title: ObeSeno_2

city: Los Angeles

first: Yao Wei

last: Lu

state: CA

address: 2011 Zonal Ave

department: Department of Medicine

institute: University of Southern California

data_processing:
Fastq files clean-up (adaptor and quality trimming) were performed by Cutadapt. Gene expression levels obtained from RNA sequencing were aligned and quantified using HISAT2 and StringTie, with GRcm38 Ensembl release 102 as reference genome.
Assembly: GRCm38 (Ensembl release 102)
Supplementary files format and content: csv, raw transcript count (CPM), all sample in one file (colum name correspond to each sample title)

source_name: Heart

growth_protocol: C57BL/6NTac female mice at 8 weeks of age were fed a control diet (69.1% kcal carbohydrate, 10.4% kcal fat, 20.5% kcal protein, Envigo®) or an obesogenic diet, which consisted of a combination of a high-fat diet (21.3% kcal carbohydrate, 60.3% kcal fat, 18.4% kcal protein, 5.1 kcal/g, Envigo®) and sweetened condensed milk (55% sugar, 13% fat, 7% protein, 3.25 kcal/g, Nestlé®) for 24 weeks (de Oliveira Silva et al., 2020).

extract_protocol:
Total RNA was isolated from the hearts using the TRIzol protocol (Invitrogen). RNA integrity and quality was assessed using the Qubit RNA.
One μg of total RNA per sample was used for the library preparations. The libraries were prepared and sequenced by GENEWIZ (Azenta Life Sciences) using Illumina (2x150bp, at least 60M reads per sample).

treatment_protocol: To assess the impact of senescent cells removal in obesity-induced metabolic and cardiac dysfunctions, we used a senolytic cocktail. After 16 weeks of obesogenic diet feeding, some obese female mice were treated with a senolytic cocktail containing dasatinib (5mg/kg) and quercetin (50mg/kg) diluted in 10% PEG400, which was administered orally (via gavage) for three consecutive days weekly (Xu et al., 2018) until the 24th week of treatment. Other obese female mice were treated with vehicle (10% PEG400) via oral gavage.

value: Heart

value: high fat diet + senolytic cocktail


title: siControl_3

status: Public on Dec 19 2024

type: SRA

city: Shenyang

first: Zhihao

last: Liu

address: No.36 in sanhao street

country: China

institute: China Medical University

description: Library name: Sample3

library_source: transcriptomic

data_processing:
Using MGISEQ-2000RS sequencing platform
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Transcrips per million (TPM) were calculated.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tpms for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: pancreatic cancer

extract_protocol:
Lysis of cells with Trizol regent and harvesting of RNA.
RNA libraries for RNA-seq were prepared using MGISEQ-2000RS protocols.

tag: tissue

value: pancreatic cancer

tag: cell line


title: Ab134 wild type, 24h, rep2

city: CHICAGO

first: Yitao

last: Dai

state: IL

address: 900 S Ashland ave Room 3106, MBRB Building 919 M/C 870

country: USA

institute: University of Illinois at Chicago

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v3.9.3)
Processed raw reads were mapped to the reference genome assembly (GCA_018282095.1_ASM1828209v1) using Geneious assembler (medium-low sensitivity / fast; advanced settings were unchanged).
Expression levels (RPKM, FPKM, and TPM) were calculated using Geneious (ambiguously mapped reads were count as partial matches).
Assembly: GCA_018282095.1 of Genome assembly ASM1828209v1
Supplementary files format and content: comma-separated values (csv) files include locus tag, protein id, raw read count, TPM, FPKM, and RPKM values of each gene for each sample.

organism: Pseudovibrio brasiliensis

growth_protocol: P. brasiliensis Ab134 wild type and mutants were cultivated at 30˚C in BD Difco™ Marine Broth 2216 (50 ml broth in 250-ml Erlenmeyer flasks) shaking at 200 rpm for 24 hours.

extract_protocol:
RNA was isolated from 24-h triplicate cultures using the RiboPure™-Bacteria kit (Thermo Fisher Scientific) following the manufacturer’s instructions.
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices.

tag: strain

tag: genotype

value: wild type


title: day30_ctrl1

city: Shanghai

first: Hanling

last: Wang

address: Shanghai

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Science

data_processing:
The mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA). And then fragmented to approximately 200bp. Subsequently, the RNA fragmentswere subjected to first strand and second strand cDNA synthesis following by adaptor ligaion and enrichment with a low-cycleaccording to instructions ofNEBNext® Ultra™ RNA Library Prep Kit for Illumina.
The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit(Thermo Fisher  Scientific, USA). The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp at Ribobio Co. Ltd (Ribobio, China).
HISAT2 was used to align the clean reads to the human reference genome hg19  with default parameters.
HTSeq was subsequently employed to convert aligned short reads into read counts for each gene
Differential expression was assessed by DESeq2 using read counts as input.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include COUNTs number, RPKM or TPM values for each Sample

source_name: LNCap cell line

growth_protocol: LNCap were cultured in RPM1640 media supplemented with 10% FBS or CSS at 37°C under 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. Total RNA was subjected to Hiseq RNA-Seq, performed by RiboBio Co., Ltd.
RNA libraries for RNA-seq were prepared according to instructions of NEBNext® Ultra™ RNA LibraryPrep Kit for Illumina (NEB, USA)

treatment_protocol:
LNCaP EV and LNCaP ZMYND8-OE cells were cultured with CSS in different time point. Each group was performed in two biological replicates.
LNCaP EV and LNCaP ZMYND8-OE cells were treated with or without FOXM1 KD. Each group was performed in two biological replicates.
LNCaP EV and LNCaP ZMYND8-OE cells were treated with or without iZMYND8-34. Each group was performed in two biological replicates.

value: LNCap cell line

tag: cell type

value: epithelial

value: WT

tag: treatment

value: EV

value: CSS

tag: time

value: Day 30


title: Ex3aERKO rep 3

type: RNA

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from ovary of ERa knockout mouse

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

organism: Mus musculus

source_name: ovary from ERa knockout mouse

label_protocol: Starting with 250-350 ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Ovaries were hymogenized in TRIzol and RNA was extracted following manufactorers protocol.

tag: age

value: 1 year

tag: organ

value: whole ovary


title: Ex3aERKO rep 2


title: siVCPIP1_2

description: Library name: Sample5


title: GCB_S5

type: genomic

city: Ulm

first: Selina

last: Glaser

address: Albert-Einstein-Allee 11

country: Germany

institute: Ulm University and Ulm University Medical Center

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation 450 Beadchip using standard Illumina protocol

scan_protocol: The arrays were scanned using a iScan device or NextSeq 550.

data_processing:
Raw idat files were read into the statistical program R (version 4.3.0) using the minfi package (version 1.46.0). Normalization was performed with the preprocessIllumina() function against the intrinsic controls and without background correction. For normalization, we placed the here the normalization sample within the first row of the sample sheet. For downstream analysis, beta values were calculated, rs loci, loci on gonosomes and loci with a detection p value > 0.01 were excluded.
processed_data: normalized (minfi, preprocessIllumina(), against instrinisc controls, without background correction) average Beta

label: Cy3, Cy5

molecule: genomic DNA

source_name: Non-neoplastic, genomic DNA, cryo preserved

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified according to commercially available kits form Qiagen according to standard instructions

tag: gender

value: Male

tag: disease state

value: non neoplastic DNA from patient with Burkitt lymphoma


title: control rep 4

description: Gene expression from control ovary with one allele of each ER


title: Ab134 wild type, 24h, rep1


title: day0_oe1

value: Day 0


title: day3_oe2

value: Day 3


title: control rep 3

source_name: control ovary with one allele of each ER


title: Obese_4

value: high fat diet


title: siControl_1

description: Library name: Sample1


title: Obese_3

value: Heart


title: Adult_CTX_H3K9me3_ChIPseq

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

library_source: genomic

data_processing:
Raw reads were trimmed using cutadapt (v2.5) and aligned to mouse reference genome mm10 using bowtie2 (v2.4.2). The duplicate reads were removed using samtools (v1.6) 55. The CUT&RUN final bigwig file was generated using makeUCSC program of HOMER and CUT&TAG bigwig files (CPM and RPKM) files were genearted using bamCoverage tool of deeptools (v.3.5.0)
SICER was used  to identify H3K9me3-enriched regions compared to H3 using parameters of W=500; G=1,500; FDR<0.001.
Assembly: mm10
Supplementary files format and content: bigWig (normalized coverage)
Supplementary files format and content: BED (peaks)

source_name: Brain Cortex

extract_protocol:
For CUT&TAG, cortices were collected from 10-week-old wild type mice, and dounced 15 times in HB buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH pH7.8, 1mM DTT, 0.15 mM spermine, 0.5 mM spermidine, Roche protease inhibitor tablets, 10mM Sodium Butyrate).  IGEPAL CA-630 (Sigma) was added to a final concentration of 0.3% and the lysates were dounced 5 more times.  The lysates were filtered through 40µm cell strainers and spun down at 500g for 5 minutes at 4C.  The pellet was resuspended in cold wash buffer 1 (WB1) (20mM HEPES pH 7.5, 150mM NaCl, 0.2% Tween-20, 0.5 mM spermidine, EDTA-free complete protease inhibitor tablet (Roche), 1mg/mL BSA).  20µl of concanavalin A beads pre-washed with binding buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2) were added to each sample and incubated for 10 minutes at room temperature to bind nuclei to beads.  The supernatant was discarded and 50µl antibody buffer (WB1 with 2mM EDTA, 0.1% Triton) (along with respective antibodies) was added to the beads and incubated overnight at 4C.  Next, the supernatant was discarded, and beads were incubated for 1 hour at room temperature with secondary antibodies diluted 100X in antibody buffer (either pig anti-rabbit antibodies (Novus Biologicals NBP172763) or rabbit anti-mouse antibodies (Abcam ab46540)). After the incubation, beads were washed 3 times with WB1.  The beads were then incubated for 1 hour at room temperature with 0.025µM pA-Tn5 adapter complex diluted in 100 µl wash buffer 2 (WB2) (20mM HEPES pH 7.5, 300mM NaCl, 0.2% Tween-20, 0.5 mM spermidine, EDTA-free complete protease inhibitor tablet (Roche), 1mg/mL BSA). The beads were next washed three times with WB2 and then were incubated for 1 hour at 37C with 300µl tagmentation buffer (WB2 with 10mM MgCl2).  After the incubation, 10ul of 0.5M EDTA, 3µl of 10% SDS, and 2.5µl of 20mg/mL proteinase K were added and incubated for 1 hour at 50°C followed by 70°C for 10 minutes.  The DNA was extracted by phenol-chloroform extractions.  The samples were PCR amplified with KAPA HiFi polymerase along with 1X KAPA HiFi Buffer, 0.3 mM dNTPs, 10µM universal primer (AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTG) and 10µM index primer (CAAGCAGAAGACGGCATACGAGAT[index]GTCTCGTGGGCTCGGAGATGT) with the following cycles: (1) 72C for 5 minutes (2) 98C for 30 seconds (3) 98C for 10 seconds (4) 63°C for 30 seconds (5) 72°C for 1 minute (6) 72°C for 5 minutes, (7) go to step 3 thirteen times (8) 12°C hold.  After the PCR, 25µl of Ampure XP beads (0.5x volume) were added and incubated for 10 minutes at room temperature. The supernatant was transferred to a new tube, and an additional 65µl of AMPure beads were added and incubated for 10 minutes at room temperature. The beads were washed twice with 80% ethanol and libraries were eluted with Qiagen EB buffer.
ChIP Libraries were constructed by using the Ovation Ultralow Library System (Nugen).  All libraries were sequenced using an Illumina NextSeq 500
CUT&RUN and CUT&TAG

treatment_protocol: CUT&RUN experiments were performed exactly as previously described by Stroud et. al, 2020 using freshly harvested cortices from adult mice (7-10 weeks). The exceptions were for control experiments. where we altered the experiments in the following ways: (1) Increased anti-MECP2 antibodies by 20-fold. (2) Increased the pA-MNase incubation time after adding CaCl2 from 30 minutes to 2 hours, (3) instead of collecting fragmented chromatin by passive diffusion out from the nuclei, we performed total DNA extraction as previously described by Skene et. al 2017). ChIP-seq experiments were performed exactly as previously described by Stroud et. al 2017

value: Brain Cortex

value: Wild type

tag: antibody

value: anti-H3K9me3 antibodies (Abcam ab8898)


title: Ex3aERKO rep 1


title: day0_ctrl1

value: LNCap cell line


title: Squalene 5

city: Zaragoza

first: Roubi Hamid

middle: Ahmad

last: AbuObeid

state: Spain

address: calle de Miguel Servet, 177

country: Spain

institute: university of Zaragoza

description: Test group:fed for 4 weeks with diet enriched with purified 1% of sunflower oil and 0.5% of squalene

data_processing:
Clean reads were mapped to reference and gene expression level for each sample was calculated using HISAT2, GATK was used to call SNP and INDEL
Supplementary_files_format_and_content: excel files

molecule: polyA RNA

organism: Oryctolagus cuniculus

source_name: fresh liver cells

extract_protocol:
Total RNA was extracted using Quick-RNA MiniPrep kit (Cat.No:R1055, ZYMO Research, Irvine, CA, USA).
The first step involves purifying the poly-A containing mRNA molecules using poly-T oligoattached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

treatment_protocol: PBS wash of liver sections

value: liver

value: Wildtype

tag: breed

value: New Zealand white rabbits

tag: diet

value: squalene


title: Z8Z8

data_processing:
Paired-end fastq files were trimmed and uniquely aligned to the hg19 human genome assembly using BWA.
After alignment, reads mapped to the same genomic positions were filtered by PICARD-MarkDuplicates (Galaxy Version 2.18.2.2)
Bam coverage was used to transform the BAM alignment files to their representative BigWig files.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Purified DNA was prepared for sequencing as per the manufacturer’s instructions (Illumina). Libraries were quantified and sequenced on the Illumina NovaSeq 6000 Sequencer.

