title: SKMEL28, MITFKO, ATAC seq, bio rep 2

city: Iowa City

first: Jeremy

last: Chang

state: IA

address: 285 Newton Rd

department: Surgery

institute: University of Iowa

data_processing:
Reads were trimmed using Trim Galore Version 0.6.3 (Developed by Felix Krueger at the Babraham Institute) and Bowtie2 version 2.1.0 (Langmead and Salzberg, 2012) was used to map the reads against the hg19 genome assembly.
Assembly: hg19
Supplementary files format and content: bigwig file

growth_protocol: cells are grown in appropriate media (SKMEL28 = RPMI, A375 = DMEM) supplemented with 10% FBS and 1% Penicillin/streptomycin at 37 degrees celcius with 5% Co2. Cells were plated into separate flasks for biologic replicates and media was changed 24 hours before harvest.

extract_protocol:
70,000MITF-WT SKMEL28 and D6 (four replicates) were lysed in ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40: Sigma). Transposition was performed directly on nuclei using 25 μl tagmentation reaction mix (Tagment DNA Buffer #15027866, Tagment DNA Enzyme #15027865 from Illumina Tagment DNA kit #20034210).
Tagged DNA was subjected to PCR amplification and library indexing, using the NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs #M0451S) with Nextera DNA CD Indexes (Illumina #20015882), according to the following program: 72°C for 5 minutes; 98°C for 30 seconds, 12 cycles of 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute. The PCR product was purified with 1.8 times the volume of Ampure XP beads (Beckman Coulter #A63881). Library quality was assessed using a BioAnalyzer 2100 High Sensitivity DNA Chip (Agilent Technologies).
All DNA libraries that exhibited a nucleosome pattern were pooled and processed for 150 bp paired-end sequencing.

value: melanoma

value: MITFKO


title: ZnO, strong agitation 3

status: Public on Mar 20 2025

type: SRA

city: Wuhan

first: Pier-Luc

last: Tremblay

state: Hubei

address: 122 Luoshi Road

department: School of Chemistry, Chemical Engineering and Life Science

country: China

institute: Wuhan University of Technology

description: Library name: Sample 3

library_source: transcriptomic

data_processing:
The quality of the raw data sequences was evaluated with FastQC
RNA-seq data was trimmed with Trimmomatic
Short reads were aligned to the reference genome with Bowtie 2
Transcript Per Million (TPM) calculation was done with the featureCounts software
Assembly: GCA_000009285.2
Supplementary files format and content: Tab-delimited text file including gene locus, gene name, annotation, TPM for each replicate, TPM mean, Log2 TPM for each replicate, Log2 TPM mean, SEM (Log2 TPM)

molecule: total RNA

organism: Cupriavidus necator H16

source_name: Bacterial cell

growth_protocol: C. necator was grown autotrophically with 0.8 g/L ZnO nanosheets under an H2:CO2:O2 atmosphere (74:13:13, 0.23 MPa)

extract_protocol:
After 36 hours of growth, bacterial cells were collected by centrifugation at 6000 × g for 5 min at 4 ℃, snap frozen with liquid nitrogen, and total RNA was extracted with the TRIzol reagent
The RNA sequencing library was prepared with the VAHTS™ Stranded mRNA-seq V2 Library Prep Kit for Illumina

treatment_protocol: C. necator H16 with ZnO nanosheets was agitated at 200 rpm with a tilting agitator to stimulate the piezocatalyst

tag: strain

value: DSM 428

tag: cell type

value: Bacterial cell

tag: genotype

value: WT

tag: treatment

value: 0.8 g/L ZnO, tilting agitation 200 rpm

tag: time


title: NS rep4 1h

city: Calgary

first: Mark

last: Giembycz

state: Alberta

address: 3280 Hospital Drive NW

department: Physiology & Pharmacology

country: Canada

institute: University of Calgary

description: Library name: A13

data_processing:
bcl2fastq v2.17.1.14 for base calling; STAR v2.4.2a for alignment and coverage counting;
Assembly: GRCh38.78
Supplementary files format and content: tab-delimited text file includes transcripts per million (TPM) values for each sample for each gene described by its HGNC symbol

organism: Homo sapiens

source_name: Lung

growth_protocol: BEAS-2B cells were grown to confluence in Dulbecco’s Modified Eagle’s Medium/Nutrient Mixture F-12 (DMEM/F12) supplemented with 10 % Canada origin FBS, L-glutamine (2.5 mM) and NaHCO3 (0.15 % w/v) followed by overnight incubation in serum-free medium.

extract_protocol:
Total RNA was extracted using NucleoSpin® RNA kit (MACHEREY-NAGEL GmbH & Co. KG, Düren, Germany) and quantified using NanoDrop 2000 (Thermo Fisher Scientific, Wilmington, DE) according to manufacturer's instructions.
Illumina TruSeq

treatment_protocol: Confluent BEAS-2B cells were treated for one, two, six and eighteen hours with vehicle (NS), indacaterol (100 nM), carbachol (10 µM), mometasone (100 nM), or the combination of mometasone and indacaterol, mometasone and carbachol, indacaterol and carbachol, or all three in combination.

tag: tissue

value: Lung

tag: cell line

value: BEAS-2B human airway epithelial cell line

value: Vehicle


title: ZnO, strong agitation 2

description: Library name: Sample 2


title: SKMEL28, wild type, ATAC seq, bio rep 4

country: USA

library_source: genomic

molecule: genomic DNA

value: wild type


title: NS rep3 18h

description: Library name: A12


title: SKMEL28, wild type, ATAC seq, bio rep 3


title: OSRC2, PT2399, Rep3

city: Boston

first: Nitin

middle: H.

last: Shirole

state: MA

address: 450 Brookline Avenue, M448, Dana Farber Cancer Institute

institute: Dana Farber Cancer Institute

description:
OSRC2_PT_6h_F._normD1.27.bw
OSRC2_PT_6h_R._normD1.27.bw

data_processing:
Dual, 6nt Unique Molecular Identifiers (UMIs) were extracted from read pairs using UMI-tools. Read pairs were trimmed using cutadapt 1.14. The UMI length was trimmed off the end of both reads to prevent read-through into the UMI of the other end of the sequence, which will happen for shorter fragments. An additional nucleotide was removed from the end of read 1 (R1), using seqtk trimfq, to preserve a single mate orientation during alignment.
The paired-end reads were then mapped to a combined genome index, including both the spike (dm6, drosophila) and primary (hg19, human) genomes, using bowtie2. Properly paired-end reads were retained. These read pairs were then separated based on the genome (i.e. spike-in vs primary) to which they mapped, and both these spike and primary reads were independently deduplicated, again using UMI-tools. Reads mapping to the reference genome were separated according to whether they were R1 or R2, sorted via samtools 1.3.1 (-n), and subsequently converted to bedGraph format using a custom script
Because R1 in PRO-seq reveals the position of the RNA 3’ end, the “+” and “-” strands were swapped to generate bedGraphs representing 3’ end positions at single nucleotide resolution. Samples displayed highly comparable recovery of spike-in reads; thus samples were normalized based on the DESeq2 size factors. Combined bedGraphs were generated by summing counts per nucleotide across replicates for each condition.
Annotated transcription start sites were obtained from human (GRCh37.87) GTFs from Ensembl. After removing transcripts with biotypes, PRO-Seq signal in each sample was calculated in the window from the annotated transcription start site (TSS) to +150 nt downstream
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: Precision Run-On (PRO)-seq

growth_protocol: OSRC2 cells were obtained from RIKEN Bioresource Research Center Cell Bank and were cultured in RPMI-1640 (Gibco 11875119) supplemented with FBS (GeminiBio 100-106), 1% penicillin-streptomycin (Gibco 15140122).

extract_protocol:
Cells (Human or Drosophila) were washed with RT PBS, trypsinized for 1-2 min at 37°C, quenched with ice-cold DMEM +10% FBS and transferred to 50 ml conical tubes. After harvesting, cells were always kept on ice. 5×106 to 1×107 cells per condition were collected by centrifugation at 300×g for 4 min at 4°C. The supernatant was removed, and the cell pellets were gently resuspended in 10 ml ice-cold PBS, followed by centrifugation at 300×g for 4 min at 4°C. The supernatant was removed, and the cells were resuspended in 250 ml wash buffer [10 mM Tris-HCl pH 8.0, 10 mM KCl, 250 mM Sucrose, 5 mM MgCl2, 1 mM EGTA, 10% (v/v) glycerol, 0.5 mM DTT (Thermo Fisher Scientific 707265ML), 0.2 ml/ml RNase inhibitor (Invitrogen AM2696) and 1× protease inhibitor (Thermo Fisher Scientific A32965)]. The cell pellets were gently pipetted using wide bore filtered pipette tips (Thermo Fisher Scientific 2079GPK) to create a single-cell suspensions. The cell suspension was passed through a cell strainer once (Falcon 352235) to avoid cell clumps. 10 ml permeabilization buffer [10 mM Tris-HCl pH 8.0, 10 mM KCl, 250 mM Sucrose, 5 mM MgCl2, 1 mM EGTA, 10% (v/v) glycerol, 0.1 % (v/v) IGEPAL CA-630, 0.05% (v/v) Tween-20, 0.5 mM DTT, 0.2 l/ml RNase inhibitor and 1× protease inhibitor] was slowly (over 5-10 seconds) added to the single-cell suspension along the wall of the conical tube. The samples were then incubated on ice for 5 min before centrifugation at 400×g for 4 min at 4°C. The supernatant was removed by gently inverting the tubes after which 1 ml of ice-cold wash buffer was added to each of the pellets to dilute out the residual permeabilization buffer followed by gently pipetting 2-3 times to achieve a single cell suspension. Next an additional 9 ml of ice-cold wash buffer was added to each tube and the samples were pelleted by centrifugation at 400×g for 4 min at 4°C. This wash procedure (1 ml wash buffer followed by 9 ml wash buffer) was repeated an additional 2 times. After the washes, the cell pellets were resuspended in 250 l freezing buffer [50 mM Tris-HCl, pH 8.0, 40% (v/v) glycerol, 5 mM MgCl2, 1.1 mM EDTA, 0.5 mM DTT, 1 l/ml RNase inhibitor] and transferred to 1.5 ml low binding tubes (Thermo Fisher Scientific Pl90410). 250 l freezing buffer/tube was also added to the 50 ml conical tubes, followed by gentle pipetting, to collect any residual cells, which were then pooled with the first resuspension (bringing the total volume to 500 l, which was further resuspended by gentle pipetting). Trypan blue-stained cell number was determined using a hemocytomer after which the cells were diluted using freezing buffer to the concentration of 1×106 cell/100 l. Aliquots of 5×106 permeabilized cells per 1.5 ml low binding tube were flash frozen in liquid nitrogen and stored at -80°C prior to use. To conduct nuclear run-ons and library preparation, aliquots of frozen permeabilized cells were thawed on ice, pipetted gently, and recounted using a Luna II automated cell counter (Logos Biosystems). For each sample, 1×106 permeabilized Human cells were used for nuclear run-ons, with 5×104 permeabilized Drosophila S2 cells added to each sample for normalization. Nuclear run-on assays and library preparation were performed as described in (Reimer et al, Mol Cell, 2021) with modifications. Briefly, nascent RNA was labeled by a run-on assay in which an equal volume of 2× nuclear run-on buffer [10 mM Tris-HCl, pH 8.0, 300 mM KCl, 1% sarkosyl, 10 mM MgCl2, 1 mM DTT, 20 M/ea biotin-11-NTPs (Perkin Elmer NEL543001EA), 0.8 U/l RNase inhibitor)] was added into permeabilized cell mixture and incubated for 5 min at 37°C. RNA was purified by the Total RNA Purification Kit (Norgen Biotek Corp 17200) per manufacturer’s instructions, eluted in 100 l H2O, and fragmented by base hydrolysis by adding 25 l 5× fragmentation solution (375 mM Tris-HCl, pH 8.3, 562.5 mM KCl, 22.5 mM MgCl2) followed by incubation for 5 min at 94°C. Fragmentation was stopped by adding 125 l ice-cold 0.1 M EDTA. To enrich for biotin-labeled nascent RNA, 10 ml of streptavidin C1 magnetic beads (Invitrogen 65001) were washed, rendered RNase free per manufacturer’s instructions, and resuspended in 50 ml binding buffer (10 mM Tris-HCl pH 7.4, 300 mM NaCl, 0.1% Triton X-100) before being added to the fragmented RNA. The samples were rotated end-to-end for 20 min at RT. The streptavidin magnetic beads were then washed twice with high salt buffer (50 mM Tris-HCl pH 7.4, 2 M NaCl, 0.5% Triton X-100), twice with binding buffer (listed above), and twice with low salt buffer (5 mM Tris-HCl pH 7.4, 0.1% Triton X-100). The beads were next resuspended in 500 ml TRIzol Reagent (Invitrogen 15596026) and incubated at 65°C for 5 min to elute RNA from the beads. This elution step was repeated once and the first and second eluates for a given sample were pooled. The RNA was subsequently purified by adding 2.75× volumes of 100% ethanol to the 400 l solution recovered from aqueous phase of TRIzol in the presence of 20 g of Ultrapure glycogen (Invitrogen 10814010). The pelleted RNA was subsequently washed per manufacturer’s instructions and resuspended in 5 l of 10 M App-VRA3_6N 3’ end adapter prepared using the 5' DNA Adenylation Kit (New England Biolabs M2611A) and ligated using T4 RNA ligase 2, truncated KQ (New England Biolabs M0373) per manufacturer’s instructions with 15% (w/v) PEG-8000 in final solution and incubated overnight at 16°C. 180 ml of betaine binding buffer [1.42g of betaine (Sigma-Aldrich 61962) in 10 ml with binding buffer] was mixed with ligations and incubated for 5 min at 65°C and then for 2 min on ice. Capture on Streptavidin beads was again performed as above to enrich for ligated nascent RNAs except for the addition of a final wash with 1× MDE buffer (New England Biolabs B0608S) after the washes with high salt buffer, binding buffer, and low salt buffer. To prepare nascent RNA for 5’ end adapter ligation, the 5’ ends of the RNA were first decapped by mRNA decapping enzyme (New England Biolabs M0608S) for 1 h at 37°C. The beads were washed once in high, once with low salt buffer, and then once in 1× T4 PNK reaction buffer. The samples were then treated with T4 polynucleotide kinase (New England Biolabs M0201) for 1 h at 37°C for 5’-hydroxyl repairs, followed by one wash with high salt buffer, one wash with low salt buffer, and one wash with 0.25× T4 RNA ligase reaction buffer prior to resuspension in 5 ml of 10 pmol 5' RNA adapter VRA5_6N. Next T4 RNA ligase 1 (New England Biolabs M0204L) was used to ligate the 5’ RNA adapter per manufacturer’s instructions with 15% (w/v) PEG-8000 in final solution and incubated overnight at 16°C. Following the 5’ end ligation, beads were washed twice with high salt buffer, twice with binding buffer, and twice with low salt buffer, then once with 0.25× SuperScript IV reaction buffer. Reverse transcription was performed using SuperScript IV Reverse Transcriptase (Invitrogen 18090010) and the cDNA was eluted from the beads by heating the samples twice for 30 seconds at 95°C.
The eluted cDNA was initially amplified for 5-cycles of "preCR" [NEBNext Ultra II Q5 master mix (New England Biolabs M0544S) with Illumina TruSeq PCR primers RP-1 and RPI-X for indexing] following the manufacturer's suggested PCR cycling protocol for library construction]. A portion of preCR was serially diluted and for test amplification to determine optimal amplification of final libraries. Libraries were amplified by 3 additional cycles of PCR (8 cycles in total). The amplified library was purified using the ProNex Size-Selective Purification System (Promega) and sequenced using the Illumina NovaSeq platform.

