leaf tissue of TRB-ZF T2 lines as well as fwa with CTAB-based method and converted using the Epitect Bisulfite kit kit (Qiagene research). Methylation level of FWA promoter region and several control regions have been amplified with primers described previously46. HiSeq 2500 (Illumina) sequencing libraries were made from purified PCR products using a Kapa Hyper DNA Library Prep kit. For McrBC of FWA tandem repeat, genomic DNA was extracted from leaf tissue with CTAB-based method, and treated with PureLink RNase (Invitrogen) and then with McrBC (NEB) for 4 hours at 37°C. FWA tandem repeat region was quantified by qPCR.

tag: tissue

value: leaf tissue

tag: developmental stage

value: 5-6 weeks

tag: ecotype


title: Livers from KO mice fed MCD diet Bio rep 3

city: Atlanta

first: Samuel

middle: Adam

last: Druzak

state: GA

address: 1510 clifton RD NE

department: Biochemistry

institute: Emory University

data_processing:
Analysis was performed by novagene.
Pathway analysis was performed using Enrichr.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include procced data values for each Sample

source_name: Primary whole liver

extract_protocol:
Total RNA was isolated from liver (10 µg) or cells using miRNeasy (QIAGEN, Hilden, Germany) following manufacturer’s instructions. cDNA was synthesized with a High-Capacity cDNA Reverse transcription Kit (Applied Biosystems, Foster City, CA, USA).
cDNA was sent to Novagene for library prep and sequencing.

value: Primary whole liver

tag: genotype

value: PCTP-/-

tag: treatment

value: MCD Diet


title: Untreated Hippocampus RNA ZT14_3814

city: Irvine

first: Matthew

last: Birnie

address: Health Sciences Road

institute: University of California-Irvine

data_processing:
Illumina Casava 1.8.2 software was used for basecalling
Sequenced reads were trimmed (to 100bp) for adaptor sequence, mapped to rn6 genome using tophat2 (version 2.0.10)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CuffDiff (version 2.2.0)
Assembly: rn6
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: Hippocampus

extract_protocol:
Hippocampi were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Qiagen miRNeasy RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq stranded Illumina protocols

treatment_protocol: Vehicle (normal drinking water) or methylprednisolone (1mg/mL) in drinking water for 5 days, ad libitum

tag: strain

value: Sprague-Dawley

value: Brain

value: Hippocampus

value: Vehicle

tag: age

value: 3-4 months

tag: timepoint


title: RNA seq data of TRB3 ZF replicate 1

description: RNA seq data of TRB3 ZF replicate 1


title: Ctrl-GFPi_8C_RNA_rep2

source_name: GFPi Control 8-cell stage embryo

value: Control


title: Untreated Hippocampus RNA ZT14_3813


title: Livers from WT mice fed MCD diet Bio rep 3

value: WT


title: Untreated Hippocampus RNA ZT18_3819


title: Ctrl-GFPi_8C_RNA_rep1


title: Untreated Hippocampus RNA ZT14_3812


title: RNA seq data of Col0 replicate 3

description: RNA seq data of Col0 replicate 3

source_name: Arabidopsis seedling tissue

value: seedling tissue

value: 2-3 weeks


title: RNA seq data of TRB2 ZF replicate 2

description: RNA seq data of TRB2 ZF replicate 2


title: Untreated Hippocampus RNA ZT14_3811


title: Livers from KO mice fed MCD diet Bio rep 2


title: RNA seq data of Col0 replicate 2

description: RNA seq data of Col0 replicate 2


title: MERVLi_4C_RNA_rep2

source_name: MERVLi 4-cell stage embryo


title: Livers from KO mice fed MCD diet Bio rep 1


title: Livers from WT mice fed MCD diet Bio rep 1


title: Livers from KO mice fed Chow diet Bio rep 3

value: Chow diet


title: MERVLi_4C_RNA_rep1

value: 2.5 dpc


title: Untreated Hippocampus RNA ZT2_3809


title: Untreated Hippocampus RNA ZT2_3810


title: Ctrl-GFPi_4C_RNA_rep2

source_name: GFPi Control 4-cell stage embryo


title: Ctrl-GFPi_4C_RNA_rep1


title: Untreated Hippocampus RNA ZT2_3808


title: RNA seq data of TRB1 ZF replicate 2

description: RNA seq data of TRB1 ZF replicate 2


title: Livers from WT mice fed MCD diet Bio rep 2


title: RNA seq data of TRB1 ZF replicate 1

description: RNA seq data of TRB1 ZF replicate 1


title: RNA seq data of TRB2 ZF replicate 1

description: RNA seq data of TRB2 ZF replicate 1


title: RNA seq data of fwa replicate 3

description: RNA seq data of fwa replicate 3


title: Livers from WT mice fed Chow diet Bio rep 3


title: MERVLi_2C_RNA_rep1

source_name: MERVLi 2-cell stage embryo

value: 1.5 dpc

value: MERVLi


title: Untreated Hippocampus RNA ZT2_3807


title: MERVLi_2C_RNA_rep2


title: RNA seq data of TRB2 ZF replicate 3

description: RNA seq data of TRB2 ZF replicate 3

value: leaf tissue

value: 5-6 weeks


title: RNA seq data of fwa replicate 2

description: RNA seq data of fwa replicate 2


title: Livers from WT mice fed Chow diet Bio rep 1

value: Primary whole liver


title: Human splenocytes, mRNA-derived cDNA

city: Vancouver

first: Megan

last: Levings

state: BC

address: 950 West 28th Avenue

country: Canada

institute: University of British Columbia

description:
mRNA and cell surface protein
R1 file contains paired-end sequence read 1; R2 file contains paired-end sequence read 2; I1 contains the index 1 (i5) reads; I2 contains the index 2 (i7) reads

data_processing:
Read alignment to the reference human genome (GRCh38/hg38) and gene expression matrices were generated by the 10X Genomics CellRanger pipeline (version 6.1.2).
Further processing was done with Seurat v4.3.0 (cell and gene filtering, dimensionality reduction, clustering, differential gene expression analysis).
Assembly: GRCh38-2020-A
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

organism: Homo sapiens

source_name: Splenocytes

extract_protocol:
Stained samples were adjusted to a concentration of 1200 cells/μL and loaded onto a Chromium controller (10X Genomics) as per manufacturer protocol for GEM generation and barcoding.
Samples were prepared for sequencing using the 10X Genomics Single Cell 5’ v2 platform in accordance with manufacturer’s instructions for capture of 12,000 cells per sample. Reverse transcription, cDNA amplification and sequencing libraries were generated using 10X Genomics Single Cell 5’ v2 reagents. Across samples, cells were sequenced to a target depth of 40,000 reads per cell. ADT and RNA libraries were sequenced in separate lanes on a shared flow cell.

treatment_protocol:
Samples were cut into small pieces using a sterile scalpel then placed into gentleMACS C-tubes with 10 mL PBS plus 2% FBS and placed in a gentleMACS dissociator using the m_spleen_01_01 setting. After dissociation, the slurry was mashed through a 70 μm cell strainer and ACK lysed to remove red blood cells. Cell pellets were resuspended in 50 mL RPMI media and 10E6 cells were removed per well, centrifuged and resuspended in 50 μL master mixes containing cell staining buffer and either flow cytometry or CITE-seq antibodies.
10E6 cells were resuspended in Cell Staining Buffer and Fc blocked as per BioLegend ADT staining protocol. TotalSeq-C antibody cocktails were prepared using concentrations determined by previous flow-cytometry titrations. The resulting cocktail was then added to cells and incubated for 30 minutes at 4C.

value: Splenocytes

tag: cell type

value: Dissociated splenocytes

tag: library type

value: RNA and ADT

tag: antibodies/tags

value: 61 TotalSeq-C antibodies contained in feature_reference.csv


title: Livers from WT mice fed Chow diet Bio rep 2


title: Human islet CD45+, Lineage- cells, mRNA-derived cDNA

source_name: Pancreatic islets

treatment_protocol:
~10,000 IEQ were dissociated by centrifugation, resuspended in trypLE, and pipetted vigorously. Immune cells were enriched using a EasySep human CD45 Depletion kit II. CD45-enriched islet cells (10E6) were stained with flow cytometry antibodies as well as the TotalSeq™-C antibody cocktail (at a 1:1 ratio) and flow sorted before sequencing. FITC-conjugated antibodies against B cells, T cells, and myeloid cells were used to differentiate these immune cells from ILCs. We also used a live/dead dye and antibodies directed against CD45, CD56, and CD127 to differentiate helper ILCs from NK cells. Cells were sorted as Live, CD45+, Lineage- and sent for sequencing.
10E6 cells were resuspended in Cell Staining Buffer and Fc blocked as per BioLegend ADT staining protocol. TotalSeq-C antibody cocktails were prepared using concentrations determined by previous flow-cytometry titrations. The resulting cocktail was then added to cells and incubated for 30 minutes at 4C.

value: Pancreatic islets

value: CD45+, ILC-enriched, flow-sorted cells


title: Ctrl-GFPi_2C_RNA_rep1

source_name: GFPi Control 2-cell stage embryo

value: Control


title: Ctrl-GFPi_2C_RNA_rep2


title: RNA seq data of fwa replicate 1

description: RNA seq data of fwa replicate 1


title: Livers from KO mice fed Chow diet Bio rep 2

value: PCTP-/-


title: Input_PE_786O_PBRM1WT_Rep5

status: Public on Feb 11 2023

city: Singapore

first: Xiaosai

last: Yao

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

library_source: genomic

data_processing:
Sequencing reads were mapped against human genome reference hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.6.2) 'mem' algorithm. Only reads with mapQ >10 and with duplicate removed by rmdup were used in the subsequent analysis
Significant peaks were called using MACS2 24 (q-value < 0.01).
Assembly: hg19
Supplementary files format and content: ChIP-seq peaks are in bed format, including 5 columns: "chromosome"  "start of region" "end of region" "peak name" "peak enrichment"

molecule: genomic DNA

source_name: Cancer cell line

growth_protocol: Cells were grown in RPMI-1640 medium (Sigma) supplemented with 10% fetal bovine serum (Gibco). Cells were maintained in a 5% CO2-humidified incubator at 37°C.

extract_protocol:
For each protein of interest, approximately 2x107 cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and stopped by adding glycine to a final concentration of 0.2M. Chromatin was extracted and sonicated to ~500bp (Vibra cell, SONICS). The total volume of immunoprecipitation was 2 ml and the amount of antibody used was 20 µg. The input DNA was precleared with protein G Dynabeads (LifeTechnologies) for 2 hours at 4°C and then incubated with antibodies overnight at 4°C. Protein G beads were added the following day and mixture was nutated for 3 hours at 4°C. The beads were washed 6 times with wash buffer at room temperature.
At least 10 ng of the amplified DNA was used with NEBNext ChIP-Seq library prep reagent set (NEB). Each library was sequenced to an average depth of 30-50 million reads on HiSeq2500 or HiSeq4000.

treatment_protocol: PBRM1 was knocked out using CRISPR-Cas9 mediated gene editing in 786-O, A498 and HK-2. Wildtype PBRM1 was cloned from normal kidney tissue. cDNA was either cloned into pbabe vector or pLenti-GFP.

