title: saline,replicate 1, snRNA-seq

city: Ningbo

first: Qiong

last: Li

state: Zhejiang

address: Kongpu

institute: Ningbo University

description: 10x Genomics

data_processing:
The raw reads were mapped to the rat reference genome (refdata-gex-Rnor6-2022) using CellRanger count (v7.0.0) with parameter “includeintrons=true”. The digital expression matrix was extracted from the “filtered_feature_bc_matrix” folder generated by the CellRanger count pipeline.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Orbitofrontal cortex

extract_protocol:
The tissues were placed in a 5 mL tube containing 2 mL of Hibernate A®/B27®/GlutaMAX™ (HEB) medium on ice to minimize degradation. The HEB medium was transferred to a 15mL conical and kept on ice for subsequent operations. Then, 2mL of chilled lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% Nonidet™ P40 Substitute in Nuclease-Free Water) were added to the tissue, followed by douncing 10 times with loose pestle to homogenize it. After homogenization, the tissue was lysed on ice for 15 minutes, swirling 2 – 3 times during this period. The reserved chilled HEB medium was then returned to the lysed tissue solution, and the tissue was further triturated with 5–7 passes through a 1mL pipette. The lysed tissue solution was filtered through a 30 µm cell strainer (MACS SmartStrainer; Miltenyi Biotech 130-110-915) that was prewashed with 1 mL of PBS to remove debris and clumps. Filtered nuclei were centrifuged at 500 g for 5 minutes at 4°C. The supernatant was removed, and the nuclei were washed in 1mL of Nuclei Wash and Resuspension Buffer (1× PBS with 1.0% BSA and 0.2U/µl Rnase Inhibitor). The nuclei were manually counted using Trypan blue and AO-PI staining to estimate of nucleus concentration after each centrifugation and resuspended.
We performed single-nucleus 3’ gene expression profiling using the Chromium Next GEM Single Cell 3’ Kit v3.1 (10× Genomics, 1000268) and the Chromium Next GEM Chip G Single Cell Kit (10× Genomics, 1000120). The nuclei suspension was loaded onto the Chromium single-nucleus controller (10× Genomics) to generate single-nucleus gel beads in the emulsion, according to the manufacturer’s protocol. The captured nucleus was lysed, and the released RNA was barcoded through reverse transcription in individual GEMs.
The nucleus-barcoded 3’ gene expression libraries were sequenced on an Illumina NovaSeq6000 system by Shanghai Biochip Co., Ltd., Shanghai, China.

value: Orbitofrontal cortex

value: Sprague-Dawley

value: Brain cells

value: saline


title: iPSC-CM_Ind4_VEH_3hr

status: Public on Feb 01 2024

type: SRA

city: Galveston

first: Michelle

middle: C.

last: Ward

email: miward@UTMB.edu, ermatthe@UTMB.edu

state: TX

address: 301 University Blvd., MRB 7.150

department: Biochemistry and Molecular Biology

country: USA

institute: UTMB-Galveston

library_source: transcriptomic

data_processing:
Reads were assessed for quality using the MultiQC package (Ewels et al. 2016) in Linux.
Reads were aligned to hg38 using the Subread package (Liao et al. 2013)  with the featureCounts function (Liao et al. 2014) used to quantify  the read number across annotated genes in R.
Assembly: hg38
Supplementary files format and content: RNA-seq counts for all individuals and conditions (72 total samples). Column 1 are Entrez gene IDs by row.  Columns 2-72 are each sample denoted by (treatment.individual.time). Eg. DOX.3.3hr is the DOX-treated sample from individual 3 at 3 hours after treatment.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Human iPSC-dervied cardiomyocytes were maintained in Cardiomyocyte Maintenance Media (500 mL DMEM without glucose (A14430-01, ThermoFisher Scientific), 50 mL FBS (MT35015CV, Corning), 990 mg Galactose (G5388, Sigma-Aldrich), 5 mL 100 mM sodium pyruvate (11360-070, ThermoFisher Scientific), 2.5 mL 1 M HEPES (H3375, Sigma-Aldrich), 5 mL 100X GlutaMAX (35050-061, ThermoFisher Scientific), and 5 mL Penicillin/Streptomycin) on Matrigel-coated dishes at 37°C, 5% CO2 and atmospheric O2.

extract_protocol:
RNA was extracted from ~1.5 million cells using the Zymo dual DNA/RNA extraction kit (D7001, Zymo, Irvine, CA, USA). All treatments and timepoints per individual were extracted in one batch resulting in 6 extraction batches of 12 samples corresponding to the 6 individuals. Median RIN scores were 9.35, 9.6, 9.3, 9.6, 9.65, and 9.55 across treatments for individuals 1-6, respectively.
RNA-seq libraries were generated using 250 ng of RNA using the NEBNext® Poly(A) mRNA Magnetic Isolation Module kit (E7490L, Ipswich, MA, USA), NEBNext Ultra II RNA library prep with Sample Purification Beads kit (E7775K) and the NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs) kit (E6440S). Libraries were prepared in batches of 12 for each individual, following the manufacturer's protocol.

treatment_protocol: 1.5 million iPSC-CMs were plated in 6-well plates. On Days 27-29, iPSC-CMs were treated with 0.5 µM DNR, DOX, EPI, MTX, TRZ, or vehicle in fresh cardiomyocyte maintenance media. iPSC-CMs and cell culture media were collected 3- and 24-hours post-treatment, resulting in 72 samples from 6 individuals.

tag: disease state

value: healthy

tag: cell line

tag: cell type

value: induced pluripotent stem cell-derived cardiomyocytes

tag: Sex

value: female

tag: treatment

value: 0.5 uM vehicle

tag: time


title: Mu-RE_10w_ALF_19.ZT16

city: Barcelona

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

country: Spain

institute: UPF

data_processing:
Sequencing reads were pre-processed using the nf-core/rnaseq v1.2 pipeline, and read quality was assessed by FastQC v0.11.8.
TrimGalore v0.5.0 was used to trim sequencing reads, eliminate Illumina adaptor remains, and discard short reads.
The resulting reads were mapped onto the mouse genome using HiSAT2 v2.1.0 and quantified using featureCounts v1.6.2.
TMM-normalized FPKM values were calculated using Bioconductor package edgeR v3.30.0 and log2-transformed with a pseudo count of 0.01.
The expression data was adjusted for biological (sex) and technical (batch) effects using the Bioconductor package limma v3.44.1.
14413 genes with average non-transformed FPKM expression > 0.5 in at least one time point of at least one experimental condition were considered for further analysis.
Genome_build: GRCm38, release 81
Supplementary_files_format_and_content: Tab-delimited text file with log2-transformed FPKM gene expression values for each sample.

molecule: total RNA

organism: Mus musculus

source_name: tibialis anterior muscle

extract_protocol:
After homogenization of tibialis anterior muscle with Qiazol reagent (Qiagen #1023537) RNA was isolated using miRNeasy Mini Kit (Qiagen #1038703). RNA quality was checked using Nanodrop and RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent).
RNA-seq libraries were sequenced in paired-end mode with a read length of 150 base pairs with an average of 2 x 25 million reads for each sample at Berry Genomics (Illumina NovaSeq 6000).

treatment_protocol: Tibialis anterior muscle was collected and snap frozen with liquid nitrogen at six different time point intervals during 24hr period (ZT0, ZT4, ZT8, ZT12, ZT16, ZT20).

tag: strain

value: male

tag: genotype

value: Bmal1(stopFL/stopFL), Hsa-Cre(-/tg)

tag: age

value: 10-12 weeks

tag: feeding

value: ad libitum

tag: zeitgeber time

tag: tissue

value: whole muscle


title: hippocampus, male, alzheimer, chow, cohort1_3

city: Atlanta

first: Marise

last: Parent

email: mbparent@gsu.edu, tanderson80@gsu.edu

state: GA

address: PO Box 5030

department: Neuroscience Institute

institute: Georgia State University

data_processing:
Cutadapt with minimum length set to 1 to exclude empty reads.
STAR (version 2.7.0a) was used to align Fastq files to the Rn6.0 genome build from UCSC genome browser with refseq annotations. To limit analyses to canonical gene alignments and generate counts for downstream analyses, “outSAMstrandField intronMotif,” “outFilterIntronMotifs RemoveNoncanonical,” and “quantMode GeneCounts” STAR options were used.
Assembly: Rn6
Supplementary files format and content: tab delimited text file including raw counts for each sample

organism: Rattus norvegicus

source_name: dorsal hippocampus

extract_protocol:
rneasy lipid tissue minikit from snap frozen dorsal hippocampus tissue chunks
PolyA enrichment and NEB Ultra II library prep

value: dorsal hippocampus

value: alzheimer

tag: diet

value: chow

tag: cohort


title: METH,replicate 1, snRNA-seq

country: China

description: 10x Genomics

library_source: transcriptomic single cell

molecule: nuclear RNA

value: METH


title: NC_22

city: Suzhou

first: Yihang

last: Shen

state: Jiangsu

address: 2666 Ludang Road

institute: Suzhou Ninth People's Hospital

description: NC

data_processing:
Cutadapt v1.18 (--max-n 0) was used for S1 removal from raw data. Trimmomatic v0.35 (SLIDINGWINDOW:4:15 LEADING:10 TRAILING:10) was used for removal of low quality reads. FastQC (in default) was used for quality control. Bowtie v1.2.2 (-v 1 -k 1 -m 1 --best --strata) was used to align sequences with human genome database (GRCh38). Removal of the repeating reads from PCR was carried out. Specifically, if one read with the same S2 sequence was aligned to the same position (namely the 5 'and 3' end positions of the sequence are the same), it was regarded as a PCR repeat and combined into the same sequence, (only one sequence was calculated in the subsequent expression values) so as to achieve the purpose of accurate quantification of miRNA. Bedtools (in default) was used to calculate reads per million (RPM) value. The given expression matrix of miRNA in every specimen was used for subsequent analysis.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw RPM for every miRNA

source_name: Serum

extract_protocol:
10 mL fasting blood was withdrawn via venipuncture and stood in non-anticoagulant serum tube (BD Biosciences, USA) for 20 min at room temperature, followed by centrifugation at 1600 g for 10 min. Supernatant was transferred into a new Eppendorf tube, and stored at -80 oC immediately. Serum miRNA was isolated using QIAamp ccfDNA/RNA Kit (QIAGEN, Germany), and the concentration was detected by NanoDropTM One/OneC (ThermoFisher Scientific, USA), and the 260/280 quality was determined using Agilent Bioanalyzer 2100 (Agilent, USA).
Qiaseq miRNA Library Kit (QIAGEN) was used for miRNA library construction. Briefly, 10 ng miRNA was diluted into 5 μL, and mixed with 1 μL RA3 adaptor (10 mM) at 70 oC for 2 min, then rapidly cooled on ice. Mixture was incubated with 2 μL ligation buffer, 1 μL RNase Inhibitor, 1 μL T4 RNA Ligase at 28 oC for 1h, and 1 μL Stop Oligo for another 15 min. RA5 adaptor containing with three parts (S1, S2 and S3) was modified and synthesized (Sangon Biotech, China). S1 was a universal connector provided by kit. S2 consisted of 15 random bases, which could produce 1.07 billion complexity to accommodate every miRNA molecule one by one. The purpose of RA5 adaptor was to remove the reads of the identical S2 and miRNA in the subsequent data analysis, because they came from the repeats generated by PCR in the process of library construction and sequencing, and could not reflect the true expression of miRNA. S3 included 4 bases “ACGA” as a recognin. 1 μL RA5 adaptor (10 mM), 1 μL ATP (10 mM) and 1 μL T4 RNA Ligase were mixed, and added into the previous 11 μL reaction system at 28 oC for 1h, followed by 1 μL RNA RT Primer at 70 oC for 2 min. The system was further added 2 μL 5 × First Strand Buffer, 0.5 μL dNTP Mix (12.5 mM), 1 μL DTT (100 mM), 1 μL RNase Inhibitor, and 1 μL SuperScript Ⅱ Reverse Transcriptase at 50 oC for 1 h. The cDNA libraries were amplified by PCR for 15 cycles, and fragments of 150-200 nt were selected by electrophoresis and sequenced with single-end 75 as the sequencing mode on Illumina Novaseq 6000 platform.