value: epithelial

tag: chip antibody

value: ZMYND8 (Bethyl, #A302-090A)


title: ObeSeno_3

value: high fat diet + senolytic cocktail


title: Cntl_4

value: control diet


title: day3_ctrl1

value: WT

value: EV

value: CSS


title: FFPE_S5

source_name: Burkitt lymphoma, genomic DNA, cryo preserved

value: Male

value: DNA from Burkitt lymphoma


title: Cntl_3

value: Heart


title: ObeSeno_1


title: siControl_2

description: Library name: Sample2

value: pancreatic cancer


title: day30_oe1

value: Day 30


title: Cntl_2


title: GCB_S3

value: non neoplastic DNA from patient with Burkitt lymphoma


title: day0_ctrl2

value: LNCap cell line

value: Day 0


title: GCB_S1


title: control rep 1

value: 1 year

value: whole ovary


title: Ex3abERKO rep 1

description: Gene expression from ovary of mouse lacking both ERa and Erb

source_name: ovary form mouse lacking both ERa and Erb


title: Cntl_1


title: FFPE_S3

value: Female


title: control 4

description: Control group:fed for 4 weeks with diet enriched with  purified 1% of sunflower oil

value: liver

value: Wildtype

value: New Zealand white rabbits

value: control


title: ATAC_EV

data_processing:
ATAC-seq libraries were sequenced on the Illumina HiSeq 2500 (125-nucleotide read length, paired end).
FastQC initially processed raw sequence reads for quality control, and then adapter sequences and poor quality reads were removed.
Quality filtered reads were then mapped to reference genome using BWA and only uniquely mapped reads were kept,
Filtered bam files were used for peak calling by MACS2 and an initial threshold q-value of 0.01 as cutoff.
Bam coverage was used to transform the BAM alignment files to their representative BigWig files.
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
Cells were collected and lysed to obtain purified nucleus; The Tn5 enzyme transposable reaction was carried out and the open regions of chromatin were fragmented; the fragmented DNA was purified; the purified DNA was amplified. The amplified DNA was sized to remove non-target fragments.
ATAC libraries were prepared for sequencing using TruePrepTM DNA Library Prep Kit V2 for Illumina kit.Purified fragmented DNA were amplified by PCR reaction,and the libraries were first purified by MinElute PCR purification column(Qiagen)and then further size-selected by VAHTS DNA Clean Beads to obtain libraries with a size distribution between 100 and 1500 bp.

value: epithelial

tag: library type

value: WT

value: EV


title: Obese_2

value: high fat diet


title: Plasma_NF_Sample7

city: Houston

first: Keila

middle: E.

last: Torres

address: 1515 Holcombe Blvd

department: Surgical Oncology

institute: The University of Texas MD Anderson Cancer Center

library_source: other

data_processing:
library strategy: cfMBD-seq
Initial quality control was performed on the sequenced files using fastqc, fastp and multiqc. The sequence reads were aligned to the human genome (hg38) using Bowtie 2 with the default settings. These bam files were further sorted and indexed using SAMtools. The duplicated reads were removed using Picard command line tool.
The indexed bam files with unique reads were converted to bed files using bamtobed command in bedtools.
Since the cfMBDseq can detect genomic regions that are hypermethylated in plasma samples, each CpG site was converted to a genomic region using UCSC_CpG_Island locations.We have identified unique CpG island location for 67 target CpG sites using Infinium HumanMethylation450K v1.2 product file annotations from illumina. We used these genomic regions covering CpG sites for further analysis.
To quantify methylation level at genomic regions covering CpG sites of interest, read count matched to each CpG site interval were called using intersectBed command lines in bedtools. These read counts were normalized to 10M total reads using total unique raw reads per sample. Further we also normalized to 100-fold methylation fold enrichment score to account for any experimental variations during library preparation. The values for total unique raw reads and methylation fold change per sample are provided in the SAMPLES section of this metadata file.
The final read counts in MPNST and NF1 groups were compared using two tailed unpaired t-test. The multiple testing was adjusted using false discovery rate (FDR) approach.
Assembly: GRCh38
Supplementary files format and content: .txt
Supplementary files format and content: The processed data file contains normalized counts for 67 target CpG sites/regions for all samples.

molecule: other

source_name: Plasma_Soft Tissue_Neurofibroma1

extract_protocol:
Approximately 2ml of purified plasma was processed for cfDNA extraction using (Qiagen QIAamp Circulating Nucleic Acid Kit) according to manufacturer protocol.
Libraries were prepared using cfMBDseq protocol as described in Huang et al., 2022. https://www.tandfonline.com/action/showCitFormats?doi=10.1080/15592294.2021.1896984

value: Plasma_Soft Tissue_Neurofibroma1

value: Plasma

tag: total unique_raw_reads_(in_millions)

tag: fold enrichment


title: FFPE_S2

value: Male

value: DNA from Burkitt lymphoma


title: GCB_S4

value: non neoplastic DNA from patient with Burkitt lymphoma


title: control 2

tag: tissue


title: control rep 2


title: GCB_S2


title: Cryo_S6

source_name: Burkitt lymphoma, genomic DNA, FFPE


title: control 1


title: Obese_1

value: Heart

tag: strain


title: Squalene 4

tag: genotype

value: squalene


title: Squalene 3


title: EVZ8

tag: cell line

value: LNCap cell line

tag: cell type

value: ZMYND8 (Bethyl, #A302-090A)


title: FFPE_S1

value: Female


title: FFPE_S6


title: ATAC_ZMYND8oe

tag: treatment


title: Squalene 2

value: liver

value: Wildtype


title: Squalene 1

value: New Zealand white rabbits


title: Adult_OSMInfused_Xenium_3

city: Vancouver

first: Freda

middle: D.

last: Miller

state: BC

department: Michael Smith Laboratories, Department of Medical Genetics

country: Canada

institute: University of British Columbia

description:
gene_panel_1.json
Mouse brain gene panel

hyb_protocol: Sections were incubated in a probe solution for 22 hours at 50°C for hybridization. The probe solution contained a set of 347 gene-targeting probes (described in methods) in TE buffer (Fisher). The rest of the Xenium workflow for fresh frozen tissue (fixation, permeabilization, ligation, amplification, etc) was performed as recommended by 10x Genomics.

scan_protocol: Full sections were imaged and analyzed using the Xenium Analyzer, software v1.7.6.0.

data_processing: Output files (transcripts, cell boundaries, features, etc) were generated directly by the Xenium onboard analysis pipeline (analysis v1.7.1.0). **Important note on file names** File names have been pre-fixed with their associated sample to ensure they are unumbigious when contained in the upload folder (e.g. "Cntl1_" for Adult_Control_Forebrain_Xenium_Biol1). However, the experiment.xenium file will try to pull paths from non-prefixed files (e.g. "morphology.ome.tif", rather than "Cntl1_morphology.ome.tif"). Hence, data users should remove these pre-fixes prior to using the data. The same gene panel was used for all samples, hence gene_panel.json is the same for all uploaded datasets.

label: Gene targeting probes

label_protocol: Single cell spatial transcriptomics was performed using a panel targeting 347 mRNA transcripts. 247 of these probes were from the mouse brain panel designed by 10x Genomics (10xgenomics.com/products/xenium-panels). An additional 100 custom probes were added which are documented in Willis et al. supplementary table 2 and in the gene_panel.json raw data file attached.

extract_protocol: For demyelination experiments, brains were dissected from adult CD-1 mice immediately following exposure to 6 weeks of cuprizone-rapamycin or control (normal chow-vehicle injection). Once dissected, brains were immediately embedded in O.C.T. compound (Tissue-Tek) on dry ice, stored at -70°C, and cryosectioned coronally onto Xenium slides (chemistry v1) to produce 10 μm sections. For in vivo ligand infusion experiments, upon infusion end point, mice were euthanized and cardiac perfusions with ice-cold PBS, followed by 4% paraformaldehyde (PFA) performed. Brains were sucrose protected and flash frozen in Optimal Cutting Temperature (OCT) embedding matrix (TissueTek). Tissues were cryosectioned coronally onto Xenium slides (chemistry v1) to produce 10 μm sections.

treatment_protocol: Control animals for demyelination experiments were exposed to Vehicle I.P injection 5 consecutive days per week (5% PEG400; 5% Tween 80; and 5% ethanol, reconstituted in PBS), normal powdered chow - for 6 weeks. Cuprizone-rapamycin (CupRap) were exposed to rapamycin I.P injection 5 consecutive days per week (10 mg/kg rapamycin, R-5000, LC Laboratories; dissolved in 5% ethanol, 5% polyethylene glycol 400 (PEG400), Sigma; 5% Tween 80, Sigma; in PBS), ad libitum 0.3% cuprizone in powdered chow for 6 weeks. All animals had no  recovery prior to collection. For in vivo ligand infusion experiments, adult CD1 mice were fitted with osmotic minipumps. Animals were then either infused with 0.1% BSA-PBS or 204ng OSM in 0.1% BSA-PBS for 7 days, with a delivery rate of 0.5ul per hour.

tag: Sex

value: M/F

tag: developmental stage

value: adult

value: brain

tag: tissue location

value: forebrain

value: OSM infused


title: control 5

value: control


title: Cryo_S4

tag: gender

value: Male

tag: disease state


title: Cryo_S3

value: DNA from Burkitt lymphoma


title: Plasma_NF_Sample2

value: Plasma_Soft Tissue_Neurofibroma1

value: Plasma


title: A673, siKCNA2, rep3

city: Nantes

first: Anaïs

last: Postec

address: 1 Rue Gaston Veil

country: France

institute: Nantes University

data_processing:
fastp v.0.19.5 (parameters: default + «--detect_adapter_for_pe -q 30»)
kallisto quant v.0.46.2 (parameters: default + «-b 100»)
Assembly: hg38 (GRCh38.p14 analysis set) and Refseq GCF_000001405.40
Supplementary files format and content: «abundance.tsv» files are the output of kallisto quant. It determines the expression of each transcript within the sample.

source_name: cell line

extract_protocol:
NucleoSpin RNA Plus Kit (Macherey-Nagel)
Illumina TruSeq Stranded mRNA Sample Preparation kit

value: cell line

value: ewing sarcoma


title: FFPE_S4


title: Cryo_S1


title: siRBFOX2_high_AC2

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Quality checks were performed using FastQC (v0.11.8), summarised with MultiQC (v1.10.1). Reads were then subsampled to 90 million reads [Mohorianu2017] . Alignment to the human reference genome (build GRCh38.p13) was performed using STAR (v2.7.10a) with default parameters. The counts of the aligned reads corresponding to exons were obtained using featureCounts against the exon annotations from the ensembl database (annotation file Homo_sapiens.GRCh38.101.gtf).
The resulting expression levels were normalised using quantile normalisation [Bolstad2003] and noise was removed using noisyR count matrix approach [Moutsopoulos2021].
Analysis of all the samples (including quality checks, differential expression, and enrichment analysis) was performed using bulkAnalyseR [Moutsopoulos2022]
Assembly: hg38 (GRCh38.p13)
Supplementary files format and content: count matrix containing raw gene expression, matrix of normalised counts

source_name: Human embryonic stem cell

growth_protocol: Human Embryonic stem cell derived Vascular Smooth Muscle Cells (neural crest lineage) were cultured in DMEM media supplemented with 10% FBS, Pen/Strep and L-GLutamine for 10-14 days post differentiation in 10cm dishes (BD Falcon) coated with 0.1% Gelatin in PBS. Protocols for differentiation from hES to Neural crest to VSMCs - refer Granata et al, 2017 (PMID 27893734).