tag: source

tag: protein

value: Input (paired end)

value: parental

tag: chip antibody


title: Input_PE_786O_PBRM1KO_Rep4


title: Input_PE_786O_PBRM1KO_Rep5


title: Input_PE_786O_PBRM1WT_Rep4


title: Livers from KO mice fed Chow diet Bio rep 1

value: Chow diet


title: Input_PE_786O_PBRM1WT_Rep2


title: H3K4me1_786O_PBRM1WT_ChIPseq_Rep2


title: Input_PE_786O_PBRM1KO_Rep2


title: H3K4me1_786O_PBRM1KO_ChIPseq_Rep2


title: H3K4me1_786O_PBRM1WT_ChIPseq_Rep1


title: H3K4me1_786O_PBRM1KO_ChIPseq_Rep1


title: RELA_786O_PBRM1KO_ChIPSeq_Rep2

value: RELA

value: RELA (Invitrogen 51-0500 Lot:WG331314)


title: RELA_786O_PBRM1WT_ChIPSeq_Rep3

value: RELA(Diagenode C15310256 Lot:24468)


title: RELA_786O_PBRM1KO_ChIPSeq_Rep3


title: RELA_786O_PBRM1WT_ChIPSeq_Rep2


title: RELA_786O_PBRM1KO_ChIPSeq_Rep1

value: RELA(Santa Cruz sc-372 Lot:#J1915)


title: BRD9_786O_PBRM1WT_ChIPSeq_Rep2

value: BRD9 (Bethyl A303-781A, Lot2)


title: BRD9_786O_PBRM1KO_ChIPSeq_Rep2


title: BRD9_786O_PBRM1KO_ChIPSeq_Rep1


title: ARID1A_786O_PBRM1KO_ChIPSeq_Rep2

value: ARID1A (Santa Cruz sc-32761 Lot:#H2217)


title: ARID1A_786O_PBRM1WT_ChIPSeq_Rep2


title: ARID1A_786O_PBRM1WT_ChIPSeq_Rep1


title: SMARCA4_786O_PBRM1KO_ChIPSeq_Rep2


title: Input_PE_786O_PBRM1KO_Rep3


title: Input_PE_786O_PBRM1WT_Rep3


title: SMARCA4_786O_PBRM1WT_ChIPSeq_Rep2


title: ARID2_786O_PBRM1KO_ChIPSeq_Rep2

value: ARID2(Bethyl, A302-230A, lot 2)


title: ARID2_786O_PBRM1WT_ChIPSeq_Rep2


title: PBRM1_786O_PBRM1KO_ChIPSeq_Rep3

value: PBRM1(Bethyl, A301-591A, lot3)


title: PBRM1_786O_PBRM1KO_ChIPSeq_Rep2


title: PBRM1_786O_PBRM1WT_ChIPSeq_Rep2


title: RELA_786O_PBRM1WT_ChIPSeq_Rep1


title: BRD9_786O_PBRM1WT_ChIPSeq_Rep1


title: OE58F

city: Guangzhou

first: ZhiJie

last: Liu

address: No. 651 Dongfengdong Road

country: China

institute: Sun Yat-sen University Cancer Center

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the (TPM) method. RSEM v1.3.1 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.24.0
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: cell line

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cell line

tag: cell line

value: nasopharyngeal carcinoma (NPC)

value: overexpression


title: ARID1A_786O_PBRM1KO_ChIPSeq_Rep1


title: NCS18

value: vector


title: Input_PE_786O_PBRM1KO_Rep1

data_processing:
Sequencing reads were mapped against human genome reference hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.6.2) 'mem' algorithm. Only reads with mapQ >10 and with duplicate removed by rmdup were used in the subsequent analysis
Significant peaks were called using MACS2 24 (q-value < 0.01).
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq peaks are in bed format, including 5 columns: "chromosome"  "start of region" "end of region" "peak name" "peak enrichment"


title: Input_PE_786O_PBRM1WT_Rep1


title: NC58F


title: H3K4me3_786O_PBRM1KO_ChIPSeq


title: H3K27ac_786O_PBRM1WT_ChIPSeq


title: Input_PE_786O_PBRM1WT(for ARID1A and SMARCC1)


title: ARID1A_786O_ChIPSeq

value: ARID1A (Santa Cruz, sc-32761, lot H2217)


title: H3K14ac_786O_PBRM1WT_ChIPSeq


title: OES18


title: H3K4me3_786O_PBRM1WT_ChIPSeq


title: H3K27ac_786O_PBRM1KO_ChIPSeq


title: BJ cells, siVDR_2

city: Beijing

first: Xiangyang

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: College of Life Sciences

institute: Peking University

data_processing:
Illumina Casava1.8 software used for basecalling.
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.At the same time, Q20, Q30 and GC content the clean data were calculated.
Clean reads were mapped to GRCh38/hg38 of human genome using Hisat v.2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: text files include fpkm values for each Sample

source_name: BJ cells

growth_protocol: Cells were cultured at 37 ℃ in 5% CO2 in Dulbecco’s modified Eagle medium (DMEM, Gibco) supplemented with 100 U ml-1 penicillin, 100 μg ml-1 streptomycin, and 20% fetal bovine serum (FBS, Gibco).

extract_protocol:
RNA was isolated from cells by TRIzol Reagent (Invitrogen) as recommended by the manual.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BJ cells

value: primary fibroblasts

value: VDR knockdown with siRNA for 24 hours


title: BJ cells, siVDR_1


title: BJ cells, Chae_2

value: 50 nM chaetocin treatment for 24 hours


title: BJ cells, Cal24h_2

value: 100 nM calcipotriol treatment for 24 hours


title: BJ cells, Cal24h_3


title: BJ cells, Chae_1


title: BJ cells, siVDR_3


title: BJ cells, Cal4h_2

value: 100 nM calcipotriol treatment for 4 hours


title: BJ cells, Cal4h_3


title: BJ cells, CTL_3

value: control


title: BJ cells, CTL_2


title: BJ cells, Chae_3


title: BJ cells, CTL_1


title: 786O_PBRM1KO_ATPasei_24hr_rep2

data_processing:
RNA-seq data were mapped to hg19 (hs37d5) using STAR 25, with GENCODE annotation (gencode.v19.annotation.gtf) and recommended settings from STAR manual. Gene expression levels were quantified with STAR. For 769-P, RNA-seq data were mapped to GRCh38 using GMAP. Log fold change of differential expression genes was computed with DESeq2 for all cell lines
Assembly: hg19
Supplementary files format and content: Deseq2 files are in tab delimited text files, including 8 standard columns "ensembleID", "GeneSymbol", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj", then followed by columns of log2(normalized counts) and columns of raw count.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini kit
RNAseq libraries were prepared using Illumina Tru-Seq Stranded Total RNA kit protocol

treatment_protocol: Cells were treated with DMSO control or 5nM bortezomib for 9 hours prior to RNA-seq. Cells were treated with DMSO control or 10uM SMARCA2/4 ATPase inhibitor (BRM014) for 24 hours prior to RNA-seq.

value: ATPase inhibitor 10uM, 24hr


title: 786O_PBRM1KO_DMSO_24hr_rep2

value: DMSO


title: 786O_PBRM1WT_DMSO_24hr_rep1


title: 786O_PBRM1KO_BTZ_9hr_rep3

value: bortezomib 5nM, 9hr


title: 786O_PBRM1WT_DMSO_24hr_rep2


title: 786O_PBRM1KO_DMSO_24hr_rep1


title: 786O_PBRM1WT_ATPasei_24hr_rep2


title: 786O_PBRM1KO_ATPasei_24hr_rep1


title: 786O_PBRM1WT_ATPasei_24hr_rep1


title: BJ cells, Cal24h_1


title: del atoC, M9, rep1

city: La Jolla

first: Cameron

last: Lamoureux

state: CA

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California San Diego

data_processing:
Raw read trimming was performed with Trim Galore using the default options, followed by FastQC on the trimmed reads.
Reads were aligned to the E. coli K-12 MG1655 reference genome (NC_000913.3) using bowtie with the following optional arguments: -X 1000, -3 3, -n 2
Read direction was inferred with RSEQC.
Read counts were generated with featureCounts with the following optional arguments: -p -B -C -P --fracOverlap 0.5
Quality control metrics were assembled with MultiQC and the final expression was reported in units of log2-transformed transcripts per million for each gene.
Assembly: NC_000913.3
Supplementary files format and content: tcs_log_tpm.csv contains log2[TPM] values for all samples and genes.
Supplementary files format and content: tcs_counts.csv contains raw read counts as computed by featureCounts for all samples and genes.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: MG1655 del_atoC

extract_protocol:
3 ml of cell broth (at an A600 ≈ 0.6) was immediately added to two volumes of Qiagen RNA-protect Bacteria Reagent (6 ml), vortexed for 5 s, incubated at room temperature for 5 min and immediately centrifuged for 10 min at 17,500 r.p.m. The supernatant was decanted, and the cell pellet was stored at −80 °C. Cell pellets were thawed and incubated with Ready-Lyse Lysozyme, SuperaseIn, protease K and 20% SDS for 20 min at 37 °C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase treatment was performed for 30 min at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA nano chip on a bioanalyser. The ribosomal RNA was removed using an Illumina Ribo-Zero rRNA removal kit for Gram-negative bacteria.
A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around 300 bp

value: MG1655 del_atoC

tag: culture type

value: batch

tag: media

tag: supplement


title: 786O_PBRM1KO_BTZ_9hr_rep2


title: 786O_PBRM1KO_BTZ_9hr_rep1


title: RRBS_ESCs_Usp7KO2

city: Illkirch

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

country: France

institute: CNRS

data_processing:
Reads were trimmed with Trim Galore (v0.4.4) in –non_directional and –rrbs mode to remove adapter sequences, two bases filled in during end-repair of MspI restriction sites, and low-quality ends with a Phred score below 20. Sequencing reads were mapped to the mouse genome (mm10) with Bismark v0.18.2 with default parameters. Methylation scores were extracted as the ratio of the number of Cs over the total number of Cs and Ts using the Bismark_methylation_extractor. CpG methylation ratios from both strands were combined and filtered for a minimum sequencing depth of 8X.
We provide IGV files containing methylation scores for all CGs with at least 8X sequencing depth.

source_name: ES cells

growth_protocol: Mouse E14TG2a embryonic stem cells were cultured in DMEM Glutamax supplemented with 15% FBS, 1,000 U/mL of LIF, 0.1 mM of non-essential amino acids, 50 U/mL of penicillin and streptomycin and 0.1 mM of 2-mercaptoethanol.