value: Serum

value: Wildtype


title: NC_23

description: NC


title: Jurkat cells, DMSO, 6 hours, RUNX3 antibody [DMSO_RUNX3_rep1]

city: Cleveland

first: Yi Fan

last: Chen

state: OH

address: 2109 Adelbert Road Biomedical Research Building 747A

institute: Case Western Reserve University School of Medicine

library_source: genomic

data_processing:
library strategy: CUT&RUN-Seq
Reads were trimmed using Trim Galore version 0.6.7 followed by alignment to hg38 genome build using bowtie2 version 2.4.5.
Reads were de-duplicated using Picard MarkDuplicates version 2.18.2.3
RPGC-normalized bigwig files and bedgraph files were generated using deeptools version 3.4.3
Peaks were called using SEACR version 1.3 under stringent conditions normalized to respective IgG controls
Assembly: hg38
Supplementary files format and content: RPGC-normalized bigwig files

molecule: genomic DNA

source_name: Peripheral blood mononuclear cells

growth_protocol: Jurkat cells were cultured in RPMI-1640 supplemented with glutamine, 10% FBS, penicillin/streptomycin, and 10 mM HEPES

extract_protocol:
Cells were fixed with 1% formaldehyde for 1 minute. After quenching and permeabilization, cells were treated with respective antibodies
Samples were treated with pA/G-Mnase to cleave target DNA sequences following antibody incubation
CUT&RUN libraries were prepared using NEBNext DNA Ultra II  Library Prep kit according to manufacturer instructions.
Libraries were amplified for 15 cycles in the thermo cycler and samples purified with magnetic purification beads (NEB  E7104S)

treatment_protocol:
Cells were activated with a cocktail of 50 nM PMA (Cayman Chemicals) and 1 uM Ionomycin (Cayman Chemicals)
1 uM SP100030 treatments were co-administered at the same time and cells were incubated for 6 hours prior ot harvest

tag: antibody

value: Peripheral blood mononuclear cells

value: Jurkat E6-1

value: T cells

value: WT

value: DMSO


title: HEK001 cultured in KSFM Day 1, rep3

type: RNA

city: Kubang Kerian

first: Ahmad

last: Azlina

state: Kelantan

address: Health Campus, Universiti Sains Malaysia

country: Malaysia

institute: School of Dental Sciences

description: Gene expression of HEK001 in KSFM at day 1

hyb_protocol: 0.825 μg of Cy3-labelled cRNA with specific activity ≥6 pmol Cy3/µg cRNA was fragmented at 60 °C for 30 min in a reaction volume of 25 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent. Then, 25 µl of the mixture were combined with 25 μl of 2x Hi-RPM Hybridization Buffer and hybridized to Agilent SurePrint G3 Human Gene Expression v3 8x60K for 17 hours at 65 °C in a rotating Agilent microarray hibridization oven

scan_protocol: Slides were scanned immediately using Agilent SureScan Microarray Scanner (G4900DA) with 3 μm resolution at wavelength of 532 nm (Cy3) using the extended dynamic range (10-100%) setting.

data_processing: The normalized intensities were extracted using the Agilent Feature Extraction Software using default parameters (protocol GE1_1200_Jun14 and grid: 072363_D_F_20150612)

source_name: Human Epithelial Keratinocyte (HEK001)

label_protocol: Cy3 labelled cRNA was purified using RNeasy Mini Kit (Qiagen, Ca) according to manufacturer's instruction

growth_protocol: Stem cells from human exfoliated deciduous teeth (SHED) (AllCells, USA) were cultured in alpha-minimum essential medium (α-MEM) (Gibco, USA) supplemented with 15% of fetal bovine serum (FBS) (Gibco, USA) and 1% of penicillin/streptomycin (Gibco, USA). Meanwhile, human epithelial keratinocyte (HEK001) (ATCC, USA) were cultured in Keratinocyte-Serum Free Medium (KSFM) (1x) (Gibco, USA) containing L-glutamine supplemented with 2.5 µg of Epidermal Growth Factor (EGF) (Gibco, USA) Human Recombinant and 25 mg of Bovine Pituitary Extract (Gibco, USA). Both cells were incubated in 37°C humidified incubator and the media inside the flask was changed every 2 days.

extract_protocol: RNA was prepared using the innuPREP RNA Mini Kit (AnalytikJena, Germany). The qualitative and quantitative analysis of the RNA samples were determined. All RNA samples are subjected to DNase I, RNase-free (Thermo Scientific, USA) to remove genomic DNA.

treatment_protocol: SHED were cultured in 6-well of Transwell with 0.4 µm pore polyester membrane insert (Corning, USA) until day 5. HEK001 were cultured at the top of the co-culture plate while SHED were cultured at the bottom of the co-culture plate. Medium used inside the co-culture was complete KSFM (Gibco, USA).

value: keratinocyte cells

tag: culture type

value: 6-well plate

tag: protocol

value: HEK001 in KSFM

value: day 1


title: Mu-RE_10w_ALF_18.ZT16

value: female

value: Bmal1(stopFL/stopFL), Hsa-Cre(-/tg)

value: 10-12 weeks

value: ad libitum


title: Mu-RE_10w_ALF_17.ZT16

value: whole muscle


title: iPSC-CM_Ind4_MTX_3hr

tag: disease state

value: healthy

value: induced pluripotent stem cell-derived cardiomyocytes

value: 0.5 uM mitoxantrone


title: NC_20

description: NC

value: Serum

value: Wildtype


title: iPSC-CM_Ind4_DOX_3hr

tag: cell line

value: 0.5 uM doxorubicin


title: iPSC-CM_Ind4_EPI_3hr

tag: cell type

value: 0.5 uM epirubicin


title: iPSC-CM_Ind4_DNR_3hr

tag: Sex

value: 0.5 uM daunorubicin


title: NC_19

description: NC


title: NC_21

description: NC


title: S16 Nr2f siRNA rep1

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

data_processing:
Reads were aligned to Rn6 genome using Hisat2 (Mortazavi et al., 2008).  FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced.
Data were analyzed using DESeq2 v1.20.0 (Anders et al., 2013) to determine differentially regulated genes between control and Nr2f1/Nr2f2 siTNA treatment (p-value < .05). The resulting P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: Rn6
Supplementary files format and content: gene count data
Supplementary files format and content: analysis of differential gene expression

growth_protocol: S16 Schwann cells  were cultured in 6-well plates in Corning DMEM containing 4.5 g/L glucose and L-glutamine without sodium pyruvate (#10-017-CV).

extract_protocol:
Schwann cells were homogenized in 500uL of Trizol (Thermo Fisher, #15596026) per well for 5 minutes on a rotator at low speed. Lysate was placed in RNAse free microcentrifuge tubes, 200uL of chloroform was added, and tubes were centrifuged at 12,000g for 15 minutes at 4°C. The aqueous layer was purified using the Zymo RNA Clean & Concentrator kit protocol (catalog #R1014, Zymo Research) at step 2.
1000 ng total RNA was sent to Novogene for library preparation after PolyA selection and Illumina sequencing (Novaseq 6000). Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis.

treatment_protocol: S16s were transfected with control siRNA (IDT DS NC1), or siRNAs for Nr2f1 (IDT, RNC.RNAI.N031130.12.3), Nr2f2 (IDT RNC.RNAI.N080778.12.1), using Mirus Transit X2 lipofectamine (MIR 6000).

value: Schwann

tag: treatment

value: Nr2f1/Nr2f2 siRNA


title: S16 control siRNA rep1

value: control siRNA


title: iPSC-CM_Ind3_VEH_24hr

value: 0.5 uM vehicle

tag: time


title: Mu-RE_10w_ALF_15.ZT12

tag: strain

value: male


title: iPSC-CM_Ind3_TRZ_24hr

value: female

value: 0.5 uM trastuzumab


title: NC_17

description: NC

tag: genotype


title: BCP

city: Guangzhou

first: chen

middle: wei

last: fen

address: 4F, Building 1, Standard Property Unit 3, International Biotech Island

institute: Forevergen

description: circRNA-seq

data_processing:
Illumina CASAVA 1.8 software used for basecalling.
Low quality which have more than 20% low base quality bases or adapter sequence contamination reads were discarded. Then high quality reads were aligned to the reference genome using BWA mem alignment module. CircRNA identify and characterize was used the CIRI2 software based on the following process. First, reads aligning contiguously to the genome without any trimming were discarded. The remaining reads were used for circRNA candidate detection. Next, terminal sequences (anchors) were extracted and re-aligned independently to find unique anchor positions. Anchors that aligned in the reverse orientation (head-to-tail) indicated circRNA splicing (back-splicing).
The following criteria were used to filter the resulting splicing events: 1) GT/AG signal flanking the splice sites; 2) unambiguous breakpoint detection; 3) no more than two mismatches in the extension procedure; 4) the breakpoint reside a maximum of two nucleotides inside an anchor; 5) less than two independent reads support the head-to-tail splice junction.
Counts of reads mapping across an identified back-splice are normalized by number of reads mapping (spliced tags reads per million mapping, TPM), which allows expression comparisons between two circRNAs. Differential expression analysis of two samples was performed using the previous statistics model. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. CircRNA with an adjusted P-value <0.05 were assigned as differentially expressed.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: Walker256 cells in the logarithmic phase were collected and washed with PBS 3 times. The cell concentration was adjusted to 1×107cells/ml and 0.5ml was injected into the peritoneal cavity of SD rats. 9-12 days later, the ascites was centrifuged to collect the Walker 256 cells and 5μl (4×105 cells) of cell suspension was injected into the bone marrow cavity 0.5cm below the tibia, while the sham operation group was injected with Walker 256 cells boiled for 20 minutes and underwent the same surgical procedure as above. The BCP group and the sham control group were each composed of 3 animals, which were kept for 21 days after surgery and subsequently anaesthetized and sacrificed.

extract_protocol:
Total RNA from the cells was isolated using the Trizol (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions, followed by a DNase I digestion for 30 minutes to remove genomic DNA
Total RNA was treated with the RiboMinus kit (Life Technologies) to remove the ribosomal RNAs; RNAs were incubation with 16 units RNase R (Sigma–Aldrich, St. Louis, MO, USA) for 15 min at 37℃ to deplete linear and enrich circRNAs; The remaining RNAs were fragmented and reverse-transcribed using random primers and reverse transcriptase; Second strand cDNA synthesis was completed using DNA polymerase I and RNase H. Sixth, the Illumina series KAPA Library Preparation Kit (Kapa Biosystems) was used to perform end repair, dA-tailing, and adapter ligation; The dUTP-marked second strand was digested at 37 °C for 30 min using Uracil Specific Excision Reagent (USER) enzyme (New England Biolabs); The cDNA was enriched by PCR amplification to create the final cDNA libraries.

value: spinal cord cells

tag: injected cell type

value: hydrostatic cancer cells

tag: injected cell line

value: BCP


title: Sham

description: circRNA-seq

value: sham


title: Mu-RE_10w_ALF_14.ZT12

value: Bmal1(stopFL/stopFL), Hsa-Cre(-/tg)

tag: age

value: 10-12 weeks

tag: feeding

value: ad libitum

tag: zeitgeber time

value: whole muscle


title: S16 Nr2f siRNA rep2


title: iPSC-CM_Ind3_MTX_24hr

value: healthy

value: induced pluripotent stem cell-derived cardiomyocytes

value: 0.5 uM mitoxantrone


title: NC_18

description: NC

tag: tissue

value: Serum

value: Wildtype


title: NC_16

description: NC


title: Mu-RE_10w_ALF_16.ZT12


title: S16 control siRNA rep2

value: Schwann

value: control siRNA


title: Mu-RE_10w_ALF_25.ZT8

value: male


title: Tg(mpx:eGFP) larvae injected with znf687a MO 2

city: Shanghai

first: Shuiyi

last: Tan

address: 197 Rui-Jin Road II, Shanghai, China

institute: CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics

data_processing:
We filter the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads. We use fastp to filter.
We use HISAT(v2.0.4) to do the mapping step.
We mapped clean reads to reference using Bowtie2(v2.2.6) , and then calculate gene expression level with RSEM(v1.2.12).
Then, we calculate pearson correlation between all samples using cor, perform hierarchical clustering between all samples using hclust, perform PCA analysis with all samples using princomp, and draw the diagrams with ggplot2 with fuctions of R.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Danio rerio

source_name: hematopoietic

growth_protocol: Wild type zebrafish (without GFP) were used as blank to determine the background values in GFP-controls.

extract_protocol:
RNA was extracted from sorted cells using RNeasy Micro (Qiagen, Manchester, UK)
1 μg total RNA was used for following library preparation. Paired-end libraries were prepared using the VAHTS® Universal V8 RNA-seq Library Prep Kit (vazyme Technology Co., Ltd., Nanjing, China) .The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

treatment_protocol: mpx+ cells isolated from Tg(mpx:eGFP) and znf687a MO injected Tg(mpx:eGFP) larvae at 48 hpf.