treatment_protocol: 3 x 106 OSRC2/dish were plated on day 0 in triplicate in 150 mm TC-treated cell culture dishes. On day 3 the media was replaced with media containing PT2399 or DMSO and the cells were harvested 6 hrs later. The cells were detached by a brief incubation with 0.25% Trypsin-EDTA (Gibco, 25200072) at 37oC. The Trypsin was then quenched with ice-cold DMEM +10% FBS. The cells were then transferred to 50 ml conical tubes and kept on ice for the remainder of their processing.

value: ccRCC

value: 6 hrs


title: ZnO, strong agitation 1

description: Library name: Sample 1


title: OSRC2, PT2399, Rep2


title: SKMEL28, wild type, ATAC seq, bio rep 2


title: SKMEL28, wild type, ATAC seq, bio rep 1


title: NS rep3 6h

description: Library name: A11


title: HT1197 PEMF Day 5 Sample 2

type: RNA

city: Winston Salem

first: Stephen

last: Walker

state: North Carolina

address: 391 Technology Way NE

department: Urology

institute: Wake Forest Institute for Regenerative Medicine

description: UC20 PEMF HT1197 D5 S2

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51C. Labeled complimentary deoxyribonucleic acid (DNA) generated from RNA was assayed on an nCounter®Tumor Signaling 360™ Panel.

scan_protocol: not provided

data_processing: Standard normalization uses a combination of Positive Control Normalization, which uses synthetic positive control targets, and CodeSet Content Normalization, which uses housekeeping genes, to apply a sample-specific correction factor to all the target probes within each sample lane.

source_name: primary urothelial carcinoma

label_protocol: not provided

growth_protocol: Rinsed cell layer with 0.25% (w/v) Trypsin-0.53mM EDTA solution to remove all traces of serum, which contains trypsin inhibitor. Added 2.0 to 3.0 mL of Trypsin-EDTA solution to flask and observe cells under an inverted microscope until cell layer is dispersed (usually within 5 to 15 minutes). Added 6.0 to 8.0 mL of complete growth medium and aspirate cells by gently pipetting. Added aliquots of the cell suspension to new culture vessels. Incubated cultures at 37°C (https://www.atcc.org/products/crl-1473).

extract_protocol:
Ribonucleic acid (RNA) was extracted from cellular samples, “RNeasy® MinElute™ Plus columns (Qiagen®) were used for RNA recovery from cell samples according to manufacturer instructions.
RNA quality was determined using a bioanalyzer (Agilent Technologies, Palo Alto, California) with a mean RNA integrity number of 9.4 ± 0.24 for all samples.

tag: age

value: 44 years

tag: Sex

value: Male

tag: status after 5 years

value: dead

tag: histology

value: stage p2, grade 4, Transitional cell carcinoma

tag: Stage

value: pulsed electromagnetic field therapy


title: HT1197 Control Day 5 Sample 1

description: UC25 CONTROL HT1197 D5 S1

value: control


title: HT1197 Control Day 5 Sample 2

description: UC26 CONTROL HT1197 D5 S2


title: OSRC2, DMSO, Rep1

description:
OSRC2_DMSO_F._normD1.12.bw
OSRC2_DMSO_R._normD1.12.bw

value: DMSO


title: A375, TFE3KO, RNAseq, bio rep 3

description: bulk RNAseq

data_processing:
Reads were mapped with RNAStar to human reference genome hg19 with default parameters.
FeatureCounts was used to calculate read counts for each individual gene from STAR output bam files.
Differential gene expression analysis was performed using DEseq2. Adjusted p-value <0.05 was used for statistically significant difference
Assembly: hg19
Supplementary files format and content: tab delinieated text files for normalized counts.

extract_protocol:
Total RNA was extracted with Rneasy Plus Kit (Qiagen)
Library construction performed by Novogene co

value: melanoma


title: HT1197 PEMF Day 5 Sample 3

description: UC21 PEMF HT1197 D5 S3


title: 9_iso_small_RNA

city: Moscow

first: Alina

last: Bespalova

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

description: Library name: Small_RNA_seq_9_iso

data_processing:
RNA-seq data processing Pre-processing of sequenced reads including RNA-seq, small RNA-seq and ChIP-seq experiments was performed using trim_galore (https://github.com/FelixKrueger/TrimGalore) including adapter and quality (≥ 20 Phred) trimming as well as filtering by length (20-29 nt) for small RNAs. Trimmed RNA-seq reads were aligned to the D. virilis genome r.1.06 (https://flybase.org/) using STAR 2.7.1a (PMID: 23104886). Counts of RNA-seq reads mapped on gene transcripts were estimated by featureCounts (PMID: 24227677) and normalized to transcript length as well as sequencing depth (RPKM, Reads Per Kilobase per Million mapped reads). Resulting values were considered as gene expression levels. Differential gene expression analysis was performed with DESeq2 (PMID: 25516281).  ChIP-seq data processing Trimmed sequenced reads were aligned to the reference genome (D. virilis r.1.06) using Bowtie2 (PMID: 22388286). Aligned reads were sorted by coordinates, filtered of most multi-mapped reads (samtools view -bh -q 10) and cleaned of duplicates (samtools rmdup) using SAMtools (PMID: 33590861). Filtered aligned reads were normalized using RPGC method (number of reads per bin / scaling factor for 1x average coverage of the genome) implemented in deepTools2 package (PMID: 27079975) with the command: bamCoverage --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize (total length of the genome) --extendReads (for paired-end data). Next, the obtained values for input samples were subtracted from treat samples using bigwigCompare script (PMID: 27079975) resulting in coverage values for each sample. Aligned reads in bigwig format for ChIP-seq, RNA-seq and small RNA-seq were visualized using the Integrative Genome Viewer (IGV) (PMID: 21221095). Peak calling was performed using MACS2 software (PMID: 18798982) with the recommended parameters for narrow and broad peak calling as well as normalization on input chromatin controls.  Small RNA-seq data processing Pre-processed reads were further subjected to subtraction of reads matching to all rRNA, tRNA, snRNA and miRNA sequences of Drosophila genus. The selected reads were mapped to the reference genome as well as annotated gene transcripts of D. virilis by Bowtie (PMID: 19261174), allowing up to 3 mismatches retaining only uniquely mapped reads (tags: --all --tryhard -v 3 -m 1 --best --strata –quiet). We considered small RNA fractions of 23-29 nt in length as piRNAs (PMID: 17346786; PMID: 20581131). Counting of piRNAs, sorting of sense and antisense piRNAs, calculation of ping-pong signatures were analyzed in accordance to the well-described technique (10.1007/978-1-0716-2380-0) using custom scripts written in R and Python. Normalization to the number of mapped reads (RPM, Reads Per Million mapped reads) was applied to obtain piRNA expression levels.
Assembly: D. virilis genome r.1.06 (https://flybase.org/)
Supplementary files format and content: tab-delimeted text file include preprocessed and normalized counts for each sample

organism: Drosophila virilis

source_name: ovaries

extract_protocol:
Total RNA for RNA-seq and small RNA-seq experiments was extracted from ovaries using Extract RNA reagent (Evrogen, Russia). The concentration of RNA was measured with a Qubit Fluorometer (Invitrogen, USA). The quality of RNA was determined with an Agilent BioAnalyzer 2100 using the RNA 6000 nano kit. The RNA Integrity Number (RIN) of all RNA samples taken for mRNA libraries preparation was not less than 8. Poly(A)-containing RNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, USA).  Chromatin from ovaries (~ 100 pairs for each IP experiment) was extracted and immunoprecipitated according to the published protocol (PMID: 16613483). ChIP experiments were carried out using commercially available antibodies anti-H3K9me3 (ab8898) (Abcam, UK).To bind antibodies Pierce protein A/G agarose (Thermo Fisher Scientific, USA) was used.  The ovarian small RNA fraction for cloning was separated from total RNA (~ 15 μg) using 15% polyacrylamide gel electrophoresis containing 8M Urea. After incubation in an ethidium bromide solution (0.5 μg/ml), gel fragments corresponding to the small RNA fraction were excised, using chemically synthesized RNA corresponding to 20 and 29 nts as size markers.
Libraries for RNA-seq were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, USA) according to the manufacturer’s guidelines. Experiments were performed in two biological replicates for each D. virilis strain. Paired-end sequencing (50+50 nts) was conducted on an Illumina NextSeq 2000 platform.  Construction of ChIP-seq libraries for sequencing was performed using DNA Library Prep for Illumina (New England Biolabs, USA). Experiments were performed in two biological replicates. Paired-end sequencing (50+50 nt) was conducted on an Illumina NextSeq 2000 platform.  Cloning of small RNA libraries was performed using the Illumina TruSeq Small RNA prep kit (Illumina, USA) according to the manufacturer's protocol.