extract_protocol:
DNA samples were extracted using the NucleoSpin RNA purification kit and NucleoSpin RNA/DNA Buffer Set for parallel RNA and DNA purification (Macherey-Nagel) according to the manufacturer's instructions.
RRBS libraries were prepared as described in Bender et al. (2021), Methods Mol Biol 2214:207-220. Briefly, 100 ng genomic DNA were digested with MspI (Thermo Fisher Scientific), end-repaired and A-tailed with Klenow fragment exo- (Thermo Fisher Scientific) and ligated to methylated adapters with T4 DNA ligase (Thermo Fisher Scientific) in Tango 1X buffer. DNA fragments ranging from 150 to 400 bp were selected by gel excision, purified using the MinElute gel extraction kit (Qiagen) and bisulfite-converted twice with the EpiTect bisulfite kit (Qiagen). The libraries were amplified using the Pfu Turbo Cx hotstart DNA polymerase (Agilent) with 12 PCR cycles and purified using Agencourt AmpureXP beads (Beckman-Coulter).

treatment_protocol: Usp7-KO clones were generated by CRISPR-Cas9.


title: RRBS_ESCs_Usp7KO1


title: RRBS_ESCs_Usp7KO3


title: RRBS_ESCs_WT4

value: WT


title: RRBS_ESCs_Usp7KO4


title: 786O_PBRM1KO_DMSO_9hr_rep3


title: 786O_PBRM1KO_DMSO_9hr_rep1


title: 786O_PBRM1KO_DMSO_9hr_rep2


title: RRBS_ESCs_WT3


title: RRBS_ESCs_WT2


title: 786O_PBRM1WT_BTZ_9hr_rep3


title: 786O_PBRM1WT_BTZ_9hr_rep2


title: RRBS_ESCs_WT1


title: RNA-seq_ESCs_Usp7KO4

data_processing:
Reads were aligned to the mouse mm10 genome with TopHat2 v2.0.13 using default parameters and a RefSeq transcriptome index.
For data visualization, bigWig files were generated using bam2wig.py from the RSeQC package v2.6.4 using the parameters -u -t 5000000000.
We provide bigWig files for visualization of RNA-seq tracks.

extract_protocol:
RNA samples were extracted using the NucleoSpin RNA purification kit and NucleoSpin RNA/DNA Buffer Set for parallel RNA and DNA purification (Macherey-Nagel) according to the manufacturer's instructions.
RNA-Seq libraries were generated from 100ng total RNA using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit and IDT for Illumina RNA UD Indexes (Illumina), according to the manufacturer’s instructions. The final libraries were generated with 13 cycles of PCR amplification and purified using SPRIselect beads (Beckman-Coulter).


title: RNA-seq_ESCs_Usp7KO3


title: 786O_PBRM1WT_DMSO_9hr_rep3


title: 786O_PBRM1WT_DMSO_9hr_rep1


title: RNA-seq_ESCs_Usp7KO2


title: 786O_PBRM1WT_DMSO_9hr_rep2


title: RELA_786O PBRM1KO_ATPasei_24hr__ChIPSeq_rep2

data_processing:
Sequencing reads were mapped against human genome reference hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.6.2) 'mem' algorithm. Only reads with mapQ >10 and with duplicate removed by rmdup were used in the subsequent analysis
Significant peaks were called using MACS2 24 (q-value < 0.01).
Assembly: hg19
Supplementary files format and content: ChIP-seq peaks are in macs2 narrowPeak format, including 10 columns: "chromosome"  "start coordinate" "end coordinate" "name" "score" "strand" "signalValue" "pValue" "qValue" "peak"

extract_protocol:
For each protein of interest, approximately 2x107 cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and stopped by adding glycine to a final concentration of 0.2M. Chromatin was extracted and sonicated to ~500bp (Vibra cell, SONICS). The total volume of immunoprecipitation was 2 ml and the amount of antibody used was 20 µg. The input DNA was precleared with protein G Dynabeads (LifeTechnologies) for 2 hours at 4°C and then incubated with antibodies overnight at 4°C. Protein G beads were added the following day and mixture was nutated for 3 hours at 4°C. The beads were washed 6 times with wash buffer at room temperature.
At least 10 ng of the amplified DNA was used with NEBNext ChIP-Seq library prep reagent set (NEB). Each library was sequenced to an average depth of 30-50 million reads on Novaseq

treatment_protocol: Cells were treated with DMSO control or 5nM bortezomib for 9 hours prior to ChIP-seq. Cells were treated with DMSO control or 10uM SMARCA2/4 ATPase inhibitor (BRM014) for 24 hours prior to ChIPseq.

value: RELA

value: SMARCA2/4 ATPase inhibitor, 10uM, 24 hr

value: RELA (Invitrogen 51-0500 Lot:WG341385)


title: RNA-seq_ESCs_WT4


title: RNA-seq_ESCs_Usp7KO1


title: RNA-seq_ESCs_WT3


title: RNA-seq_ESCs_WT2


title: RELA_786O PBRM1KO_DMSO_24hr__ChIPSeq_rep2


title: RNA-seq_ESCs_WT1


title: SMARCA4_786O PBRM1KO_DMSO_24hr__ChIPSeq_rep2


title: RELA_786O PBRM1WT_DMSO_24hr_ChIPSeq_rep2


title: RRBS_ESCs_siRNA_Dnmt1_rep2

growth_protocol: Mouse embryonic stem cell line E14TG2a was cultured in DMEM Glutamax supplemented with 15% FBS, 1,000 U/mL of LIF, 0.1 mM of non-essential amino acids, 50 U/mL of penicillin and streptomycin and 0.1 mM of 2-mercaptoethanol.

treatment_protocol: ES cells were transfected with ON-TARGETplus SMART pool siRNAs using lipofectamine 2000, and cells were harvested 72 hours after transfection for nucleic acid extraction.

tag: sirna


title: 786O_PBRM1WT_BTZ_9hr_rep1


title: SMARCA4_786O PBRM1WT_DMSO_24hr_ChIPSeq_rep2


title: RELA_786O PBRM1WT_ATPasei_24hr_ChIPSeq_rep2


title: RELA_786O PBRM1KO_ATPasei_24hr_ChIPSeq_rep1


title: SMARCA4_786O PBRM1KO_ATPasei_24hr_ChIPSeq_rep1


title: RRBS_ESCs_siRNA_Usp7_rep3


title: RRBS_ESCs_siRNA_Usp7_rep1


title: RRBS_ESCs_siRNA_ctrl_rep3

value: non-targeting control


title: RRBS_ESCs_siRNA_Dnmt1_rep1


title: RELA_786O PBRM1KO_DMSO_24hr__ChIPSeq_rep1


title: SMARCA4_786O PBRM1WT_ATPasei_24hr_ChIPSeq_rep2


title: SMARCA4_786O PBRM1KO_ATPasei_24hr__ChIPSeq_rep2


title: RRBS_ESCs_siRNA_Usp7_rep2


title: RRBS_ESCs_siRNA_Dnmt1_rep3


title: RELA_786OPBRM1WT_ATPasei_24hr__ChIPSeq_rep1


title: RRBS_ESCs_siRNA_ctrl_rep1


title: RNA-seq_ESCs_siRNA_Shfm1_rep3

extract_protocol:
RNA samples were extracted using the NucleoSpin RNA purification kit and NucleoSpin RNA/DNA Buffer Set for parallel RNA and DNA purification (Macherey-Nagel) according to the manufacturer's instructions.
RNA-seq libraries were prepared from 400 ng total RNA using the TruSeq Stranded Total RNA Library Prep Gold kit with Ribo-Zero rRNA removal and TruSeq RNA Single Indexes kits A and B (Illumina), according to the manufacturer's instructions. The final libraries were generated with 12 cycles of PCR amplification and purified using AMPure XP beads (Beckman-Coulter).


title: RRBS_ESCs_siRNA_ctrl_rep2


title: RELA_786O PBRM1WT_24hr_DMSO_ChIPSeq_rep1


title: RNA-seq_ESCs_siRNA_Shfm1_rep2


title: R2_RNS_siGFP

city: Heidelberg

first: Jonathan

last: Bohlen

address: Im Neuenheimer Feld 581

country: Germany

institute: DKFZ

description: Total RNA

data_processing:
Adapter sequences and randomized nucleotides (Nextflex) or polyA stretches (Clonentech/Takara) were trimmed from raw reads using cutadapt (https://doi.org/10.14806/ej.17.1.200). Nuclear and mitochondrial Ribosomal RNA and tRNA reads were removed by alignment to human tRNA and rRNA sequences using bowtie2 (22388286). Then, the remaining reads were separately aligned to the human transcriptome (Ensembl transcript assembly 94) and human genome (hg38) using BBmap (sourceforge.net/projects/bbmap/). Multiple mappings were allowed. Secondary mappings were counted when analyzing single transcripts, but not counted in metagene plots to avoid biasing genes with many transcript isoforms or reads with low sequence complexity. Metagene plots, single transcript traces and grouped analyses were carried out or created with custom software written in C, supplied in Supplemental Dataset 1. Read counts for metagene plots of whole transcripts that encompass 5’UTRs, ORFs and 3’UTRs were normalized for the length of each of these features to make them comparable. 70 of the 41.314 transcripts were excluded from the analyses because PCR artefacts mapped to these transcripts. 2-D metagene plots were visualized using Fiji (Schindelin et al., 2012). The same, linear color gradient was always used to indicate read counts at each position in these 2-D metagene plots. Importantly, the maximum intensity of the color gradient was adjusted for the library size of the sample displayed so that 2-D metagene plots can be compared across panels. For 80S plots, only reads with footprint lengths between 26 to 37 nt were counted. For 5’UTR plots, only 40S footprints larger than 29 nt were counted because of the occurrence of artefacts and misaligned reads in the shorter population.
Translated uORFs were defined by the presence of any 80S ribosome footprints in a 10-nucleotide window around the uORF start codon. Only ATG initiated uORFs were considered. uORFs annotated by uORF-Tools (31513641) were downloaded from supplemental table 2 and filtered for uORFs with an intercistronic space > 80 nt.
Assembly: Ensemble transcript assembly 94
Supplementary files format and content: Excel files: Tables of the raw counts for each ENSEMBL transcript in each sample counted in coding sequence (80S and RNA-seq) or 5'UTR (40S).

source_name: HeLa

growth_protocol: We cultured HeLa cells in DMEM +10% fetal bovine serum (FBS) +100 U/ml Penicillin/Streptomycin (Gibco 15140122). We sub-cultured the cells using Trypsin-EDTA. HeLa cells were tested negative for mycoplasma and authenticated using SNP typing.