value: hematopoietic

value: mpx+

value: neutrophil

value: znf687a knowdown

value: znf7687a MO


title: NC_15

description: NC


title: Mu-RE_10w_ALF_13.ZT12

value: female

value: Bmal1(stopFL/stopFL), Hsa-Cre(-/tg)


title: Mu-RE_10w_ALF_12.ZT8

value: 10-12 weeks

value: ad libitum


title: Tg(mpx:eGFP) larvae injected with znf687a MO 1

value: znf687a  MO


title: iPSC-CM_Ind3_DOX_24hr

value: healthy

value: induced pluripotent stem cell-derived cardiomyocytes

value: 0.5 uM doxorubicin


title: Mu-RE_10w_ALF_11.ZT8

value: whole muscle


title: Tg(mpx:eGFP) 2

value: WT

value: control


title: NC_12

description: NC

value: Serum

value: Wildtype


title: NC_13

description: NC


title: iPSC-CM_Ind3_DNR_24hr

value: 0.5 uM daunorubicin


title: iPSC-CM_Ind3_VEH_3hr

value: 0.5 uM vehicle


title: Mu-RE_10w_ALF_10.ZT8

value: male


title: Tg(mpx:eGFP) 1

value: hematopoietic

value: mpx+

value: neutrophil


title: iPSC-CM_Ind3_TRZ_3hr

value: female

value: 0.5 uM trastuzumab


title: NC_11

description: NC


title: Mu-RE_10w_ALF_9.ZT8

value: Bmal1(stopFL/stopFL), Hsa-Cre(-/tg)

value: 10-12 weeks

value: ad libitum


title: Mu-RE_10w_ALF_7.ZT4


title: SAM_SD, rep2

city: Milan

first: Matteo

last: Chiara

address: via celoria 26

department: Biosciences

country: Italy

institute: University of Milan

data_processing:
Reads were aligned to the MSU reference of the Os-Nipponbare-Reference-IRGSP-1.0 genome as available from http://rice.uga.edu/, by means of the bowtie2 software;
gene expression levels were estimated by RSEM.
Differential analyses of gene expression were executed by means of the edgeR; the Genewise Negative Binomial Generalized (glmQLFTest) was  applied to test for statistically significant differences.
P-values were corrected using the Benjamini Hochberg procedure for the control of the False Discovery Rate.
Only genes showing a p-value <= 0.05 following the FDR adjustment were considered to be differentially expressed (DEGs).
Assembly: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary files format and content: csv file includes raw reads counts for each Sample

organism: Oryza sativa

source_name: apical meristem cells

growth_protocol: Plants were grown at 16h/day light for 8 weeks

extract_protocol:
NucleoZOL
RNA was extracted using NucleoZOL (Macherey-Nagel) and DNA removed using DNase I (Turbo™ DNAse, Invitrogen). Stranded cDNA library was prepared and sequenced with 50 bp single-end reads (about 35M pairs of reads per sample were obtained). Sequencing was performed on an Illumina HiSeq2500 machine

treatment_protocol:
Shift to 10h/day light (samples 15,24,25)
10µM dexamethasone solution + 0.2% Tween  (samples 4-6, 10-12)
0.2% Tween solution (samples 1-3, 7-9)

tag: cultivar

value: Nipponbare

value: apical meristem cells

value: Shift to short days


title: iPSC-CM_Ind3_EPI_3hr

value: healthy

value: induced pluripotent stem cell-derived cardiomyocytes

value: 0.5 uM epirubicin


title: iPSC-CM_Ind3_EPI_24hr


title: Mu-RE_10w_ALF_8.ZT4

value: whole muscle


title: iPSC-CM_Ind3_MTX_3hr

value: 0.5 uM mitoxantrone


title: NC_9

description: NC

value: Serum

value: Wildtype


title: NC_10

description: NC


title: SAM_LD, rep3

value: WT


title: NC_14

description: NC


title: iPSC-CM_Ind3_DOX_3hr

value: 0.5 uM doxorubicin


title: SAM_LD, rep2


title: Mu-RE_10w_ALF_6.ZT4

value: male


title: Mu-RE_10w_ALF_5.ZT4

value: female


title: NC_8

description: NC


title: NC_7

description: NC


title: iPSC-CM_Ind3_DNR_3hr

value: 0.5 uM daunorubicin


title: Mu-RE_10w_ALF_3.ZT0

value: Bmal1(stopFL/stopFL), Hsa-Cre(-/tg)

value: 10-12 weeks


title: SAM_SD, rep3

value: Nipponbare


title: Hd3a_DEX, rep2

value: apical meristem cells

value: dexamethasone

value: 5 days


title: Hd3a_DEX, rep3


title: Mu-RE_10w_ALF_4.ZT0

value: ad libitum


title: iPSC-CM_Ind2_TRZ_24hr

value: healthy

value: induced pluripotent stem cell-derived cardiomyocytes

value: 0.5 uM trastuzumab


title: NC_6

description: NC

value: Serum


title: SAM_SD, rep1

value: Shift to short days


title: Mu-RE_10w_ALF_2.ZT0

value: whole muscle


title: NC_4

description: NC

value: Wildtype


title: NC_3

description: NC


title: iPSC-CM_Ind2_DOX_24hr

value: 0.5 uM doxorubicin


title: Hd3a_DEX, rep1


title: Mu-RE_10w_ALF_1.ZT0

value: female


title: WT_26w_ALF_24.ZT20

value: wild-type

value: 26 weeks


title: Hd3a_mock, rep2

value: mock solution


title: iPSC-CM_Ind2_EPI_24hr

value: 0.5 uM epirubicin


title: Hd3a_mock, rep1

value: Nipponbare

value: apical meristem cells


title: WT_26w_ALF_23.ZT20


title: SAM_LD, rep1

value: WT


title: iPSC-CM_Ind2_VEH_24hr

value: 0.5 uM vehicle


title: iPSC-CM_Ind2_MTX_24hr

value: healthy

value: 0.5 uM mitoxantrone


title: NC_5

description: NC


title: PT_37

description: PT


title: Hd3a_mock, rep3

value: 5 days


title: NC_2

description: NC

value: Serum


title: WT_26w_ALF_22.ZT20

value: male

value: ad libitum


title: RFT1_DEX, rep3

value: dexamethasone

value: 2 days


title: iPSC-CM_Ind2_VEH_3hr

value: induced pluripotent stem cell-derived cardiomyocytes

value: female


title: WT_26w_ALF_20.ZT16

value: wild-type

value: 26 weeks

value: whole muscle


title: iPSC-CM_Ind2_DNR_24hr

value: 0.5 uM daunorubicin


title: PT_36

description: PT

value: Wildtype


title: iPSC-CM_Ind2_TRZ_3hr

value: 0.5 uM trastuzumab


title: WT_26w_ALF_19.ZT16


title: iPSC-CM_Ind2_MTX_3hr


title: NC_1

description: NC


title: RFT1_DEX, rep1

value: Nipponbare

value: apical meristem cells


title: iPSC-CM_Ind2_EPI_3hr

value: healthy

value: 0.5 uM epirubicin


title: WT_26w_ALF_18.ZT16


title: PT_35

description: PT

value: Serum


title: WT_26w_ALF_17.ZT16


title: PT_34

description: PT


title: RFT1_mock, rep2

value: mock solution


title: PT_33

description: PT


title: iPSC-CM_Ind2_DOX_3hr

value: 0.5 uM doxorubicin


title: WT_26w_ALF_16.ZT12

value: ad libitum


title: RFT1_mock, rep3

value: 2 days


title: PT_32

description: PT


title: iPSC-CM_Ind1_TRZ_24hr

value: induced pluripotent stem cell-derived cardiomyocytes


title: PT_30

description: PT


title: 1205Lu-R PLX+Corin-1

city: Boston

first: Robert

last: Fisher

state: MA

address: 609 Albany St

department: Dermatology

institute: Boston University

data_processing:
Paired-end RNA-Seq reads were quality- and adapter-trimmed using trimmomatic
Gene expression was quantified using the salmon software package against the GENCODE v32 transcriptome  summarized to the gene level.
Differential expression analysis for pairwise cell type/treatment conditions was conducted using DESeq2 modeling counts as a function of treatment vs the relevant control
Genes with a false discovery rate < 0.01 were considered significant.
Assembly: hg38/GENCODEv32
Supplementary files format and content: CSV DESeq2 FoldChange Values

growth_protocol: Grown to 80% confluency in DMEM supplemented with 10% FBS

extract_protocol:
Qiagen Rneasy Plus Mini Kit
Completed by Azenta

treatment_protocol: 2.5 uM corin or DMSO for 24 h

value: PLX+Corin


title: WT_26w_ALF_15.ZT12

value: male

value: wild-type


title: RFT1_mock, rep1


title: PT_31

description: PT


title: RFT1_DEX, rep2

value: dexamethasone


title: WT_26w_ALF_14.ZT12

value: female

value: 26 weeks

value: whole muscle


title: PT_28

description: PT

value: Wildtype


title: iPSC-CM_Ind2_DNR_3hr

value: 0.5 uM daunorubicin


title: iPSC-CM_Ind1_DOX_24hr

value: healthy


title: WT_26w_ALF_13.ZT12


title: 1205Lu-R PLX+Corin-2


title: WT_26w_ALF_9.ZT8


title: iPSC-CM_Ind1_MTX_24hr

value: 0.5 uM mitoxantrone


title: 1205Lu-R PLX-2

value: PLX


title: PT_27

description: PT

value: Serum


title: WT_26w_ALF_11.ZT8


title: iPSC-CM_Ind1_VEH_24hr

value: 0.5 uM vehicle


title: WT_26w_ALF_8.ZT4

value: ad libitum


title: iPSC-CM_Ind1_DNR_24hr


title: PT_26

description: PT


title: 451Lu-R PLX+Corin-2


title: iPSC-CM_Ind1_VEH_3hr


title: WT_26w_ALF_7.ZT4


title: iPSC-CM_Ind1_EPI_24hr

value: 0.5 uM epirubicin


title: WT_26w_ALF_10.ZT8


title: PT_24

description: PT


title: WT_26w_ALF_6.ZT4


title: 451Lu-R PLX+Corin-1


title: PT_23

description: PT


title: PT_25

description: PT


title: 451Lu-R PLX-2


title: PT_29

description: PT


title: iPSC-CM_Ind1_TRZ_3hr

value: induced pluripotent stem cell-derived cardiomyocytes

value: 0.5 uM trastuzumab


title: WT_26w_ALF_5.ZT4


title: iPSC-CM_Ind1_MTX_3hr


title: 451Lu-R PLX-1


title: CHP134 RNA-seq C38b 4 day rep3

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
ChIP-seq reads were aligned to the hg19 or mm10 genome assembly using Bowtie2 after adapter trimming.
Peaks were called by MACS2 with a q-value of 0.01.
Differential binding peaks were identified using DiffBind.
SLAM-seq was processed using SLAMdunk.
Assembly: hg19, mm10
Supplementary files format and content: ChIP-seq: one peak file per Sample
Supplementary files format and content: RNA-seq: tab-delimited text file include raw counts for each Sample
Supplementary files format and content: SLAM-seq: tab-delimited text file include raw counts for each Sample

growth_protocol: Media for all cell lines was supplemented with 100 IU/ml Penicillin and 100μg/ml streptomycin.