value: ovaries


title: 84_small_RNA

description: Library name: Small_RNA_seq_84


title: A375, TFE3KO, RNAseq, bio rep 1

description: bulk RNAseq


title: HT1197 PEMF Day 5 Sample 1

description: UC19 PEMF HT1197 D5 S1


title: 62_small_RNA

description: Library name: Small_RNA_seq_62


title: NS rep3 2h

description: Library name: A10

value: WT


title: SKMEL28, MITFKO, ATAC seq, bio rep 1

value: MITFKO


title: A375, wild type, RNAseq, bio rep 3

description: bulk RNAseq


title: NS rep2 18h

description: Library name: A8

value: Lung


title: A375, wild type, RNAseq, bio rep 2

description: bulk RNAseq


title: A375, wild type, RNAseq, bio rep 1

description: bulk RNAseq


title: 6_small_RNA

description: Library name: Small_RNA_seq_6


title: NS rep2 6h

description: Library name: A7

value: BEAS-2B human airway epithelial cell line


title: SKMEL28, MITFKO, TFE3KO, clone 13, RNAseq, bio rep 3

description: bulk RNAseq

value: MITFKO, TFE3KO


title: 44_small_RNA

description: Library name: Small_RNA_seq_44


title: HT1197 Control Day 5 Sample 3

description: UC27 CONTROL HT1197 D5 S3


title: SKMEL28, MITFKO, TFE3KO, clone 13, RNAseq, bio rep 2

description: bulk RNAseq


title: NS rep2 2h

description: Library name: A6

value: Vehicle


title: SKMEL28, MITFKO, TFE3KO, clone 13, RNAseq, bio rep 1

description: bulk RNAseq


title: SKMEL28, MITFKO, TFE3KO, clone 3, RNAseq, bio rep 3

description: bulk RNAseq


title: 39_small_RNA

description: Library name: Small_RNA_seq_39


title: A375, TFE3KO, RNAseq, bio rep 2

description: bulk RNAseq


title: NS rep3 1h

description: Library name: A9


title: 140_iso_small_RNA

description: Library name: Small_RNA_seq_140_iso


title: NS rep2 1h

description: Library name: A5


title: 30_small_RNA

description: Library name: Small_RNA_seq_30


title: NS rep1 6h

description: Library name: A3


title: NS rep1 2h

description: Library name: A2


title: 2630-Liver_vehicle

city: Austin

first: Anna

last: Warden

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

description: Library name: 2630-Liver

data_processing:
Reads were mapped to the mouse reference genome (UCSC, GRCm39) using the alignment tool STAR (v2.7.10b). Raw RNA-sequencing files were evaluated for quality control using FastQC (v0.12.0). HTSeq (v.0.2.0) and python (v.2.7) was used for counting mapped sequencing reads. RSeQC (v5.0.1) was used to further quality control mapped sequenced reads.
Quantified read counts were normalized and analyzed using DESeq2 (v1.12.3) to determine differential expression between groups, within the R statistical computing environment (v4.2.2)
Pairwise differential expression analysis were performed with DESeq2. Identical read filtering parameters were used for different organs, and genes with read counts < 5 in at least half of the samples per treatment group were removed.
Assembly: mm39
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA from tissue was isolated using the PureLink RNA mini kit using manufacturer’s instructions (Invitrogen). Genomic DNA was removed using RapidOut DNA Removal Kit (ThermoFisher).
Sequencing libraries were constructed using a 3’ Tag-based approach (TagSeq), targeting the 3’ end of mRNA fragments.
3’ TagSeq was performed by the University of Texas Genomic Sequencing and Analysis Facility (RRID#: SCR_021713) . Libraries were quantified using the Quant-it PicoGreen dsDNA assay (ThermoFisher) and pooled equally for subsequent size selection at 350-550bp on a 2% gel using the Blue Pippin (Sage Science).  The final pools were checked for size and quality with the Bioanalyzer High Sensitivity DNA Kit (Agilent) and their concentrations were measured using the KAPA SYBR Fast qPCR kit (Roche). Samples were then sequenced on the NovaSeq 6000 (Illumina) instrument with single-end, 100-bp reads.

value: Liver

value: total homogenate

value: vehicle


title: 2630-SI_vehicle

description: Library name: 2630-SI

source_name: Small Intestine

value: Small Intestine

value: Male


title: F1_9x140_rep1

description: Library name: RNA_seq_F1_9x140_rep1

molecule: polyA RNA


title: SKMEL28, MITFKO, TFE3KO, clone 3, RNAseq, bio rep 1

description: bulk RNAseq


title: NS rep1 18h

description: Library name: A4


title: F1_9x140_rep2

description: Library name: RNA_seq_F1_9x140_rep2


title: SKMEL28, MITFKO, RNAseq, bio rep 2

description: bulk RNAseq


title: SKMEL28, MITFKO, RNAseq, bio rep 1

description: bulk RNAseq


title: SKMEL28, MITFKO, RNAseq, bio rep 3

description: bulk RNAseq


title: 2629-Liver_vehicle

description: Library name: 2629-Liver

value: Female


title: 2630-Brain_vehicle

description: Library name: 2630-Brain

source_name: Brain

value: Brain


title: NS rep1 1h

description: Library name: A1


title: SKMEL28, MITFKO, TFE3KO, clone 3, RNAseq, bio rep 2

description: bulk RNAseq


title: SKMEL28, wild type, RNAseq, bio rep 3

description: bulk RNAseq

value: wild type


title: SKMEL28, wild type, RNAseq, bio rep 4

description: bulk RNAseq


title: 2629-Brain_vehicle

description: Library name: 2629-Brain


title: Heart - HFpEF

city: Chicago

first: Edward

last: Thorp

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

description:
Library name: Sample 4
10X Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were performed using CellRanger v3.0.2 (Heart) or CellRanger v4.0.0 (Spleen)
Aligned reads were then filtered for valid barcodes and UMIs to generate gene-cell matrices used for downstream analysis. To filter low-quality cells from the dataset, gene-cell matrices were read into R using Seurat (v4.3.0) R toolkit
Cells that expressed less than 1100 unique molecular identifiers, less than 900 unique genes, log10(GenesperUMI) less than 0.8, and greater than 15% mitochondrial gene content were removed. Additionally, features that were not detected in at least ten single cells were removed.
Next, we normalized for cell cycle variation and used sctransform (v0.3.5) based normalization to recover sharper biological distinctions compared to log-normalization. To mitigate potential batch effects that are common for scRNAseq data, each dataset for each sample was integrated using Seurat’s FindIntegrationAnchors and IntegrateData function.
Assembly: Mouse mm10
Supplementary files format and content: tab-separated values files and matrix files

source_name: Heart

growth_protocol: Heart: Adult C57BL/6J males were subjected to Chow diet, HFD only, LNAMe only, or HFD+LNAME (HFpEF) for five weeks (n=5 per group, per organ). Hearts were collected and enzymatically digested to obtain a single cell solution. F4/80+ cells were enriched using magnetic bead selection (Stem Cell). Biological replicates in the same conditions were pooled together by condition for processing in the 10X Genomics Chromium System. A targeted number of 8,000 cells were loaded for each experimental condition. Single cell mRNA sequencing libraries were prepared using the 10X Genomics Chromium Next GEM Single Cell 3′ Library and Gel Bead Kit (v3.1) pipeline following manufacturer protocols.                      Spleen: Adult C57BL/6J males were subjected to Chow diet, HFD only, LNAME only, or HFD+LNAME (HFpEF) for five weeks (n=5 per group, per organ). Spleens were collected and triturated through a 40um cell filter to obtain a single cell solution. cKIT+ stem cells were enriched by magnetic bead selection. Biological replicates in the same conditions were pooled together by condition for processing in the 10X Genomics Chromium System. A targeted number of 10,000 cells were loaded for each experimental condition. Single cell mRNA sequencing libraries were prepared using the 10X Genomics Chromium Next GEM Single Cell 3′ Library and Gel Bead Kit (v3.1) pipeline following manufacturer protocols.

extract_protocol:
scRNA-seq
Library was performed following manufacturer's instructions (Single cell 3' v3, 10X Genomics)

value: Heart

value: HFpEF

value: 12-15 weeks

value: male


title: SKMEL28, wild type, RNAseq, bio rep 2

description: bulk RNAseq

value: melanoma


title: 2628-SI_vehicle

description: Library name: 2628-SI


title: Heart - LNAME

description:
Library name: Sample 3
10X Genomics

value: L-NAME


title: 9_rep2

description: Library name: RNA_seq_9_rep2

value: ovaries


title: Heart - HFD

description:
Library name: Sample 2
10X Genomics

value: HFD


title: 2628-Liver_vehicle

description: Library name: 2628-Liver


title: 2629-SI_vehicle

description: Library name: 2629-SI


title: 9_rep1

description: Library name: RNA_seq_9_rep1


title: 140_rep2

description: Library name: RNA_seq_140_rep2


title: SKMEL28, wild type, RNAseq, bio rep 1

description: bulk RNAseq


title: 2628-Brain_vehicle

description: Library name: 2628-Brain


title: XRGIC67_D_P8

city: London

first: James

last: Nicholson

address: 4 Newark St

department: Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

description: Xenograft derived GICs; modelled-recurrence, PDX seeded with primary GICs; patient 67

data_processing:
Reads were quality trimmed using trimgalore v0.6.5
Reads were aligned with STAR v2.7.9a
Reads were counted using FeatureCounts of the Rsubread v2.16.0 package
Differential expression analysis was performed in DESeq2 using the Wald test
Assembly: GRCh38.release109
Supplementary files format and content: comma separated values of log(cpm+1)

source_name: cells

growth_protocol: GIC were maintained in NeuroCult NS-A Proliferation kit medium, 1% Pen/Strep, 2µg/ml Heparin, 20ng/ml murine EGF and 10ng/ml human FGF. iNSC were cultured in 0.5X Advanced DMEM/F-12 , 0.5X Neurobasal medium, 1X Neurobasal Induction supplement and 1X pen/strep

extract_protocol:
DNA and RNA were extracted from tissue samples using the FFPE RNA/DNA Purification Plus Kit (Norgen, 54300) as per manufacturer protocol. For cells (GICs/GICRs/XGICs/XGICRs/IRGICs) both DNA and RNA were extracted from pellets containing one well of a 6-well plate (confluency 80%) using the RNA/DNA/Protein Purification Plus Kit (Norgen, 47700) following the instructions provided by the manufacturer.
RNA library is formed by polyA capture (or rRNA removal for the FFPE samples) and reverse transcription of cDNA. Illumina PE150 technology

value: Glioblastoma initiating cells


title: F1_140x9_rep2

description: Library name: RNA_seq_F1_140x9_rep2


title: Heart - Chow

description:
Library name: Sample 1
10X Genomics

value: Chow


title: BMSCs, Dexamethasone 48h-4

city: shanghai

first: Rongtai

last: Zuo

address: No.600, Yishan Road, Xuhui District, Shanghai

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

data_processing:
The libraries were sequenced as 51-bp paired-end reads using Illumina Novaseq6000.
For raw reads, adapters and poor quality bases were trimmed off using Skewer version 0.2.2.
The clean reads were aligned to the genome reference genome downloaded from the Ensembl website using Bowtie version 1.0 and comprehensive gene annotation GTF file from Ensembl website.
The clean data were aligned to the miRBase database using Bowtie version 1.0 to obtain the miRNAs expression counts.
The clean data were annotated in the Rfam database to show the distribution of different RNA class in small RNA sequencing data.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text file include raw counts for each sample
Supplementary files format and content: tab-delimited text file include CPM values for each sample

organism: Rattus norvegicus

source_name: bone marrow mesenchymal stem cells

extract_protocol:
Total RNA was extracted from each sample using a miRNA kit (Qiagen, Germany), and a total amount of 1ug could be used for the construction of sequencing libraries.
RNA libraries for sequencing were constructed by VAHTS™ Total RNA-seq (H/M/R) Library Prep Kit for Illumina® platforms.