extract_protocol:
Selective 40S and 80S ribosome footprinting was carried out as published in (Bohlen et al., 2020a; Bohlen et al., 2020b) [Nature Protocols] and as briefly below.
Preparation of non-denaturing cell lysates: We seeded Hela cells at 1.5 million cells per 15 cm dish in 20 ml growth medium two days before cell harvest. For cell harvest, we poured off growth medium and washed cells quickly with ice-cold washing solution (1x PBS 10 mM MgCl2, 800 µM Cycloheximide). After quickly pouring off the washing solution, we added freshly prepared crosslinking solution (1x PBS, 10 mM MgCl2, 0.025% PFA, 0.5 mM DSP, 200 µM Cycloheximide) to the cells. We incubated cells with crosslinking solution for 15 minutes at room temperature while slowly rocking. We poured the crosslinking solution off and inactivated the remaining crosslinker for 5 minutes with ice-cold quenching solution (1x PBS, 10 mM MgCl2, 200 µM Cycloheximide, 300 mM Glycine). After removal of the quenching solution we added 150 µl of lysis buffer (0,25 M HEPES pH 7.5, 50 mM MgCl2, 1 M KCl, 5% NP40, 1000 μM Cycloheximide) to each 15 cm dish, resulting in 750µL of lysate. Lysis was carried out at 4°C. Then we scraped cells off the dish and collected the lysate. After brief vortexing, we clarified lysates by centrifugation at 20.000xg for 10 minutes at 4°C.
Sucrose gradient centrifugation: We collected Supernatant and determined the approximate RNA concentration using a Nanodrop photo-spectrometer. We added 100 U of Ambion RNase 1 per 120 µg of measured RNA. To obtain polysome profiles, we did not add RNase. We incubated the Lysates for 5 minutes at 4°C and then loaded them onto 17.5%-50% sucrose gradients and centrifuged them for 5 hours at 35.000 rpm in a Beckman Ultracentrifuge in the SW40 rotor. Then we fractionated Gradients using a Biocomp Gradient Profiler system. We collected 40S and 80S fractions for immunoprecipitation and footprint isolation. We used 40S and 80S fractions corresponding to roughly one or two 15 cm dishes for direct extraction of RNA for total footprint sample and we used 40S and 80S fractions corresponding to roughly ten 15 cm dishes for immunoprecipitation of initiation factor bound ribosomes, to these fractions, we added NP40 to 1% final concentration.
Immunoprecipitation: For immunoprecipitation, we bound antibodies to protein A or protein G magnetic dynabeads (Thermo) according to the manufacturer’s instructions. For PRRC2C selective ribosome footprinting, we used 40 µl antibody (Biomol #A303-315A) for each the 40S and 80S immunoprecipitation. We washed Beads three times and then added them to the cell lysates or 40S or 80S fractions. We incubated Solutions with beads for 2 hours or over-night, rotating at 4°C. Then we washed the beads three times with bead wash buffer (20 mM Tris pH 7.4, 10 mM MgCl2, 140 mM KCl, 1% NP40), including a change of reaction-vessel during the last wash. We increased the Bead volume to ~500µl with bead wash buffer. Then we subjected total footprint fractions and IPed fractions to crosslink removal and RNA extraction: we added 55 µl (1/9th of volume) of crosslink-removal solution (10% SDS, 100 mM EDTA, 50 mM DTT), 600 µl Acid-Phenol Chloroform (Ambion) and incubated the mixture at 65°C, 1300 rpm shaking for 45 minutes. We then placed Tubes on ice for 5 minutes, spun for 5 min at 20.000 g and washed the supernatant once with acid-phenol chloroform and twice with chloroform. Then we precipitated RNA with Isopropanol and subjected it to library preparation (see below).We used the organic phase to isolate the precipitated or total proteins. We added 300 µl of ethanol, then 1,5 ml of isopropanol and incubated the solutions at -20°C for 1 hour. We then sedimented the precipitated proteins by centrifugation at 20.000g for 20 minutes, washed them twice with 95% ethanol 0,3 M Guanidine HCl, dried and resuspended them in 1x Laemmli buffer.
Deep-sequencing library preparation: After RNA extraction from total and IP-purified fractions, we determined the RNA quality and integrity on an Agilent Bioanalyzer using the total RNA Nano 6000 Chip. For size selection, we ran the RNA on 15% Urea-Polyacrylamide gels (Invitrogen) and excised fragments of size 25-35 nt (80S libraries) and 20-80 nt (40S libraries) using the Agilent small RNA ladder as a reference. We extracted RNA from the gel pieces by smashing the gels into small pieces with gel smasher tubes and extracting the RNA in 0.5 ml of 10 mM Tris pH 7 at 70°C for 10 minutes. We removed Gel pieces and precipitated RNA using isopropanol. We then dephosphorylated the Footprints using T4 PNK (NEB) for 2 hours at 37°C in PNK buffer without ATP. Then we again precipitated and purified the Footprints using isopropanol. For 40S footprints, we depleted contaminating 18S rRNA fragments as follows. We used prevalent 18S rRNA fragments from the first round of 40S footprinting to design complementary Biotin-TEG-DNA oligonucleotides (sequences listed in (Bohlen et al., 2020a)), ordered from Sigma-Aldrich). We then hybridized 100ng of RNA footprints to a mixture (proportional to occurrence of the fragment) of these DNA oligos (in 40x molar excess) in (0.5M NaCl, 20mM Tris pH7.0, 1mM EDTA, 0.05% Tween20) by denaturing for 90 sec at 95°C and then annealing by reducing the temperature by -0.1°C/sec down to 37°C, then incubating 15min at 37°C. We pulled out Hybridized species using Streptavidin magnetic beads (NEB) by incubating at room temperature for 15 minutes, and purifying the remaining RNA by isopropanol precipitation. We then assayed Footprints using an Agilent Bioanalyzer small RNA chip and Qubit smRNA kit. We used 25 ng or less of footprint RNA as input for library preparation with SMARTer smRNA-SeqKit for Illumina from Takara / Clontech Laboratories according to the manufacturer’s instructions. We sequenced Deep-sequencing libraries on the Illumina Next-Seq 550 system.
For RNA-seq libraries, we extracted total cell RNA using TRIzol and performed library preparation using the Illumina TruSeq Stranded library preparation kit. We also sequenced these RNA-seq libraries on the Illumina Next-Seq 550 system.
Polyadenylation-based, oligo dT primer Reverse transcription, followed by PCR amplification.

treatment_protocol: Cells were transfected with Lipofectamine RNAimax for siRNA mediated knockdowns. We seeded cells at 200.000 cells per 6-well, transfected them with 3 µl 10 µM siRNA (or siRNA Tetraplex) and 9 µl Lipofectamine reagent. We then re-seeded cells for experiments 72 hours post transfection. Sequences of siRNAs are provided in the publication.

value: HeLa

value: GFP

tag: fraction

value: Total RNA

tag: antibody


title: SMARCA4_786O PBRM1KO_9hr_BTZ_ChIPSeq_rep2

tag: treatment


title: SMARCA4_786O PBRM1WT_24hr_DMSO_ChIPSeq_rep1


title: SMARCA4_786O PBRM1KO_DMSO_24hr_ChIPSeq_rep1


title: RNA-seq_ESCs_siRNA_Shfm1_rep1

tag: strain


title: SMARCA4_786O PBRM1WT_9hr_BTZ_ChIPSeq_rep2


title: SMARCA4_786O PBRM1KO_9hr_DMSO_ChIPSeq_rep2


title: RNA-seq_ESCs_siRNA_Erh_rep3

value: Erh


title: R2_80S_siABC

description: 80S Footprints

data_processing:
Adapter sequences and randomized nucleotides (Nextflex) or polyA stretches (Clonentech/Takara) were trimmed from raw reads using cutadapt (https://doi.org/10.14806/ej.17.1.200). Nuclear and mitochondrial Ribosomal RNA and tRNA reads were removed by alignment to human tRNA and rRNA sequences using bowtie2 (22388286). Then, the remaining reads were separately aligned to the human transcriptome (Ensembl transcript assembly 94) and human genome (hg38) using BBmap (sourceforge.net/projects/bbmap/). Multiple mappings were allowed. Secondary mappings were counted when analyzing single transcripts, but not counted in metagene plots to avoid biasing genes with many transcript isoforms or reads with low sequence complexity. Metagene plots, single transcript traces and grouped analyses were carried out or created with custom software written in C, supplied in Supplemental Dataset 1. Read counts for metagene plots of whole transcripts that encompass 5’UTRs, ORFs and 3’UTRs were normalized for the length of each of these features to make them comparable. 70 of the 41.314 transcripts were excluded from the analyses because PCR artefacts mapped to these transcripts. 2-D metagene plots were visualized using Fiji (Schindelin et al., 2012). The same, linear color gradient was always used to indicate read counts at each position in these 2-D metagene plots. Importantly, the maximum intensity of the color gradient was adjusted for the library size of the sample displayed so that 2-D metagene plots can be compared across panels. For 80S plots, only reads with footprint lengths between 26 to 37 nt were counted. For 5’UTR plots, only 40S footprints larger than 29 nt were counted because of the occurrence of artefacts and misaligned reads in the shorter population.
Translated uORFs were defined by the presence of any 80S ribosome footprints in a 10-nucleotide window around the uORF start codon. Only ATG initiated uORFs were considered. uORFs annotated by uORF-Tools (31513641) were downloaded from supplemental table 2 and filtered for uORFs with an intercistronic space > 80 nt.
Assembly: Ensemble transcript assembly 94
Supplementary files format and content: Excel files: Tables of the raw counts for each ENSEMBL transcript in each sample counted in coding sequence (80S and RNA-seq) or 5'UTR (40S).
Library strategy: Ribo-seq

value: PRRC2A + PRRC2B + PRRC2C


title: R2_RNS_siABC

description: Total RNA


title: SMARCA4_786O PBRM1KO_9hr_BTZ_ChIPSeq_rep1


title: R2_80S_siGFP

description: 80S Footprints


title: SMARCA4_786O PBRM1WT_ATPasei_24hr_ChIPSeq_rep1


title: SMARCA4_786O PBRM1WT_9hr_BTZ_ChIPSeq_rep1


title: SMARCA4_786O PBRM1WT_9hr_DMSO_ChIPSeq_rep2


title: RNA-seq_ESCs_siRNA_Erh_rep1


title: RNA-seq_ESCs_siRNA_Erh_rep2


title: SMARCA4_786O PBRM1KO_9hr_DMSO_ChIPSeq_rep1


title: BJ cells, Cal4h_1

value: BJ cells

value: primary fibroblasts

value: 100 nM calcipotriol treatment for 4 hours


title: SMARCA4_786O PBRM1WT_9hr_DMSO_ChIPSeq_rep1

value: DMSO


title: R2_80S_IPC

description: 80S Footprints


title: RNA-seq_ESCs_siRNA_Dnmt1_rep2


title: RELA_786O_PBRM1KO_BTZ_9hr_ChIPSeq_rep2

value: bortezomib 5nM, 9hr


title: R2_40S_siABC

description: 40S Footprints


title: R2_40S_siGFP

description: 40S Footprints


title: RELA_786O_PBRM1WT_BTZ_9hr_ChIPSeq_rep2


title: RELA_786O_PBRM1WT_DMSO_9hr_ChIPSeq_rep2


title: RNA-seq_ESCs_siRNA_Dnmt1_rep3


title: R2_40S_IPC

description: 40S Footprints


title: RELA_786O_PBRM1KO_BTZ_9hr_ChIPSeq_rep1


title: RNA-seq_ESCs_siRNA_Dnmt1_rep1


title: R1_RNS_siGFP

description: Total RNA


title: RELA_786O_PBRM1KO_DMSO_9hr_ChIPSeq_rep1


title: RNA-seq_ESCs_siRNA_Usp7_rep3


title: RELA_786O_PBRM1WT_DMSO_9hr_ChIPSeq_rep1


title: RELA_786O_PBRM1WT_BTZ_9hr_ChIPSeq_rep1


title: R1_RNS_siABC

description: Total RNA


title: RNA-seq_ESCs_siRNA_Usp7_rep2


title: HeLa_NT_WCE_1

city: Pozzuoli

first: Francesco

last: Panariello

state: Napoli

address: Via Campi Flegrei 34

country: Italy

institute: TIGEM

data_processing:
Basecalls performed using bcl2fastq v2.20.0.422
Paired sequencing reads were aligned on human hg38 reference genome using BWA
Reads were filtered with samtools to remove unmapped read pairs, not primary alignment, reads failing platform quality, with mapping quality score below 30 and duplicate reads were then removed using picard MarkDuplicates
Each sample was equally split in two pseudoreplicates and peaks were called with MACS2 with p < 0.1 on both samples and pseudoreplicates and filtered after Irreproducible Discovery Rate analysis with a threshold of 0.01
Each pair of replicated sample was combined and and filtered after Irreproducible Discovery Rate analysis with a threshold of 0.01;  coordinates from each replicate and from the combined peak lists were merged using bedtools and peaks supported by at least two out of the three were selected
bigWig IP vs input fold change signal profiles were produced using macs2 bdgcmp and then converted with UCSC bedGraphToBigWig tool
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input and Histone Modification samples)