extract_protocol:
ChIP-seq assays (performed as described in Weissmiller, et. al. Nat Commun,10, Article number: 2014 (2019)): Briefly, cross-linking was carried out with 0.75% formaldehyde (Sigma-Aldrich; in PBS pH 7.4) at room temperature for 10 minutes. The reaction was quenched with 125 mM glycine for 10 minutes at room temperature, after which cells were washed twice with ice-cold PBS. Nuclei were prepared by incubating cells in Nuclear Lysis Buffer A (1 M HEPES pH 7.9, 1 M KCl, 0.5 M EDTA, 0.4% NP-40, PMSF, Na3VO4, and Complete Protease Inhibitor Cocktail) for 5 minutes on ice, after which they were collected by centrifugation. Nuclei were then lysed in Formaldehyde Lysis Buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1% SDS, PMSF, Na3VO4, and Complete Protease Inhibitor Cocktail) for 15 minutes on ice. Chromatin was sheared by 17–24 minute sonication (BioRuptor UCD-200, Diagenode; on highest setting, alternating between 30 seconds on and 30 seconds off) to yield a mean chromatin size of ~250 bp. After sonication, debris was cleared by centrifugation, and sheared chromatin diluted 10-fold in Formaldehyde Lysis Buffer without SDS. Chromatin from 107 cells was used per immunoprecipitation reaction. Immunoprecipitation reactions were performed with either 0.8 µL of IgG or 4.0 µL of α-WDR5 antibody as indicated. Immune complexes were recovered on Protein A agarose beads (Roche) and washed sequentially with Low Salt Wash buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, PMSF, and Complete Protease Inhibitor Cocktail), High Salt Wash Buffer (20 mM Tris pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, PMSF, and Complete Protease Inhibitor Cocktail), LiCl Wash buffer (10 mM Tris pH 8.9, 250 mM LiCl, 1 mM EDTA, 1% Triton X-100, PMSF, and Complete Protease Inhibitor Cocktail) and TE (10 mM Tris pH 8.0, 1 mM EDTA, supplemented with PMSF and Complete Protease Inhibitor Cocktail). Protein–DNA complexes were de-crosslinked overnight at 65°C in 50 µL Elution Buffer (10 mM Tris pH 8.0, 1 mM EDTA, 200 mM NaCl, 0.1% SDS, and 20 µg Proteinase K (740506, Clontech).  ---   RNA-seq assays: CHP134 cells were lysed in Trizol (ThermoFisher), after which RNA was isolated using the Direct-zol RNA MiniPrep Kit (Zymo Research) with on-column DNase digestion, following the manufacturer's instructions. RNA-Seq analysis (with rRNA reduction) was performed at GENEWIZ. Library preparation with rRNA depletion and paired-end 150 base pair sequencing on an Illumina HiSeq was performed by GENEWIZ.   ---   SLAM-seq assays: Nascent RNA was labeled using the SLAMseq Kinetics Kit–Anabolic Kinetics Module (061, Lexogen).  LoVo cells were pretreated with 25 uM C6, C6nc, or 0.1% DMSO prior to a three hour labeling with 1 mM 4-Thiouridine (S4U). Following the manufacturer's instructions, total RNA was isolated, alkylated with iodoacetamide, flash frozen, and shipped to Lexogen for analysis.
For analysis of ChIP-Seq, de-crosslinked DNA samples from three ChIP reactions were pooled (a total of 3 x 107 cellular equivalents per sample), and DNA purified by phenol-chloroform extraction and recovered by ethanol precipitation. Indexed libraries were then made using the DNA Ultra II Library Prep Kit for Illumina (E7645, New England Biolabs). Library quality was assessed using the 2100 Bioanalyzer (Agilent) and libraries quantitated using KAPA Library Quantification Kits (KAPA Biosystems). Pooled libraries were subject to 75 bp single-end sequencing according to the manufacturer’s protocol (Illumina NextSeq500). Sequencing was performed by the Vanderbilt Technologies for Advanced Genomics (VANTAGE) Shared Resource. Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.   ---   RNA-Seq analysis (with rRNA reduction) was performed at GENEWIZ. Library preparation with rRNA depletion and paired-end 150 base pair sequencing on an Illumina HiSeq was performed by GENEWIZ. RNA-Seq for CHP-134 cells was completed with three biological replicates.   ---    For analysis of SLAM-seq: After quality control analyses, libraries were prepared (250 ng RNA per sample) using Lexogen’s QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina, following the User Guide (015UG009V0251) recommendations. Sequencing was performed by Lexogen on an Illumina NextSeq 500 system, using the SR75 High Output Kit. The SLAMdunk analysis pipeline (34) was used to analyze SLAMseq sequencing data. SLAM-Seq completed with three biological replicates.

treatment_protocol: Treatment that occurred is noted in SAMPLES section.

value: 5 uM C38b


title: PT_22

description: PT


title: CHP134 RNA-seq C38b 4 day rep1


title: WT_26w_ALF_3.ZT0

value: wild-type


title: 1205Lu-R PLX-1


title: PT_21

description: PT


title: WT_26w_ALF_2.ZT0


title: iPSC-CM_Ind1_EPI_3hr


title: WT_26w_ALF_4.ZT0

value: male


title: iPSC-CM_Ind1_DOX_3hr

value: female

value: 0.5 uM doxorubicin


title: LZ11 (YAP-deficient M50 rep 3)

city: Cincinnati

first: Yuhang

last: Zhang

address: 3230 Eden Ave

institute: University of Cincinnati

data_processing:
FASTQ files were uploaded on the AIR platform (https://transcriptomics.sequentiabiotech.com/) for prosscing and then analyzed using DESeq2 method.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample

growth_protocol: CAFs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1X P/S in a humidified incubator with 5% CO2 at 37 degree

extract_protocol:
Total RNA was extracted using PureLink RNA mini Kit (Invitrogen 12183018A) following standard protocol.
RNA libraries for RNA-Seq were prepared using standard Illumina protocols

treatment_protocol:
CAFs and YAP-deficient CAFs were treated with 500 ng/ml doxycycline for 72 hours to induce YAP silencing in YAP-deficient CAFs.
After three days, the cells were collected and processed for RNA extraction.

value: melanoma-associated fibroblast

value: YAP silencing by shRNA

value: Doxycycline

value: Day 3


title: CHP134 RNA-seq C38b 4 day rep2


title: LZ7 (YAP-deficient M50 rep 2)


title: PT_20

description: PT

value: Wildtype


title: 58_DMSO_24h

city: Berlin

first: Andreas

last: Schlicker

address: Muellerstr 178

department: Translational Sciences Oncology Computational Biology

country: Germany

institute: Bayer AG

description: fpkm.tsv

data_processing:
Sample quality of the raw data (FASTQ) was checked through the internal NGS QC pipeline.
Reads were mapped to the human reference genome (assembly hg19) using STAR aligner alignment tool (version 2.4.2a).
FeatureCounts (version 1.4.6-p2) from the Subread package was used to compute the total read counts per gene based on the gene annotation downloaded from Gencode (version 19).
The Bioconductor package DESeq2 was used for the computation of FPKM expression values using CDS lengths from Gencode release 24.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes FPKM values for all genes and samples

source_name: breast cancer

extract_protocol:
Total RNA was extracted using the RNAeasy Kit (Qiagen, #74181), and cDNA was prepared using the LunaScript® RT SuperMix Kit (New England Biolabs, #E3010) according to manufacturer’s instructions.
TruSeq Stranded mRNA Library Prep (Illumina, RS-122-2103) was used to construct cDNA libraries starting with an input of 400 ng of total RNA per sample. cDNA libraries were pooled and clustered to a single-read sequencing flow cell (Illumina cBOT, HiSeq SR Cluster Kit v4, GD-401-4001 and sequenced on an Illumina HiSeq 2500 instrument (HiSeq SBS Kit v4 (50 Cycle Kit), FC-401-4002).

value: breast cancer

value: breast cancer cell line

value: DMSO


title: 60_DMSO_24h

description: fpkm.tsv


title: PT_19

description: PT

value: Serum


title: iPSC-CM_Ind1_DNR_3hr

value: healthy

value: 0.5 uM daunorubicin


title: 59_DMSO_24h

description: fpkm.tsv


title: WT_26w_ALF_1.ZT0

value: 26 weeks

value: ad libitum

value: whole muscle


title: WT_10w_ALF_24.ZT20

value: wild-type

value: 10-12 weeks


title: LZ3 (YAP-deficient M50 rep 1)


title: WT_10w_ALF_22.ZT20

value: male


title: PT_17

description: PT


title: 57_DMSO_24h

description: fpkm.tsv


title: PT_16

description: PT


title: 56_DMSO_24h

description: fpkm.tsv


title: LZ1 (M50 rep 1)

value: melanoma-associated fibroblast

value: WT


title: LZ9 (M50 rep 3)

value: Doxycycline


title: PT_18

description: PT


title: 55_DMSO_24h

description: fpkm.tsv


title: LZ5 (M50 rep 2)

value: Day 3


title: WT_10w_ALF_23.ZT20

value: female


title: PT_15

description: PT

value: Wildtype


title: 53_DMSO_6h

description: fpkm.tsv

value: breast cancer

value: breast cancer cell line


title: PT_14

description: PT

value: Serum


title: PT_12

description: PT


title: WT_10w_ALF_18.ZT16


title: 54_DMSO_6h

description: fpkm.tsv

value: DMSO


title: RPTEC uninfected, 2

city: Novara

first: Francesco

last: Favero

state: NO

address: Corso Trieste 15/A

department: Translational Medicine - CAAD (Center for Translational Research on Autoimmune and Allergic Diseases)

institute: University of Eastern Piedmont

description:
RPTEC-MOCK-2_S4
RPTEC uninfected rep.2

data_processing:
Fastq files were analyzed with RSEM v. 1.3.1 in order to obtain normalized counts of expressed genes in TPM. RSEM has been launched using STAR aligner 2.7.1a
Reads were aligned against the human GRCh38 / hg38 genome (Ensembl_database)
RSEM was launched with the following parameters –paired-end --strandedness reverse --calc-ci --ci-memory 12288 --estimate-rspd --append-names –star
Genome_build: human GRCh38 / hg38 annotated with Homo_sapiens.GRCh38.100.gtf (Ensembl_database)
Supplementary_files_format_and_content: all.data.matrix.TPM.xlsx = File containing the normalized counts expressed in TPM in all samples obtained by RSEM.

source_name: renal proximal tubule epithelial cells

growth_protocol: 786-O were cultured in RPMI, 10% of FBS. RPTEC were immortalized with hTERT and manteined in ProxUp, with 0,5% FBS

extract_protocol:
mRNA was extracted following the instruction of the kit miRNeasy Tissue/Cells Advanced Kits – QIAGEN
Library was prepared according to Illumina TruSeq Stranded mRNA kit using 500 ng of total RNA per sample.

treatment_protocol: 50.000 cells were plated and infected for 48h at MOI1 with HCMV TR strain

tag: agent

value: renal proximal tubule epithelial cells


title: PT_13

description: PT


title: WT_10w_ALF_21.ZT20


title: RPTEC uninfected, 1

description:
RPTEC-MOCK-1_S2
RPTEC uninfected rep.1


title: 52_DMSO_6h

description: fpkm.tsv


title: PT_11

description: PT


title: WT_10w_ALF_19.ZT16


title: 51_DMSO_6h

description: fpkm.tsv


title: RPTEC infected  with HCMV (MOI1 48h), 1

description:
RPTEC-TR-1_S1
RPTEC infected rep.1

value: HCMV


title: RPTEC infected  with HCMV (MOI1 48h), 2

description:
RPTEC-TR-2_S3
RPTEC infected rep.2


title: WT_10w_ALF_16.ZT12

value: ad libitum


title: PT_10

description: PT


title: 50_DMSO_6h

description: fpkm.tsv


title: 49_DMSO_6h

description: fpkm.tsv


title: WT_10w_ALF_20.ZT16

value: whole muscle


title: PT_9

description: PT


title: hMe-Seal SGBS_day07_rep1_background

city: Heidelberg

first: Clarissa

last: Feuerstein-Akgoz

address: Im Neuenheimer Feld 280

institute: DKFZ

data_processing:
Library strategy: hMeSEAL-seq
After sequencing, read-through adapter sequences were trimmed off using Cutadapt v1.16 and reads <30 bp were filtered out.
The remaining sequences were aligned to the human reference genome hg19/GRCh37 using Bowtie2 v.2.2.6.
Duplicate reads were marked by SAMtools v1.3.1 (RmDup) and collapsed to allow one read per alignment position.
Mapped reads with a mapping quality score of >10 were retained for further analysis.
Raw data of WAT samples will be available from the corresponding author upon reasonable request.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: For bigwig files, sequencing reads overlapping with the ENCODE blacklist were removed and bw files were generated with the deeptools function bamCoverage with the options -p max -bs 20 --smoothLength 40 –e --normalizeUsing RPGC. For hMeSeal_WAT.bw mean values of 5 samples are given.

source_name: SGBS cells at day 7 of adipocyte differentiation

growth_protocol: Human Simpson-Golabi-Behmel syndrome (SGBS) pre-adipocytes were grown to confluency in Dulbecco’s Modified Eagle’s Medium (DMEM)/F-12Nutrient Mixture (Ham) supplemented with 10 % fetal bovine serum  (FBS), 33 µM biotin, 17 µM pantothenate, 100 U/ml penicillin, 100 µg/ml streptomycin, 1ng/µl fibroblast growth factor (FGF) 1, and 90 µg/ml heparin. Three days post-confluency (day 0), SGBS cells were washed three times with PBS and stimulated to differentiate with serum-free growth medium, supplemented with 10 nM insulin, 200 pM triiodothyronine, 1 µM cortisol, 2 µM rosiglitazone/BRL49653, 500 µM 1-methyl-3-isobuthylxanthine (IBMX), 250 nM dexamethasone (Dex), and 0.01 mg/ml human transferrin. After 6 days, FGF-1, Heparin, IBMX, Dex, rosiglitazone were removed from the medium. Cells were harvested at day 0, 1, 7 and 11.