value: bone marrow mesenchymal stem cells

value: Dexamethasone


title: tumor tissue of adamantinomatous craniopharyngioma from case CP5, biological replicate1

city: minatoku toranomon

first: Tatsuma

last: Matsuda

address: tokyo

country: Japan

institute: toranomon hospital

description:
Library name: CP5rep1
10x Genomics

data_processing:
ASTQ files were aligned using the 103 Genomics CellRanger 6.0.0. pipeline to the human GRCh38 reference transcriptome to generate gene-expression count matrices with the ‘‘exclude the introns’’ option.
Assembly: GRCh38
Supplementary files format and content: separated barcode file and features file, matrix file

source_name: tumor tissue

extract_protocol:
A single-cell suspension of the craniopharyngioma samples was digested via stirring at 37_x000E_C for 90 min using collagenase I 60 (160 mL, 100 mg/ mL) and collagenase VII 61 (400 mL, 100 mg/mL; Worthington, OH, USA) immediately after surgical removal. The suspension was then filtered through a 40-mm cell strainer (Corning, NY, USA) to remove debris and undigested large tissue fragments. After allowing the cells to settle, red blood cells were isolated using ACK lysing buffer (Thermo Fisher Scientific, MA, USA), and dead cells were removed using a dead cell removal kit (Miltenyi Biotec, Bergisch Gladbach, Germany); the resultant cell suspension contained approximately 20,000 cells per sampl
The obtained cell suspension was prepared following the specifications of 103 Genomics, using 103 Chromium Next GEM single-cell 3ʹ re- agent kits and the library construction kit (103 Genomics, CA, USA). The cell suspension was loaded into the 103 Genomics Chromium Controller, creating gel beads in emulsion (GEM). After generating the GEM, the suspension was incubated at 53_x000E_C for 45 min in a thermal cycler (Veriti, Applied Biosystems, MA, USA). A barcode-linked polyA cDNA with barcodes at the 5ʹ end was produced via adding template switch oligos linked to cell barcodes and unique molecular identifiers (UMIs). The GEMs were then disrupted, and single-stranded cDNA was cleaned using DynaBeads MyOne Silane Beads (Thermo Fisher Scientific). The cDNA was amplified (98_x000E_C for 3 min, 11 cycles of 98_x000E_C for 15 s, 63_x000E_C for 20 s, and 72_x000E_C for 1 min) and the quality was assessed using Agilent TapeStation (Agilent Technologies, CA, USA). The cDNA was enzymatically fragmented, end-repaired, A-tailed, and subjected to size selection on both ends using SPRIselect beads (Beckman Coulter, CA, USA). It was then ligated with adapters provided in the kit. Sample-specific indices were introduced into each library via 14-cycle poly- merase chain reaction amplification using kit-supplied indices (98_x000E_C for 45 s, 14 cycles of 98_x000E_C for 20 s, 54_x000E_C for 30 s, 72_x000E_C for 20 s, 72_x000E_C for 1 min, and holding at 4_x000E_C). Indexed libraries underwent a second round of size selection. The library was quantified and quality was assessed using Agilent TapeStation. Libraries were clustered on a NovaSeq 6000 paired-end read flow cell (Illumina, CA, USA). Sequencing was per- formed with reads for R1 (containing 103 barcodes and UMIs), I7 index (8 cycles; sample index), and R2 (89 cycles; transcript). The 103 Ge- nomics Cell Ranger Single-Cell Software was used for sample demultiplexing, alignment to the human reference genome (hg19), filtering, UMI counting, single-cell 3ʹ end gene counting, and QC as per manufacturer’s instructions.

value: tumor tissue

value: female


title: 2627-SI_vehicle

description: Library name: 2627-SI

value: Small Intestine

value: total homogenate

value: vehicle

value: Male


title: 140_rep1

description: Library name: RNA_seq_140_rep1


title: BMSCs, Dexamethasone 48h-3


title: 2627-Liver_vehicle

description: Library name: 2627-Liver

value: Liver


title: XRGIC67_D_P7

value: Xenograft derived GICs; modelled-recurrence, PDX seeded with primary GICs; patient 67


title: 140_input_rep2

description: Library name: Chip_Dvir_140_H3K9me3_input_rep2


title: XRGIC67_A_P6


title: BMSCs, Dexamethasone 48h-2


title: 2627-Brain_vehicle

description: Library name: 2627-Brain

value: Brain


title: 140_input_rep1

description: Library name: Chip_Dvir_140_H3K9me3_input_rep1


title: XRGIC67_A_P5


title: BMSCs, Dexamethasone 48h-1


title: 2603-SI_Mn50

description: Library name: 2603-SI


title: 140_H3K9me3_treat_rep2

description: Library name: Chip_Dvir_140_H3K9me3_treat_rep2


title: BMSCs, Control-4

value: Control


title: XGIC67R_D_P6

description: Xenograft derived GICs; PDX seeded with recurrent GICs; patient 67


title: 2603-Liver_Mn50

description: Library name: 2603-Liver


title: BMSCs, Control-3


title: XGIC67R_D_P5

value: Xenograft derived GICs; PDX seeded with recurrent GICs; patient 67


title: F1_140x9_rep1

description: Library name: RNA_seq_F1_140x9_rep1

value: ovaries


title: 140_H3K9me3_treat_rep1

description: Library name: Chip_Dvir_140_H3K9me3_treat_rep1


title: 2603-brain_Mn50

description: Library name: 2603-brain


title: OSRC2, HIF2a-KI, Rep2

data_processing:
Sequence tags were aligned with Burrows-Wheeler Aligner (BWA) to build hg19 and uniquely mapped, non-redundant reads were retained. These reads were used to generate binding sites with Model-Based Analysis of ChIP-Seq 2 (MACS v2.1.1.20160309), with a q-value (FDR) threshold of 0.01
Evaluated multiple quality control criteria based on alignment information and peak quality: (i) sequence quality score, (ii) uniquely mappable reads (reads that could only map to one location in the genome), (iii) uniquely mappable locations (locations that could only be mapped by at least one read), (iv) peak overlap with Velcro regions, a comprehensive set of locations – also called consensus signal artifact regions – in the genome that have anomalous, unstructured high signal or read counts in next-generation sequencing experiments independent of cell line and of experiment type, (v) number of total peaks (each sample had >3,000 peaks, passing the minimum requirement of 1000), (vi) high-confidence peaks (the number of peaks that were enriched tenfold over the background), (vii) percentage overlap with known DHS sites derived from the ENCODE Project (samples meet the minimum 80% threshold), and (viii) peak conservation (a measure of sequence similarity across species based on the hypothesis that conserved sequences are more likely to be functional). All samples in this study passed quality control criteria.
To identify HIF2a peak location bed file was extended by 1 kb, 5 kb, 10 kb for each peak region using BEDOPS tool
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
For ChIP sample preparation, 1×107 adherent cells were washed with PBS, trypsinized, transferred to Eppendorf tubes and collected by centrifugation at 300×g for 5 min at RT. Cell pellets were washed once with RT PBS-complete [PBS supplemented with 1× protease inhibitor (Sigma PIC0006) and 5mM sodium butyrate], resuspended in 2 mM of disuccinimidyl glutarate (DSG, Thermo Fisher Scientific 20593) diluted in PBS, and then agitated at 850 rpm on a Fisherbrand Isotemp Heat/Cool Programmable Thermal Mixer II (Thermo Fisher Scientific) at RT for 45 min. The cell pellets were collected by centrifugation at 300×g for 5 min at RT. The supernatant was removed, and the cell pellets were resuspended in freshly made 1% formaldehyde (Thermo Fisher Scientific 28908) diluted in PBS followed by agitation at 850 rpm on a Fisherbrand Isotemp Heat/Cool Programmable Thermal Mixer II for 10 min at RT. The crosslinking was quenched by adding glycine to a final concentration of 0.125 M with agitation at 850 rpm on a Fisherbrand Isotemp Heat/Cool Programmable Thermal Mixer II for 5 min at RT. The cell pellets were collected by centrifugation at 300×g for 5 min at 4°C. Cell pellets were washed once with ice-cold PBS-complete. Crosslinked cells were then pelleted, snapfrozen and stored at -80°C.   Aliquots of frozen pellets were thawed on ice, resuspended in 500 l of 1% SDS lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% SDS, 1× protease inhibitor, 5 mM sodium butyrate) and lysed on ice for 10-15 min. The lysates were transferred to 1 ml Adaptive Forced Acoustics (AFA) fiber milliTUBEs (Covaris 520135) and sonicated at the following settings: 140 peak incident power, 5% duty factor and 200 cycles per burst) using Covaris E220 sonicator. Sonication lasted for 10 min. Post sonication, the lysates were transferred to Eppendorf tubes and cleared by centrifugation at 17,000×g for 15 min at 4°C.   To determine the amount of precleared chromatin to be used for ChIP-Seq experiments, 10 l of the lysates were aliquoted (INPUT) and 90 l of TE was added to make 100 l solution. 1 l RNase A (Invitrogen AM2696) was added to the samples and incubated for 30 min at 37°C, then 5 l Proteinase K (20 mg/ml, Thermo Fisher Scientific EO0492) was directly added to the mixture and incubated at 65°C for 16 h with constant agitation at 850 rpm on a Fisherbrand Isotemp Heat/cool Programmable Thermal Mixer II at the indicated temperatures. Next the chromatin was purified using PCR Purification Kit (Qiagen 28104). Briefly, 500 l PB buffer was added to each 100 l sample and the mixture was mixed and loaded onto the purification column. The purified chromatin was eluted using 32 l EB buffer. Chromatin (INPUT) concentration was determined using a Qubit High Sensitivity Kit (Life Technologies A33231) on a Qubit 4 Fluorometer (Invitrogen Q33239). 40 g chromatin (INPUT) was immunoprecipitated with 5 g of FLAG antibody (Sigma-Aldrich F1804). Antibody-bead conjugation was done by first taking 30 l of protein G beads (Life Technologies 10004D) per sample and washing them three times with 500 l ice-cold 0.5% BSA diluted in PBS. The beads were then resuspended in 500 l ice-cold 0.5% BSA diluted in PBS with the desired number of antibodies and rotated end-to-end for 4-6 h at 4°C, followed by two additional washed with ice-cold 0.5% BSA diluted in PBS to remove unbound antibodies. Lysates containing the desired amount of chromatin/protein were diluted 10-fold using ChIP dilution buffer (20 mM Tris-HCl pH 8.0, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 1× protease inhibitor, 5 mM sodium butyrate), added to pre-washed antibody-bead conjugates and then rotated end-to-end overnight at 4°C. The next day, the bead-bound chromatin-antibody complexes were washed twice with RIPA 0 buffer (10 mM Tris-HCl pH 7.4, 1 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate), twice with RIPA 0.3 buffer (10 mM Tris-HCl pH 7.4, 1 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate, 0.3 M NaCl), twice with LiCl buffer (10 mM Tris-HCl pH 7.4, 1 mM EDTA pH 8.0, 0.5% NP40, 0.5% sodium deoxycholate, 0.25 M LiCl), and then eluted with 100 l pre-warmed (37°C) ChIP elution buffer (1% SDS, 0.1 M NaHCO3 in H2O). 1 l RNase A was added to the samples and incubated for 30 min at 37°C, then 5 l Proteinase K was added to the samples and incubated at 65°C for 16 h. For RNase A and Proteinase K incubation, the samples were constantly agitated at 850 rpm on Fisherbrand Isotemp Heat/cool Programmable Thermal Mixer II. The supernatant was purified using a MinElute PCR Purification Kit (Qiagen 28004), eluted in 12 l H2O, and quantified using a Qubit High Sensitivity Kit (Invitrogen Q33230).
A 5 l sample was used for ChIP-seq library preparation with a Swift DNA Library Prep Kit (Swift Biosciences 1002). 75 bp paired-end reads were sequenced on a NextSeq instrument (Illumina).