extract_protocol:
Cells were harvested by trypsinization and resuspended in FACS buffer (1% FBS in PBS supplemented with 2mM EDTA. Cells were sorted (BD FACSAria III) for Low, medium and High intensity GFP and collected in FACS Buffer. Sorted cells were spun down and resuspended in RLT buffer (RNAeasy, Qiagen) and frozen. All samples were extracted simultaneously using the RNeasy kit and resuspended in RNAse free water.
NovaSeq, PolyA selection beforehand (NEBNext® Poly(A) mRNA Magnetic Isolation Module, E7490),  NEBNext® Ultra8482 II Directional RNA Library Prep Kit for Illumina (E7760)

treatment_protocol: VSMCs were grown either untreated (NO dox) or treated with 0.2ug/ml Doxycycline for 10-14 days post differentiation in media containing 10% FBS. siRNA treatments were conducted for 5 days - with 2 treatments 72h apart, of 100pmol per well of a 6-well plate. Control or anti-RBFOX2 siRNAs were used.

value: Human embryonic stem cell

tag: type

tag: rbpms

value: High

tag: replicate


title: control 3

value: liver

tag: breed

tag: diet


title: Plasma_NF_Sample6

tag: total unique_raw_reads_(in_millions)

tag: fold enrichment


title: Adult_BSAInfused_Xenium_5

tag: strain

tag: tissue

value: BSA infused


title: day0_oe2

tag: cell line

value: LNCap cell line

value: epithelial

tag: genotype

value: WT

value: CSS

tag: time

value: Day 0


title: siRBFOX2_low_AC4

tag: cell type

value: Low


title: A673, siCT, rep2

tag: treatment

value: siCT


title: Plasma_NF_Sample5


title: Cryo_S5

value: Male


title: Plasma_NF_Sample4


title: A673, siCT, rep1


title: Plasma_NF_Sample3


title: A673, siCT, rep3


title: Plasma_MPNST_Sample2

source_name: Plasma_Soft Tissue_MPNST

value: Plasma_Soft Tissue_MPNST


title: siRBFOX2_low_AC2


title: siRBFOX2_high_AC8


title: Adult_OSMInfused_Xenium_2

tag: Sex

value: M/F

tag: developmental stage

value: adult

value: brain

tag: tissue location

value: forebrain

value: OSM infused


title: Ctrl_high_AC8

value: Human embryonic stem cell

tag: type

value: Control

value: High


title: Animal R312, T Cells, Liver, VDJ

city: Boston

first: Rene

last: Bermea

state: MA

address: 55 Fruit St

department: Pulmonary and Critical Care Medicine

institute: Massachusetts General Hospital

description:
Library name: R312_Liver_TCells_VDJ
TCR seq (VDJ)
01_pre_filtered_object.hdf5
02_final_filtered_object.hdf5
03_shared_clonotype_object.hdf5

data_processing:
Cellranger multi (10x Genomics, v7.0.0) and Cellranger aggregate (10x Genomics, v7.0.0) were used on GEX and VDJ libraries from 5 lung samples and 6 liver samples.  The Cellranger multi pipeline was run on the Terra Cloud Computing Platform and can be found here: https://portal.firecloud.org/?return=terra#methods/Alignment/Cellranger_Multi/11.  The Cellranger aggregate pipeline was run on the Terra Cloud Computing Platform and can be found here: https://portal.firecloud.org/?return=terra#methods/Alignment/Cellranger_Aggregate_For_Multi_Samples/16
Assembly: MMulatta Ensembl v107
Supplementary files format and content: Tab-separated values, matrix files, and hdf5 files for scRNA-seq samples; fasta and csv files for  VDJ-seq samples.

organism: Macaca mulatta

source_name: Liver

extract_protocol:
MHC-haploidentical HCT and autologous HCT underwent pre-transplant conditioning with 1040 cGy total body irradiation prior to transplantation with an apheresis-derived peripheral blood stem cell product. Transplant recipients were not given immunosuppression. Animals were euthanized when they met a pre-set experimental endpoint on day 8 or prespecified clinical endpoints. The lungs and liver were cut into small pieces and digested with Dnase I and type I collagenase at 37°C for 1 hour, and passed through a metal strainer, then 100-, 70-, and 40-μm nylon strainers. The resulting cell suspension was layered into a 70% and 30% Percoll gradient and the leukocytes were collected at the interphase between the layers. The cells were washed and immediately analyzed or cryopreserved in 10% DMSO in FBS and stored in liquid nitrogen.
Cells were processed for single cell sequencing using the Next GEM 5’ v2 Gel Beads and either i7 Multiplex Plate (Single Index) or Single Cell 5’ v2 Sample Index Plate TT (Dual Index). All products used in the preparation of the samples are available from 10x Genomics, except the NHP TCR specific custom designed primers that were developed as previously described (DOI 10.3389/fimmu.2021.804932). These NHP TCR specific custom primer set were substituted for the provided primers in the T Cell Mix 1 and 2 premixed primers.

value: Liver

value: T-cell


title: siRBFOX2_high_AC4

tag: rbpms


title: A673, siKCNA2, rep1

value: cell line

value: ewing sarcoma


title: Adult_OSMInfused_Xenium_1


title: Plasma_NF_Sample1

value: Plasma_Soft Tissue_Neurofibroma1

value: Plasma


title: Cryo_S2

tag: gender

tag: disease state

value: DNA from Burkitt lymphoma


title: Plasma_MPNST_Sample5


title: Animal R276, T Cells, Liver, VDJ

description:
Library name: R276_Liver_TCells_VDJ
TCR seq (VDJ)
01_pre_filtered_object.hdf5
02_final_filtered_object.hdf5
03_shared_clonotype_object.hdf5


title: siRBFOX2_low_AC8

value: Low

tag: replicate


title: CB65_MLL_AF9_DMSO

city: Saarbrücken

first: Julia

middle: Maria

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

institute: Saarland University

data_processing:
Raw fastq files were processed with nfcore/rna-seq v3.10.1 using the Star-Salmon option.
Assembly: GRCh39
Supplementary files format and content: tab-separated text file with raw counts per gene and sample

source_name: cord blood-derived CD34+ cells

growth_protocol: t(9;11) cells derived from cord blood and bone marrow were maintained in StemMACS™ HSC Expansion Media (Miltenyi) supplemented with 10% FCS, 1% Penicillin/Streptomycin, human cytokines (IL-3, IL-6, SCF, FLT3L, SCF, G-CSF, 50 ng/ml each), SR-1 and UM-729 (0.75 µM each).

extract_protocol:
Total RNA was isolated using NucleoSpin RNA Kit (Macherey-Nagel) according to the manufacturer’s instructions. All samples were examined for quality assessment using Nanodrop One (Thermo Fisher Scientific) and Bioanalyzer (Agilent, Santa Clara, CA, USA). Only samples with an RNA integrity number (RIN) of 7 and higher were used for sequencing library preparation.
NEBnext Ultra II directional RNA library preparation kit

treatment_protocol: t(9;11) cells were seeded in 48-well plates at a density of 1,0x10^6/ml in appropriate media. Volasertib (selleck chemicals LLC) was diluted with DMSO up to 50nM and added to the cells. Incubation for 72h before readout.

value: cord blood-derived CD34+ cells

value: hematopoietic stem and progenitor cells

value: DMSO


title: Adult_BSAInfused_Xenium_6

value: M/F

value: adult

value: brain

value: BSA infused


title: Normalization_sample 1

source_name: peripheral blood

value: Male

value: normal DNA from healthy donor


title: Plasma_MPNST_Sample4

value: Plasma_Soft Tissue_MPNST

tag: total unique_raw_reads_(in_millions)


title: Adult_BSAInfused_Xenium_2

value: forebrain


title: CB65_MLL_AF9_50nM

value: 50nM volasertib


title: Adult_BSAInfused_Xenium_4


title: Plasma_MPNST_Sample3

tag: fold enrichment


title: Animal R235, T Cells, Liver, VDJ

description:
Library name: R235_Liver_TCells_VDJ
TCR seq (VDJ)
01_pre_filtered_object.hdf5
02_final_filtered_object.hdf5
03_shared_clonotype_object.hdf5

value: Liver

value: T-cell


title: Animal R312, T Cells, Lung, VDJ

description:
Library name: R312_Lung_TCells_VDJ
TCR seq (VDJ)
01_pre_filtered_object.hdf5
02_final_filtered_object.hdf5
03_shared_clonotype_object.hdf5

source_name: Lung

value: Lung


title: CB29_MLL_AF9_50nM


title: CB29_MLL_AF9_DMSO


title: Adult_CupRap_NoRecovery_Xenium_1

tag: strain

value: forebrain. cuprizone-rapamycin


title: Animal R232, T Cells, Liver, VDJ

description:
Library name: R232_Liver_TCells_VDJ
TCR seq (VDJ)
01_pre_filtered_object.hdf5
02_final_filtered_object.hdf5

tag: tissue


title: HepaRG cells, Control, rep3

city: Nan jing

first: jing

last: ye

address: Jiangsu Province Nanjing,Qixia District, Xianlin Road No.163

institute: Nanjing University

description:
NC_3
A_NC_FPKM.txt

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation
System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s
instructions. After cluster generation, the library preparations were sequenced on an Illumina
Novaseq platform and 150 bp paired-end reads were generated.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts and FPKMs for each sample

source_name: liver

extract_protocol:
Cells were calculated and RNA samples were extracted from 1 × 10^6 HepaRG cells and mus hepatocytes using trizol. cDNA libraries were prepared using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
cDNA libraries were prepared using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions

value: liver

tag: cell line

value: HepaRG

value: hepatocyte

value: WT

value: lentivirus HepaRG-NC


title: Ctrl_high_AC4

value: Human embryonic stem cell

value: Control

value: High


title: Animal R276, T Cells, Lung, VDJ

description:
Library name: R276_Lung_TCells_VDJ
TCR seq (VDJ)
01_pre_filtered_object.hdf5
02_final_filtered_object.hdf5
03_shared_clonotype_object.hdf5


title: Adult_BSAInfused_Xenium_1

value: M/F

value: adult

value: brain

value: BSA infused


title: Adult_BSAInfused_Xenium_3

value: forebrain


title: Adult_Control_NoRecovery_Xenium_1


title: CB102_MLL_AF9_DMSO

value: cord blood-derived CD34+ cells

value: hematopoietic stem and progenitor cells

tag: genotype

value: DMSO


title: Animal R230, T Cells, Liver, VDJ

description:
Library name: R230_Liver_TCells_VDJ
TCR seq (VDJ)
01_pre_filtered_object.hdf5
02_final_filtered_object.hdf5
03_shared_clonotype_object.hdf5

value: Liver

value: T-cell


title: Adult_CupRap_NoRecovery_Xenium_3

value: forebrain. cuprizone-rapamycin


title: CB102_MLL_AF9_50nM

value: 50nM volasertib


title: Ctrl_high_AC2


title: Animal R235, T Cells, Lung, VDJ

description:
Library name: R235_Lung_TCells_VDJ
TCR seq (VDJ)
01_pre_filtered_object.hdf5
02_final_filtered_object.hdf5
03_shared_clonotype_object.hdf5

value: Lung


title: Adult_CupRap_Forebrain_Xenium_Biol1

description:
Mouse brain gene panel
Xenium In Situ Analyzer

extract_protocol: Brains were dissected from adult CD-1 mice following exposure to 6 weeks of cuprizone-rapamycin or control (normal chow-vehicle injection) with 3 weeks recovery. Once dissected, brains were immediately embedded in O.C.T. compound (Tissue-Tek) on dry ice, stored at -70°C, and cryosectioned coronally onto Xenium slides (chemistry v1) to produce 10 μm sections.

treatment_protocol: Control animals were exposed to Vehicle I.P injection 5 consecutive days per week (5% PEG400; 5% Tween 80; and 5% ethanol, reconstituted in PBS), normal powdered chow - for 6 weeks. Cuprizone-rapamycin (CupRap) were exposed to rapamycin I.P injection 5 consecutive days per week (10 mg/kg rapamycin, R-5000, LC Laboratories; dissolved in 5% ethanol, 5% polyethylene glycol 400 (PEG400), Sigma; 5% Tween 80, Sigma; in PBS), ad libitum 0.3% cuprizone in powdered chow for 6 weeks. All animals had 3 weeks recovery prior to collection.