extract_protocol:
DNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions, including an RNase A digest (RNase A solution, Qiagen) and Proteinase K digest  (Puregene Proteinase K, Qiagen). DNA  quality was checked by Agilent Bioanalyzer ( Agilent Technologies, Santa Clara, CA, USA) and quantified by Qubit fluorimetry (Thermo Scientific, Wilmington, USA).
Enrichment of hydroxymethylated DNA by selective chemical labeling (hMeSEAL) and spike-in amplicon generation was performed as described by Song et al. 2017 with minor modifications. Briefly, fragmented genomic (11 – 20 ng) DNA was subjected to library preparation using the KAPA HyperPrep Kit with KAPA Dual-Indexed Adapters for Illumina platforms (Roche, Mannheim, Germany). Sequencing adapters were ligated for 15 hours at 16°C, followed by library purification through double-sided size selection. The ligated DNA was spiked with unmethylated, methylated and hydroxymethylated amplicons (15 pg per amplicon) and incubated with 30 U T4 phage β-glucosyltransferase (T4-BGT), 1x NEBuffer 4 (NEB, Ipswich, MA, USA) and 3 nmol UDP-glucose (Active Motif, Carlsbad, CA, USA) for one hour at 37°C. Next, samples were purified using AMPure XP beads (Beckman Coulter, Brea, USA) and incubated for 1.5 hours at 37°C with 5 nmol dibenzylcyclooctyne-polyethylenglycol-4-distearlyether-biotin conjugate (DBCO-PEG4-biotin) (Jena Bioscience, Jena, Germany). Following AMPure XP bead-based purification, biotin-tagged DNA fragments were immobilized on streptavidin-coupled magnetic Dynabeads™ M270 (ThermoFisher Scientific, Waltham, MA, USA), pre-blocked with 50 µg sheared salmon sperm DNA. 5 µL Dynabeads™ M270 in 150 µL Buffer 1 (5 mM Tris-HCl (pH 7), 1 M NaCl, 0.5 mM EDTA, and 0.2% Tween-20) were added and rotated for 30 min at room temperature. Afterwards, the beads underwent four 5-min washing cycles at room temperature (using Buffer 1, Buffer 2 (Buffer 1 without NaCl), Buffer 3 (Buffer 1 with pH 9) and Buffer 4 (Buffer 3 without NaCl)) and were then resuspended in 27 µL water. The success of the reaction was validated by qPCR-based detection of recovered spike-in amplicons using 2 µL enriched DNA per sample. The enriched hydroxymethylated DNA fragments were amplified using 14 PCR cycles and purified by AMPure XP beads. Background libraries were prepared from the same fragmented genomic DNA (2 ng) by direct PCR amplification (11 cycles), without hydroxymethylation enrichment. Amplified libraries were subjected to paired-end 75 bp sequencing on the Illumina NextSeq 550 instrument (Illumina, San Diego, CA, USA).

value: SGBS

tag: day

tag: experiment

tag: replicate

tag: enrichment

value: background


title: hMe-Seal SGBS_day07_rep2_background

tag: cell type

value: SGBS cells at day 7 of adipocyte differentiation

tag: disease state


title: WT_10w_ALF_15.ZT12

tag: Sex

value: male

value: wild-type

value: 10-12 weeks


title: PT_8

description: PT


title: 48_DMSO_3h

description: fpkm.tsv

tag: cell line

tag: time

tag: treatment


title: WT_10w_ALF_14.ZT12

tag: strain

tag: genotype


title: hMe-Seal SGBS_day01_rep3_background

source_name: SGBS cells at day 1 of adipocyte differentiation


title: hMe-Seal SGBS_day01_rep2_background

value: SGBS cells at day 1 of adipocyte differentiation


title: 46_DMSO_3h

description: fpkm.tsv


title: WT_10w_ALF_12.ZT8

value: female

tag: age

tag: feeding


title: hMe-Seal SGBS_day00_rep3_background

source_name: SGBS cells at day 0 of adipocyte differentiation


title: PT_5

description: PT

tag: tissue

value: Wildtype


title: PT_6

description: PT


title: 47_DMSO_3h

description: fpkm.tsv

value: breast cancer


title: WT_10w_ALF_11.ZT8

tag: zeitgeber time


title: WT_10w_ALF_17.ZT16


title: PT_4

description: PT


title: hMe-Seal SGBS_day00_rep1_background

value: SGBS cells at day 0 of adipocyte differentiation


title: WT_10w_ALF_10.ZT8


title: 44_DMSO_3h

description: fpkm.tsv

value: breast cancer cell line


title: hMe-Seal SGBS_day27_rep3

source_name: SGBS cells at day 27 of adipocyte differentiation

value: hmC


title: WT_10w_ALF_9.ZT8


title: 43_DMSO_3h

description: fpkm.tsv

value: DMSO


title: hMe-Seal SGBS_day27_rep1

value: SGBS cells at day 27 of adipocyte differentiation


title: PT_3

description: PT

value: Serum


title: PT_2

description: PT


title: WT_10w_ALF_8.ZT4

value: ad libitum

value: whole muscle


title: PT_7

description: PT


title: PT_1

description: PT


title: WT_10w_ALF_13.ZT12


title: 42_DMSO_1h

description: fpkm.tsv


title: hMe-Seal SGBS_day11_rep3

source_name: SGBS cells at day 11 of adipocyte differentiation

value: SGBS


title: 41_DMSO_1h

description: fpkm.tsv


title: WT_10w_ALF_7.ZT4


title: hMe-Seal SGBS_day11_rep2

value: SGBS cells at day 11 of adipocyte differentiation


title: CPP_28

description: CPP


title: CPP_27

description: CPP


title: 39_DMSO_1h

description: fpkm.tsv


title: hMe-Seal SGBS_day11_rep1


title: 45_DMSO_3h

description: fpkm.tsv


title: CPP_26

description: CPP


title: WT_10w_ALF_5.ZT4

value: male


title: WT_10w_ALF_6.ZT4

value: wild-type


title: hMe-Seal SGBS_day07_rep3

value: SGBS cells at day 7 of adipocyte differentiation


title: 38_DMSO_1h

description: fpkm.tsv


title: CPP_25

description: CPP


title: hMe-Seal SGBS_day07_rep2


title: WT_10w_ALF_4.ZT0

value: 10-12 weeks


title: 36_BAY2506856_1uM_24h

description: fpkm.tsv


title: hMe-Seal SGBS_day07_rep1


title: hMe-Seal SGBS_day01_rep3

value: SGBS cells at day 1 of adipocyte differentiation


title: 35_BAY2506856_1uM_24h

description: fpkm.tsv


title: hMe-Seal SGBS_day01_rep2


title: CPP_24

description: CPP

value: Wildtype


title: WT_10w_ALF_1.ZT0

value: female


title: CPP_22

description: CPP


title: CPP_23

description: CPP


title: hMe-Seal SGBS_day01_rep1


title: CPP_21

description: CPP


title: 33_BAY2506856_1uM_6h

description: fpkm.tsv

value: breast cancer


title: hMe-Seal SGBS_day00_rep3

value: SGBS cells at day 0 of adipocyte differentiation


title: 34_BAY2506856_1uM_24h

description: fpkm.tsv

value: breast cancer cell line


title: hMe-Seal SGBS_day00_rep1

value: hmC


title: CPP_20

description: CPP


title: Organoid.KO.minus_DHT.rep_3

city: Reno

first: Pier Paolo

last: Pandolfi

address: 75 Pringle Way

institute: Renown Institute for Cancer

data_processing:
Reads were aligned and quantified with Salmon v0.13.1
Genome_build: hg38
Supplementary_files_format_and_content: text files contain raw read count data for each sequencing sample

source_name: prostate

growth_protocol: For maintenance of organoid samples, prostate anterior lobes were dissected from the prostates of 3-month-old mice and digested in a collagenase type II solution. Single cells were then resuspended in Matrigel and cultured in prostate organoid medium (advanced DMEM/F12, N-acetylcysteine, EGF, Noggin, R-Spondin, A83-01, Y27632, GlutaMAX, penicillin-streptomycin, (dihydro)testosterone and  B27). For mouse samples, RNA was extracted directly from mouse prostate anterior lobes for RNA-Seq

extract_protocol:
RNA was isolated from mouse tissues and organoids using PureLink RNA Mini Kit (ThermoFisher Scientific, 12183025) according to the manufacturer’s recommendations
RNA libraries were prepared for sequencing using standard Illumina protocols, conducted by the Molecular Biology Core Facilities at Dana-Farber Cancer Institute

value: prostate

value: prostate organoid_minus_DHT


title: Mouse.HET.rep_2

value: prostate tissue


title: CPP_19

description: CPP

value: Serum


title: WT_10w_ALF_2.ZT0

value: ad libitum

value: whole muscle


title: CPP_18

description: CPP


title: Mouse.KO.rep_2


title: 37_DMSO_1h

description: fpkm.tsv

value: DMSO


title: 31_BAY2506856_1uM_6h

description: fpkm.tsv


title: Organoid.WT.minus_DHT.rep_3

value: wild type


title: 30_BAY2506856_1uM_3h

description: fpkm.tsv


title: Organoid.WT.plus_DHT.rep_3

value: prostate organoid_plus_DHT


title: MAC2A_IgG_NP11513

city: Memphis

first: Brian

middle: J

last: Abraham

address: 262 Danny Thomas Blvd

department: Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
Raw sequencing reads were aligned to the hg19 revision of the human reference genome using bowtie v1.2.2 in paired-end mode with parameters -k 2 -m 2 --best -X 600
Read alignments were converted into fragments using samtools view, samtools sort, and bedtools bamtobed
Fragment coverage was calculated in 50bp bins genome-wide using bedtools makewindows and bedtools intersect and were normalized to the millions of mapped reads
Assembly: hg19
Supplementary files format and content: bigWig files contain reads-per-million-normalized coverage of fragments in 50bp bins
Library strategy: CUT&RUN-Seq

source_name: ALCL

growth_protocol: Cells were grown in T75 flasks in RPMI media containing 10% FBS and 1% pen-strep

extract_protocol:
Live cells were washed and incubated with activated concanavalin A beads for 10 min at room temperature. Cells were then resuspended in antibody buffer containing 0.01% digitonin, 1 ml of each antibody was added to individual cell aliquots, and tubes were rotated at 4°C overnight. The following day, targeted chromatin digestion and release were performed with 2.5 ml of Cutana pA/G-MNase and 100 mM CaCl2. Retrieved genomic DNA was purified with a MinElute PCR purification kit and eluted in 10 ml of buffer EB.
Swift 2S automated library prep (manufacturer's instructions)

value: ALCL


title: 29_BAY2506856_1uM_3h

description: fpkm.tsv


title: CPP_17

description: CPP


title: CPP_16

description: CPP


title: MAC2A_H3K27me3_NP11513


title: 28_BAY2506856_1uM_3h

description: fpkm.tsv


title: JB6_IgG_NP11513


title: 40_DMSO_1h

description: fpkm.tsv


title: CPP_15

description: CPP


title: 32_BAY2506856_1uM_6h

description: fpkm.tsv


title: 27_BAY2506856_1uM_1h

description: fpkm.tsv


title: CPP_14

description: CPP


title: 26_BAY2506856_1uM_1h

description: fpkm.tsv


title: JB6_H3K27me3_NP11513


title: Organoid.WT.plus_DHT.rep_1


title: 25_BAY2506856_1uM_1h

description: fpkm.tsv


title: Organoid.WT.minus_DHT.rep_2


title: Organoid.HET.minus_DHT.rep_3


title: 23_BAY2506856_300nM_24h

description: fpkm.tsv


title: Organoid.KO.plus_DHT.rep_3


title: APOE 4/4 iMG LD low PE 2 [RNA-seq]

city: Stanford

first: Tony

last: Wyss-Coray

state: CA

address: 290 Jane Stanford Way

department: Neurology

institute: Stanford University

data_processing:
Reads were mapped to the human hg38 reference genome using STAR (v.2.5.1b).
Raw read counts were generated with STAR using the GeneCounts function.
Differential expression in RNA-seq was analyzed using the R package DESeq2.
assembly: hg38

source_name: iMG

extract_protocol:
iMicroglia RNA was isolated from the cell pellets using an RNeasy Plus Micro kit (Qiagen, 74034). mRNA was transcribed into full-length complementary DNA using a SMART-Seq v4 Ultra Low Input RNA kit (Clontech) according to the manufacturer’s instructions. Full-length cDNA (150 pg) was processed using a Nextera XT DNA library preparation kit (Illumina) according to the manufacturer’s protocol. Library quality was verified using the Agilent 2100 Bioanalyzer and the Agilent High Sensitivity DNA kit.
Sequencing was carried out using an Illumina NexSeq 550, paired-end, 2× 100 bp depth sequencer.

treatment_protocol: For Aβ treated conditions, iMG were exposed to 5 μM Aβ fibrils for 24 hours or DMSO before RNA isolation. For LD high vs low conditions iMG were exposed to 5 μM Aβ fibrils for 24 hours, stained with LipidSpot 488 as described above and top 10% highest and 10% lowest Lipidspot fluorescent cells were separated by FACS (Sony, MA900).