value: ccRCC

tag: chip antibody

value: anti-FLAG


title: XGIC67R_C_P6

value: Glioblastoma initiating cells


title: OSRC2, HIF2a-KI, Rep1


title: 2602-SI_Mn50

description: Library name: 2602-SI


title: BMSCs, Control-2

value: bone marrow mesenchymal stem cells


title: XGIC67R_C_P5


title: OSRC2, Parental, Rep2

value: Parental


title: XGIC67R_B_P6


title: XGIC67R_B_P5


title: 2602-Brain_Mn50

description: Library name: 2602-Brain


title: OSRC2, Parental, Rep1


title: 2601-liver_Mn50

description: Library name: 2601-liver


title: CJ_SKO911

city: Luzhou

first: Yan

last: Yang

address: Xianglin Road

institute: South-West Medical University

description: 10x Genomics

data_processing:
Data were processed following standard protocols using Cell Ranger version 6.0.0.
Cellranger mkfastq was used to demultiplex raw base call files into fastq files.
Cellranger count was used to perform alignment, filtering, barcode counting, UMI counting, and to generate feature-barcode matices.
Supplementary files format and content: TSV data for genes and barcodes; MTX data for gene expression matrix

source_name: femoral artery

extract_protocol:
We performed scRNA-seq of MA, AA and FA cells respectively from WKY/N and SHR/N rat of young and old group (male, 16-18 weeks old and 72-weeks old, 7-8 rats in each group). Only male rats were included to avoid the sex influence on experiment results. Rats were anaesthetized with intraperitoneal injection of 50 mg/kg sodium pentobarbital. The adequacy of anaesthesia throughout the procedure was confirmed by the lack of reflex response to toe stretch. Direct blood pressure was measured and recorded with a heparinized fluid-filled catheter that was inserted into the isolated femoral artery. While still being under 50 mg/kg intraperitoneal sodium pentobarbital anaesthesia, the rats were sacrificed by exsanguination via transcardial perfusion with 50 mL phosphate buffered saline (PBS) and subsequent heart excision. All branches of superior and inferior MAs (excluding the superior and inferior MAs themselves), AA (thoracic artery and abdominal artery; aortic arch is not included) and FA (Below the iliac artery branch) were collected and perivascular tissues were carefully cleaned. Pooled tissue from each group and artery type, respectively, was obtained. As described before(Gu et al., 2019), the arteries were digested with 2 mg/mL collagenase I (Invitrogen; 17018-029) and 2 mg/mL dispase II (Sigma; D4693) in Hank’s balanced salt solution (with calcium and magnesium) at 37 ℃ for 30 minutes on a shaker at the speed of 100 rpm. Digested mix was passed through 40 μm strainer and stained with LIVE/DEAD Fixable Near-IR (APC/Cy7 channel) Dead Cell Stain Kit (Invitrogen; L34975, 1:1000) and Hoechst 33342 (Invitrogen; H3570, 1:1000) for 20 minutes. Unstained cells and single stained cells served as control. After 1 wash in PBS for 5 minutes, cells resuspended in PBS were sorted with FACS Aria II (BD Biosciences). Single nucleated live cells (Hoechst+/APC/Cy7-population) were sorted into PBS with 0.04% BSA. After centrifugation at 300 g for 5 min, the cells were loaded to 10x Genomics Chromium chip following manufacturer’s recommendations with target capture of 6,000 cells. Standard 10x Chromium Single Cell 3′ v2 (10x Genomics) protocols were followed for scRNA-seq for reverse transcription and library preparation. The generated scRNA-seq library was sequenced with Nova PE150 with the sequencing depth of 30 million per cell.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: femoral artery

value: nucleated living cells

value: spontaneously hypertensive

value: male

value: 16 weeks old


title: CJ_WK823

description: 10x Genomics

value: Wistar Kyoto


title: XGIC67R_A_P6


title: CJ_OSM10

description: 10x Genomics

source_name: mesenteric artery

value: mesenteric artery

value: 72 weeks old


title: sgASH1L-3_2

city: Houston

first: Di

last: Zhao

state: Tx

address: Zayed Building Z7. 4018

institute: MD Anderson Cancer Center

data_processing:
The reads were aligned to the human genome (hg38) using TopHat (version 2.0.10).
The number of fragments for each gene from GENCODE (V37) was quantified using htseq-count from the HTSeq package (version 0.6.0). Genes with fewer than 10 fragments in all samples were excluded.
Normalized fragment counts were estimated by the R/Bioconductor package DESeq (version 1.18.0).
Assembly: hg38
Supplementary files format and content: The first column is Ensembl gene id. The second column is gene symbol. The other columns are normalized fragment counts (estimated by DESeq) for all the genes in each sample.

growth_protocol: PC-3M human prostate cancer cells were cultured  in Dulbecco’s modified Eagle’s (DMEM) medium with 10% FBS and 1% penicillin/streptomycin and incubated at 37 °C under 5% CO2.

extract_protocol:
Control and ASH1L-knockout PC-3M cells were lysed with TRIzol, and total RNAs were extracted using the RNeasy Mini Kit (Qiagen, 74104).
Library preparation and sequencing were performed by ATGC next-generation sequencing core facility at MD Anderson, using a 2x75 bases paired-end protocol on a NextSeq500 instrument.

treatment_protocol: PC-3M Ctrl and ASH1L knockout stable cell lines were generated using CRISPR-Cas9 system and selected by puromycin

value: human prostate cancer cells

value: ASH1L Knockout

value: stable cell line


title: sgASH1L-3_3


title: sgASH1L-3_1


title: XGIC67R_A_P5

value: Xenograft derived GICs; PDX seeded with recurrent GICs; patient 67


title: 2600-SI_Mn50

description: Library name: 2600-SI

value: Small Intestine

value: total homogenate

value: Female


title: CJ_OSK16

description: 10x Genomics


title: 2601-brain_Mn50

description: Library name: 2601-brain

value: Brain

value: Male


title: 2600-Liver_Mn50

description: Library name: 2600-Liver

value: Liver


title: XGIC67_D_P6

description: Xenograft derived GICs; PDX seeded with primary GICs; patient 67

value: Glioblastoma initiating cells


title: sgASH1L-2_3


title: BMSCs, Control-1

value: bone marrow mesenchymal stem cells

value: Control


title: 2602-Liver_Mn50

description: Library name: 2602-Liver


title: sgASH1L-2_2


title: CJ_OWM10

description: 10x Genomics

value: nucleated living cells

value: male


title: 2600-Brain_Mn50

description: Library name: 2600-Brain


title: XGIC67_C_P6

value: Xenograft derived GICs; PDX seeded with primary GICs; patient 67


title: XGIC67_D_P5


title: sgASH1L-2_1


title: CJ_OWK15

description: 10x Genomics

value: femoral artery

value: Wistar Kyoto

value: 72 weeks old


title: 2578-Liver_Mn50

description: Library name: 2578-Liver


title: XGIC67_C_P5


title: 2578-SI_Mn50

description: Library name: 2578-SI


title: XGIC67_B_P6


title: sgCtrl_2

value: human prostate cancer cells

value: Ctrl

value: stable cell line


title: 2578-Brain_Mn50

description: Library name: 2578-Brain

value: total homogenate


title: sgCtrl_3


title: E320K-ELK1-D_Replicate3_Timepoint 2

city: New Haven

first: Jaylissa

middle: Marie

last: Torres Robles

state: CT

address: 333 Cedar St. Department of Pharmacology, Yale School of Medicine

department: Chemistry and Pharmacology

institute: Yale University

description: Library name: Sample_19

library_source: other

data_processing:
Sequences were aligned using an internal barcode allowing for one base mismatch and trimmed. Barcode-matched sequences were mapped to the ELK1 D-site library and unique sequences were counted using the FASTX toolkit, Perl and the Yale Center for Genome Analysis shRNA Analysis Pipeline through Yale Center for Research Computing, Ruddle cluster.
Starting Library raw sequencing data files were concatenated into a single file before proceeding with trimming and barcode alignments -/+1 mismatch.
Assembly: A custom sequence library was used.
Supplementary files format and content: Table of raw counts is in .xslx format, containing the total number of counts of each sequence within our library under indicated conditions, timepoints, and replicates

molecule: other

growth_protocol: Yeast two-hybrid strain PJ694-A was cultured in yeast synthetic complete media supplemented with 2% glucose

extract_protocol:
Extracted DNA was PCR-amplified with Illumina indexing primers and a second internal primer for sequence alignment.
An oligonuclotide pool encoding short linear motifs from the human proteome  with common flanking sequence was amplified by PCR, restriction digested and ligated into the yeast two-hybrid prey plasmid encoding ELK1 between the SpeI and AgeI sites, replacing the native ELK1 D-site. MAX Efficiency DH10B electrocompetent E. coli (ThermoFisher) were transformed with the ligation reaction product. Transformed cells were spread on 15 cm Luria-Bertani Broth (LB) agar plates supplemented with 0.1 mg/ml ampicillin and grown overnight at 37°C. Plasmid DNA was isolated from pooled colonies (Qiagen Maxi prep kit). Colony counts from serial dilution plates confirmed the presence of at least 50 transformants per library sequence. The variable sequence was PCR-amplified and sequenced (Illumina HiSeq 4000) to verify clone representation of all library components. Yeast two hybrid stran PJ694A harboring ERK2 D319N or E320K mutant bait plasmids was transformed with the library plasmid pool for competitive growth Y2H screens.

treatment_protocol: For library screens, yeast harboring bait plasmids were transformed with the ELK1 D-site library plasmid pool and selected on agar plates containing SD-Leu-Trp media. Transformants were suspended in SD-Leu-Trp liquid media and grown at 30 °C. When the culture reached an OD600 of 1.0, it was used to inoculate 50 mL of selective media (SD-Leu-Trp-His + 50 μM 3-AT) and 50 mL of non-selective media (SD-Leu-Trp) at an OD600 of 0.1. Yeast cultures were subjected to two growth and dilution cycles, with 25 mL aliquots reserved for DNA extraction each time.

value: Yeast


title: XGIC67_B_P5


title: CJ_OSA16

description: 10x Genomics

source_name: thoracic aorta

value: thoracic aorta

value: spontaneously hypertensive


title: 2577-SI_Mn50

description: Library name: 2577-SI

value: Small Intestine

value: Male


title: sgCtrl_1


title: XGIC67_A_P6

value: Glioblastoma initiating cells


title: Treated 48hr replicate 2, scRNA-seq

city: Hong Kong

first: Xinlei

last: Wang

state: Hong Kong

address: Clear Water Bay, Sai Kung,

department: LIFS

institute: HKUST

description: 10x Genomics

data_processing:
The raw data were processed using Cell Ranger 4.0.0, which includes demultiplexing of raw base call (BCL) files into FASTQ files, alignment, and Unique Molecular Identifier (UMI) counting. Reads were aligned to the Homo sapiens genome assembly GRCh38 (hg38).
Assembly: GRCh38  and chrEBV_Akata_inverted (https://github.com/flemingtonlab/public/blob/master/annotation/chrEBV_Akata_inverted_2.fa)
Supplementary files format and content: gene expression mtx, gene annotation tsv, cell barcode tsv, UMAP coordinates csv, and cell annotations csv

source_name: NPC tumors

growth_protocol: NPC43, established from nasopharyngeal carcinoma (NPC) tissue of a 64-year-old male patient, was cultured in RPMI 1640 medium (Gibco 23400021) supplemented with 10% fetal bovine serum (FBS) (Gibco 10270106) and 1% penicillin-streptomycin (10000 U/mL) (Gibco 15140122) in the presence of 4 μM Rho kinase inhibitor Y-27632 dihydrochloride (Abcam 120129).

extract_protocol:
Cells were harvested from T75 flasks, washed twice with 1x phosphate-buffered saline (PBS) (Gibco 10010049), and filtered using a Falcon strainer (Falcon 100-0087). Cell viability was assessed using an automated cell counter with trypan blue staining. Subsequently, cells were diluted to a concentration of 5 × 105 cells/ml in PBS, and dead cells were labeled with Propidium iodide (PI, 3 μM). Single cells were isolated using the BD Influx cell sorter before being loaded onto the 10X Chromium Controller.
The single-cell RNA-seq (scRNA-seq) library was prepared following the Chromium Single Cell 3’ Reagent Kits User Guide (V3 Chemistry) from 10X GENOMICS.

treatment_protocol: To induce the lytic cycle of Epstein-Barr virus (EBV) in NPC43, we replaced the RPMI 1640 medium without Y-27632 and supplemented it with 40 ng/ml tetradecanoyl phorbol acetate (TPA) (Sigma-Aldrich, P8139). After the induction treatment, cells were maintained in the same medium for 24 or 48 hours.