tag: sample type

value: CD-1, M/F, adult, brain, forebrain, cuprizone-rapamycin


title: Adult_Control_NoRecovery_Xenium_3


title: Ctrl_low_AC8

tag: cell type

value: Human embryonic stem cell

value: Low


title: Adult_CupRap_NoRecovery_Xenium_2


title: Plasma_MPNST_Sample1

value: Plasma_Soft Tissue_MPNST

value: Plasma


title: HepaRG cells, HSD17B13, rep3

description:
A_3
A_NC_FPKM.txt

value: liver

value: HepaRG

value: hepatocyte

value: WT

tag: treatment

value: lentivirus HepaRG-HSD17B13


title: HepaRG cells, HSD17B13, rep2

description:
A_2
A_NC_FPKM.txt


title: Adult_Control_Forebrain_Xenium_Biol2

value: CD-1, M/F, adult, brain, forebrain, control


title: HepaRG cells, Control, rep2

description:
NC_2
A_NC_FPKM.txt

value: lentivirus HepaRG-NC


title: Ctrl_low_AC4

value: Control


title: BM56_MLL_AF9_DMSO

source_name: bone marrow-derived CD34+ cells

value: bone marrow-derived CD34+ cells

value: hematopoietic stem and progenitor cells

value: DMSO


title: Animal R312, T Cells, Lung, GEX

description:
Library name: R312_Lung_TCells_GEX
gene expression (GEX)
01_pre_filtered_object.hdf5
02_final_filtered_object.hdf5
03_shared_clonotype_object.hdf5

library_source: transcriptomic single cell

value: Lung

value: T-cell


title: Animal R233, T Cells, Lung, VDJ

description:
Library name: R233_Lung_TCells_VDJ
TCR seq (VDJ)
01_pre_filtered_object.hdf5
02_final_filtered_object.hdf5


title: CB106_MLL_AF9_DMSO

value: cord blood-derived CD34+ cells


title: Animal R227, T Cells, Liver, VDJ

description:
Library name: R227_Liver_TCells_VDJ
TCR seq (VDJ)

value: Liver


title: Ctrl_low_AC2

value: Human embryonic stem cell

value: Low


title: Adult_Control_NoRecovery_Xenium_2

tag: Sex

value: M/F

value: adult

value: brain

value: forebrain


title: BM55_MLL_AF9_DMSO


title: Adult_Control_Forebrain_Xenium_Biol1


title: CB106_MLL_AF9_50nM

value: 50nM volasertib


title: SY5609_120_R3

city: Boulder

first: Taylor

middle: K

last: Jones

state: CO

address: 3415 Colorado Ave

institute: University of Colorado Boulder

description:
RNA-seq from OV90 cells
rnaseq_ercc_normalized_counts.txt

data_processing:
Mapping of PRO-seq data was performed using the NascentFlow Pipeline (DOI 10.17605/OSF.IO/NDHJ2)
Assembly: hg38
Supplementary files format and content: NOT PROVIDED

source_name: wild type OV90 cells

growth_protocol: Roughly 7 million early-passage wild-type OV90 cells were grown in MCDB 105 media 1:1 with Medium 199 and supplemented with 15% FBS and 1% Pen-strep per ATCC guidelines.

extract_protocol:
RNA-seq: Cells were then harvested by washing with cold D-PBS, scraped in D-PBS into 15mL conical tubes, and centrifuged at 1000rpm for 5min 4C. RNA was extracted with TRIzol according to the manufacturer’s instructions. DNaseI digestion was then performed with the RNeasy kit (Qiagen) using the on-column protocol (Rimel et al., 2020). RNA was eluted in 50µL RNase-free water and samples analyzed by Qubit and TapeStation. PRO-seq: As previously described in (Levandowski, C. B.; Jones, T.; Gruca, M.; Ramamoorthy, S.; Dowell, R. D.; Taatjes, D. J, 2021), after treatment the cells were washed 3x with ice cold PBS, and then treated with 10 ml (per 15 cm plate) ice-cold lysis buffer (10 mM Tris–HCl pH 7.4, 2 mM MgCl2, 3 mM CaCl2, 0.5% NP-40, 10% glycerol, 1 mM DTT, 1x Protease Inhibitors (1mM Benzamidine (Sigma B6506-100G), 1mM Sodium Metabisulfite (Sigma 255556-100G), 0.25mM Phenylmethylsulfonyl Fluoride (American Bioanalytical AB01620), and 4U/mL SUPERase-In). Cells were centrifuged with a fixed-angle rotor at 1000xg for 15 min at 4◦C. Supernatant was removed and pellet was resuspended in 1.5 mL lysis buffer to a homogenous mixture by pipetting 20-30X before adding another 8.5 mL lysis buffer. Suspension was centrifuged with a fixed-angle rotor at 1000xg for 15 min at 4◦C. Supernatant was removed and pellet was resuspended in 1 mL of lysis buffer and transferred to a 1.7 mL pre-lubricated tube (Costar cat. No. 3207). Suspensions were then pelleted in a microcentrifuge at 1000xg for 5 min at 4◦C. Next, supernatant was removed and pellets were resuspended in 500 μL of freezing buffer (50 mM Tris pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, 4U/ml SUPERase-In). Nuclei were centrifuged 2000xg for 2 min at 4◦C. Pellets were resuspended in 100 μL freezing buffer. To determine concentration, nuclei were counted from 1 μL of suspension and freezing buffer was added to generate 100 μL aliquots of 10x106 nuclei. Aliquots were flash frozen in liquid nitrogen and stored at −80◦C.
RNA-seq: Samples were concentrated, 300-400ng/µL, and of high quality, RIN values >8.6. For deep mRNA sequencing to asses splicing alterations, poly(A) selection was performed with the KAPA mRNA HyperPrep Kit with 1µg of RNA containing 1:100 diluted ERCC RNA spike-in mix (Invitrogen Thermo Fisher). KAPA mRNA HyperPrep Kit, NovaSEQ6000, using a paired-end 150- bp cycle (2x150). PRO-seq: Nuclear run-on experiments were performed as described previously (Mahat, D. B., Kwak, H., Booth, G. T., Jonkers, I. H., Danko, C. G., Patel, R. K., et al. (2016). Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nature Protocols, 11(8), 1455–1476. with the following modifications: the final concentration of non-biotinylated CTP was raised from 0.25 μM to 25 μM, a clean-up and size selection was performed using 1X AMPure XP beads (1:1 ratio) (Beckman) prior to test PCR and final PCR amplification, and the final library clean-up and size selection was accomplished using 1X AMPure XP beads (1:1 ratio) (Beckman).

treatment_protocol: RNA-seq: Cells were then treated in T-75 flasks with one of 3 CDK7 inhibitors or the equivalent DMSO for 30min at 37C, heat-shocked for 30min at 42C, and recovered for 1hr at 37C. RNA-seq experiments with SY5609 also were completed with a no heat-shock condition or were heat-shocked continuously for 2hrs (Xu et al., 2021; Cardiello et al., 2018). PRO-seq: Cells were then treated in T-75 flasks with SY5609 or the equivalent DMSO for 30min at 37C, heat-shocked for 0min, 20min or 45min at 42C with no heat-shock recovery.

value: Wild-type OV90 cells

value: ovarian cancer

value: 30min pretreatment with SY5609 at 37C followed by a 42C heat shock for 120min with a 0min recovery at 37C

tag: time


title: RNA-Seq of mus musculus: adult 8wo male immortalized Alport Syndrome podocytes, set 2

city: Miami

first: Alla

last: Mitrofanova

state: Florida

address: 1580 NW 10th Ave, Batchelor Bldg, 6th floor

institute: University of Miami

data_processing:
Total RNA was quantified and qualified using the Nugen Universal Plus mRNA-Seq (M01442 v2) to have an RNA integrity score (RIN) above 7.
The quality of the reads was determined with FASTQC software for per base sequence quality, duplication rates, and overrepresented k-mers
Illumina adapters were trimmed from the ends of the reads using Trim Galore! package.
Gene count quantification for total RNA was performed using the GeneCounts function within STAR against the GENCODE vM35 transcript file.
Gene count data were input into edgeR software for differential expression analysis, and gene counts were normalized against total aligned reads for each sample to generate counts per million (cpm) expression value for each gene in each sample.
Assembly: mm39
Supplementary files format and content: counts

source_name: kidney

growth_protocol: Immortalized murine podocytes, both IMWT and IMAS, were maintained in DMEM/F12 media supplemented with 10% fetal bovine serum (FBS), 2% penicilin/streptomycin and 20U/mL INF gamma in humidified atmosphere with 5% CO2 at 33C and differentiated for 14 days at 37C.

extract_protocol:
RNA was extracted using RNeasy mini plus kit (Qiagen). 1.5ug of total RNA was used to construct the sequencing libraries.
Total RNA was prepared with the Nugen Universal Plus mRNA-Seq (M01442 v2) using 100ng via Qubit and 15 cycles PCR.

value: kidney

value: IMAS

value: immortalized podocyte

value: AS - Col4a3-/-


title: A673, siKCNA2, rep2

value: cell line

value: ewing sarcoma


title: Animal R276, T Cells, Liver, GEX

description:
Library name: R276_Liver_TCells_GEX
gene expression (GEX)
01_pre_filtered_object.hdf5
02_final_filtered_object.hdf5
03_shared_clonotype_object.hdf5

value: Liver

value: T-cell


title: SY5609_120_R2


title: Animal R230, T Cells, Lung, VDJ

description:
Library name: R230_Lung_TCells_VDJ
TCR seq (VDJ)
01_pre_filtered_object.hdf5
02_final_filtered_object.hdf5
03_shared_clonotype_object.hdf5

value: Lung


title: BM54_MLL_AF9_DMSO

value: bone marrow-derived CD34+ cells

value: hematopoietic stem and progenitor cells

value: DMSO


title: HepaRG cells, Control, rep1

description:
NC_1
A_NC_FPKM.txt

value: liver

value: HepaRG

value: hepatocyte

value: WT

value: lentivirus HepaRG-NC


title: Adult_CupRap_Forebrain_Xenium_Biol2

value: CD-1, M/F, adult, brain, forebrain, cuprizone-rapamycin


title: RNA-Seq of mus musculus: adult 8wo male immortalized wildtype podocytes, set 3

value: kidney

value: IMWT


title: Animal R235, T Cells, Liver, GEX

description:
Library name: R235_Liver_TCells_GEX
gene expression (GEX)
01_pre_filtered_object.hdf5
02_final_filtered_object.hdf5
03_shared_clonotype_object.hdf5


title: RNA-Seq of mus musculus: adult 8wo male immortalized Alport Syndrome podocytes, set 1

value: IMAS

value: immortalized podocyte

value: AS - Col4a3-/-


title: DMSO_120_R3

value: Wild-type OV90 cells

value: ovarian cancer

value: 30min pretreatment with DMSO at 37C followed by a 42C heat shock for 120min with a 0min recovery at 37C


title: Animal R233, T Cells, Lung, GEX

description:
Library name: R233_Lung_TCells_GEX
gene expression (GEX)
01_pre_filtered_object.hdf5
02_final_filtered_object.hdf5

value: Lung

value: T-cell


title: RNA-Seq of mus musculus: adult 8wo male immortalized wildtype podocytes, set 2


title: AU565_AR_GSK3

city: Birmingham

first: Kelly

last: Chiang

address: Vincent Drive

department: Institute of Cancer and Genomic Sciences

institute: University of Birmingham

data_processing:
alignment to hg38 using STAR
rMATs to identify differential splicing
read count extraction by featureCounts
DESeq2 to identify differential expression
Assembly: hg38
Supplementary files format and content: xlsx files contain rMATs output
Supplementary files format and content: csv file of DESeq2 output

growth_protocol: MCF7 and AU565 cells were maintained in DMEM/10%FBS/1%Glut/1%Pen/Strep. For AR isolation, cells were plated on poly-HEMA coated 15cm dishes for 16hrs in DMEM/F12/1XB27 supplement -VitA. Cells were incubated at 37oC and 5% CO2

extract_protocol:
Total RNA was extracted using the GenElute Mammalian Total RNA Isolation Kit (Merck)
NEBNext Ultra II DNA library prep kit

treatment_protocol: Cells were pretreated with DMSO or 0.5uM GSK591 for three days prior to AR isolation. GSK591 treatment was maintained throughout AR isolation

value: cell line

value: Her2+ breast cancer cell


title: BM56_MLL_AF9_50nM

value: bone marrow-derived CD34+ cells

value: hematopoietic stem and progenitor cells

value: 50nM volasertib


title: Animal R312, T Cells, Liver, GEX

description:
Library name: R312_Liver_TCells_GEX
gene expression (GEX)
01_pre_filtered_object.hdf5
02_final_filtered_object.hdf5
03_shared_clonotype_object.hdf5