value: iMG

value: iMicroglia

value: APOE 4/4

value: APOE 4/4 iMG LD low


title: CPP_11

description: CPP

value: Wildtype


title: CPP_13

description: CPP


title: APOE 4/4 iMG LD high PE 1 [RNA-seq]

value: APOE 4/4 iMG LD high


title: Mouse.KO.rep_1


title: CPP_12

description: CPP


title: CPP_10

description: CPP


title: 21_BAY2506856_300nM_6h

description: fpkm.tsv

value: breast cancer

value: breast cancer cell line


title: Mouse.WT.rep_2

value: prostate


title: Organoid.WT.plus_DHT.rep_2


title: APOE 3/3 iMG LD high PE 1 [RNA-seq]

value: APOE 3/3

value: APOE 3/3 iMG LD high


title: APOE 4/4 iMG LD high PE 2 [RNA-seq]


title: Organoid.KO.plus_DHT.rep_2


title: APOE 4/4 iMG LD low PE 1 [RNA-seq]


title: CPP_7

description: CPP

value: Serum


title: 19_BAY2506856_300nM_6h

description: fpkm.tsv


title: 22_BAY2506856_300nM_24h

description: fpkm.tsv


title: APOE 3/3 iMG LD low PE 2 [RNA-seq]

value: APOE 3/3 iMG LD low


title: Organoid.WT.minus_DHT.rep_1

value: prostate organoid_minus_DHT


title: CPP_6

description: CPP


title: Organoid.KO.minus_DHT.rep_2


title: Organoid.HET.plus_DHT.rep_3


title: 17_BAY2506856_300nM_3h

description: fpkm.tsv


title: CPP_5

description: CPP


title: APOE 3/3 iMG LD high PE 2 [RNA-seq]


title: Organoid.HET.minus_DHT.rep_2


title: CPP_4

description: CPP


title: APOE 3/3 iMG LD low PE 1 [RNA-seq]


title: CPP_9

description: CPP


title: CPP_8

description: CPP


title: 16_BAY2506856_300nM_3h

description: fpkm.tsv


title: CPP_3

description: CPP


title: 20_BAY2506856_300nM_6h

description: fpkm.tsv


title: AB_GNE1 GNE-317, fAB treated APOE 4/4 iMG PE  [RNA-seq]

value: GNE-317, fAB treated


title: 24_BAY2506856_300nM_24h

description: fpkm.tsv


title: AB_GNE2 GNE-317, fAB treated APOE 4/4 iMG PE  [RNA-seq]


title: Organoid.HET.minus_DHT.rep_1


title: AB_GNE3 GNE-317, fAB treated APOE 4/4 iMG PE [RNA-seq]


title: CPP_2

description: CPP


title: Organoid.HET.plus_DHT.rep_2

value: prostate organoid_plus_DHT


title: Organoid.KO.minus_DHT.rep_1


title: 18_BAY2506856_300nM_3h

description: fpkm.tsv


title: Organoid.HET.plus_DHT.rep_1


title: 15_BAY2506856_300nM_1h

description: fpkm.tsv


title: CPP_1

description: CPP


title: sgDHX9, input, rep 3

city: Philadelphia

first: Israel

last: Canadas

state: PA

address: 333 Cottman Ave.

department: Nuclear Dynamics and Cancer Program

institute: Fox Chase Cancer Center

data_processing:
For analysis of RE expression from RIP-seq data, FASTQ reads were trimmed by TrimGalore (version 0.6.4).
The trimmed FASTQ reads were mapped against H. sapiens UCSC hg19 using the Bowtie 2 (version 2.3.5) alignment software.
The counts of RE were calculated by RepEnrich2 using default settings, and were normalized by one million reads as CPM (counts per million).
Assembly: hg19
Supplementary files format and content: Expression data in excel format

extract_protocol:
Scramble or sgDHX9 H446 cells were harvested, and RNA immunoprecipitation (RIP) was conducted with J2 or isotype control antibody using a Magna RIP RNA-Binding Protein Immunoprecipitation kit, according to the manufacturer’s instructions.
Illumina sequencing libraries were prepared by Novogene, with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). Libraries were quantified using the Qubit 2.0 Fluorometer (Life Technologies).

treatment_protocol: H446 cells were infected with lentivirus containing Scramble or sgDHX9 vector.

value: Small Cell Lung Cancer

value: input


title: Mouse.HET.rep_1

value: prostate tissue


title: Organoid.KO.plus_DHT.rep_1


title: AB3 fAB treated APOE 4/4 iMG PE  [RNA-seq]

value: iMG

value: iMicroglia

value: APOE 4/4

value: fAB treated


title: 13_BAY2506856_300nM_1h

description: fpkm.tsv

value: breast cancer


title: AB2 fAB treated APOE 4/4 iMG PE  [RNA-seq]


title: AB1 fAB treated APOE 4/4 iMG PE  [RNA-seq]


title: 12_BAY2506856_100nM_24h

description: fpkm.tsv

value: breast cancer cell line


title: NT3 Untreated APOE 4/4 iMG PE  [RNA-seq]

value: untreated


title: sgDHX9, input, rep 2


title: Mouse.WT.rep_1

value: prostate

value: wild type


title: NT1 Untreated APOE 4/4 iMG PE  [RNA-seq]


title: 9_BAY2506856_100nM_6h

description: fpkm.tsv


title: VF-23_Vehicle

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

description: NonStrandedCounts-withNames-proteinCoding.txt

data_processing:
Data was processed using Laxy (https://laxy.io)
Alignment and mapping was performed using STAR v.2.5.2b and to the mouse reference genome GRCm38 or hg19 for human samples
Read counting was performed using FeatureCounts
Differential Gene expression analysis was performed using Degust.
Genome_build: GRCm38 and hg19
Supplementary_files_format_and_content: text file containing matrix of genes and read counts

source_name: CD34+ pro-erythroblasts

growth_protocol: Generation of Jak2V617F knockin mice is summarized here Mullally et al 2010. All animal experiments were approved by the AMREP (Alfred Medical Research and Education Precinct) Animal Ethics Committee. Bone marrow was isolated from Jak2VF (CD45.2) or WT (CD45.1) mice aged 6-12 weeks. Bone marrow cells were mixed at an ∼3:1 ratio (Jak2VF:WT) and injected into lethally irradiated C57BL/6-Ly5.1 (CD45.1 positive) recipient mice. Recipient mice received 950 Rads total body irradiation in equal divided doses, at least 3 hours apart within 24 hours of transplantation. All transplanted cells were injected by lateral tail vein. Chimerism was determined 5 weeks after injection. Mice were maintained on antibiotic (Neomycin) water for 3 weeks after transplantation. Human CD34+ cells were isolated from human bone marrow using a MiniMACS magnetic cell sorting system (Miltenyi Biotec) and maintained in StemSpan SFEM II (STEMCELL Technologies Inc.) supplemented with Penicillin/Streptomycin (10,000 µg/ml, Gibco), L-Glutamine (200 mM, Gibco) Human SCF (100 ng/ml, R&D systems), Human IL-3 (5 ng/ml, R&D systems) Epoetin alfa (3U/ml, EPREX) and Dexamethasone (2 µM, Sigma) for up to 14 days.

extract_protocol:
bone marrow cells were recovered by flushing both femurs with 1 mL of ice-cold PBS and Total RNA was extracted using TriZol method according to manufacturer's instructions.
MGIEasy V2 Library preparation was performed as per manufacturer's instructions.

treatment_protocol: Female C57Bl6 mice 6-8 weeks of age, were divided into five groups (n=6 mice per group) and were treated for 11 days with either vehicle or CTX-0391034 at 10, 30 or 100 mg/kg b.i.d. via oral gavage. A fifth group of mice was treated with CTX-0391034 100 mg/kg b.i.d. for 11 days and then drug was withdrawn for seven days. All groups were harvested 12 h after the final dose. Human CD34+ cells were treated with either DMSO or CTX-034 (1 microM) for 72 hours before harvesting for RNA-seq analysis.

value: CD34+ pro-erythroblasts

value: Vehicle

tag: dose


title: sgDHX9, input, rep 1


title: 8_BAY2506856_100nM_6h

description: fpkm.tsv


title: VF-20_CTX-0391034

value: 100 mg/kg b.i.d. of drug


title: 14_BAY2506856_300nM_1h

description: fpkm.tsv


title: 10_BAY2506856_100nM_24h

description: fpkm.tsv


title: sgDHX9, J2, rep 2


title: sgDHX9, J2, rep 3


title: HOS,shM1-2,INPUT,rep2

city: Canton

first: jieyi

last: Ma

state: Guangdong province

address: No.58 Zhong Shan Er Road

department: 1Department of Otolaryngology

institute: the First affiliated hospital of Sun Yat-sen University

description: cleavagescore_for TRAC-seq

data_processing:
For the RNA-seq, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode.
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015).
Assembly: hg19,hg38
Supplementary files format and content: xlsx
Library strategy: TRAC-seq

source_name: HOS

growth_protocol: HOS cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was extracted by TRIZol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HOS cells were  transfected with shRNA for stable knockdown of METTL1. HOS cells expressing normal METTL1 level were used as control.

value: HOS

value: mesenchymal stem cells

value: METTL1 knockdown

value: demethylated by ALKB


title: HOS,shNC,INPUT,rep2

description: cleavagescore_for TRAC-seq

value: Wild type


title: sgDHX9, J2, rep 1

value: Small Cell Lung Cancer


title: sgDHX9, IgG

value: IgG-IP


title: HOS,shM1-2,INPUT,rep1

description: cleavagescore_for TRAC-seq


title: VF-13_CTX-0391034


title: Scramble, input, rep 3

value: Scramble

value: input


title: hMe-Seal SGBS_day00_rep2

value: SGBS cells at day 0 of adipocyte differentiation

value: SGBS

tag: day

value: hmC


title: VF-14_CTX-0391034


title: 6_BAY2506856_100nM_3h

description: fpkm.tsv

value: breast cancer

value: breast cancer cell line


title: 11_BAY2506856_100nM_24h

description: fpkm.tsv


title: VF-16_CTX-0391034

value: CD34+ pro-erythroblasts


title: VF-15_Vehicle

value: Vehicle


title: Scramble, input, rep 2


title: 4_BAY2506856_100nM_3h

description: fpkm.tsv


title: Scramble, input, rep 1


title: 3_BAY2506856_100nM_1h

description: fpkm.tsv


title: Akata BCR anti-H3K4Me3

city: New Orleans

first: Erik

middle: K

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

description: anti H3K4Me3; CST (9751S)

data_processing:
Reads were aligned to hg38 and EBV genomes using bowtie2.
Duplicates were marked and removed using Picard
Assembly: hg38 and chrEBV_Akata_inverted
Supplementary files format and content: bigWig

source_name: Akata

extract_protocol:
DNA was sheared using Covaris 220 sonication device to an average length of 150-300bp, then immunoprecipitated using an anti-H3K4Me3 antibody (CST)
Libraries were constructed by BGI

value: Akata

tag: antibody

value: anti-IgG


title: HOS,shM1-2,TRAC,rep2

description: cleavagescore_for TRAC-seq

value: HOS

value: mesenchymal stem cells

value: demethylated by ALKB; NaBH4/Aniline induced reduction and cleavage


title: 2_BAY2506856_100nM_1h

description: fpkm.tsv


title: Scramble, J2, rep 3


title: HOS,shM1-1,INPUT,rep2

description: cleavagescore_for TRAC-seq

value: METTL1 knockdown

value: demethylated by ALKB


title: 1_BAY2506856_100nM_1h

description: fpkm.tsv


title: VF-10_Vehicle


title: HOS,shM1-1,TRAC,rep2

description: cleavagescore_for TRAC-seq


title: VF-11_Vehicle


title: 5_BAY2506856_100nM_3h

description: fpkm.tsv


title: HOS,shNC,TRAC,rep2

description: cleavagescore_for TRAC-seq

value: Wild type


title: NT2 Untreated APOE 4/4 iMG PE  [RNA-seq]

value: iMG

value: iMicroglia

value: APOE 4/4

value: untreated


title: Scramble, J2, rep 2

value: Small Cell Lung Cancer

value: Scramble


title: MU1

description:
Stranded
mutu_bcr_24h_gene_expression.tpm.tsv

data_processing:
Kallisto
Assembly: hg38 + chrEBV_Akata_inverted
Supplementary files format and content: transcripts per million matrix

source_name: B cell lymphoma

extract_protocol:
RNA was extracted from cell pellets using TRIzol Reagent (ThermoFisher Scientific, cat no. 15596018) according to the manufacturer's protocol
Libraries were prepared by the Beijing Genomics Institute. Briefly, RNA fragmentation followed by reverse transcription, end repair and adaptor ligation, PCR, single strand separation and cyclization, then DNA nanoball synthesis and sequencing