value: NPC tumors

value: epithelial cells

value: WT

value: TPA treated for 48 hours


title: XGIC67_A_P5

value: Xenograft derived GICs; PDX seeded with primary GICs; patient 67


title: E320K-ELK1-D_Replicate2_Timepoint 2

description: Library name: Sample_16


title: 2577-Brain_Mn50

description: Library name: 2577-Brain

value: Brain


title: E320K-ELK1-D_Replicate3_Timepoint 1

description: Library name: Sample_18


title: Treated 48hr replicate 1, scRNA-seq

description: 10x Genomics


title: XGIC39R_E_P6

description: Xenograft derived GICs; PDX seeded with recurrent GICs; patient 39


title: E320K-ELK1-D_Replicate2_Timepoint 1

description: Library name: Sample_15


title: Treated 24hr replicate 1, scRNA-seq

description: 10x Genomics

value: TPA treated for 24 hours


title: 2576-SI_Mn50

description: Library name: 2576-SI

value: Female


title: XGIC39R_E_P5

value: Xenograft derived GICs; PDX seeded with recurrent GICs; patient 39


title: E320K-ELK1-D_Replicate2_Timepoint 0

description: Library name: Sample_14


title: 2576-Liver_Mn50

description: Library name: 2576-Liver

value: Liver


title: CJ_OWA910

description: 10x Genomics

value: nucleated living cells

value: Wistar Kyoto

value: male

value: 72 weeks old


title: Untreated, replicate 2, scRNA-seq

description: 10x Genomics

value: Untreat


title: E320K-ELK1-D_Replicate1_Timepoint 2

description: Library name: Sample_13

value: Yeast


title: XGIC39R_D_P6

value: Glioblastoma initiating cells


title: Untreated, replicate 1, scRNA-seq

description: 10x Genomics

value: NPC tumors


title: XGIC39R_D_P5


title: E320K-ELK1-D_Replicate1_Timepoint 1

description: Library name: Sample_12


title: XGIC39R_C_P6


title: E320K-ELK1-D_Replicate3_Timepoint 0

description: Library name: Sample_17


title: 2575-SI_Mn50

description: Library name: 2575-SI

value: Small Intestine

value: total homogenate


title: Healthy Subject.C CD+ T cells + Tconv-EVs

city: Napoli

first: Paola

last: De Candia

address: via Pansini 5

country: Italy

institute: UNIVERSITA' DEGLI STUDI DI NAPOLI FEDERICO II - Dipartimento di Medicina molecolare e Biotecnologie mediche

description:
Healthy Subject.C
Dynabeads™ Regulatory CD4+/CD25+ T Cell Kit Isolated

data_processing:
Following sequencing, intensity correction and base calling (into BCL files), FASTQ files were generated using the appropriate bcl2fastq software (Illumina Inc.) which includes quality scoring of each individual base in a read.
Assembly: h.sapiens, hg19 / GRC37, UCSC Genome Browser
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample

source_name: CD+ T cells + Tconv-EVs

growth_protocol: CD4+ T cells from 3 healthy subjects (A, B and C) were isolated by Dynabeads™ Regulatory CD4+/CD25+ T Cell Kit Isolation kit, and cultured in vitro for 24 hours in the presence of anti-CD3/anti-CD28 beads (TCR stimulation).

extract_protocol:
RNA was extracted using the RNeasy Micro Kit from QIAGEN, according to manufacturer’s instructions. RNA samples were then quantified and quality tested by Agilent 2100 Bioanalyzer RNA assay (Agilent technologies, Santa Clara, CA).
Libraries were prepared by mRNA enrichment and poly-A tailing.
Libraries were then processed and sequenced on single-end 1x50 mode on NextsSeq500 (Illumina, San Diego, CA) following the manufacturer’s instructions.

treatment_protocol: TCR-stimulated CD4+ T cells were treated with EVs released by either Treg cells, or Tconv cells, or with particles isolated from unconditioned medium (controls, or mock EVs).

value: Caucasian

value: adult

value: Whole blood


title: 2577-Liver_Mn50

description: Library name: 2577-Liver

value: Male


title: 2576-Brain_Mn50

description: Library name: 2576-Brain

value: Brain

value: Female


title: E320K-ELK1-D_Replicate1_Timepoint 0

description: Library name: Sample_11


title: XGIC39R_C_P5

value: Xenograft derived GICs; PDX seeded with recurrent GICs; patient 39


title: 2575-Liver_Mn50

description: Library name: 2575-Liver

value: Liver


title: D319N-ELK1-D_Replicate3_Timepoint 2

description: Library name: Sample_10


title: D319N-ELK1-D_Replicate3_Timepoint 1

description: Library name: Sample_9


title: Healthy Subject.C CD+ T cells + mock EVs

source_name: CD+ T cells + mock EVs


title: XGIC39R_B_P6


title: Healthy Subject.C CD+ T cells + Treg-EVs

source_name: CD+ T cells + Treg-EVs


title: 2574-SI_vehicle

description: Library name: 2574-SI

value: vehicle


title: Healthy Subject.B CD+ T cells + Tconv-EVs

description:
Healthy Subject.B
Dynabeads™ Regulatory CD4+/CD25+ T Cell Kit Isolated


title: D319N-ELK1-D_Replicate3_Timepoint 0

description: Library name: Sample_8


title: 2574-Liver_vehicle

description: Library name: 2574-Liver


title: Healthy Subject.B CD+ T cells + Treg-EVs


title: XGIC39_C_P6

description: Xenograft derived GICs; PDX seeded with primary GICs; patient 39


title: XGIC39R_B_P5


title: D319N-ELK1-D_Replicate2_Timepoint 2

description: Library name: Sample_7


title: 2574-Brain_vehicle

description: Library name: 2574-Brain


title: XGIC39_C_P5

value: Xenograft derived GICs; PDX seeded with primary GICs; patient 39


title: D319N-ELK1-D_Replicate2_Timepoint 1

description: Library name: Sample_6


title: Healthy Subject.A CD+ T cells + Tconv-EVs

description:
Healthy Subject.A
Dynabeads™ Regulatory CD4+/CD25+ T Cell Kit Isolated


title: XGIC39_B_P6


title: 2573-SI_vehicle

description: Library name: 2573-SI


title: Healthy Subject.A CD+ T cells + Treg-EVs


title: 2573-Liver_vehicle

description: Library name: 2573-Liver


title: D319N-ELK1-D_Replicate1_Timepoint 2

description: Library name: Sample_4


title: XGIC39_B_P5


title: Healthy Subject.A CD+ T cells + mock EVs


title: 2575-Brain_Mn50

description: Library name: 2575-Brain


title: D319N-ELK1-D_Replicate1_Timepoint 1

description: Library name: Sample_3


title: 2572-SI_vehicle

description: Library name: 2572-SI


title: Healthy Subject.B CD+ T cells + mock EVs


title: 10_day_dark_IN

city: La Jolla

first: Laura

last: Sancho

state: CA

address: 10010 N Torrey Pines

institute: Salk Institute for Biological Studies

description:
whole ROI homogenate (input)
10_day_dark_IN

data_processing:
Raw sequencing data was demultiplexed and converted into FASTQ files using CASAVA (v1.8.2), and quality tested with FASTQC v0.11.2.
Alignment to the mm10 genome was performed using the STAR aligner version 2.5.1b (Dobin et al., 2013). Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read), and a high ratio of uniquely mapped reads (>75%) was confirmed with exonic alignment inspected to ensure that reads were mapped predominantly to annotated exons.
Raw and normalized (FPKM) gene expression was quantified across all genes (RNAseq) using the top-expressed isoform as proxy for gene expression using HOMER v4.10 (Heinz et al.,2010),resulting in 10-55 million uniquely mapped reads in exons.
Principal Component Analysis was carried out with prcomp in R 3.4.3 on normalized counts. Differential gene expression was carried out using the DESeq2[1] package version 1.14.1 using the HOMER getDiffExpression.pl script with default normalization and using replicates to compute within-group dispersion. Significance for differential expression was defined as adjusted P<0.05, calculated using Benjamini-Hochberg's procedure for multiple comparison adjustment.
Assembly: mm10
Supplementary files format and content: Excel Table with normalized gene counts

source_name: visual cortex

growth_protocol:
10 days of dark exposure (24h dark)
ad lib access to standard mouse chow

extract_protocol:
1% PFA perfusion then brain microdissection in cold physiological buffer, then RNA extracted (input) or ribosomal pulldown via Ribotag protocol (Sanz et al PNAS 2009): HA-tagged ribosome pulled down with Cst Rb anti-HA antibody, isolated via Pierce IgG beads. All RNA extracted with Qiagen RNeasy Micro kit.
standard Illumina protocol (PolyA beads)

value: visual cortex

value: post natal day 120

tag: manipulation

value: 10 day dark exposure

value: 73.12 GFAP-cre x RPL22-HA


title: D319N-ELK1-D_Replicate1_Timepoint 0

description: Library name: Sample_2

value: Yeast


title: 2572-Liver_vehicle

description: Library name: 2572-Liver


title: XGIC39_A_P6

value: Glioblastoma initiating cells


title: 10_day_dark_4

description:
from astrocyte ribome pulldown
10_day_dark_4


title: ELK1-D Starting Library_5

description: Library name: Sample_1e


title: GIC67R_p9

description: Recurrent GICs patient 67

value: Recurrent GICs patient 67


title: 10_day_dark_3

description:
from astrocyte ribome pulldown
10_day_dark_3


title: 2572-Brain_vehicle

description: Library name: 2572-Brain

value: total homogenate


title: ELK1-D Starting Library_4

description: Library name: Sample_1d


title: XGIC39_A_P5


title: GIC67R_p8

description: Recurrent GICs patient 67


title: EMT6 tumors, LLY283&Olaparib&anti-PD1-treated

city: Hangzhou

first: Sheyu

last: Zhang

address: Dongfang Road 150

institute: Hangzhou Institute of Medicine Chinese Academy of Sciences

description:
Library name: Sample 2
10x Genomics

data_processing:
Results from Illumina sequencing offline were converted to FASTQ format using bcl2fastq software (version 5.0.1). The scRNA-seq sequencing data were compared to reference genome using CellRanger software, and cellular and individual cellular 3' end transcripts were identified and counted in the sequenced samples. (https://support.10xgenomics.com/single-cell-gene expression/software/pipelines/latest/what-is cell-ranger , version 7.0.0) The output CellRanger expression profile matrix was loaded into Seurat (version 4.1.0) for filtering of low quality cells from scRNA-seq data, and the filtered data was downscaled and clustered. Filtering low cell quality thresholds: number of genes expressed per cell >500, mitochondrial genes expressed in <25% of cells. Cells were projected into 2D space using t-SNE or UMAP
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: subcutaneous tumor

extract_protocol:
The obtained tissues were transferred to a Petri dish (Petri dish was placed on wet ice) pre-spiked with 1×PBS (without RNase and Ca, Mg ions) and washed with 1XPBS to remove blood stains, grease and other adherents from the tissue surface. The tissue was then cut into 0.5 mm2 pieces and washed again with 1×PBS. The washed pieces were added with dissociation solvent (0.35% collagenase IV5, 2 mg/ml papain, 120 Units/ml DNase I) and reacted for 20 min at 37°C in a water bath shaker (100 rpm). PBS (containing 10% fetal bovine serum) was used to terminate the dissociation. The cells were repeatedly puffed 5-10 times with a pipette gun (gentle handling to prevent cell death due to shear force). The cell suspension was filtered through a 70-30um cell sieve and subsequently centrifuged at 300g for 5 min at 4°C. After centrifugation, the cell sediment was collected and the cells were resuspended by adding 100ul of 1× PBS (0.04% BSA) solution. To remove erythrocytes, 1 ml of 1X erythrocyte lysis solution (MACS 130-094-183, 10×) was added and reacted at room temperature or on wet ice for 2-10 min. After lysis, the cells were centrifuged at 300g for 5 min at 4°C, and the cell precipitate was collected after centrifugation. Add 100μl of Dead Cell Removal MicroBeads (MACS 130-090-101), mix well and incubate for 15min at room temperature. At the end of incubation, Binding Buffer was added, after MS Columns (130-042-201) to remove reagents, and dead cells.Cell precipitates were collected by centrifugation at 300g for 5min at 4°C. Subsequently 1×PBS (0.04% BSA) was used to resuspend the cell precipitate and centrifuged at 4°C 300g for 5min (repeated twice). The candidate cells were obtained after tissue dissociation, lysis of erythrocytes and removal of dead cells, and 100 μl of 1×PBS (0.04% BSA) was added to form a cell suspension. The cell activity was detected by trypan blue staining method, and the cell activity was required to be >85%. The number of cells was counted using a hemocytometer or Countess II Automated Cell Counter, and the cell concentration was 700-1200 cells/μl.
Single-cell suspension was added to the 10x Chromium chip according to the instructions for the 10X Genomics Chromium Single-Cell 3' kit (V3), with the expectation of capturing 8,000 cells. cDNA amplification and library construction were performed according to standard protocols. Libraries were sequenced by LC-Bio Technology (Hangzhou, China) on an Illumina NovaSeq 6000 sequencing system (double-end sequencing, 150 bp) at a minimum depth of 20,000 reads per cell.