value: Liver


title: RNA-Seq of mus musculus: adult 8wo male immortalized wildtype podocytes, set 1


title: Animal R232, T Cells, Liver, GEX

description:
Library name: R232_Liver_TCells_GEX
gene expression (GEX)
01_pre_filtered_object.hdf5
02_final_filtered_object.hdf5


title: AU565_AR_GSK2

value: WT


title: HepaRG cells, HSD17B13, rep1

description:
A_1
A_NC_FPKM.txt

value: liver

value: HepaRG

value: hepatocyte

value: lentivirus HepaRG-HSD17B13


title: AU565_AR_GSK1


title: Animal R276, T Cells, Lung, GEX

description:
Library name: R276_Lung_TCells_GEX
gene expression (GEX)
01_pre_filtered_object.hdf5
02_final_filtered_object.hdf5
03_shared_clonotype_object.hdf5


title: AU565_AR_DMSO3

value: DMSO


title: PT_stock_21_4

city: Norwich

first: Hannah

middle: Rae

last: Thomas

address: Norwich Research Park, Colney Lane

department: Cell and Developmental Biology

institute: John Innes Centre

data_processing:
Fasta files were quality checked using FastQC 0.12.1.
TruSeq3 adaptors trimmed with Trimmomatic v0
39 with a head crop setting of 12, trailing setting of 3, minimum length of 52, and a sliding window of 4:20
The polyA tail was trimmed using Prinseq v0.20.4 with the left and right tail length (i.e. trim_trail_left) of 8 and the minimum length of 40.
Genome indexes were built for tomato and pepper using the ITAG4 and CM334 models respectively. Reads were aligned using STAR 2.7.10b  with two pass mode.
Files were sorted using Samtools 1.18.
Files were assembled using Strintie version 2.2.1.
Assembly: ITAG4.0 4081, Capsicum annuum 4072
Supplementary files format and content: raw reads matrix file for tomato and pepper

organism: Solanum lycopersicum

source_name: Stock

growth_protocol: Solanum lycopersicum var. M82 (tomato) and Capsicum annuum var. California Wonder(pepper) seeds were straitified with 50% bleach. Tomato seeds were germinated in moist phytatrays and pepper seeds were germinated on soil on heatmaps. Tomato and pepper seedlings were grown in climate-controlled chambers set to 23 C with 16:8 day/night light cycles. 21 day old pepper and 14 day old tomato seedlings were grafted and allowed to heal in the dark for 3 days.

extract_protocol:
Tissue was flash frozen and hand ground with a mortal and pestle.  Total RNA was purified from Trizol-extracted samples using the Monarch Total RNA Miniprep Kit.
Libraries were built by the Cornell Institute of Biotechnology, Biotechnology Resource Centre using the Lexogen QuantSeq FWD prep kit and Poly(A) RNA Selection Kit V1
5 and subjected to high-throughput sequencing with the Illumina NextSeq 500/550 High-output kit

treatment_protocol: A 0.5 cm of tomato:tomato, pepper:pepper, tomato:pepper, and pepper tomato scion and stock were collected at 7, 14, and 21 days after grafting. Ungrafted tomato and pepper stems of the same age were also collected for tomato and pepper. Each sample had between 3-5 bioreplicates.

value: 21 DAG

value: Stock


title: AU565_AR_DMSO2


title: PT_stock_21_2


title: RNA-Seq of mus musculus: adult 8wo male immortalized Alport Syndrome podocytes, set 3

value: kidney

value: IMAS

value: immortalized podocyte

value: AS - Col4a3-/-


title: SY5609_30_R1

value: Wild-type OV90 cells

value: ovarian cancer

value: 30min pretreatment with SY5609 at 37C followed by a 42C heat shock for 30min with a 60min recovery at 37C


title: PT_stock_21_1


title: BM55_MLL_AF9_50nM

value: bone marrow-derived CD34+ cells

value: hematopoietic stem and progenitor cells

value: 50nM volasertib


title: T4

first: Liwen

last: Fu

address: 800 Dongchuan RD. Minhang District

institute: Shanghai Jiao Tong University

description: Torin2-treated sample

data_processing:
fastp; 0.20.1; --length_required 50
RseQC; 4.0.0; default
fastqc; v0.11.9; default
hisat2; 2.1.0; --rna-strandness rf --fr
samtools; 1.9; mpileup -uRf -d 1000000
htseq-count; 0.11.2; -s reverse
DESeq2; 1.22.2; qvalue(pvalue)<0.05, |log2FoldChange|>1
DESeq; 1.34.1; qvalue(pvalue)<0.05, |log2FoldChange|>1
Assembly: ITAG4.1
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: entire plant

growth_protocol: Sterilized seeds were plated on solid 1/2 Murashige and Skoog (MS) medium and placed in a growth chamber (Jiupu, China) programmed for a long-day (LD, 16 h:8 h, light: dark photoperiod) condition (300 μmol·m-2·s-1 at 25 ± 1 ˚C) for

extract_protocol:
10-day-old tomato seedlings treated with or without 5 μM Torin2 were used for RNA extraction. Total RNA was isolated using RNA isolater Total RNA Extraction Reagent (Vazyme, Cat no. R401) according to the manufacturer’s protocol.
The RNA-Seq libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s protocol.

treatment_protocol: The solid 1/2 MS medium was supplied with 5 μM Torin2 or 0.1% DMSO

value: entire plant

tag: cultivar

value: Micro-Tom

value: WT

value: 5 μM Torin2


title: BM54_MLL_AF9_50nM


title: MCF7_Bulk_GSK2

value: cell line

value: ER+ breast cancer cell


title: TP_scion_21_3

source_name: Scion

value: 21 DAG

value: Scion


title: MCF7_Bulk_GSK1


title: T2

description: Torin2-treated sample


title: DMSO_30_R1

value: 30min pretreatment with DMSO at 37C followed by a 42C heat shock for 30min with a 60min recovery at 37C


title: DMSO_120_R2

value: 30min pretreatment with DMSO at 37C followed by a 42C heat shock for 120min with a 0min recovery at 37C


title: TP_scion_21_1


title: DMSO_120_R1


title: AU565_AR_DMSO1

value: Her2+ breast cancer cell

value: DMSO


title: T1

description: Torin2-treated sample


title: m4

description: mock-treated sample

value: water with 0.1% DMSO


title: Animal R235, T Cells, Lung, GEX

description:
Library name: R235_Lung_TCells_GEX
gene expression (GEX)
01_pre_filtered_object.hdf5
02_final_filtered_object.hdf5
03_shared_clonotype_object.hdf5

value: Lung

value: T-cell


title: SY5609_120_R1

value: Wild-type OV90 cells

value: ovarian cancer

value: 30min pretreatment with SY5609 at 37C followed by a 42C heat shock for 120min with a 0min recovery at 37C


title: Animal R230, T Cells, Lung, GEX

description:
Library name: R230_Lung_TCells_GEX
gene expression (GEX)
01_pre_filtered_object.hdf5
02_final_filtered_object.hdf5
03_shared_clonotype_object.hdf5


title: SY5609_30_R3

value: 30min pretreatment with SY5609 at 37C followed by a 42C heat shock for 30min with a 60min recovery at 37C


title: MCF7_AR_GSK2

description:
MCF7_AR_filtered_GSK_DMSO.xlsx
DESeq2_MCF7_AR_GSK_DMSO.csv

value: ER+ breast cancer stem cell

value: WT


title: SY5609_0_R1

value: 30min pretreatment with SY5609 at 37C followed by a 42C heat shock for 0min with a 0min recovery at 37C


title: SY5609_30_R2


title: TT_stock_21_3

value: Stock


title: DMSO_0_R3

value: 30min pretreatment with DMSO at 37C followed by a 42C heat shock for 0min with a 0min recovery at 37C


title: Animal R227, T Cells, Liver, GEX

description:
Library name: R227_Liver_TCells_GEX
gene expression (GEX)

value: Liver


title: MCF7_AR_GSK1

value: cell line


title: m1

description: mock-treated sample

value: entire plant

value: Micro-Tom


title: TP_scion_21_4

value: 21 DAG

value: Scion


title: T3

description: Torin2-treated sample

value: 5 μM Torin2


title: DMSO_30_R2

value: 30min pretreatment with DMSO at 37C followed by a 42C heat shock for 30min with a 60min recovery at 37C


title: MCF7_Bulk_DMSO1

value: ER+ breast cancer cell

value: DMSO


title: TT_stock_21_1


title: TP_scion_21_2


title: DMSO_30_R3

value: Wild-type OV90 cells

value: ovarian cancer


title: MCF7_AR_DMSO3

value: ER+ breast cancer stem cell


title: SY5609_0_R3


title: MCF7_Bulk_DMSO2

value: WT


title: MCF7_AR_GSK3


title: SY5609_0_R2

value: 30min pretreatment with SY5609 at 37C followed by a 42C heat shock for 0min with a 0min recovery at 37C


title: SY5609_45_R2 [PRO-seq]

description:
PRO-seq from OV90 cells
proseq_virtual_spikein_normalized_counts.txt

data_processing:
library strategy: PRO-seq
Mapping of PRO-seq data was performed using the NascentFlow Pipeline (DOI 10.17605/OSF.IO/NDHJ2)
Assembly: hg38
Supplementary files format and content: NOT PROVIDED

value: 30min pretreatment with SY5609 at 37C followed by a 42C heat shock for 45min with a 0min recovery at 37C

tag: molecule subtype

value: Nascent RNA


title: MCF7_AR_DMSO1


title: TT_stock_21_4

value: Stock


title: TT_stock_21_5


title: DMSO_0_R2

value: 30min pretreatment with DMSO at 37C followed by a 42C heat shock for 0min with a 0min recovery at 37C


title: TT_scion_21_4


title: m2

description: mock-treated sample

value: entire plant

value: water with 0.1% DMSO


title: Animal R230, T Cells, Liver, GEX

description:
Library name: R230_Liver_TCells_GEX
gene expression (GEX)
01_pre_filtered_object.hdf5
02_final_filtered_object.hdf5
03_shared_clonotype_object.hdf5

value: Liver

value: T-cell


title: Pt3_PD_Tumor-FB

city: Tampa

first: Dongliang

last: Du

address: 111 Magnolia

institute: Moffitt

description:
Pt3_PD_Tumor_barcodes.tsv.gz
Pt3_PD_Tumor_features.tsv.gz
Pt3_PD_Tumor_matrix.mtx.gz

data_processing:
For single-cell RNA-seq data, Cell Ranger (v3.0, 10X Genomics) was used for sequencing reads mapping against GRCh38 human transcriptome, UMI counting, and barcodes filtering. Only barcodes with UMI counts passing threshold for cell detection were imported to Seurat v4.070 for analysis. Then cells with less than 200 genes detected or greater than 10% mitochondrial UMIs were filtered out; genes detected in less than three cells were also excluded. Doublets were detected using Scrublet71, doubletCells implemented in scran72, DoubletFinder73, and scDblFinder74, assuming 0.08% doublet rate for every 1000 cells sequenced in 10X experiments. Cells identified as doublets by >=2 methods were removed from further analysis. Raw UMI counts were log normalized and top 500 variable genes were detected in each sample independently. T cell receptor and immunoglobulin genes were removed from the variable gene list to prevent clustering based on V(D)J transcripts. S and G2/M cell cycle phase scores were assigned to cells using CellCycleScoring() function. To remove batch effects between samples, individual patient samples were further integrated using FindIntegrationAnchors() and IntegrateData() functions75 with parameter anchor.features =8000. Scaled z-scores for each gene were calculated using ScaleData() function by regressing against % of mitochondrial UMIs, cell cycle phases score, and total reads count. Principal component analysis was performed on the integrated data. A shared nearest neighbor (SNN) graph was constructed based on the first 30 principle components. A total of 23 clusters were identified using the FindClusters() function by Louvain clustering76 at resolution=0.9. Uniform manifold approximation and projection (UMAP) was used to visualize clustering and gene expression.
Assembly: GRCh38
Supplementary files format and content: tsv and matrix files

source_name: Tumor

growth_protocol: TIL was cultured at Moffitt Cell Therapy Facility, following a previously described protocol (https://doi.org/10.1038/s41591-021-01462-y).