growth_protocol: HeLa cells were maintained in DMEM High Glucose supplemented with 10% fetal bovine serum (FBS) heat-inactivated and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes at room temperature. Samples for ChIP-seq were prepped as previously described (Cesana et al. 2018)
Libraries were prepared from 10 ng of DNA using the NEBNext® Ultra™ II DNA Library Prep Kit following the manufacturer protocol

value: epithelial cell

value: NT


title: HeLa_STV_WCE_1

value: HBSS starvation


title: HeLa_NT_WCE_2


title: HeLa_H3K4me3_STV_2


title: R1_80S_siGFP

description: 80S Footprints


title: RNA-seq_ESCs_siRNA_Usp7_rep1


title: RNA-seq_ESCs_siRNA_ctrl_rep3


title: HeLa_STV_WCE_2


title: R1_80S_siABC

description: 80S Footprints


title: HeLa_H3K4me3_NT_2


title: HeLa_H3K4me3_STV_1


title: HeLa_H3K4me3_NT_1


title: RNA-seq_ESCs_siRNA_ctrl_rep1


title: HeLa_H3K4me1_STV_2


title: RELA_786O_PBRM1KO_DMSO_9hr_ChIPSeq_rep2

value: RELA


title: HeLa_H3K4me1_NT_2


title: R1_80S_IPC

description: 80S Footprints


title: RNA-seq_ESCs_siRNA_ctrl_rep2


title: R1_40S_siGFP

description: 40S Footprints


title: R1_40S_IPC

description: 40S Footprints


title: R1_40S_siABC

description: 40S Footprints


title: HeLa_H3K4me1_NT_1


title: BRD7_786O_PBRM1KO_ChIPSeq_Rep2

value: BRD7(Bethyl, A302-304A, lot 1)


title: HeLa_H3K27ac_STV_1


title: BRD7_786O_PBRM1WT_ChIPSeq_Rep2

value: parental


title: hTERT-RPE1, sh_Ctrl (Empty pLKO_3), Soft

city: Milano

first: Paolo

last: Maiuri

address: via Adamello 16

institute: IFOM

data_processing:
Reads were aligned to the GRCh38/hg38 assembly human reference genome using the STAR aligner (Dobin et al. 2013) with default settings and quantifier using Salmon (Patro et al. 2017).
Assembly: GRCh38/hg38 assembly
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Cells seeded on different substrates (Fibronectin coated glass or Fibronectin coated hydrogel 2.3 kPa)

extract_protocol:
RNA extraction performed with commercial kit (ThermoFischer)
For each experimental sample, totRNA was extracted using the RNeasy Prep kit (QIAGEN), and its abundance was measured using Qubit 4.0 and integrity assessed using Agilent Bioanalyzer 2100 using Nano RNA kit (RIN > 8). An indexed- fragment library was prepared starting from 500ng totalRNA using Illumina Stranded mRNA Prep ligation kit (Illumina) according to manufacturer’s instructions. Indexed libraries were quantified with Qubit HS DNA kit and controlled for proper size using Agilent Bioanalyzer 2100 High Sensitivity Dna kit prior to normalization and equimolar pooling to perform a multiplexed sequencing run.

treatment_protocol: Growth for 24h on different surfaces, 3 replicates for each conditions. PIP4K2B was silenced using 3 different sh_RNAi sequences

value: Cells transduced with Ctrl shRNA

tag: substrate

value: Fibronectin coated Gel 2.3kPa

value: hTERT-immortalized retinal pigment epithelial cell


title: HeLa_H3K27ac_NT_2

value: HeLa


title: HeLa_H3K27ac_STV_2


title: BRD7_786O_PBRM1KO_ChIPSeq_Rep1


title: hTERT-RPE1, sh_Ctrl (Empty pLKO_2), Soft


title: BRD7_786O_PBRM1WT_ChIPSeq_Rep1


title: hTERT-RPE1, sh_Ctrl (Empty pLKO_1), Soft


title: HeLa_EGR1_NT_3

description:
HeLa_EGR1_NT_IP.fc.signal.bw
HeLa_EGR1_NT_IP_union_I0.01_named.sorted.bed


title: HeLa_EGR1_NT_WCE


title: HeLa_H3K27ac_NT_1


title: HeLa_H3K4me1_STV_1


title: hTERT-RPE1, sh_Ctrl (Empty pLKO_2)

value: Fibronectin coated glass


title: Dsim_testis_RNAseq_replicate2

city: New Yor

first: Jeffrey

last: Vedanayagam

state: NY

address: 1275 York Avenue

department: Department of Developmental Biology

institute: Sloan-Kettering Institute

description: Dsim testis RNA replicate 2

data_processing:
RNA-seq data: Paired-end RNA-seq reads was mapped to PacBio genome assemblies for Dsim using hisat2 aligner with the following command hisat2 -x indexed_genome_assembly -1 $ read1.fastq.gz -2 read2.fastq.gz -S file.sam. The alignment file in SAM format was then converted to a compressed BAM file using SAMTOOLS1 with the following commands: (1) samtools view -bS file.sam > file.bam (2) samtools sort file.bam > file_sorted.bam (3) samtools index file_sorted.bam. Mapping statistics for the BAM alignment files were obtained using bam_stat.py script from the RSeqQC package2.
small RNA data: sRNA reads were processed as follows: Raw sequence reads were adapter trimmed using Cutadapt software (https://cutadapt.readthedocs.io/en/stable/). After clipping the adapter sequence, we removed the 4bp random-linker sequence inserted at 5’ and 3’ of the sRNA sequence (total 8bp). After filtering <=15 nt reads, we mapped the small RNA data to PacBio genome assemblies using Bowtie (with –v0 –best –strata options.) The resulting small RNA alignments in SAM format were converted to BED for downstream processing using the BEDops software and visualized on IGV.
Assembly: Data was mapped to PacBio genome assembly (Chakraborty et al. Genome Research 2021) for D. simulans.
Supplementary files format and content: The processed data files are in bigWig format for viewing in the IGV browser

organism: Drosophila simulans

source_name: D. simulans testis

growth_protocol: All flies were raised in 25C for testis extraction

extract_protocol:
For small RNA analysis, we extracted RNA from testes and accessory glands of 7-day-old Dsim w[XD1] strain using Trizol (Invitrogen). 1 μg of total RNA was used to prepare small RNA libraries as described3, with the addition of QIAseq miRNA Library QC Spike-ins for normalization (Qiagen). Adenylation of 3' linker was performed in a 40 µL reaction at 65°C for 1 hr containing 200 pmol 3' linker, 1X 5' DNA adenylation reaction buffer, 100 nM ATP and 200 pmol Mth RNA ligase and the reaction is terminated by heated to 85°C for 5 min. Adenylated 3' linker was then precipitated using ethanol and was used for 3' ligation reaction containing 10% PEG8000, 1X RNA ligase buffer, 20 µM adenylated 3' linker and 100 U T4 RNA Ligase 2 truncated K227Q. The 3' ligation reaction was performed at 4°C overnight and the products were purified using 15% Urea-PAGE gel. The small RNA-3' linker hybrid was then subjected to 5' ligation reaction at 37°C for 4 hr containing 20% PEG8000, 1X RNA ligase buffer, 1 mM ATP, 10 µM RNA oligo, 20 U RNaseOUT and 5 U T4 RNA ligase 1. cDNA synthesis reaction was then proceeded immediately by adding following components to the ligated product: 2 μl 5x RT buffer, 0.75 μl 100 mM DTT, 1 μl 1 μM Illumina RT Primer, and 0.5 μl 10 mM dNTPs. The RT mix was incubated at 65 C for 5 min and cooled to room temperature and transfer on to ice. 0.5 µL of superscript III RT enzyme and 0.5 µL RNase OUT were added to the RT mix and the reaction was carried out at 50°C for 1 hr. cDNA libraries were amplified using 15 cycles of PCR with forward and illumine index reverse primers and the amplified libraries were purified by 8% non-denaturing acrylamide gel. Purified libraries were sequenced on HiSeq2500 using SR50 at the New York Genome Center.
We used Dsim w[XD1], which were used for PacBio genome sequencing (Chakraborty et al. Genome Research 2021). We isolated total RNA from ~ 5-day-old flies and for Dsim samples. We extracted RNA from testes (dissected free of accessory glands) using Trizol (Invitrogen). We made two independent dissections to generate biologically replicate RNA samples, whose quality was assessed by Bioanalyzer. We used the Illumina TruSeq Total RNA library Prep Kit LT to make RNA-seq libraries from 650 ng of total RNA. Manufacturer's protocol was followed except for using 8 cycles of PCR to amplify the final library instead of the recommended 15 cycles, to minimize artifacts caused by PCR amplification. All samples were pooled together, using the barcoded adapters provided by the manufacturer, over 2 flow cells of a HiSeq2500 and sequenced using PE75 at the New York Genome Center.
Single-end sequencing for small RNA sequencing and paired-end sequencing for RNA sequencing data

tag: tissue

value: testis

tag: genotype

value: wildtype


title: HeLa_EGR1_NT_2

tag: cell type


title: hTERT-RPE1, sh_Ctrl (Empty pLKO_1)


title: PBRM1_786O_PBRM1WT_ChIPSeq_Rep3

value: PBRM1(Bethyl, A301-591A, lot3)


title: Dsim_testis_RNAseq_replicate1

description: Dsim testis RNA replicate 1


title: hTERT-RPE1, sh_Ctrl (Empty pLKO_3)


title: HeLa_EGR1_HBSS_WCE_2


title: HeLa_EGR1_HBSS_WCE_1


title: Dsim_testis_sRNA_replicate2

description: Dsim testis sRNA replicate 2


title: hTERT-RPE1, sh_RNA#2 for PIP4K2B

value: Cells transduced with shRNA#2 targeting PIP4K2B


title: hTERT-RPE1, sh_RNA#3 for PIP4K2B

value: Cells transduced with shRNA#3 targeting PIP4K2B


title: HeLa_EGR1_HBSS_2

description:
HeLa_EGR1_HBSS_IP.fc.signal.bw
HeLa_EGR1_HBSS_IP_union_I0.01_named.sorted.bed


title: Dsim_testis_sRNA_replicate1

description: Dsim testis sRNA replicate 1


title: HeLa_EGR1_HBSS_1


title: hTERT-RPE1, sh_RNA#1 for PIP4K2B

value: Cells transduced with shRNA#1 targeting PIP4K2B


title: HeLa_STV_8 hrs_3

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw counts

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) and 250 ng of total RNA was used for the construction of sequencing libraries.
3'DGE mRNA-seq research grade sequencing service (Next Generation Diagnostic srl)

treatment_protocol: HeLa cells were washed twice using PBS Ca2+/Mg++ free and starved using HBSS supplemented with HEPES  for the indicated time points.