value: subcutaneous tumor

value: TNBC


title: ELK1-D Starting Library_3

description: Library name: Sample_1c


title: GIC67_p9

description: Primary GICs patient 67

value: Primary GICs patient 67


title: D319N-ELK1-D_Replicate2_Timepoint 0

description: Library name: Sample_5


title: 10_day_dark_1

description:
from astrocyte ribome pulldown
10_day_dark_1


title: p45_DR_IN

description:
whole ROI homogenate (input)
p45_DR_IN

growth_protocol:
24h dark from birth
ad lib access to standard mouse chow

value: post natal day 45

value: dark rearing


title: EMT6 tumors, LLY283&Olaparib-treated

description:
Library name: Sample 1
10x Genomics


title: GIC67_p10

description: Primary GICs patient 67


title: ELK1-D Starting Library_2

description: Library name: Sample_1b


title: GIC39R_p8

description: Recurrent GICs patient 39

value: Recurrent GICs patient 39


title: p45_DR_6

description:
from astrocyte ribome pulldown
p45_DR_6


title: Spleen - HFpEF

description:
Library name: Sample 8
10X Genomics

source_name: Spleen

value: Spleen

value: HFpEF

value: 12-15 weeks

value: male


title: ELK1-D Starting Library_1

description: Library name: Sample_1a


title: GIC39R_p6

description: Recurrent GICs patient 39


title: p45_DR_5

description:
from astrocyte ribome pulldown
p45_DR_5

value: visual cortex


title: Spleen - LNAME

description:
Library name: Sample 7
10X Genomics

value: L-NAME


title: TUHR4TKB, PT2399, 48hr, Rep2

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.
Paired-end fastq files were aligned to the hg38 genome using HISAT2. Gene-level read counts were quantified with featureCounts and normalized with DESeq2.
Assembly: hg38
Supplementary files format and content: tab delimited csv file with normalised counts for each sample

growth_protocol: OSRC2 cells were obtained from RIKEN Bioresource Research Center Cell Bank and were cultured in RPMI-1640 (Gibco 11875119) supplemented with FBS (GeminiBio 100-106), 1% penicillin-streptomycin (Gibco 15140122). TUHR4TKB cells were obtained from RIKEN Bioresource Research Center Cell Bank and were cultured in DMEM (Gibco 11995065) supplemented with FBS (GeminiBio 100-106), 1% penicillin-streptomycin (Gibco 15140122).

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini Kits (Qiagen, 74106).
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit  for Illumina (New England Biolabs, E7770L) according to the manufacturer’s instructions.

treatment_protocol: 1 x 106 cells/dish were plated in 100 mm tissue culture (TC)-treated cell culture dishes (Corning, 353003) and treated with either DMSO or 2 mM PT2399 in triplicate for 24 or 48 hrs. The cells were then washed twice with ice-cold Dulbecco’s Phosphate Buffer Saline (DPBS) (Gibco, 14190094) and scraped into 1 mL of ice-cold DPBS

value: ccRCC

value: 48 hrs


title: p45_DR_4

description:
from astrocyte ribome pulldown
p45_DR_4

value: 73.12 GFAP-cre x RPL22-HA


title: GIC39_p9

description: Primary GICs patient 39

value: Primary GICs patient 39

value: Glioblastoma initiating cells


title: Spleen - HFD

description:
Library name: Sample 6
10X Genomics

value: HFD


title: Spleen - Chow

description:
Library name: Sample 5
10X Genomics

value: Chow


title: TUHR4TKB, PT2399, 48hr, Rep1


title: GIC39_p8

description: Primary GICs patient 39


title: p45_DR_1

description:
from astrocyte ribome pulldown
p45_DR_1


title: TUHR4TKB, PT2399, 24hr, Rep3

value: 24 hrs


title: p45_DR_2

description:
from astrocyte ribome pulldown
p45_DR_2

value: post natal day 45


title: ulcer tissue, DU+FH_5

city: xianyang

first: keshen

last: qu

address: shiji road

institute: shaanxi university of Chinese medicine

data_processing:
ClC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Qualty limit:0.05)
Trimmed sequence reads were mappedto GrcM38/mm10 using CLC genomic benchwork (parameters- mismath cost:2 inseion cost: 3 deletion cost: 3 length fraction. 0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: ulcer tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).1.3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols.

value: ulcer tissue

value: saline+Fu Huang ointment


title: GBM67R

description: Recurrent GBM tumor patient 67

source_name: FFPE tumor

value: Recurrent GBM tumor patient 67

value: Glioblastoma


title: ulcer tissue, DU+FH_3


title: ulcer tissue, DU+FH_4


title: TUHR4TKB, PT2399, 24hr, Rep2


title: p45_NR_IN

description:
whole ROI homogenate (input)
p45_NR_IN

growth_protocol:
Normal 12h:12h light/ dark rearing
ad lib access to standard mouse chow

value: normal rearing


title: ulcer tissue, DU+FH_2


title: GBM39R

description: Recurrent GBM tumor patient 39

value: Recurrent GBM tumor patient 39


title: TUHR4TKB, DMSO, Rep3

value: DMSO


title: TUHR4TKB, PT2399, 48hr, Rep3


title: ulcer tissue, DU+FH_1


title: GBM39

description: Primary GBM tumor patient 39

value: Primary GBM tumor patient 39


title: TUHR4TKB, DMSO, Rep2

value: ccRCC


title: p45_NR_1

description:
from astrocyte ribome pulldown
p45_NR_1

value: visual cortex


title: ulcer tissue, DU_5

value: saline


title: XRGIC67_sc2

description: GBM cells isolated from modelled-recurrence Xenograft seeded with primary GICs; patient 67

data_processing:
The Cell Ranger 2.0.1 pipeline was used to align reads to the GRCh38 human reference genome and produce count matrices for downstream pre-processing and analysis using the Seurat v5.0.1 R package
Assembly: GRCh38 human reference genome
Supplementary files format and content: cellranger output series matrix files

growth_protocol: NOD SCID CB17-Prkdcscid/J mice between 10 to 15 weeks-old were anesthetised through intraperitoneal (IP) injection with a cocktail of anaesthetic/analgesic drugs (Propofol: 60mg/kg, Medetomidine: 1mg/kg, Fentanyl: 200ug/kg). Once mice reached a deep sleep state we proceeded with the intracranial (IC) injection of hGICs. 5x105 cells were resuspended in 10 μl of PBS and slowly injected with a 26-gauge Hamilton syringe needle into the right cerebral hemisphere (stereotaxic coordinates from the bregma suture: 2 mm posterior, 2 mm lateral, 4 mm deep, 10° angle). Each mouse was then sutured using 4-0 Coated Vicryl Suture (Ethicon) and then subcutaneously injected with an antidote solution (Atipamezol: 1mg/kg, Butorphanol: 2mg/kg; diluted in PBS) able to reverse the anaesthetic effect. Mice were allowed to recover from the surgery on a heat-map until fully awake. Post-operative checks were performed twice daily for seven days, and body weight was monitored once a week thereafter until appearance of first symptoms. For survival experiments, mice were kept on tumour watch until symptoms developed and they were euthanized by neck dislocation.

extract_protocol:
Selected mice for scRNAseq were culled by neck dislocation and the brains were dissected and placed into HBSS (Gibco, 14175095) in petri dishes. Brains were cut into small pieces with a surgical blade and then dissociated into single cell suspension using the Brain Tumour Dissociation Kit (P) (Miltenyi Biotec,130-095-942) following the manufacturer’s protocol. Cells were centrifuged at 300g x for 10 minutes, followed by cell debris removal using the Debris Removal Solution (Miltenyi Biotec, 130-109-398) as per protocol instructions. Mouse cells were removed using the Mouse Cell Depletion Kit (Miltenyi Biotec, 130-104-694) as per manufacturer instructions with minor adaptations. Cells were centrifugeds and manually counted. 30000 cells were isolated, when possible, centrifuged again at 300g x 5 minutes and re-suspended in 0.04% BSA in PBS at a concentration of 1000 cells/µl.
Library preparation was performed at the Single Cell Genomics Facility (UCL, Cancer Institute) using the Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics, 1000268) along with the Chromium Next GEM Chip G Single Cell Kit (10X Genomics, 1000120) according to the manufacturer’s instructions. Pooled samples libraries were sequenced with lane sequencing on Novaseq 6000 S4 (Novogene).

treatment_protocol: The full treatment schedule used for the induced-recurrence model(XR_GBM samples only) was a focal irradiation of the forebrain using SARRP at a 10 Gy dose, followed by two days of recovery and the 5 consecutive days of drug treatment with 50mg/Kg of Temozolomide (TMZ). The time course of  the whole treatment was decided in a patient-specific way, based on when the specific cell-line showed a Luciferase signal after in vivo engraftment.

value: PDX-GIC-sample


title: TUHR4TKB, DMSO, Rep1

value: 48 hrs


title: XRGIC67_sc1

source_name: GBM cells isolated from modelled-recurrence Xenograft seeded with primary GICs; patient 67


title: ulcer tissue, DU_4


title: OSRC2, PT2399, 48hr, Rep3


title: GBM67

description: Primary GBM tumor patient 67

value: Primary GBM tumor patient 67


title: XGIC67R_sc2

description: GBM cells isolated from Xenograft seeded with recurrent GICs; patient 67


title: ulcer tissue, DU_3


title: 2D_MD_IPSI_2

description:
from astrocyte ribome pulldown
2D_MD_IPSI_2

growth_protocol:
2 days of monocular deprivation, ipsilateral hemisphere to deprived eye
ad lib access to standard mouse chow

value: post natal day 28

value: monocular deprivation

value: 73.12 GFAP-cre x RPL22-HA


title: OSRC2, PT2399, 48hr, Rep2


title: ulcer tissue, DU_2

value: ulcer tissue


title: 2D_MD_IPSI_1

description:
from astrocyte ribome pulldown
2D_MD_IPSI_1


title: p45_NR_3

description:
from astrocyte ribome pulldown
p45_NR_3

value: post natal day 45


title: TUHR4TKB, PT2399, 24hr, Rep1

value: 24 hrs


title: XGIC67_sc2

description: GBM cells isolated from Xenograft seeded with primary GICs; patient 67


title: p45_NR_2

description:
from astrocyte ribome pulldown
p45_NR_2


title: 2D_MD_CONTRA_IN

description:
whole ROI homogenate (input)
2D_MD_CONTRA_IN

growth_protocol:
2 days of monocular deprivation, contralateral hemisphere to deprived eye
ad lib access to standard mouse chow


title: ulcer tissue, DU_1


title: OSRC2, PT2399, 24hr, Rep3


title: 2D_MD_CONTRA_3

description:
from astrocyte ribome pulldown
2D_MD_CONTRA_3


title: XGIC67_sc1

source_name: GBM cells isolated from Xenograft seeded with primary GICs; patient 67


title: D3

city: San Antonio

first: Nu

state: Texas

address: 7703 Floyd Curl, Medical Building/ 5.025V

institute: UT Health Science Center

description: Old female Treg 3

data_processing:
Aligned the reads with refernece genome using Kallisto
Assembly: mm10
Supplementary files format and content: xls file include raw counts for each sample along with ENSEMBL id and gene name

source_name: spleen

extract_protocol:
RNA was extracted using zymol RNA extraction kit
RNA libraries were prepared using Takara bio's high sensitivity kit SMARTER-seq as per manufactures protocol

value: spleen

value: Old

value: female

value: WT


title: 2D_MD_IPSI_IN

description:
whole ROI homogenate (input)
2D_MD_IPSI_IN


title: OSRC2, PT2399, 24hr, Rep2

city: Boston

first: Nitin

address: 450 Brookline Avenue, M448, Dana Farber Cancer Institute

institute: Dana Farber Cancer Institute


title: XRGIC39_sc2

description: GBM cells isolated from modelled-recurrence Xenograft seeded with primary GICs; patient 39


title: 2D_MD_CONTRA_2

description:
from astrocyte ribome pulldown
2D_MD_CONTRA_2


title: 2D_MD_IPSI_3

description:
from astrocyte ribome pulldown
2D_MD_IPSI_3


title: D2

description: Old female Treg 2


title: OSRC2, PT2399, 24hr, Rep1


title: XRGIC39_sc1

source_name: GBM cells isolated from modelled-recurrence Xenograft seeded with primary GICs; patient 39


title: D1

description: Old female Treg 1


title: XGIC67R_sc1

source_name: GBM cells isolated from Xenograft seeded with recurrent GICs; patient 67


title: 2D_MD_CONTRA_1

description:
from astrocyte ribome pulldown
2D_MD_CONTRA_1


title: C3

description: Young female Treg 3

value: Young


title: OSRC2, DMSO, Rep3

value: ccRCC

value: DMSO


title: XGIC39R_sc2

description: GBM cells isolated from Xenograft seeded with recurrent GICs; patient 39


title: XGIC39R_sc1

source_name: GBM cells isolated from Xenograft seeded with recurrent GICs; patient 39


title: OSRC2, DMSO, Rep2


title: C2

description: Young female Treg 2


title: OSRC2, PT2399, 48hr, Rep1


title: Virgin_WT_2

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

description: 10x Genomics Chromium

data_processing:
Demultiplexing, barcoding, alignment, and feature counting were performed with 10x Genomics CellRanger software v5.0.1 mkfastq and count commands.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: Matrix files

source_name: Ileum

growth_protocol: Mice were fed a standard diet whilst breeding or in maintenance colonies; RM3 during breeding and RM1 for maintenance and experiment (Special Diets Services)

extract_protocol:
Cells were partitioned and barcoded using the 10X Genomics Chromium Controller, according to the manufacturer’s instructions. The harvested cDNA was assessed and quantified using the Agilent 2100 Bioanalyser and library construction performed using the 10X Single Cell 3' Library Kit v3.1. Libraries were quality controlled by shallow sequencing, balanced, and deep-sequenced.
scRNA-Seq libraries were prepared according to the manufacturer's instructions using the 10X Single Cell 3' Library Kit v3.1

treatment_protocol: Lactating mice of Slc5a4a KO (-/-) and WT (+/+) at day 7 lactation and age-matched virgin females were used.