value: B cell lymphoma

value: Mutu

value: cell line


title: Healthy 3

city: Luzhou

first: Ke

last: Yu

address: 2, Jiangyang Nan Road, Luzhou, PR China

department: Implant Department

data_processing:
acBot Cluster Generation System
The clustering of the index-coded samples was performed on acBot Cluster Generation System using TruSeq PE Cluster Kitv3-cBot-HS(Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced onan Illumina Hiseq platform and paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-houseperl scripts.
Clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include count and RPKM values for each Sample

source_name: Healthy gingival tissues 3

extract_protocol:
RNA was harvested using RNA extraction reagent(TRIzol, Invitrogen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNextRUltraTMDirectional RNA Library Prep Kit for IlluminaR(NEB) following manufacturer’s recommendations

value: oral cavity; gingival

value: WT


title: HOS,shM1-1,TRAC,rep1

description: cleavagescore_for TRAC-seq

value: HOS


title: HOS,shM1-1,INPUT,rep1

description: cleavagescore_for TRAC-seq

value: mesenchymal stem cells


title: HOS,shNC,INPUT,rep1

description: cleavagescore_for TRAC-seq


title: B-ALL cells, siANXA1, rep3

city: Guiyang

first: Yunsheng

last: Ran

state: Guizhou

address: No. 9 Beijing Road, Guiyang City, Guizhou Province

department: Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D

institute: Guizhou Medical University

data_processing:
Eukaryotic mRNA sequencing is based on the HiSeq platform
The double-stranded cDNA structure has sticky ends, which are patched to flat ends by adding End Repair Mix, followed by an A-base at the 3' end for the Y-junction
TBS380 (Picogreen) quantification, mixed on the machine in proportion to the data
TBS380 (Picogreen) quantification, mixed on the machine in proportion to the data
Assembly: mm10
Supplementary files format and content: tab-delimited xlsx files include count values for each Sample

source_name: peripheral blood

growth_protocol:
Human ANXA1-silencing RNA (si-ANXA1) from Genechem Co., Ltd. (Shanghai, China). The infection of B-ALL cells with lentivirus vectors was performed the protocols.
Expansion and maintenance in RPMI-1640 medium with 10% FBS supplement

extract_protocol:
Total RNA was isolated from pellets using the Trizol reagent (Invitrogen) according to the manufacturer’s instructions
Sequencing experiments The Illumina TruseqTM RNA sample prep Kit was used for library construction.

treatment_protocol: The transfection of CCRF-SB with an empty vector (EV) was performed as a control. After 5 days of expansion and maintenance in RPMI-1640 medium with 10% FBS supplement, Puromycin selected the stable B-ALL cell lines expressing si-ANXA1

value: peripheral blood

value: CCRF-SB

value: Lymphoblast-like

value: ANXA1 down-regulated

value: Day 5


title: Scramble, J2, rep 1


title: MU2


title: HOS,shNC,TRAC,rep1

description: cleavagescore_for TRAC-seq

value: Wild type

value: demethylated by ALKB; NaBH4/Aniline induced reduction and cleavage


title: MI3

value: anti-IgM


title: H446 cells, sgDHX9, rep 1

data_processing:
Paired-end sequenced reads were checked by FastQC.
Estimation of transcripts was performed using Kallisto.
The expression matrix was constructed and normlized by Tximport in R.
Assembly: hg19
Supplementary files format and content: Expression data in excel format

extract_protocol:
Total RNAs were extracted and purified using the Rneasy MiniKit (QIAGEN) from the cells at day 7 post-selection. Using a 2100 Bioanalyzer RNA 6000 Nano assay (Agilent), quality of RNA was assessed. RNA concentration was measured using a Qubit 2.0 Fluorometer (Life Technologies).
Illumina sequencing libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: Cells were infected with lentivirus containing Scramble or sgDHX9 vector.

value: Small Cell Lung Cancer


title: MZ5

description:
Stranded
mutu_24h_zta_gene_expression.tpm.tsv

value: 24h Zta


title: H446 cells, sgDHX9, rep 2


title: Peri-implantitis 3

source_name: Peri-implantitis inflammatory tissues 3

value: Peri-implantitis


title: MI2

value: B cell lymphoma

value: Mutu


title: B-ALL cells, siControl, rep3


title: B-ALL cells, siANXA1, rep2


title: MU3

value: cell line


title: RNAseq_TET1.var-rep2

first: Hao

last: Wu

address: 415 Curie Boulevard

department: Genetics

institute: University of Pennsylvania

data_processing:
Fastq files were mapped to hg38 with strand-specific and single-end mode by Hisat2 (v2.2.1). Unique mapped reads were kept and sorted by samtools (v1.7). featureCounts (v2.0.1) was used to quantify reads from exon.
Assembly: hg38
Supplementary files format and content: comma-delimited csv files include read counts for each Sample

growth_protocol: Human HEK293T cells were maintained at 37°C with 5% CO2 in CO2 incubators (Thermo Scientific, 51-033-774) in Dulbecco’s Modified Eagle’s Medium (DMEM) (Gibco, 11965084), supplemented with 10% fetal bovine serum (Gibco, 16000044), 5% L-glutamine (Gibco, 25030081), 5% nonessential amino acid (Gibco, 11140050), and 5% sodium pyruvate (Gibco, 11360070) in 10-cm dishes and passaged every 2-3 days at 70% confluency with PBS and 0.05% Trypsin-EDTA (Gibco, 25300054).

extract_protocol:
RNA was extracted from GFP+/DAPI- FAC-sorted transient transfected HEK293T cells with ZR-Duet DNA/RNA MiniPrep Kit (Zymo Research, D7001).
RNA-seq libraries were prepared using SMARTer Stranded total RNA-seq Kit v3 (Clontech, 634486) per the manufacturer’s instructions. Library concentration and complexity was validated with a Qubit Fluorometer and Agilent Bioanalyzer 2100 (Agilent, 5067-4626). Libraries were diluted to 4nM and pooled together for sequencing on Illumina NextSeq 500.

treatment_protocol: For FACS-sorted All-in-one experiments, 2ug of Suntag platform containing scrambled or RHOXF2B sgRNA expressing constructs, and pTY-GFP (transfection control) were transiently transfected in suspension with dissociated 2x106cells per sample in Opti-MEM I Medium (Thermo Fisher Scientific, 31985062), with Lipofectamine 2000 (Invitrogen, 11668019) per manufacturer’s recommendation into 12-well plates. However, Lipofectamine 2000-DNA complexes were incubated for 45 minutes as opposed to manufacturer’s instruction. 24-hours post-transfection, the cells were expanded onto-6 well plates and incubated for an additional 48-hours prior to GFP+/DAPI- gated FACS followed by gDNA/RNA (Zymo Research, D7001), and protein isolation.

value: TET1-var overexpression


title: B-ALL cells, siControl, rep2

value: WT


title: RNAseq_TET1.mut-rep1

value: TET1-mut overexpression


title: HOS,shM1-2,TRAC,rep1

description: cleavagescore_for TRAC-seq

value: HOS

value: mesenchymal stem cells

value: METTL1 knockdown


title: MI1


title: RNAseq_TET1.var-rep1


title: B-ALL cells, siANXA1, rep1

value: peripheral blood

value: CCRF-SB

value: Lymphoblast-like

value: ANXA1 down-regulated


title: H446 cells, Scramble, rep 2

value: Scramble


title: H446 cells, Scramble, rep 1

value: Small Cell Lung Cancer


title: RNAseq_TET1.mut-rep2


title: MZ1

value: 24h Zta


title: H82 cells, Scramble, rep 1


title: 7_BAY2506856_100nM_6h

description: fpkm.tsv

source_name: breast cancer

value: breast cancer

value: breast cancer cell line


title: H82 cells, sgDHX9, rep 2


title: MZ3

value: B cell lymphoma

value: Mutu


title: RNAseq_Ctrl-rep2

value: GFP overexpression


title: H196 cells, sgDHX9, rep 2


title: B-ALL cells, siControl, rep1

value: WT

value: Day 5


title: Peri-implantitis inflammatory tissues 2

description: Peri-implantitis 2

source_name: oral cavity

extract_protocol:
RNA was harvested using RNA extraction reagent(TRIzol, Invitrogen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB) following manufacturer’s recommendations

value: gingival

value: Peri-implantitis


title: MZ2

value: cell line


title: RNAseq_TET1.wt-rep2

value: TET1-wt overexpression


title: Healthy gingival tissues 2

description: Healthy 2


title: MC3

value: 24h Ctl


title: H196 cells, sgDHX9, rep 1


title: H82 cells, Scramble, rep 2


title: Healthy gingival tissues 1

description: Healthy 1


title: MC2


title: WS, KAS-Seq, biol rep2

city: Chicago

first: Mark

last: Applebaum

state: IL

address: 900 E 57th St

department: Pediatrics, Section of Hematology/Oncology

institute: University of Chicago

data_processing:
reads were trimmed using the trim-galore package in single-end mode.
Trimmed reads were aligned to hg38 using bowtie2 (v2.3.0) with standard parameters and sorted to bam files using samtools sort (v1.9)
samtools rmdup (v1.9) was utilized to get unique mapped reads, which were then extended to 150 bp
bigWig files were generated using deepTools bamCoverage, normalized to RPKM. Blacklist regions (obtained from ENCODE) were excluded.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: KAS-Seq

source_name: NBL-W-S

growth_protocol: Cells were grown at 5% CO2 in RPMI1640 medium (Life Technologies) supplemented with 10% heat-inactivated FBS, 2 mmol/L l-glutamine, and 1% penicillin/streptomycin

extract_protocol:
cells were incubated for 5–10 min at 37 °C, 5% CO2  in complete culture medium containing 5 mM N3-kethoxal. Using the PureLink genomic DNA mini kit (Thermo, K182002), genomic DNA (gDNA) was isolated from collected cells.
Accel-NGS Methyl-seq DNA library kit (Swift, 30024) was used for library construction on eluted DNA and corresponding input.

value: NBL-W-S

value: neuroblastoma cell line, MYCN-amplified

tag: chip antibody


title: WS, KAS-Seq, biol rep1


title: MC4


title: RNAseq_TET1.wt-rep1


title: 24hrUninduced-3

description:
Stranded
akata_24h_bcr_induction_gene_expression.tpm.tsv

value: Akata


title: H196 cells, Scramble, rep 2

value: Small Cell Lung Cancer

value: Scramble


title: Renal organoids, d24, scRNA-seq, batch 3

city: Cambridge

first: Katja

last: Röper

state: Cambridgeshire

address: Cambridge Biomedical Campus,, Francis Crick Ave

department: Cell Biology Division

country: United Kingdom

institute: MRC LMB

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger ARC software v2.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly:hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Single cell preparations were generated as above, then further processed for single nucleus isolation by centrifugation at 300g for 4 min at 12oC and resuspension in 100µL freshly prepared ice-cold lysis buffer (10mM Tris-HCL, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20, 1 % BSA, 1mM DTT, 1 U/µL Protector RNase Inhibitor (Sigma, 3335402001), 0.1% Nonidet P40 Substitute (Sigma, 74385) and 0.01% Digitonin in nuclease-free H2O) followed by incubation on ice for 5 min. Lysis was halted by addition of 900µL chilled wash buffer (10mM Tris-HCL, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20, 1 % BSA, 1mM DTT, 1 U/µL Protector RNase Inhibitor in H2O), followed by 3 rounds of centrifugation at 500g for 5 min at 4oC and resuspension in chilled wash buffer, with the final resuspension in 50µL chilled 1x Nuclei Buffer (10X Genomics, 2000153) with 1mM DTT and 1 U/µL Protector RNase Inhibitor in H2O, according to the 10x Genomics demonstrated protocol for Nuclei Isolation for Single Cell Multiome (ATAC + GEX) sequencing (CG000365, RevA). After resuspension in 1x Nuclei Buffer, nuclei were stained with Trypan Blue and counted using a Countess II (Life Technologies) to confirm complete lysis and to achieve a targeted nuclei recovery of 1,600 nuclei per sample for batch 2, and 5,000 nuclei per sample for batch 3.
Nuclei were processed for library preparation using a 10X Chromium scMultiome kit (10X Genomics) at the Cancer Research UK Genomics Facility.

value: iPSC-derived renal organoids

tag: time point

value: day 24


title: MC1

value: B cell lymphoma

tag: cell type


title: iPGRMC1-WT-rep2

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

data_processing:
We trimmed the 3’ sequencing adapters from the reads (AAAAAAAA for the A-tailing methods). For the libraries we used SMARTer oligo-based template switching, and we trimmed the first 7 nt, including the random 4 nt and the 3 locked Gs in the 5’ sequencing adapters. The trimmed reads were mapped to the reference genome (hg38) and the GENCODE-defined transcriptome using STAR (version 2.1.0). We used HTSeq (version 0.9.1) to generate gene-level read counts.
Assembly: hg38
Supplementary files format and content: HTSeq count file

growth_protocol: MCF-7 cells were cultured in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and maintained in a humidified incubator at 37 ℃ with 5% CO2.