extract_protocol:
1. For isolated TIL: Tumor was minced and carefully mixed in digestion medium with collagenase (type II and type IV), hyaluronidase and DNAase (Thermo Fisher Scientific). Then undigested tumor was filtered from the cell suspension to generate a single-cell suspension. Intact cells were enriched with a Ficoll-Hypaque (GE Healthcare Bio-Sciences) gradient and viable tumor cells were enumerated by trypan blue exclusion. The tumor digested was stained with anti-human CD3 and Zombie NIR. Isolated TIL was sorted as the CD3+ Zombie NIR- population and sent for single cell sequencing.  2. For cultured TIL: Samples were stained with anti-human CD3 and Zombie NIR, and flow sorting was conducted to sort CD3+Zombie NIR- TIL for single cell sequencing.
The cell suspension was loaded onto the 10X Genomics Chromium Single Cell Controller (10X Genomics, Inc., Pleasanton, CA) at a concentration of about one thousand cells per microliter and the single cells, reagents, and 10x Genomics gel beads were encapsulated into individual nanoliter-sized Gelbeads in Emulsion (GEMs).  Revers transcription of poly-adenylated mRNA was performed inside each droplet, and cDNA generated from cells encapsulated with a 10X Genomics Chromium NextGEM Single Cell V(D)J Reagent Kit was enriched using VDJ primers provided in the kit.  A portion of the DNA library generated from antibody-labeled cells was amplified using primers provided by 10X Genomics to prepare a cell surface protein library, and the cDNA, feature barcoding and VDJ-enriched libraries were completed in bulk reactions using the 10X Genomics Chromium NextGEM Single Cell 3’ or 5’ V(D)J Reagent Kits.

value: Tumor

value: TIL

value: T cells

value: isolated


title: m3

city: Shanghai

description: mock-treated sample

value: Micro-Tom


title: DMSO_0_R1

value: Wild-type OV90 cells

value: ovarian cancer


title: TT_scion_21_5

value: 21 DAG

value: Scion


title: MCF7_AR_DMSO2

value: cell line

value: ER+ breast cancer stem cell

value: WT

value: DMSO


title: TT_stock_21_2

value: Stock


title: Pt3_Baseline_Tumor-FB

description:
Pt3_Baseline_Tumor_barcodes.tsv.gz
Pt3_Baseline_Tumor_features.tsv.gz
Pt3_Baseline_Tumor_matrix.mtx.gz


title: Pt3_Baseline_Tumor-VDJ


title: Hipocampo 77

city: San Sebastián

first: David

last: Otaegui

state: Guipuzcoa

address: Paseo Dr begiristain s/n

department: Neurosciences

institute: Biodonostia Research institute

hyb_protocol: Affymetrix

scan_protocol: Affymetrix  Scanner 3000 7G

data_processing: RMA + DABG (Human Only)

label: biotin

source_name: Hippocampus

label_protocol: Flash Tag Biotin Labeling

growth_protocol: Not applicable

extract_protocol: Trizol

treatment_protocol: Not applicable

tag: age

value: Male


title: SY5609_45_R1 [PRO-seq]

value: 30min pretreatment with SY5609 at 37C followed by a 42C heat shock for 45min with a 0min recovery at 37C

value: Nascent RNA


title: TT_scion_21_3


title: Hipocampo 85

tag: gender


title: Hipocampo 82


title: TT_scion_21_2


title: Ungraft_T_21_4

source_name: Ungrafted stem

value: Ungrafted stem


title: Hipocampo 322


title: DMSO_45_R1 [PRO-seq]

value: 30min pretreatment with DMSO at 37C followed by a 42C heat shock for 45min with a 0min recovery at 37C


title: Pt3_PD_Tumor-VDJ

value: Tumor

value: TIL

value: T cells


title: Ungraft_T_21_2


title: SY5609_20_R1 [PRO-seq]

value: Wild-type OV90 cells

value: 30min pretreatment with SY5609 at 37C followed by a 42C heat shock for 20min with a 0min recovery at 37C


title: Ungraft_T_21_1

value: 21 DAG


title: Pt3_PD_Tumor-RNA

value: isolated


title: Hipocampo 152


title: Hipocampo 80


title: DMSO_20_R2 [PRO-seq]

value: ovarian cancer

value: 30min pretreatment with DMSO at 37C followed by a 42C heat shock for 20min with a 0min recovery at 37C


title: 009 HIPOCAMPO

value: Female


title: DMSO_20_R1 [PRO-seq]


title: Hipocampo 229


title: Cornea, AALhigh

first: Pablo

last: Argueso

address: 150 Harrison Avenue

institute: Tufts Medicine

description: 10X Genomics

data_processing:
Raw base call files generated by Illumina sequencers were de-multiplexed into FASTQ files using Cell Ranger mkfastq. Cell Ranger Single-Cell Software was used for sample demultiplexing, barcode processing, single-cell 3’gene counting, and mapping to the Human Reference Genome GRCh38.
Assembly: GRCh38
Supplementary files format and content: comma-separated value files and matrix files

source_name: Cornea

extract_protocol:
Cells were harvested directly from donor corneas as above and suspended in flow buffer (2% FBS in DPBS no calcium, no magnesium supplemented with 1mM EDTA). Cells were incubated with 1µg/mL fluorescein conjugated AAL on ice for 30 minutes, with gentle mixing every 10 minutes. Cells were collected by centrifugation, washed, centrifuged, and resuspended in flow buffer. Immediately before sorting, cells were again filtered with a cell strainer.  Addition of 3 µM propidium iodide (Thermo Fisher Scientific) was used to exclude dead cells. The stained cells were sorted by a Coulter ELITE cell sorter (Miami, FL, USA) calibrated for two-color fluorescence. The cells were sorted into two populations, cells with relatively low AAL binding (AALlow)and cells with relatively high AAL binding (AALhigh). Single cell suspensions of AAL-sorted corneal limbal epithelial cells were passed through a 35 µm nylon cell strainer, centrifuged for 5 min at 400× g and resuspended in 1 mL PBS on ice. The cells were again centrifuged for 5 min at 400× g and resuspended in ice-cold PBS at a ratio of 200 μL PBS per 1 × 106 cells followed by the dropwise addition of ice-cold methanol, at a ratio of 800 μL per 1 × 106 cells. The cells were stored at − 80 °C until sequencing.
Single-cell mRNA sequencing was performed by the BWH Center for Cellular Profiling according to standard 10X Genomics 3’ V3.1 chemistry protocol. Prior to loading the cells on the 10X Chromium controller, cells were rehydrated in rehydration buffer. Cells were then counted to assess cell integrity and concentration. Approximately 3,400 AALlow and 1,200 AALhigh cells from three donor corneas were separately loaded and the resulting sequencing libraries were prepared following a standard 10X Genomics protocol. Briefly, samples were processed through GEM wells and libraries generated and sequenced.

value: Cornea

tag: cell subpopulation

value: AALhigh


title: Pt3_Baseline_Tumor-RNA


title: SY5609_20_R2 [PRO-seq]


title: PT_stock_14_3

value: 14 DAG

value: Stock


title: Ungraft_T_21_5


title: SY5609_0_R2 [PRO-seq]

value: 30min pretreatment with SY5609 at 37C followed by a 42C heat shock for 0min with a 0min recovery at 37C

value: Nascent RNA


title: Cornea, AALlow

description: 10X Genomics

value: AALlow


title: 008 HIPOCAMPO

value: Male


title: 007 HIPOCAMPO


title: SY5609_0_R1 [PRO-seq]


title: HepG2 D312A rep3 (input)

first: Yunsun

last: Nam

state: Texas

department: Biochemistry

institute: UTSouthwestern Medical Center

data_processing:
Library strategy: m6A-seq
The quality of resulting m6A-seq datasets were assessed using the FastQC (version 0.11.2) and FastQ Screen (version 0.4.4)
The low-quality reads and sequencing adapter was removed by Trim Galore (version 0.4.4)
The reads were aligned to the human reference genome (hg38) using STAR (version 2.7.9a), with the parameters set for aligning reads once. The duplicated alignments were eliminated using Picard toolkit.
Uniquely mapped reads were called peaks for the IP populations against its input by MACS (version 2.1.2) with additional parameters (--nomodel --extsize 66 -p 1.00e-05).
The resulting summits from peak-calling were defined as the center of the 50-nt peaks, which is the default peak-length in this m6A-seq study. The 50-nt peaks overlapped among three replicates (at least 1-nt with at least one other replicate) derived from the same cell line were assembled as intersectional population using HOMER (version 4.9) mergePeaks function. Each peak summit of newly defined intersectional populations was the average of three original summit coordinates, which participated in overlap. The peak region of the newly defined intersectional population was expanded to 50-nt around its summit.
The peak population unique to each cell line (non-overlapping with any peak from the other three cell lines) was obtained by another round of HOMER mergePeaks analysis.
For the discovery of methylation site sequence consensus of the unique population from each cell line, the strand information of the summits was retrieved from the source of GTF files on Genecode. The actual 50-nt sequences of the peaks were extracted using BEDtools (version 2.17.0) getfasta function with appropriate strand orientation.
For RNA-seq analysis, mapped-reads from three replicates of input RNA samples of each cell line in m6A-seq experiment (METTL14 WT: X_2, S_10, S_18; METTL14 R298P: X_3, S_11, S_19) were counted by featureCounts module of Rsubread package (version 1.4.6). ComBat-seq was used for correcting batch effects between libraries prepared and sequenced at different times. Differential RNA expression analysis between METTL14 (R298P) and METTL14 (WT) overexpressing cell line was performed using edgeR. The transcripts with zero count were eliminated and Log2 fold change was calculated using counts per million (CPM) of METTL14 (R298P) divided by CPM of METTL14 (WT).
Genome_build: hg38
Supplementary_files_format_and_content: bed files of m6A peaks summit coordinates for each sample
Supplementary_files_format_and_content: fasta sequence files of m6A sites (50-nt) unique to each type of cell line
Supplementary_files_format_and_content: read-count of gene, log2 fold change, and p-value of RNA-seq analysis on METTL14 (R298P) vs. METTL14 (WT)

source_name: Liver cancer cell

growth_protocol: HepG2 cells were cultured in MEM with EBSS, 2 mM L-glutamine (Cytiva SH30024) supplemented with 1% non-essential amino acids (Gibco 11140-050) and 10% FBS (Corning 35-011-CV) under standard mammalian cell culture conditions (37 ℃, 5% CO2).

extract_protocol:
Three biological replicates of 40 million (2✕ 150 mm plates) HepG2 cells of stable overexpression of EGFP, METTL14 (WT), METTL14 (R298P) and METTL14 (D312A) were lysed by Trizol and the total RNA was extracted. The total RNA was treated by DNase I (5 U per 100 µg total RNA) and mRNAs were enriched by NEBNext Poly(A) mRNA magnetic isolation module (NEB E7490L).
8-10 µg of mRNA from each sample was fragmented to the size of ~120-nt by Ambion Fragmentation reagent (Thermo Scientific AM8740) in a proportional volume (10 µl reaction per 1 µg mRNA) at 70 ℃ for 7 min then precipitated in 75% ethanol with 10% volume of sodium acetate (3 M, pH 5.5) and GlycoBlue (1 µl, Invitrogen AM9515). The RNA fragments were dissolved in nuclease-free H2O at a concentration of 100 ng/µl, and 200 ng from each sample was spared as input. 5 µg of RNA fragment was denatured and incubated with 15 µg of anti-m6A antibody (Abcam ab151230) in immunoprecipitation (IP) buffer (10 mM Tris pH 7.5, 150 mM NaCl, 0.1% NP-40, 5 mM EDTA pH 8.0, 0.2 U/µl SUPERase·In) for 4 h at 4 ℃. The complex was incubated with 100 µl slurry of protein A/G beads blocked by BSA (0.5 mg/ml in IP buffer) at 4 ℃ overnight. The beads were washed by 0.9 ml, twice of each IP buffer, high-salt buffer (10 mM Tris pH 7.5, 1 M NaCl, 1% NP-40, 0.5% sodium deoxycholate), low-salt buffer (10 mM Tris pH 7.5, 50 mM NaCl, 0.1% NP-40), and FastAP buffer (10 mM Tris pH 8.0, 5 mM MgCl2, 100 mM KCl, 0.02% Triton X-100). The IP samples were dephosphorylated on-bead by 5 U of FastAP (Thermo Scientific EF0615) in 100 µl slurry at 37 ℃ for 30 min in a thermomixer with 15 s pulse-shaking at 1200 r.p.m. every 5 min, then washed by FastAP buffer and T4 RNA ligase buffer (50 mM Tris pH 7.5, 10 mM MgCl2, 1 mM DTT). A linker RNA oligonucleotides purchased from IDT was pre-adenylated at 5’ -end by T4 RNA ligase I (NEB 0437) using a method described previously {Song, 2015 #6827}. The pre-adenylated linker RNA (100 pmol) was added to the 3’ -end of IP RNAs on-bead by 500 U of T4 RNA ligase 2, truncated K227Q (NEB M0351) in 50 µl slurry (with a 25% final concentration of PEG8000) at 16 ℃ for an overnight-incubation in a thermomixer with pulse-shaking, then washed by T4 RNA ligase buffer and high-salt buffer. The input samples were dephosphorylated and ligated to the pre-adenylated linker RNA similarly in tubes, except the reactions were scaled-down 5-time and 2.5-time, respectively. Precipitation of RNA in 80% ethanol was performed after both reactions for the input samples. The IP RNA on-bead was eluted twice by incubation with 100 µg proteinase K in an 100 µl slurry (50 mM Tris pH 8.0, 50 mM NaCl, 1 mM EDTA, 1% SDS, 0.4 U/µl SUPERase·In) at 50 ℃ for 1 h in a thermomixer with pulse-shaking then extracted by acid phenol-chloroform and precipitated in 75% ethanol with GlycoBlue and 0.1✕ volume of NaCl (2 M). Input and IP RNA were reversed transcribed by RT primer using SuperScript III and the excessive RT primer was removed by ExoSAP-IT. The RNA template in RT reactions was removed by NaOH (3 µl, 1 M) hydrolysis at 70 ℃ for 12 min and the reaction was neutralized by 3 µl HCl (1 M). The resulting first-strand was cleaned by MyONE Silane beads (Invitrogen 37002D) before ligated to an ssDNA adaptor fused with 10-random-nucleotide UMI (60 pmol) by T4 RNA ligase 1 (45 U) in a 30 µl reaction with 20% PEG8000, and cleaned again by MyONE Silane beads after ligation. The standard Nextera i5 and i7 barcodes were added to the adapted cDNA by a 13-cycle of PCR amplification. The dsDNAs were resolved on 2% agarose gel, and the fragments within the 175-250 bp range were eluted and pooled for Illumina NextSeq500 single-end 75-bp sequencing with expected sequencing depth of 25 million reads.