value: Ileum

tag: mating status

value: Virgin

value: Female


title: OSRC2, DMSO, Rep1

last: Shirole

value: 48 hrs


title: C1

description: Young female Treg 1


title: XGIC39_sc2

description: GBM cells isolated from Xenograft seeded with primary GICs; patient 39

value: PDX-GIC-sample


title: XGIC39_sc1

source_name: GBM cells isolated from Xenograft seeded with primary GICs; patient 39


title: B2

description: Old male Treg 2

value: male


title: Lactating_WT_9

description: 10x Genomics Chromium

value: Lactating


title: sgCtrl_input_for_H3K4me3

data_processing:
3' ends adapter sequences were removed using Trim Galore! (version 0.6.5) and Cutadapt (version 2.8).
The reads were then mapped to the spike-in genome (sacCer3) initially, and the remaining reads were subsequently mapped to the human genome (hg38) using Bowtie (version 1.1.2) with the following parameters: "--allow-contain --maxins 2000 -v 2 -m 1 --best --strata".
To avoid PCR bias, only one copy of multiple fragments mapped to the same genomic position was retained for further analysis. Fragments longer than 800 bp (less than 1% of the total) were excluded from subsequent analysis.
To generate the signal landscape, each fragment was resized to a length of 151 bp, spanning from -75 bp to +75 bp around its midpoint. The count of fragments covering each genomic position was multiplied by 1x10-6 divided by a library size. These values were then averaged over a 10 bp resolution and written in bigWig files.
For the bigWig files (v1), the library size is the number of uniquely mapped fragments after deduplication. For the bigWig files (v2) of H3K4me3, the library size is the number of fragments uniquely mapped to the spike-in genome. For the bigWig files (v2) of H3K36me3, the library size is the number of fragments uniquely mapped to the common significant gene bodies . A list of common significant gene bodies in all H3K36me3 samples was determined by comparing against IgG and input samples using a binomial test with FDR ≤ 0.05.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
CUT&RUN was carried out using the CUT&RUN Assay Kit (Cell Signaling Technology,86652) as per the manufacturer’s instructions
Sequencing libraries were prepared using the DNA Library Prep Kit (Cell Signaling Technology, 56795) for Illumina Platforms

value: human prostate cancer cells

value: Ctrl

value: stable cell line

tag: cut&run antibody


title: Lactating_WT_8

description: 10x Genomics Chromium


title: A3

description: Young male Treg 3

value: spleen


title: sgCtrl_input_for_H3K36me3


title: Lactating_WT_7

description: 10x Genomics Chromium


title: sgCtrl_igG_for_H3K4me3

value: IgG control (Cell Signaling Technology, 66362)


title: Sample LL_2

city: Yangling

first: Yuxuan

last: Song

state: Shaanxi

address: No. 22 Xinong Road

institute: Northwest A&F University

description: Library name: Sample 4

data_processing:
Primary data processing involved demultiplexing (Cell Ranger v5.0.1), STAR-based alignment to the Ovis aries reference genome (ARS-UI_Ramb_v2.0), and read down-sampling for cross-sample normalization. Initial quality filtering excluded cells with <200 detected genes, <1,000 UMIs, or log10(Genes/UMI) ratios below 0.7, retaining 39,521 high-quality cells. Subsequent analyses were conducted in Seurat v3.2.0, including data integration, dimensionality reduction, and cluster identification. Following initial clustering of the entire dataset, immune cells were subset based on expression of pan-immune markers (PTPRC). Subset data were re-normalized using SCTransform and scaled to regress out mitochondrial gene content. Potential doublets were identified and removed using the DoubletFinder package. Principal component analysis (PCA) was applied to the 2000 most variable genes identified, using the ‘RunPCA’ function. Significant principal components were selected based on p-values from the ‘JackStraw’ function, and these components were used for cell clustering through the ‘FindClusters’ function. Visualization of the clustering was performed in two-dimensional space using the ‘RunUMAP’ function to map cell diversity. For integrative analysis, we assessed batch effects before combining scRNA-seq datasets across different conditions. Batch correction was performed using the Harmony package to mitigate batch effects. Marker genes for each cluster were identified using the ‘FindMarkers’ function, followed by manual annotation based on known cell type markers. Clusters with similar marker expression were merged to streamline the analysis and ensure consistency across datasets.
Assembly: Ovis aries reference genome (ARS-UI_Ramb_v2.0)
Supplementary files format and content: A sparse matrix file containing gene expression values for each gene and cell, accompanied by a gene annotation file (.tsv) and cell metadata file (.csv) including cell type
Supplementary files format and content: tab-separated values files and matrix files

organism: Ovis aries

source_name: mammary gland

extract_protocol:
The single-cell RNA sequencing extraction method is as follows: First, generate GEMs and barcode labeling using the Master Mix, which includes reverse transcriptase reagents, template switch oligos, reducing agent B, and reverse transcriptase enzyme. A total of 33.4 碌L of Master Mix is prepared. Next, load the Master Mix and cell suspension onto the 10x single-cell chip in sequence, distributing them across different wells. Gel Beads and Partitioning Oil are added, and the chip is sealed. Following this, reverse transcription and cDNA amplification are carried out under specific conditions, with the reaction set at 53掳C for 45 minutes. Amplification Reaction Mix is then added for cDNA amplification through PCR, with temperature cycling as follows: 98掳C for 3 minutes, 63掳C for 20 seconds, and 72掳C for 1 minute. Finally, the cDNA is purified and collected to complete the process. These steps ensure efficient single-cell capture and transcriptome analysis.
First, DNA fragmentation is performed using appropriate enzymes and buffers to generate small fragments. End repair and A-tailing are then carried out. Next, an adaptor ligation mix is added for adaptor ligation, incorporating sample barcodes. Following this, PCR amplification is performed through the Sample Index PCR step to add sample-specific barcodes. After amplification, the library is purified using SPRIselect Reagents to remove impurities and unligated adaptors. Finally, the library is quality-controlled by measuring concentration with Qubit and performing gel electrophoresis to confirm that the fragment size is within the range of 400-600 bp. The final product is a library ready for high-throughput sequencing.

value: mammary gland


title: Sample LL_1

description: Library name: Sample 3


title: Sample LH_2

description: Library name: Sample 2


title: Virgin_WT_3

description: 10x Genomics Chromium

value: WT


title: Sample LH_1

description: Library name: Sample 1


title: A2

description: Young male Treg 2

value: Young


title: Lactating_WT_11

description: 10x Genomics Chromium


title: A1

description: Young male Treg 1


title: MLE12_H2Bub_IP_hetRnf20_Rep2

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

country: Germany

institute: Medical Faculty Mannheim/University of Heidelberg

data_processing:
Raw reads using Trimmomatic (Bolger et al. 2014), min lengh of 60 bp and Quality score of minimum 15, remove Illumina Adapters TruSeq3.
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 default settings
samtools were used to convert sam files to bam files, after sorted bam files
PCR duplicates were removed using MarkDuplicates.jar from picard-tools-1.119
bam files were merged with bamtools merge (default settings).
bamCoverage was used to create bigWig files with the following settings (-bs 20 --smoothLength 40 -p max --normalizeUsing RPKM -e 150)
Peaks were annotated with annotatePeaks.pl default setting
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: MLE12 cells were fixed and harvested on the plate

extract_protocol:
107 control, Rnf20+/-, and Rnf20+/-HIF1   KD MLE12 cells were fixed with 1% methanol-free formaldehyde for 10 min at room temperature. 125 mM glycine was added to quench the fixation. After three washes with PBS, cells were suspended in cold PBS at a concentration of 5  106/ml. Equal volume of 2   lysis buffer (100 mM Tris-HCl pH8, 300 mM NaCl, 2% Triton X-100, 10 mM CaCl2) was added for 10 min on ice with gentle shaking. The nuclei were washed with cold PBS and centrifuged at 2500 g, 4   C for 5 min. Chromatin was sheared using a Covaris Ultrasonicator (10% duty factor, 200 cycles, 75 A) for 6 min and the samples were clarified at 16 000g for 15 min. Next, the extracts were pre-cleaned with 75   l protein G beads for 2 h at 4  C, then incubated with 0.5   g Pol II antibody (14958S, Cell Signalling), 1   g Pol II p-Ser5 (ab5131, Abcam), 1   g Pol II p-Ser2 (13499s, Cell Signalling), 1   g H2Bub1 (5546S, Cell Signalling) or 1   g H3K4me3 (ab8580, Abcam) antibodies overnight at 4  C, followed by binding to 75   l BSA-coated protein G beads. Immunoprecipitates were washed twice with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH7.5, 150 mM NaCl), three times with high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH7.5, 500 mM NaCl), twice with LiCl buffer (10 mM Tris-HCl pH7.5, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 20 mM EDTA) and then eluted with Elution buffer (50 mM Tris-HCl pH8.0, 10 mM EDTA pH8.0, 1% SDS). Samples were treated with RNase A for 1 h at 37   C, followed by Protein K digestion for 2 h at 37   C, and cross-linking was reversed by incubation at 65   C overnight. DNA was purified by using the Qiagen mini elute PCR purification kit (Qiagen, 28004).
Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S/L, E7103S/L) according to the manufacturer's instructions.

tag: antibody

value: Ubiquityl-Histone H2B (Lys120) (D11) XP® Cell Signalling


title: Lactating_WT_10

description: 10x Genomics Chromium


title: sgCtrl_H3K4me3_2

value: H3K4me3 (Cell Signaling Technology, 9751)


title: TRIB1 ASO rep3

city: Ottawa

first: Ruth

last: McPherson

state: Ontario

address: 40 Ruskin

institute: UOHI

hyb_protocol: Samples were hybridized to a Clariom_D array (Affymetrix) and scanned at the Centre for Applied Genomics (TCAG), Toronto

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Relative expression changes assessed by Expression Console

label: Biotin

source_name: HepaRG cell line

label_protocol: Standard Affymetrix protocol

growth_protocol: Confluent HepaRGs were maintained in William's E, 10% serum, pen/strep and 2% DMSO for 2 weeks

extract_protocol: High Pure RNA isolation using Trizol and cartridges

treatment_protocol: On days 11-14 after 2%DMSO supplementation, HepaRG in 24 well plates were treated for 72 h with 60 nM final of cognate ASOs.  ASOs targeting TRIBAL /TRIB1AL (TRIBALASO2), TRIB1 (TRIB1ASO2) or a control (NTASO).

value: HepaRG 2D cell culture


title: Virgin_WT_1

description: 10x Genomics Chromium

value: Ileum

value: Virgin


title: sgCtrl_H3K4me3_1


title: MLE12_H2Bub_IP_CTR_Rep2

value: control


title: TRIB1 ASO rep2