value: epithelial cell

value: WT

tag: time

value: 8 hrs


title: Hp-KRAS+, 12 wk, fresh

city: Seattle

first: Taran

last: Gujral

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutch Cancer Center

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were done using Cell Ranger software (10x Genomics)
The normalizing, intergrating, clustering and visualizing were done using Seurat
Assembly: mm10
Supplementary files format and content: CellRanger processed data
Supplementary files format and content: Comma-separated values files and matrix files

source_name: stomach

extract_protocol: Stomachs from mice +/- H. pylori infection, +/- induction of active KRAS in Mist1-expressing cells were used for gastric single-cell RNA-sequencing. Samples were obtained six and 12 weeks after infection/KRAS induction. Six samples were frozen, then thawed before sequencing (and in some cases pooled from multiple mice) and two samples were freshly prepared and never frozen before sequencing.

value: stomach

tag: Sex

value: male

value: Mist1-CreERT2; LSL-K-ras G12D

tag: age

value: 18.9 weeks

value: Hp-KRAS+, 12 wk, fresh


title: PBRM1_A498_ChIPSeq

tag: source

tag: protein

value: parental

tag: chip antibody


title: HeLa_EGR1_NT_4

tag: cell line

value: HeLa

value: NT


title: Input_NCC010_PBRM1_ChIPSeq

value: NCC010 (in house derived cancer cell line)

value: Input

value: pbabe PBRM1


title: HeLa_EGR1_NT_1


title: HeLa_STV_8 hrs_2

value: HBSS starvation


title: GAD_ctrl3

city: New York

first: Marina

last: Schernthanner

state: New York

address: 1230 York Ave.

institute: The Rockefeller University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 genome assembly using STAR version 2.5.3a
Reads falling on each gene are counted by HT-Seq

source_name: brain

extract_protocol:
TRAP
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hippocampus

value: bound


title: Hp-KRAS+, 6 wk, freeze/thaw

value: 15.7 weeks

value: Hp-KRAS+, 6 wk, freeze/thaw


title: Hp+KRAS+, 12 wk, fresh

value: 19.7 weeks

value: Hp+KRAS+, 12 wk, fresh


title: GAD_ctrl2


title: HeLa_STV_8 hrs_1

value: epithelial cell

value: WT

value: 8 hrs


title: GAD_ctrl1


title: HeLa_STV_6 hrs_2

value: 6 hrs


title: HeLa_STV_6 hrs_3


title: Hp+KRAS+, 6 wk, freeze/thaw

value: stomach

value: female

value: Mist1-CreERT2; LSL-K-ras G12D

value: 17.4 weeks

value: Hp+KRAS+, 6 wk, freeze/thaw


title: UBGS9

value: Unbound


title: Hp+KRAS+, 12 wk, freeze/thaw

value: pooled male and female

value: 19.9 weeks

value: Hp+KRAS+, 12 wk, freeze/thaw


title: Input_NCC010_EV_ChIPSeq

value: NCC010 (in house derived cancer cell line)

value: Input

value: empty vector


title: Hp+KRAS-, 12 wk, freeze/thaw

value: 18.0 weeks

value: Hp+KRAS-, 12 wk, freeze/thaw


title: UBS8

value: hippocampus


title: PBRM1_NCC010_PBRM1_ChIPSeq

value: pbabe PBRM1

value: PBRM1(Bethyl, A301-591A, lot4)


title: HeLa_STV_6 hrs_1

value: HeLa

value: epithelial cell

value: WT

value: HBSS starvation

value: 6 hrs


title: HeLa_STV_4 hrs_3

value: 4 hrs


title: Hp-KRAS-, 12 wk, freeze/thaw

value: stomach

value: pooled male and female

value: Mist1-CreERT2; LSL-K-ras G12D

value: 17.6 weeks

value: Hp-KRAS-, 12 wk, freeze/thaw


title: PBRM1_NCC432_PBRM1_ChIPSeq

value: NCC432 (in house derived cancer cell line)


title: VkoM5

value: cKO


title: HeLa_STV_4 hrs_1


title: HeLa_STV_4 hrs_2


title: PDK1KO (NC)

city: Kobe

first: Yusei

last: Hosokawa

address: 7-5-2 Kusunoki-cho, Chuo-ku

department: Division of Diabetes and Endocrinology, Department of internal medicine

institute: Kobe University graduate school of medicine

data_processing:
Using DRAGEN Bio-IT Platform v3.6.3 software.
Read sequences obtained by sequence analysis were mapped to the genome sequence.
Gene expression levels were calculated based on the information obtained by mapping and the gene annotation file (gencode.vM25.primary_assembly.annotation.gtf).
Assembly: GRCm38
Supplementary files format and content: Text files include TPM values for each Sample

source_name: epididymal white adipose tissue

growth_protocol: Mice were housed at 21°C-25°C on a 12-hr light/dark cycle in the animal facility at Kobe University Graduate School of Medicine.

extract_protocol:
Total RNA was extracted from tissues with RNeasy minikit (QIAGEN). 6.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Nextera XT DNA Library Prep kits following manufacturer's protocols.

treatment_protocol: After weaning at 4 weeks old, control mice and A-PDK1KO mice were fed normal chow or GAN diet for 16 weeks.

value: epididymal white adipose tissue

value: fed normal chow


title: PDK1KO (GAN)

value: fed GAN diet


title: HeLa_STV_2 hrs_3

value: 2 hrs


title: PBRM1_NCC432_EV_ChIPSeq

extract_protocol:
For each protein of interest, approximately 2x107 cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and stopped by adding glycine to a final concentration of 0.2M. Chromatin was extracted and sonicated to ~500bp (Vibra cell, SONICS). The total volume of immunoprecipitation was 2 ml and the amount of antibody used was 20 µg. The input DNA was precleared with protein G Dynabeads (LifeTechnologies) for 2 hours at 4°C and then incubated with antibodies overnight at 4°C. Protein G beads were added the following day and mixture was nutated for 3 hours at 4°C. The beads were washed 6 times with wash buffer at room temperature.
At least 10 ng of the amplified DNA was used with NEBNext ChIP-Seq library prep reagent set (NEB). Each library was sequenced to an average depth of 30-50 million reads on HiSeq2500 or HiSeq4000.

value: empty vector

value: PBRM1(Bethyl, A301-591A, lot4)


title: PBRM1_NCC010_EV_ChIPSeq

value: NCC010 (in house derived cancer cell line)


title: Hp-KRAS+, 12 wk, freeze/thaw

value: 22.0 weeks

value: Hp-KRAS+, 12 wk, freeze/thaw


title: Input_NCC432_PBRM1_ChIPSeq

value: Input

value: pbabe PBRM1


title: UBGS8

value: hippocampus

value: Unbound


title: Input_NCC432_EV_ChIPSeq


title: Control (GAN)

value: Control


title: Input_NCC2112_PBRM1_ChIPSeq

value: NCC2112 (in house derived cancer cell line)

value: plenti PBRM1


title: HeLa_STV_2 hrs_2

value: HeLa

value: epithelial cell

value: WT

value: HBSS starvation


title: Control (NC)

value: epididymal white adipose tissue

value: fed normal chow


title: Input_NCC2112_EV_ChIPSeq

value: empty vector


title: UBS7


title: VkoM2

value: cKO


title: HeLa_STV_2 hrs_1

value: 2 hrs


title: PBRM1_NCC2112_EV_ChIPSeq

value: PBRM1(Bethyl, A301-591A, lot3)


title: HeLa_FED_3

value: FED


title: VkoM4


title: VwtM3


title: HeLa_FED_2


title: Input_SE_786O_PBRM1KO_ChIPSeq

value: Input (single end)


title: OSUMMER11_Melanocyte, TN61R

city: Columbus

first: Christin

last: Burd

state: Ohio

address: 460 West 12th Avenue

department: Molecular Genetics

institute: Ohio State University Wexner Medical Center

data_processing:
Reads were aligned to mm39 using STAR
Duplicates were removed using Picard
Assembly: mm39
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

molecule: polyA RNA

source_name: Ohio State University-Moffitt Melanoma Exposed to Radiation (OSUMMER) cell line

extract_protocol:
RNA was extracted from cultured melanocytes using the Zymo Quick RNA MiniPrep Kit (Zymo R1054)
Library preparation was conducted by Novogene Co. (Sacramento, CA)

value: melanocyte

value: F


title: OSUMMER13_Melanocyte, TN61R

value: Ohio State University-Moffitt Melanoma Exposed to Radiation (OSUMMER) cell line


title: HeLa_FED_1


title: OSUMMER10_Melanocyte, TN13R


title: Input_SE_786O_PBRM1WT_ChIPSeq

data_processing:
Sequencing reads were mapped against human genome reference hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.6.2) 'mem' algorithm. Only reads with mapQ >10 and with duplicate removed by rmdup were used in the subsequent analysis
Significant peaks were called using MACS2 24 (q-value < 0.01).
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq peaks are in bed format, including 5 columns: "chromosome"  "start of region" "end of region" "peak name" "peak enrichment"

value: parental


title: PBRM1_NCC2112_PBRM1_ChIPSeq

value: NCC2112 (in house derived cancer cell line)

value: plenti PBRM1


title: VkoM3

value: hippocampus


title: VkoM1


title: SMARCC1_786O_ChIPSeq

value: SMARCC1(Santa Cruz, sc-32763, lot K1617)


title: OSUMMER9_Melanocyte, TN61L

value: M


title: 769-P gARID2 3 [SAM24314128]

data_processing:
For all cell lines other than 769-P, RNA-seq data were mapped to hg19 (hs37d5) using STAR 25, with GENCODE annotation (gencode.v19.annotation.gtf) and recommended settings from STAR manual. Gene expression levels were quantified with STAR. For 769-P, RNA-seq data were mapped to GRCh38 using GMAP. Log fold change of differential expression genes was computed with DESeq2 for all cell lines
Assembly: hg19
Supplementary files format and content: Deseq2 files are in tab delimited text files, including 8 standard columns "ensembleID", "GeneSymbol", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj", then followed by columns of log2(normalized counts) and columns of raw count. There are usually 4 columns of log2(normalized counts) and 4 columns of raw count, corresponding to 2 replicates per each condition of two conditions (with and without PBRM1).