treatment_protocol: For the generation of stable overexpression of EGFP, METTL14 (WT), METTL14 (R298P) and METTL14 (D312A) HepG2 cell lines, 2.5 million cells were seeded on each 100 mm plate 24 h before the viral transduction. The viral transduction was accomplished by incubating cells with a mixture of 10% (v/v) virus-containing media and complete growth media in the presence of Polybrene (10 µg/ml, Sigma TR-1003-G) for 48 h. Puromycin (3 µg/ml) was added to the growth media for selection. The selection lasted 8 days when fresh puromycin-containing media was provided every 48 hours. Cells were subcultured as needed to maintain the cell confluence between 20% to 80%.

value: Liver cancer

value: Expressing METTL14 (D312A) by integrating lentivirus cassette

tag: m6a-seq antibody

value: none (input)


title: 006 HIPOCAMPO


title: 005 HIPOCAMPO


title: TP_scion_14_4

value: Scion


title: HepG2 D312A rep3 (IP)

value: anti-m6A antibody (Abcam ab151230)


title: DMSO_0_R1 [PRO-seq]

value: Wild-type OV90 cells

value: 30min pretreatment with DMSO at 37C followed by a 42C heat shock for 0min with a 0min recovery at 37C


title: HepG2 R298P rep3 (input)

value: Expressing METTL14 (R298P) by integrating lentivirus cassette


title: TP_scion_14_3


title: SGC7901 cells,△IDR,biol rep 2

city: baoding

first: yukun

last: wang

state: hebei

address: hebei

institute: hebei university

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp.
HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38
The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters.
The differentially expressed mRNAs were selected  by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: hg38
Supplementary files format and content: tab text files include FPKM values for each Sample

growth_protocol: SGC7901cells were cultured in DMEM medium with 10% fetal bovine serum, penicillin (100U/ml), streptomycin (100g/ml)  and cultivated at 37 °C in 5% CO2 (v/v).

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase.The average insert size for the final cDNA library was 300±50 bp.

value: human gastric cancer cell line


title: SGC7901 cells,△IDR,biol rep 3


title: DMSO_0_R2 [PRO-seq]

value: ovarian cancer


title: HepG2 WT rep3 (IP)

city: Dallas

address: 5323 Harry Hines Blvd

value: Expressing METTL14 (WT) by integrating lentivirus cassette


title: TP_scion_14_1

value: 14 DAG


title: HepG2 WT rep3 (input)


title: TT_stock_14_5

value: Stock


title: PT_stock_14_2


title: RNA-Seq of Drosophila melanogaster: larval head and thoracic epidermal cells 11

city: Seattle

first: Jay

middle: Z

last: Parrish

state: WA

address: 3747 W Stevens Way NE

institute: University of Washington

description: Library name: head_11

data_processing:
Reads were demultiplexed with CASAVA (Illumina) and read quality was assessed using FastQC and MultiQC. Reads containing adapters were removed using Cutadapt version 2.4 and reads were mapped to the D. melanogaster transcriptome, FlyBase genome release 6.29, using Kallisto version 0.46.0 with default parameters.
Assembly: FlyBase genome release 6.29
Supplementary files format and content: txt file with raw counts

organism: Drosophila melanogaster

source_name: epidermal cells

growth_protocol: Larvae were reared at 25 C under 12 h light / dark cycle on standard cornmeal/molassess media and isolated for dissection at 96 h after egg laying.

extract_protocol:
Larvae with cytoplasmic GFP expressed in different epidermal subsets were microdissected and dissociated in collagenase type I (Fisher 17-100-017) into single cell suspensions, largely as previously described, with the addition of 1% BSA to the dissociation mix. After dissociation, cells were transferred to a new 35 mm petri dish with 1 mL 50% Schneider’s media, 50% PBS supplemented with 1% BSA. Under a fluorescent stereoscope, individual fluorescent cells were manually aspirated with a glass pipette into PBS with 0.5% BSA, and then serially transferred until isolated without any additional cellular debris present. Ten cells per sample were aspirated together, transferred to a mini-well containing 3ul lysis solution (0.2 % Triton X-100 in water with 2 U / µL RNAse Inhibitor), lysed by pipetting up and down several times, transferred to a microtube, and stored at -80º C. For the picked cells, 2.3 µL of lysis solution was used as input for library preparation.
RNA-Seq libraries were prepared from the picked cells following the Smart-Seq2 protocol for full length transcriptomes. To minimize batch effects, primers, enzymes, and buffers were all used from the same lots for all libraries. Libraries were multiplexed, pooled, and purified using AMPure XP beads, quality was checked on an Agilent TapeStation, and libraries were sequenced as 51-bp single end reads on a HiSeq4000 at the UCSF Center for Advanced Technology.

treatment_protocol: Epidermal cells were isolated from larvae with different genotypes

value: epidermal cells

value: R38F11-GAL4, UAS-GFP (head and thorax)


title: SGC7901 cells,△IDR,biol rep 1


title: SGC7901 cells,WT,biol rep 3


title: TT_stock_14_4


title: RNA-Seq of Drosophila melanogaster: larval head and thoracic epidermal cells 10

description: Library name: head_10


title: HepG2 EGFP rep3 (input)

value: Expressing EGFP by integrating lentivirus cassette


title: SGC7901 cells,WT,biol rep 2


title: 001 HIPOCAMPO

value: Male


title: PT_stock_14_1


title: 003 HIPOCAMPO


title: 004 HIPOCAMPO

value: Female


title: HepG2 R298P rep3 (IP)

value: Liver cancer


title: TP_scion_14_2


title: HepG2 EGFP rep3 (IP)


title: RNA-Seq of Drosophila melanogaster: larval head and thoracic epidermal cells 9

description: Library name: head_9


title: HepG2 D312A rep2 (input)

value: Expressing METTL14 (D312A) by integrating lentivirus cassette

value: none (input)


title: RNA-Seq of Drosophila melanogaster: larval head and thoracic epidermal cells 8

description: Library name: head_8


title: 002 HIPOCAMPO


title: HepG2 D312A rep2 (IP)

value: anti-m6A antibody (Abcam ab151230)


title: SGC7901 cells,Vector,biol rep 3

value: overexpression-Vector


title: TT_stock_14_1


title: HepG2 R298P rep2 (input)


title: SGC7901 cells,Vector,biol rep 2


title: RNA-Seq of Drosophila melanogaster: larval head and thoracic epidermal cells 6

description: Library name: head_6


title: TT_scion_14_5

value: Scion


title: SGC7901 cells,WT,biol rep 1


title: TT_scion_14_3


title: HepG2 WT rep2 (input)


title: HepG2 R298P rep2 (IP)

value: Expressing METTL14 (R298P) by integrating lentivirus cassette


title: SGC7901 cells,△IDR,H3K4me3

data_processing:
Raw sequencing data were cleaned to filter adapters and low quality reads using FASTQC (v0.11.5) and the unique mapped reads were harvested by mapping the cleaned reads to genome with no more than two mismatches by Bowtie 2.
MACS2 (v2.1.1) was used to call peak, giving a robust and high resolution ChIP-Seq peak predictions. Peaks were annotated related genes using Homer (v4.10).
deepTools (v2.4.1) was used to plot gene coverage of the reads near TSS and TES. ChIPseeker (v1.5.1) was used to depict the reads distribution on chromosomes.
Assembly: hg38
Supplementary files format and content: txt

source_name: cell line

extract_protocol:
All tissue was harvested for the immunoprecipitation (IP) reaction. The tissue preparation and ChIP protocol closely adhered to the steps outlined in the SimpleChIP® Plus Sonication Chromatin IP System manual (Cell Signaling Technology, # 56383).
A total amount of 50ng DNA per sample was used as input material for the ChIP sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer's recommendations and index codes were added to attribute sequences to each sample.The library preparations were sequenced on an Illumina platform and 2x150bp paired-end sequencing reads were generated.

value: cell line

value: human gastric cancer cell line

value: {delta}IDR

tag: chip antibody


title: TT_scion_14_2

value: 14 DAG


title: SGC7901 cells,Vector,biol rep 1


title: RNA-Seq of Drosophila melanogaster: larval head and thoracic epidermal cells 4

description: Library name: head_4


title: SGC7901 cells,WT,H3K4me3

value: WT


title: RNA-Seq of Drosophila melanogaster: larval head and thoracic epidermal cells 3

description: Library name: head_3

value: epidermal cells


title: HepG2 EGFP rep2 (input)


title: TT_stock_14_3

value: Stock


title: TT_scion_14_1


title: SGC7901 cells,Vector,H3K4me3

value: Vector


title: RNA-Seq of Drosophila melanogaster: larval head and thoracic epidermal cells 2

description: Library name: head_2

value: R38F11-GAL4, UAS-GFP (head and thorax)


title: TT_stock_14_2


title: HepG2 WT rep2 (IP)

value: Expressing METTL14 (WT) by integrating lentivirus cassette


title: RNA-Seq of Drosophila melanogaster: larval head and thoracic epidermal cells 7

description: Library name: head_7


title: Ungraft_T_14_5

value: Ungrafted stem


title: HepG2 EGFP rep2 (IP)

value: Liver cancer

value: Expressing EGFP by integrating lentivirus cassette


title: RNA-Seq of Drosophila melanogaster: larval head and thoracic epidermal cells 1

description: Library name: head_1


title: SGC7901 cells,△IDR,FLAG

value: FLAG,Sigma


title: Ungraft_T_14_4


title: Ungraft_T_14_3


title: RNA-Seq of Drosophila melanogaster: larval head and thoracic epidermal cells 5

description: Library name: head_5


title: SGC7901 cells,WT,FLAG


title: RNA-Seq of Drosophila melanogaster: larval ventral epidermal cells 12

description: Library name: vent_12

value: R38F11-GAL4, UAS-GFP (ventral)


title: HepG2 D312A rep1 (input)

value: Expressing METTL14 (D312A) by integrating lentivirus cassette

value: none (input)


title: SGC7901 cells,Vector,FLAG

value: cell line


title: HepG2 D312A rep1 (IP)

value: anti-m6A antibody (Abcam ab151230)


title: RNA-Seq of Drosophila melanogaster: larval ventral epidermal cells 10

description: Library name: vent_10


title: HepG2 R298P rep1 (input)

value: Expressing METTL14 (R298P) by integrating lentivirus cassette


title: Ungraft_T_14_1

value: 14 DAG


title: S.1303.AHK7

first: MIKEL

last: GARCIA PUGA

address: Paseo Dr. Begiristain sn

institute: Biodonostia HRI

data_processing:
Mapping, Hisat2, v2.0.4
Quantitative expression, cuffquant,cuffnorm, v2.2.1
Differential expression analysis, DESeq2, v1.10.1
Genome_build: hg38
Supplementary_files_format_and_content: count

source_name: Skin primary fibroblasts

growth_protocol: fibroblasts were cultured in Dulbecco’s modified Eagle medium (DMEM, Gibco) containing 10% fetal bovine serum (Sigma-Aldrich, St Louis, MO, USA), 1% L-glutamine (Gibco), and 1% penicillin–streptomycin (Gibco)

extract_protocol:
Trizol
'For library construction, RNA was extracted from a sample first. After DNase I treatment and performing quality control (QC), 200 ng of high-quality total RNA was proceed to library construction. Magnetic beads with Oligo (dT) are used to isolate mRNA (for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). The mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer after adding dNTPs, RNase H and DNA polymerase I. Short fragments are purified and resolved with EB buffer for end repair and single nucleotide A (adenine) addition. After that, the short fragments are connected with sequencing adapters. The double-stranded cDNA library is completed through size selection and PCR enrichment. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. Lastly, the qualified RNA-seq libraries are sequenced using Illumina NovaSeq6000 in CD Genomics (Shirley, NY) after pooling according to its effective concentration and expected data volume

treatment_protocol: fibroblasts were seeded in T75-flasks and after 14-16 h were treated with 0.1 µM AHK7 for 72 h.