extract_protocol:
Total RNA was extracted with a Direct-zol RNA kit (Zymo Research), and mRNAs were then isolated using Oligo(dT)25 magnetic beads (New England Biolabs) according to the manufacturer's instructions.
Purified mRNAs were fragmented with a NEBNext Mg2+ RNA fragmentation module (New England Biolabs) at 94 ℃ for 4 min. Fragmented RNAs were then precipitated overnight at -20 ℃ by adding 0.1 volume of 3 M sodium acetate, 10 mg of glycoblue, and 1.2 volumes of isopropanol. RNA fragments were re-suspended, and RNA-seq libraries were generated using the previously described A-tailing and SMARTer oligo-based template switching method as described in Li et al, Genome Research, 2022.

value: breast cancer cell

value: iPGRMC1 overexpression


title: Renal organoids, d14, CHIR, multi-ome-seq, batch 3

description: 10X Genomics

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger ARC software v2.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly:hg38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: snMulti-ome-seq (paired snRNA-seq and snATAC-seq)

molecule: other

value: day 14

value: 3micoM CHIR from day 12-14


title: Peri-implantitis inflammatory tissues 1

description: Peri-implantitis 1

value: gingival


title: SY5Y, KAS-Seq, biol rep2

value: neuroblastoma cell line, MYCN-non-amplified


title: Renal organoids, d14, DMSO, multi-ome-seq, batch 3

description: 10X Genomics

value: DMSO from day 12-14


title: WN, KAS-Seq, biol rep2

source_name: NBL-W-N

value: NBL-W-N


title: 24hrUninduced-2

value: cell line


title: iPGRMC1-Ctrl-rep2

value: iPGRMC1 control


title: RNAseq_Ctrl-rep1

value: Non-transfection control (NTC)


title: WN, KAS-Seq, biol rep1

value: neuroblastoma cell line, MYCN-amplified


title: iPGRMC1-WT-rep1


title: 24hrInduced-2

value: Akata

value: anti-IgG


title: H82 cells, sgDHX9, rep 1

value: Small Cell Lung Cancer


title: iPGRMC1-Ctrl-rep1


title: uSLC35A4-Ctrl2-rep2

value: uSLC35A4 control2


title: H196 cells, Scramble, rep 1

value: Scramble


title: 24hrInduced-3

value: B cell lymphoma


title: uSLC35A4-WT-rep2

value: breast cancer cell

value: uSLC35A4 overexpression


title: 24hrInduced-1


title: DG75-Z4

description:
Stranded
dg75_cntl_rta_zta_gene_expression.tpm.tsv

value: 24h Zta


title: Renal organoids, d12, multi-ome-seq, batch 3

description: 10X Genomics

value: iPSC-derived renal organoids

value: day 12


title: uSLC35A4-WT-rep1


title: NBLS, KAS-Seq, biol rep2

source_name: NBL-S

value: NBL-S

value: neuroblastoma cell line, MYCN overexpressing


title: SY5Y, KAS-Seq, biol rep1

value: neuroblastoma cell line, MYCN-non-amplified


title: Renal organoids, d24, scRNA-seq, batch 2

description: 10X Genomics

value: day 24


title: uSLC35A4-Ctrl2-rep1


title: SHEP, KAS-Seq, biol rep2

source_name: SHEP

value: SHEP


title: Renal organoids, d10, multi-ome-seq, batch 3

description: 10X Genomics

value: day 10


title: uSLC35A4-Ctrl1-rep2

value: uSLC35A4 control1


title: DG75-Z2

value: cell line


title: Renal organoids, d14, multi-ome-seq, batch 2

description: 10X Genomics

value: day 14


title: NBLS, KAS-Seq, biol rep1


title: DG75-Z1


title: DG75-R4

value: 24h Rta


title: SHEP, KAS-Seq, biol rep1


title: uSLC35A4-Ctrl1-rep1


title: Renal organoids, d12, multi-ome-seq, batch 2

description: 10X Genomics


title: Renal organoids, d14, scRNA-seq, batch 1

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly:hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
For each sample, ~5000 organoids were collected in 15ml tubes, washed once with PBS then dissociated to single cells in 500µL Bacillus Licheniformis protease (Sigma, P5380) on ice for 20 min (Adam et al., 2017), with gentle agitation by pipetting every 2 min, followed by resuspension in PBS with 10% FBS to neutralise the protease. Cells were centrifuged at 300g for 5 min, then resuspended in PBS with 10% FBS and filtered through a 30µm strainer prior to centrifugation and final resuspension in PBS with 0.5% BSA. Cells were counted with Countess II (Life Technologies) to ensure cell viability > 90% and to achieve a targeted cell recovery of 1,600 cells per sample for batches 1 and 2, and 5,000 cells per sample for batch 3.
Cells were processed for library preparation using a 10X Chromium sc 3’mRNA kit (v3, 10X Genomics) at the Cancer Research UK Genomics Facility, Cambridge, UK.


title: Renal organoids, d10, multi-ome-seq, batch 2

description: 10X Genomics


title: BE2, KAS-Seq, biol rep2

value: neuroblastoma cell line, MYCN-amplified


title: DG75-Z3

value: B cell lymphoma


title: KYSE150 - DMSO-1

city: Hong Kong

first: Xiaodan

last: Zhang

address: No.5 Sassoon Road, Pokfulam,

institute: Hong Kong University

data_processing:
Sequenced reads were mapped to hg38 genome (grch38_genome_tran file downloaded from http://daehwankimlab.github.io/hisat2/download/, which created by Homo_sapiens.GRCh38.84.gtf) using hisat2 v2.1.0 with default parameters.
multi-mapped reads will be filtered out from hisat2 created sam files with parameter "awk -v header=$header 'NR<=header{print $0} NR>header{if($5 > 30 && ($2==147 || $2==163 || $2==83 || $2==99)) print $0}'" and export to bam format files, then raw counts matrix was created from filtered bam files by HTSeq v0.12.4 with parameters --stranded=no --format=bam --order=pos --idattr=gene_name --mode=intersection-nonempty  -q and Homo_sapiens.GRCh38.84.gtf file as reference.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: ESCC

extract_protocol:
Total RNA was extracted and purified with TRIzol (Invitrogen) as per the manufacturer’s instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: KYSE150 cells were seeded into 6-well plates and cultured for 12–24 h until 70–80% confluence, and then starved in serum-free medium overnight followed by incubation with TPA (10 ng/ml, Sigma) for another 24 h

value: DMSO


title: KYSE150 - DMSO-2


title: DG75-R2


title: BE2, KAS-Seq, biol rep1


title: DG75-R3


title: Renal organoids, d10, scRNA-seq, batch 1

description: 10X Genomics


title: 55N, KAS-Seq, biol rep2


title: 55N, KAS-Seq, biol rep1


title: DG75-R1


title: KYSE150 - TPA-1

value: TPA


title: Renal organoids, d24, scRNA-seq, batch 1

description: 10X Genomics


title: KYSE150 - TPA-2


title: KYSE150 - TPA-3


title: Tonsil 2, freeze-thawing, rep1, scRNAseq

city: Huddinge

first: Christopher

middle: Thomas

last: Stamper

address: Alfred Nobels Allè 8

department: Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tonsil

extract_protocol:
Freshly resected tonsil tissue was washed in PBS, any visible signs of pus, blood, or burns were cut away and then tissue was further cut into smaller pieces before being mechanically disrupted by grinding and filtering. The filtered cell suspension was washed in 50 ml PBS, pelleted by centrifugation and resuspended in 20mL PBS and layered onto 30mL Ficoll (Cytiva) and centrifuged. The lymphocyte layer was harvested and washed with 50mL PBS before being pelleted by centrifugation and resuspended in 50mL PBS. 500 million cells were stained with Fc Block (Miltenyi Biotec) for 15 minutes, washed, and then stained with Miltenyi MACS anti-CD19 magnetic beads according to manufacturer’s instructions. After staining cells were washed and B cells were depleted using Miltenyi MACS LD columns according to manufacturer’s instructions. Aftewards cells were cells were frozen in FBS/10% DMSO overnight at -80 before being transferred to LN2 for at least one week. Cells were then thawed by being submerged halfway into a waterbath at 37 degrees until partially thawed. They were then removed and allowed to finish thawing at room temperature. The cells were gently pipetted from the cryovial into a 50ml tube using a wide bore pipette tip. The cryotube was then rinsed with 1ml of IMDM 10% FBS prewarmed to 37 °C and this media was then added dropwise to the cells while gently swirling the 50ml tube. The cells were then sequentially diluted an additional four times using a 1:1 volume addition of prewarmed IMDM 10% FBS each time. The media for each dilution was added at 1ml/sec while the tube was gently swirled, cells were allowed to rest for one minute following each dilution. Afterwards, cells were pelleted by centrifugation at 300 RCF for 5 minutes. Cells were resuspended and incubated with live/dead cell marker (DCM; Invitrogen) and surface protein antibodies at 4 °C for 30 min, washed with PBS and resuspended in FACS buffer (PBS with 2% FBS). Cells were sorted into eppendorf tubes containg Sort Buffer (PBS with 0.2% BSA and 5mM EDTA). Cells were sorted on a FACSAria III sorter (BD Biosciences), with FACS Diva version 9 software.
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics)

value: Tonsil

value: mixed sample (ILCs, NKs, T cells)

value: freeze-thawing


title: KYSE150 - DMSO-3


title: CD3+ cells, PMA Ionomycin + SP100030, 6 hours, NFAT1 antibody [PMA_Iono_SP_NFAT1_primary_2]

city: Cleveland

first: Yi Fan

last: Chen

address: 2109 Adelbert Road Biomedical Research Building 747A

institute: Case Western Reserve University School of Medicine

data_processing:
Reads were trimmed using Trim Galore version 0.6.7 followed by alignment to hg38 genome build using bowtie2 version 2.4.5.
Reads were de-duplicated using Picard MarkDuplicates version 2.18.2.3
RPGC-normalized bigwig files and bedgraph files were generated using deeptools version 3.4.3
Peaks were called using SEACR version 1.3 under stringent conditions normalized to respective IgG controls
Assembly: hg38
Supplementary files format and content: RPGC-normalized bigwig files
Library strategy: CUT&RUN

growth_protocol: Jurkat cells were cultured in RPMI-1640 supplemented with glutamine, 10% FBS, penicillin/streptomycin, and 10 mM HEPES

extract_protocol:
Cells were fixed with 1% formaldehyde for 1 minute. After quenching and permeabilization, cells were treated with respective antibodies
Samples were treated with pA/G-Mnase to cleave target DNA sequences following antibody incubation
CUT&RUN libraries were prepared using NEBNext DNA Ultra II  Library Prep kit according to manufacturer instructions.
Libraries were amplified for 15 cycles in the thermo cycler and samples purified with magnetic purification beads (NEB  E7104S)

treatment_protocol:
Cells were activated with a cocktail of 50 nM PMA (Cayman Chemicals) and 1 uM Ionomycin (Cayman Chemicals)
1 uM SP100030 treatments were co-administered at the same time and cells were incubated for 6 hours prior ot harvest

value: Peripheral blood mononuclear cells

value: T cells

value: WT

value: PMA Ionomycin + SP100030


title: Tonsil 1, freeze-thawing, rep1, scRNAseq

description: 10x Genomics


title: DG75-R-C3

value: 24h Ctl


title: 5S input 2

data_processing:
raw read quality was assessed using fastqc (version 0.11.5)
Trimmomatic (version 0.36) was used to filter raw reads with a minimum Phred score of 33
Reads were aligned to GRCh38 using Bowtie2 (version 2.3.0) with default settings
Duplicate reads were eliminated using picard (version 2.18.29) with default settings.
bigWig files were generated using deepTools bamCoverage, normalized to RPKM. Blacklist regions (obtained from ENCODE) were excluded.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes and quenched with 0.125 M glycine. After cell lysis, chromatin was sonicated using a Diagenode Bioruptor (30 seconds on and 30 seconds off) for 10 minutes in precooled conditions. Lysates were pelleted at 4˚C and the supernatant was collected.
DNA was purified using Qiagen PCR kit (Qiagen 28104). ChIP DNA libraries were made using Ovation® Ultralow System V2 kit (Tecan Genomics 0344NB-32).

treatment_protocol: Cells were treated with tazemetostat 600nM for 72 hours.


title: DG75-R-C4


title: DG75-R-C2