treatment_protocol: PBRM1 was knocked out using CRISPR-Cas9 mediated gene editing in 786-O, A498, HK-2 and 769-P. Wildtype PBRM1 was cloned from normal kidney tissue. cDNA was either cloned into pbabe vector or pLenti-GFP.  ARID2 was knocked out during CRISPR-Cas9 mediated gene editing in 769-P cells. RELA was knocked down in 786-O cells using shRNA.

value: gARID2 3

value: Cancer cell line


title: AOA3

city: Fuzhou

first: Zhiren

state: Fujian

address: 20 Chazhong Road

institute: the First Affiliated Hospital of Fujian Medical University

description: blastulation failure embryo in AOA group

data_processing:
The quality-control filtration of raw reads was performed by fastp (https://github.com/OpenGene/fastp).
The remaining clean reads for each sample were mapped to the annotated human genome (GRCh38) with HISAT2.
Fragment counts normalized per kilobase of exon per million mapped fragments (FPKM) were estimated using FeatureCounts.
Supplementary files format and content: gene expression level files include FPKM values for each Sample

source_name: embryo

extract_protocol:
RNALib Single cell WTA Kit (Lifeint, China) was used to synthesize and amplify cDNA based on total RNA from individual embryos.
Lifeint Transpose DNA Library Prep Kit for Illumina and Lifeint Library Prep Index Kit V1 for Illumina (Lifeint, China) were utilized to prepare a cDNA library.

treatment_protocol: The oocytes of the AOA+ICSI group were artificially activated by exposure to 10 uM ionomycin for 10 minutes within 30 min after the injection

value: embryo

value: Artificial oocyte activation


title: AOA2


title: 769-P gARID2 2 [SAM24314127]

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini kit
RNAseq libraries were prepared using Illumina Tru-Seq Stranded Total RNA kit protocol

value: gARID2 2


title: Pol_II_786O_PBRM1KO_ChIPSeq

value: Pol II


title: OSUMMER7_Melanocyte, TN61R


title: VwtM2

value: WT


title: AOA1


title: OSUMMER6_Melanocyte, TN61R


title: SMARCA4_786O_PBRM1KO_ChIPSeq_Rep1


title: control2

description: blastulation failure embryo in non-AOA group


title: 769-P gPBRM1 4 [SAM24314125]

value: gPBRM1 4


title: OSUMMER5_Melanocyte, TN61R

value: melanocyte


title: control3


title: 769-P gPBRM1 3 [SAM24314124]

value: gPBRM1 3


title: 769-P gPBRM1 2 [SAM24314123]

value: gPBRM1 2


title: Pol_II_786O_PBRM1WT_ChIPSeq

value: parental


title: ARID2_786O_PBRM1KO_ChIPSeq_Rep1

value: ARID2(Bethyl, A302-230A, lot 2)


title: OSUMMER4_Melanocyte, TN61R

value: Ohio State University-Moffitt Melanoma Exposed to Radiation (OSUMMER) cell line


title: OSUMMER8_Melanocyte, TN61K

value: F


title: ARID2_786O_PBRM1WT_ChIPSeq_Rep1


title: 769-P gARID2 1 [SAM24314126]

value: gARID2 1


title: OSUMMER3_Melanocyte, TN61R


title: 769-P gPBRM1 1 [SAM24314122]

value: gPBRM1 1


title: HeLa FLCN KO_TRAMETINIB_3

source_name: Hela

growth_protocol: HeLa FLCN KO cells were maintained in DMEM High glucose supplemented with 10% fetal bovine serum (FBS) heat-inactivated and antibiotics in humidified atmosphere with 5% CO2 at 37C

treatment_protocol: Trametinib or DMSO were added at final concentration of 10uM and cells were harvest after 4 days of treatment

value: Hela

value: epithelial cell

value: FLCN KO

value: Trametinib treatment


title: PBRM1_786O_PBRM1KO_ChIPSeq_Rep1

value: PBRM1(Bethyl, A301-591A, lot3)


title: SMARCA4_786O_PBRM1WT_ChIPSeq_Rep1


title: OSUMMER2_Melanocyte, TN61R


title: HeLa FLCN KO_TRAMETINIB_2


title: PBRM1_786O_PBRM1WT_ChIPSeq_Rep1


title: 769-P control 4 [SAM24314121]

value: control 4

value: Cancer cell line


title: control1

value: embryo


title: OSUMMER1_Melanocyte, TN61R

value: melanocyte

value: M


title: 769-P control 3 [SAM24314120]

value: control 3


title: HeLa FLCN KO_TRAMETINIB_1


title: 769-P control 2 [SAM24314119]

value: control 2


title: 769-P control 1 [SAM24314118]

value: control 1


title: Ctrl_Sham_2

city: Chengdu

first: Ping

last: Lyu

address: NO.14, 3rd Section of Ren Min Nan Rd. Chengdu, Sichuan

institute: West China Hospital of Stomatology, Sichuan University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: FPKM values and gene count for each Sample

source_name: tissue

extract_protocol:
PowerLyzer 24 Homogenizer (Qiagen) was used for lysis and homogenization of alveolar bone samples and Trizol (Invitrogen) was used for mRNA extraction according to the manufacturer’s protocol. NanoDrop ND-1000 (Thermo fisher Scientific) was used to quantify RNA concentration.
High-quality RNA samples with RIN number > 7.0 were used to construct sequencing library. After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR  by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following  the vendor's recommended protocol.

value: alveolar bone tissue

value: Eleven-week-old


title: HeLa FLCN KO_DMSO_3

value: DMSO treatment


title: mRNA_natrinema sp. J7-1_MMC_9h-3

city: wuhan

first: chen

last: zhao

state: huibei

address: luojiashan

department: college of life sciences

institute: wuhan university

data_processing:
SOAP(V2.21) was used to compare the second-generation sequence of each sample after quality control to the reference genome
Using RSEM(27), the bowtie2 comparison results were used for statistics
the number of Reads compared to each transcript of each sample was obtained, and FPKM(28) (Fragments Per Kilobase Per Million bases) conversion was performed
edgeR（V3.6.8） was used for differential expression significance analysis, and the screening threshold was FDR（false discovery rate）＜0.05， log2FC（fold change）＞1 or ＜-1.
Assembly: GCA_000493245.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Natrinema sp. J7-1

growth_protocol: strains were cultured in Halo-2 medium  at 45℃

extract_protocol:
total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) as described by the manufacturer, RNA purity and integrity was monitored by NanoDrop 2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and a Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA library was constructed, Qubit 2.0 was used for preliminary quantification, and the library was diluted to 1.5 ng/μL. Then Agilent 2100 BioAnalyzer was used to detect the insert size of the library

treatment_protocol: strains were cultured to middle exponential phase (OD600=0.6-0.8) in Halo-2 medium and treated with a final concentration of 1 μg/mL MMC for 30 min. Cells were collected by centrifugation and washed twice in the same volume of Halo-2 medium to remove MMC. Cell pellets were resuspended in Halo-2 medium and cultured at the same condition

value: WT

value: mitomycin C-9h


title: Ctrl_Sham_1


title: HeLa FLCN KO_TRAMETINIB_4

value: Hela

value: epithelial cell


title: HeLa FLCN KO_DMSO_4

value: FLCN KO


title: Ctrl_AP_2

source_name: apical periodontitis model was built on the first molar

value: Apical periodontitis model was built on eight-week-old mice for three weeks.


title: mRNA_natrinema sp. J7-1_MMC_9h-1


title: HeLa FLCN KO_DMSO_2


title: Ctrl_AP_1


title: mRNA_natrinema sp. J7-1_MMC_4h-3

value: mitomycin C-4h


title: mRNA_natrinema sp. J7-1_MMC_4h-2


title: HeLa FLCN KO_DMSO_1


title: 15h-OGD treated astrocyte enriched culture cells 02

type: RNA

city: setagaya-ku

first: Kengo

last: Moriyama

address: 2-1-6 kamikitazawa

institute: Tokyo metropolitan institute of medical science

description: Gene expression after 15h OGD treatment

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was fragmented and then hybridized to the Mouse Gene Expression 4 × 44K v2 Microarray (G4846A; Agilent Technolorgies) using Gene Expression Hybridization Kit (Agilent Technologies). Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned immediatry after washing on the SureScan Microarray Scanner (Agilent Technologies).

data_processing: The scanned TIFF-images were processed using Agilent’s Feature Extraction software (v11.5.1.1) with set to default for all parameters.

source_name: AEC 15h OGD 02

label_protocol: 200 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacture’s protocol.

extract_protocol: Total RNA was extracted from untreated or OGD-treated cells using the RNeasy Mini kit (Qiagen, Tokyo, Japan) according to the supplier's protocol. The quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Astrocyte-enriched cultures seeded on 6-well plate were either untreated or treated with 15h oxygen-glucose deprivation at 37 ºC in a humidified incubator with 5% CO2.

value: brain

value: Astrocyte-enriched cultures

value: 15h exposure of OGD


title: mRNA_natrinema sp. J7-1_MMC_9h-2


title: mRNA_natrinema sp. J7-1_MMC_4h-1


title: HeLa_scramble_STV 6hrs_3

treatment_protocol: siRNA transfection was performed in suspension using Lipofectamine RNAiMAX Transfection Reagent for 72hrs and subjected to starvation for additional 6 hours

value: HeLa

value: siSCR transfection


title: HeLa_scramble_STV 6hrs_4


title: Control, replicate 1, scRNAseq

description:
Primary cell of wildtype mouse.
10x Genomics

data_processing:
We used Cellranger (v3.1, 10x Genomics) to compare reads to the mouse genome mm10 and for detection of cells using default parameters. Next, we used the Seurat package (v3.1) for further analysis of the scRNA-seq.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: mandibular alveolar bone

extract_protocol:
Twenty C57/B6 male mice were used to acquire single-cell suspensions as control group. Mandibles were dissected under a stereo microscope 19 (Leica). Specifically, soft tissues, molars, incisors and bone behind the condyle were removed. Then, mandibular alveolar bone tissue was cut into small pieces and digested with 3 mg/mL collagenase type I (Gibco) and 4 mg/mL dispase II (Sigma) for 60 min at 37°C as previously described (Cui et al., 2020; Yamaza et al., 2011). Red blood cells were lysed with 1 mL Red Cell Lysis Solution (Biosharp). Cells were centrifuged and resuspended in 1% BSA solution. The final concentration of cells was 1 x 10^6 cells per mL.
Cellular suspensions were loaded into Chromium microfluidic chips and barcoded with a 10x Chromium Controller (10x Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v3 reagent kit (10x Genomics) and sequenced with the NovaSeq system (Illumina).

value: MSC, B cell, T cell, monocyte, macrophage et al.