tag: agent

value: 0.1 µM AHK7


title: RNA-Seq of Drosophila melanogaster: larval ventral epidermal cells 11

description: Library name: vent_11

value: epidermal cells


title: S.1303


title: HepG2 R298P rep1 (IP)


title: RNA-Seq of Drosophila melanogaster: larval ventral epidermal cells 8

description: Library name: vent_8


title: PT_stock_7_5

value: 7 DAG

value: Stock


title: RNA-Seq of Drosophila melanogaster: larval ventral epidermal cells 9

description: Library name: vent_9


title: S.1029


title: HepG2 WT rep1 (input)


title: S.1029.AHK7

value: 0.1 microM AHK7


title: RNA-Seq of Drosophila melanogaster: larval ventral epidermal cells 7

description: Library name: vent_7


title: HepG2 WT rep1 (IP)

value: Expressing METTL14 (WT) by integrating lentivirus cassette


title: S.1115.AHK7


title: PT_stock_7_1


title: S.1115


title: HepG2 EGFP rep1 (input)


title: TP_scion_7_5

value: Scion


title: RNA-Seq of Drosophila melanogaster: larval ventral epidermal cells 6

description: Library name: vent_6


title: HepG2 EGFP rep1 (IP)

value: Liver cancer


title: RNA-Seq of Drosophila melanogaster: larval ventral epidermal cells 5

description: Library name: vent_5


title: STRIPE-seq + SLAM-seq BAC2 PAA 72hpi R2

city: Würzburg

first: Christopher

middle: Sebastian

last: Jürges

state: BY

address: Versbacher Straße 7

department: Institut für Virologie und Immunbiologie

institute: Julius-Maximilians-Universität Würzburg

data_processing:
STAR was used to align all reads to the human genome (Enxembl version 90), ribosomal rRNA, and HCMV genome (KF297339)
Peaks were called by using the tool iTiSS and merged using iTiSS TiSSMerger2
Genome_build: KF297339.1
Supplementary_files_format_and_content: tsv, called TSS

source_name: human foreskin fibroblasts (HFF)

growth_protocol: Primary human foreskin fibroblasts were cultured in DMEM supplements with 10% FBS. Cells were infected with HCMV strain TB40 and BAC2 at an MOI of 10.

extract_protocol:
Cells were lyzed using Trizol and total cellular RNA was isolated.
Sequencing libraries were prepared using the dRNA-seq and STRIPE-seq and SLAM-seq inhouse protocols.

treatment_protocol: Cells were infected using an MOI of 10. 4sU labelling at 500uM for 1 hour prior to lysis. GCV and PAA treatment was conducted at 12 hpi using 50 uM and 250 ug/mL, respectively

value: primary fibroblasts

value: 4sU + IAA + PAA

tag: time post infection

value: HCMV 72 h p.i.

tag: replicate

value: Replicate 2


title: RNA-Seq of Drosophila melanogaster: larval ventral epidermal cells 4

description: Library name: vent_4

value: R38F11-GAL4, UAS-GFP (ventral)


title: Ungraft_T_14_2

tag: tissue

value: Ungrafted stem


title: STRIPE-seq + SLAM-seq BAC2 PAA 72hpi R1

value: Replicate 1


title: TP_scion_7_4


title: ipi1-R70H, micafungin, biol_rep2

city: Miyazaki

first: Taiga

last: Miyazaki

address: 5200 Kihara, Kiyotake

department: Department of Internal Medicine

country: Japan

institute: University of Miyazaki

description:
gene-R70H.MFG.nega_R70H.MFG.posi_DESeq2.txt
gene-CBS138.MFG.posi_R70H.MFG.posi_DESeq2.txt

data_processing:
RNA-seq libraries were sequenced using paired end reads (150 nt of read1 and read2) on a DNBSEQ-G400RS instrument (MGI Tech).
Obtained raw reads were trimmed and quality-filtered using the Trim Galore! (version 0.6.7), Trimmomatic (version 0.39), and cutadapt (version 3.7) software.
Trimmed reads were then mapped to the C. glabrata CBS138 genome using STAR (version 2.7.10a).
Reads on annotated genes were counted using featureCounts (version 2.0.1).
FPKM values were calculated from mapped reads by normalizing to total counts and transcript. Differentially expressed genes were detected using the DESeq2 package (version 1.20.0).
Assembly: Candida_glabrata_CBS138_s05-m01-r09
Supplementary files format and content: tab-delimited text files include data obtained by DESeq2 analysis

organism: Nakaseomyces glabratus

extract_protocol:
Total RNA of C. glabrata cells was extracted using RNeasy mini kit (Qiagen). Qualities of total RNA were assessed by Bioanalyzer (Agilent) to ensure that RIN (RNA integrity number) is over 7.0.
After poly (A) + RNA enrichment by NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs), double-stranded cDNA libraries (RNA-seq libraries) were prepared using SMARTer stranded RNA-Seq kit (Clontech) and MGIEasy Universal Library Conversion Kit (MGI Tech) according to the manufacturer’s instruction.

tag: strain

tag: genotype

value: G209A in IPI1

value: micafungin


title: ipi1-R70H, micafungin, biol_rep3


title: TP_scion_7_3


title: RNA-Seq of Drosophila melanogaster: larval ventral epidermal cells 3

description: Library name: vent_3

tag: cell type


title: PT_stock_7_3


title: STRIPE-seq + SLAM-seq BAC2 GCV 72hpi R2

tag: treatment

value: 4sU + IAA + GCV


title: RNA-Seq of Drosophila melanogaster: larval ventral epidermal cells 2

description: Library name: vent_2

value: epidermal cells


title: ipi1-R70H, micafungin, biol_rep1


title: PT_stock_7_2

value: 7 DAG


title: TP_scion_7_2


title: RNA-Seq of Drosophila melanogaster: larval ventral epidermal cells 1

description: Library name: vent_1


title: STRIPE-seq + SLAM-seq BAC2 GCV 72hpi R1


title: TP_scion_7_1


title: STRIPE-seq + SLAM-seq BAC2 72hpi R2

value: 4sU + IAA


title: ipi1-R70H, no-drug, biol_rep2

description:
gene-R70H.MFG.nega_R70H.MFG.posi_DESeq2.txt
gene-CBS138.MFG.nega_R70H.MFG.nega_DESeq2.txt

value: no-drug


title: ipi1-R70H, no-drug, biol_rep1


title: STRIPE-seq + SLAM-seq BAC2 72hpi R1


title: RNA-Seq of Drosophila melanogaster: larval dorsal epidermal cells 12

description: Library name: ush_12

value: ush-GAL4, UAS-GFP


title: RNA-Seq of Drosophila melanogaster: larval dorsal epidermal cells 11

description: Library name: ush_11


title: WT, micafungin, biol_rep3

description:
gene-CBS138.MFG.nega_CBS138.MFG.posi_DESeq2.txt
gene-CBS138.MFG.posi_R70H.MFG.posi_DESeq2.txt

value: wild-type


title: STRIPE-seq + SLAM-seq BAC2 24hpi R2

value: HCMV 24 h p.i.


title: RNA-Seq of Drosophila melanogaster: larval dorsal epidermal cells 10

description: Library name: ush_10


title: TT_stock_7_2

value: Stock


title: WT, micafungin, biol_rep2


title: TT_stock_7_3


title: TT_stock_7_5


title: RNA-Seq of Drosophila melanogaster: larval dorsal epidermal cells 9

description: Library name: ush_9


title: RNA-Seq of Drosophila melanogaster: larval dorsal epidermal cells 8

description: Library name: ush_8


title: WT, micafungin, biol_rep1


title: STRIPE-seq + SLAM-seq BAC2 24hpi R1

value: primary fibroblasts


title: TT_scion_7_5

value: Scion


title: STRIPE-seq + SLAM-seq TB40 PAA 72hpi R2

value: 4sU + IAA + PAA

value: HCMV 72 h p.i.

value: Replicate 2


title: TT_scion_7_3


title: ipi1-R70H, no-drug, biol_rep3


title: STRIPE-seq + SLAM-seq TB40 PAA 72hpi R1

value: Replicate 1


title: WT, no-drug, biol_rep3

description:
gene-CBS138.MFG.nega_CBS138.MFG.posi_DESeq2.txt
gene-CBS138.MFG.nega_R70H.MFG.nega_DESeq2.txt


title: RNA-Seq of Drosophila melanogaster: larval dorsal epidermal cells 6

description: Library name: ush_6


title: TT_scion_7_2


title: WT, no-drug, biol_rep2


title: STRIPE-seq + SLAM-seq TB40 GCV 72hpi R2


title: TT_scion_7_1


title: RNA-Seq of Drosophila melanogaster: larval dorsal epidermal cells 5

description: Library name: ush_5


title: WT, no-drug, biol_rep1


title: STRIPE-seq + SLAM-seq TB40 GCV 72hpi R1


title: DMSO_45_R2 [PRO-seq]

tag: cell line

value: Wild-type OV90 cells

value: ovarian cancer

value: 30min pretreatment with DMSO at 37C followed by a 42C heat shock for 45min with a 0min recovery at 37C

value: Nascent RNA


title: STRIPE-seq + SLAM-seq TB40 72hpi R2


title: cmnac-nor45DAP_3

city: Beijing

first: Jinfang

last: Wang

address: No.50 Zhanghua Road, Haidian District

institute: Beijing Academy of Agricultural and Forestry Sciences

data_processing:
NovaSeq 6000
fastx_toolkit_0.0.14/SeqPrep/Sickle were used for estimating sequencing quality to gain clean reads.
TopHat2 / HISAT2 were used to analysis the mapped data quality.
The mapped reads were spliced using StringTie or Cufflinks software
TPM （Fragments Per Kilobases per Millionreads）values were used to show gene expression level.
Genome_build: http://cucurbitgenomics.org/organism/18
Supplementary_files_format_and_content: text files include TPM values for each Sample

organism: Cucumis melo

source_name: Cucumis melo L.

growth_protocol: The wild type (WT) and cmnac-nor mutant fruits were harveseted at 15 DAP,25 DAP,35 DAP and 45 DAP  (days after pollination)

extract_protocol:
RNA was extracted from WT and cmnac-nor mutant fruits at 15,25,35 and 45 DAP with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed
The 24 libraries were built by TruseqTM RNA sample prep kit (Illumina, USA).

value: fruit flesh

value: 45 days after pollination

value: cmnac-nor mutant


title: RNA-Seq of Drosophila melanogaster: larval dorsal epidermal cells 2

description: Library name: ush_2

value: epidermal cells

value: ush-GAL4, UAS-GFP


title: Ungraft_T_7_3

tag: time

value: 7 DAG

value: Ungrafted stem


title: STRIPE-seq + SLAM-seq TB40 72hpi R1

value: primary fibroblasts

value: 4sU + IAA


title: RNA-Seq of Drosophila melanogaster: larval epidermal bands 12

description: Library name: 38793_12

value: R51F10-GAL4, UAS-GFP


title: cmnac-nor45DAP_2


title: cmnac-nor45DAP_1


title: STRIPE-seq + SLAM-seq TB40 24hpi R2

value: HCMV 24 h p.i.


title: Ungraft_T_7_1


title: RNA-Seq of Drosophila melanogaster: larval epidermal bands 11

description: Library name: 38793_11


title: Ungraft_T_7_2


title: WT45DAP_3

value: wild type


title: STRIPE-seq + SLAM-seq TB40 24hpi R1

value: Replicate 1


title: STRIPE-seq + SLAM-seq mock R2

value: Mock

value: Replicate 2


title: WT45DAP_2