value: mandibular alveolar bone

tag: diagnosis

value: control

value: wildtype

value: 8 weeks

value: male


title: AP, replicate 1, scRNAseq

extract_protocol:
Twenty C57/B6 male mice with apical periodontitis were used to acquire single-cell suspensions. Mandibles were dissected under a stereo microscope 19 (Leica). Specifically, soft tissues, molars, incisors and bone behind the condyle were removed. Then, mandibular alveolar bone tissue was cut into small pieces and digested with 3 mg/mL collagenase type I (Gibco) and 4 mg/mL dispase II (Sigma) for 60 min at 37°C as previously described (Cui et al., 2020; Yamaza et al., 2011). Red blood cells were lysed with 1 mL Red Cell Lysis Solution (Biosharp). Cells were centrifuged and resuspended in 1% BSA solution. The final concentration of cells was 1 x 10^6 cells per mL. Cellular suspensions were loaded into Chromium microfluidic chips and barcoded with a 10x Chromium Controller (10x Genomics).
Cellular suspensions were loaded into Chromium microfluidic chips and barcoded with a 10x Chromium Controller (10x Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v3 reagent kit (10x Genomics) and sequenced with the NovaSeq system (Illumina).

value: apical periodontitis


title: RNF138 knockout RAW264.7 cells, LPS 3h

first: Wei

address: 5 Dongdan Santiao Road

institute: Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

data_processing:
Illumina CASAVA 1.8 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mouse genome (GRCm38/mm10).
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10

source_name: RAW264.7 cells

growth_protocol: RAW264.7 cells were cultured in DMEM (Corning) supplemented with 10% fetal bovine serum (FBS) (Gibco).

extract_protocol:
RNA was harvested using Trizol reagent, total  RNA was used for RNA-seq.
Library was constructed by Novogene China Co. Ltd. Briefly, fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: RAW264.7 cells were treated with LPS for 3 hours and then washed with ice-cold PBS.

value: RAW264.7 cells

value: murine macrophage  cell line

value: RNF138 knockout

value: LPS (100ng/ml)

value: 3 hours


title: 786O_KO_PBRM1_Rep3

city: Singapore

first: Xiaosai

address: 60 Biopolis Street, Genome, #02-01

institute: Genome Institute of Singapore

data_processing:
RNA-seq data were mapped to hg19 (hs37d5) using STAR 25, with GENCODE annotation (gencode.v19.annotation.gtf) and recommended settings from STAR manual. Gene expression levels were quantified with STAR 26. Log fold change of differential expression genes was computed with DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Deseq2 files are in tab delimited text files, including 8 standard columns "ensembleID", "GeneSymbol", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj", then followed by columns of log2(normalized counts) and columns of raw count. There are usually 4 columns of log2(normalized counts) and 4 columns of raw count, corresponding to 2 replicates per each condition of two conditions (with and without PBRM1).

source_name: Cancer cell line

value: plenti PBRM1


title: HeLa_scramble_STV 6hrs_2

value: epithelial cell

value: WT


title: mRNA_natrinema sp. J7-1_MMC_1h-2

value: mitomycin C-1h


title: mRNA_natrinema sp. J7-1_MMC_1h-3


title: 786O_KO_PBRM1_Rep2


title: No treated astrocyte enriched culture cells 02

description: Gene expression with no treated

source_name: AEC CTRL 02

value: brain

value: Astrocyte-enriched cultures


title: PCB126

city: Hangzhou

first: Fengjun

last: Xu

state: Zhejiang

address: No.866, Yuhangtang Road

department: College of Environmental & Resource Sciences

institute: Zhejiang Univeristy

data_processing:
Raw sequence data (bcl files) were firstly converted into fastq files and demultiplexed by the mkfastq command in CellRanger v6.1.1.
The count command in CellRanger v6.1.1 was used to perform the unique molecular identifiers (UMIs) and cell barcode deconvolution, as well as generate other outputs (barcordes.tsv.gz, features.tsv.gz and matrix.mtx.gz) used in downstream steps.
Downstream analyses (e.g., quality control, normalization) were all performed by using Seurat v4.0.1 in R language.
Genome_build: ref-data-gex-mm-2020-A provided on the 10x Genomics website was chosen as the reference sequence.
Supplementary_files_format_and_content: Processed data used for Seurat in R language, matrix, barcodes and features files

source_name: Liver

growth_protocol: Before the experiment, mice were allowed to acclimatize for at least seven days. Two mice were involved in the experiment. Mice were given a synthetic common diet, and treated by one-time gavage with peanut oil (vehicle control) or PCB 126 (20 µg/kg/day), respectively. Mice were housed with constant temperature (21℃-25℃) and humidity (45%-65%) in a light-controlled room (with light from 8:00 to 20:00), provided with food and water ad libitum. The exposure lasted for five weeks.

extract_protocol:
After the five-week exposure followed with a twelve-hour overnight fast, mice were treated with the anesthetic tribromoethanol (500 mg/kg) to facilitate the collection of blood from arteria femoralis. Mice were then killed by cervical dislocation. The livers were carefully collected, rinsed and preserved in 1× PBS at 2℃ to 8 ℃, ready for downstream procedures. After the collection, livers were dissociated by using TissueLyser Type-TM Enzyme Blends under the manufacturer's instruction. Subsequently, centrifugation and filtration were performed to filter out hepatocytes. In brief, the liver suspension was centrifuged at 300 g for 5 min for several times and then passed through a 30 µm nylon cell strainer. Red blood cells were lysed by the treatment of 0.8% NH4Cl.
All procedures were processed based on the general protocols of 10x Genomics. Briefly speaking, prior to loading onto the 10x Genomics single-cell-A chip, qualified samples were diluted to an appropriate volume in which each sample was calculated for a targeted capture of 6,000 cells. After the droplet generation performed by a single-cell microfluidic chip, samples were transferred onto a pre-chilled 96-well plate. Subsequently, cDNA libraries were prepared following the Single Cell 3′ Reagent Kits v3.1 user guide with minor modifications. Reverse transcription, cDNA purification and amplification were then performed successively. Finally, sequencing was conducted on the platform Illumina NovaSeq. 6000.

value: Liver

value: Treated with PCB126 (20 microg/kg/day)

value: post natal day 21


title: 15h-OGD treated astrocyte enriched culture cells 01

description: Gene expression after 15h OGD treatment

source_name: AEC 15h OGD 01

value: 15h exposure of OGD


title: Control

value: Untreated


title: HeLa_siEGR1_STV 6hrs_3

source_name: HeLa

value: HeLa

value: siEGR1 transfection


title: 786O_KO_PBRM1_Rep1

last: Yao


title: 786O_KO_EV_Rep3

value: plenti empty vector


title: No treated astrocyte enriched culture cells 01

description: Gene expression with no treated

source_name: AEC CTRL 01


title: mRNA_natrinema sp. J7-1_MMC_0h-2

value: mitomycin C-0h


title: 786O_KO_EV_Rep2


title: OSUMMER12_Melanocyte, TN61R

value: Ohio State University-Moffitt Melanoma Exposed to Radiation (OSUMMER) cell line

value: melanocyte

value: F


title: Wild type RAW264.7 cells, LPS 3h

city: Beijing

last: Liu

value: RAW264.7 cells

value: murine macrophage  cell line

value: LPS (100ng/ml)

value: 3 hours


title: 786O_KO_EV_Rep1


title: HeLa_siEGR1_STV 6hrs_2

value: epithelial cell

value: WT


title: NCC432_PBRM1_Rep2

value: NCC432 (in house derived cell line)

value: pbabe PBRM1


title: HeLa_siEGR1_STV 6hrs_1


title: HeLa_EGR1 OE_3

treatment_protocol: HelLa cells were infected in the presence of polybrene at MOI of 1 and 1ug of puromycin was used to select infected cells

value: EGR1 overexpression


title: HeLa_EGR1 OE_4


title: C. elegans_DCL289_rep3

city: Nanjing

first: Zi

last: Wang

state: Jiangsu

address: 12 Xue-Fu Road, Pukou District , Nanjing, Jiangsu

department: Model Animal Research Center

institute: Nanjing University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Read quality was checked for each sample by using FastQC v 0.11.5.
Reads were aligned to the C.elegans genome (version Wbcel235) using TopHat2 with parameters -r 30 -G -p 8 --microexon-search --library-type fr-unstranded.
Raw counts of sequencing reads were generated by using the python script HTSeq.
Differential expression and dataset normalization were performed using the Bioconductor package DESeq2.
Assembly: Wbcel235
Supplementary files format and content: tab-delimited text files include raw counts for each sample

organism: Caenorhabditis elegans

growth_protocol: C. elegans animals were growing at 20°C until the late L4 stage before collection.

extract_protocol:
Total RNAs were extracted using the Trizol reagent (Takara) and Direct-zol RNA mini prep kit (ZYMO Research).
RNA libraries for RNA-seq were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, NR605).


title: C. elegans_DCL289_rep2


title: HeLa_siEGR1_STV 6hrs_4


title: HeLa_scramble_STV 6hrs_1

value: siSCR transfection


title: mRNA_natrinema sp. J7-1_MMC_1h-1

value: mitomycin C-1h


title: C. elegans_DCL33_rep3


title: NCC432_PBRM1_Rep1

treatment_protocol: PBRM1 was knocked out using CRISPR-Cas9 mediated gene editing in 786-O, A498 and HK-2. Wildtype PBRM1 was cloned from normal kidney tissue. cDNA was either cloned into pbabe vector or pLenti-GFP.


title: mRNA_natrinema sp. J7-1_MMC_0h-3


title: NCC432_EV_Rep2

value: pbabe empty vector


title: C. elegans_DCL289_rep1


title: C. elegans_DCL33_rep2


title: HeLa_EGR1 OE_2

value: HeLa


title: C. elegans_DCL33_rep1


title: NCC432_EV_Rep1


title: HeLa_EGR1 OE_1


title: NCC2112_PBRM1_Rep2

value: NCC2112 (in house derived cell line)

value: plenti PBRM1


title: HeLa_CTRL_4

value: control


title: long_RNA_Kdm3 GLKD 3-5h progeny biol rep 2

city: PARIS

first: Antoine

last: Boivin

address: 9 quai St Bernard

department: IBPS

institute: Sorbonne Universite CNRS

data_processing:
A DeSEq2 analyze on all D. mel. genes (release 6.36) was performed using the two biological replicates for each genotype, control or Kdm3 GLKD progeny.
Assembly: dm6_clean
Supplementary files format and content: bigWig, DEseq2 result for biological triplicates as a tab-delimited text file

organism: Drosophila melanogaster

growth_protocol: Flies were raised at 25°C on cornmeal medium. Embryos were collected on same medium plus fresh yeast.

extract_protocol:
Total RNA was extracted from 100 ul of embryos using TRIzol (Life Technologies) and 1 µg was treated with DNase (Fermentas).
Libraries were prepared using the RNA RiboZero Stranded protocol by Fasteris.

value: embryo

value: Kdm3 GLKD progeny


title: NCC2112_PBRM1_Rep1


title: long_RNA_Kdm3 GLKD 3-5h progeny biol rep 1


title: NCC2112_EV_Rep2

value: plenti empty vector


title: long_RNA_w GLKD 3-5h progeny biol rep 2

value: w GLKD progeny


title: HeLa_CTRL_2

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw counts

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) and 250 ng of total RNA was used for the construction of sequencing libraries.
3'DGE mRNA-seq research grade sequencing service (Next Generation Diagnostic srl)


title: HeLa_CTRL_1


title: long_RNA_w GLKD 3-5h progeny biol rep 1


title: 786O_KO_shRELA_Rep2

value: shRNA against RELA

value: Cancer cell line