title: Batch2, 40 day, young ablated, central brain

city: College Station

first: Alex

last: Keene

state: Texas

address: 3258 TAMU Department of Biology Butler Hall 203A

department: Biology

institute: Texas A&M University

description:
Library name: Batch2-Old_abl
Batch2-Old_abl

data_processing:
The snRNA-seq raw sequencing files were processed using CellRanger 6.0 (10x Genomics; Pleasanton, CA) and then mapped to the Drosophila reference genome (Flybase r6.31).
Assembly: GCF_000001215.4
Supplementary files format and content: .tar file includes filtered feature matrix and barcodes for each sample

molecule: nuclear RNA

source_name: Central brain

extract_protocol:
Central brains from either axotomized or intact flies were dissected at the age of 5 and 40 days and then placed into 1.5 mL RNase-free Eppendorf tubes, flash-frozen in liquid nitrogen, and then stored at -80°C. All dissections were performed between ZT0 and ZT4. Approximately 120-140 central brains were collected for each treatment and stored on dry ice.
Tissue was homogenized and lysed with Triton X-100 in RNase-free water to isolate nuclei. The nuclei were then purified, centrifuged, resuspended in PBS with RNase Inhibitor, and then diluted to ~700 nuclei/µL. Next, standardized 10x capture and library preparation were performed using the 10x Genomics Chromium Next GEM 3’ Single Cell Reagent kit v3.1 (10x Genomics; Pleasanton, CA).

treatment_protocol: Flies of the indicated age and genotype were gently anesthetized on CO2 for less than one minute at ZT0-2. Next, using forceps, the third segments of both antennae were removed. Controls received the same treatment without ablation.

value: Central brain

value: ablated


title: A549 cells,RNAseq_ADAR_OE_SFTSV,rep1

status: Public on Jan 07 2026

type: SRA

city: wuhan

first: han

middle: shao

last: qing

address: whu

country: China

institute: school

description:
Library name: sample45
EXE1

library_source: transcriptomic

data_processing:
The Illumina sequencing reads were initially processed with cutadapt v4.3 to remove adapters and perform quality-based trimming.
After trimming adapters and filtering out low-quality reads, all the cleaned FASTQ files were aligned to either the human reference genome hg38 or miRBase version 22, utilizing STAR version 2.7.5a and Bowtie2.
Gene expression levels were quantified using featureCounts v2.0.6.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: A549 cells

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, 15596018) according to the manufacturer’s instructions
RNA sample were subjected to library construction using SMARTer Stranded Total RNA-Seq Kit v2—Pico Input Mammalian according to the manufacturer’s protocol. miRNA-seq libraries construction were used VAHTS® Small RNA Library Prep Kit for Illumina (NR801). All of the quality-ensured libraries were sequenced on the Illumina Nova seq 6000 platform in 150 bp paired-end mode (sequenced by Genewiz).

tag: cell line

value: A549 cells


title: A549 cells,RNAseq_ADAR_OE_nonSFTSV,rep3

description:
Library name: sample44
EXC3


title: 11dpf, replicate 2, scRNA-seq

city: Zhan Jiang

first: Xiaoyu

last: Li

state: Guangdong

address: 57 People's Avenue

institute: Affiliated Hospital of Guangdong Medical University

description: Library name: sample_11dpf_2

library_source: transcriptomic single cell

data_processing:
10X Genomics Cell Ranger software (version 3.1.0) was used to convert raw BCL files to FASTQ files, alignment and counts quantification. Briefly, reads with low-quality barcodes and UMIs were filtered out and then mapped to the reference genome. Reads uniquely mapped to the transcriptome and intersecting an exon at least 50% were considered for UMI counting.Before quantification, the UMI sequences would be corrected for sequencing errors, and valid barcodes were identified based on the EmptyDrops method.The cell by gene matrices were produced via UMI counting and cell barcodes calling.The cell by gene matrices for each sample were individually imported to Seurat  for downstream analysis.Quality control, removing doublets, empty droplets, and cells with higher mitochondrial containment, was performed by utilizing the Seurat (v. 4.3.0) package in R with the thresholds calculated by scuttle::isOutlier function
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: matrix files

molecule: polyA RNA

organism: Danio rerio

source_name: brain

extract_protocol:
At 3, 6, and 11 dpf, zebrafish larvae were anesthetized in the E3 medium, and brain tissues were isolated within 30 min. 1500-2000 brain tissues were isolated from the above zebrafish at the corresponding time point and incubated at 37℃ with tissue digestion solution containing 2 mg/L of papain for about 25 min. Then the tissues were incubated with DMEM containing 5% fetal bovine serum (FBS) to terminate the digestion. Cell suspensions were centrifugated at 500 g for 30 min at 4℃ and resuspended with DMEM medium containing 5% FBS. Then cell suspensions were filtered through 70 μm, 40 μm cell strainer to prepare single cell suspensions. All filtration procedures were performed on ice to preserve cell viability. eGFP positive cells were sorted by FACS aril III and collected with DMEM medium containing 5% FBS.
Cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Upon dissolution of the Gel Bead in a GEM, primers containing (i) an Illumina® R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded, full-length cDNAs were then reverse-transcribed from poly-adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full-length, barcoded cDNAs were then amplified by PCR to generate sufficient mass for library construction. R1 (read 1 primer sequence) were added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produced Illumina-ready sequencing libraries. A Single Cell 3’ Library comprised standard Illumina paired-end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI were encoded in Read 1, while Read 2 was used to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read. Read 1 and Read 2 were standard Illumina® sequencing primer sites used in paired-end sequencing.

tag: tissue

value: brain

value: primary cell

tag: cell type

value: endotheliall cell

tag: genotype

value: Wild Type


title: Batch2, 5 day, young ablated, central brain

country: USA

description:
Library name: Batch2-Young_abl
Batch2-Young_abl

organism: Drosophila melanogaster

tag: treatment

tag: batch


title: 20-week SN Grin2a WT Sample 8

city: Cambridge

first: Ally

last: Nicolella

state: MA

address: 75 Ames St

department: Stanley Center for Psychiatric Research

institute: Broad Institute

description: Library name: grin2a_20w-SN-WT8

data_processing:
Reads were aligned to RefSeq M25/GRCm38.p6 and gene and isoform level expression values were estimated using RSEM v1.3.0
Assembly: RefSeq M25/
Supplementary files format and content: tab-delimited text files include TPM and FPKM values for each Sample

organism: Mus musculus

source_name: Substantia Nigra

growth_protocol: Brain dissection was performed in the cryostat using frozen brain tissues collected from Grin2b mutant mice. RNA was prepared from microdissected tissues using RNeasy Mini Kit (Qiagen). 200 ng of isolated total RNA from each sample was used for the construction of sequencing libraries.

extract_protocol:
RNA libraries for RNA-seq were prepared using an Illumina TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions.
RNA-seq

value: Substantia Nigra

value: Grin2a WT


title: Batch2, 40 day, young intact, central brain

description:
Library name: Batch2-Old_int
Batch2-Old_int

value: intact control


title: 11dpf, replicate 1, scRNA-seq

data_processing:
10X Genomics Cell Ranger software (version 3.1.0) was used to convert raw BCL files to FASTQ files, alignment and counts quantification.
Briefly, reads with low-quality barcodes and UMIs were filtered out and then mapped to the reference genome. Reads uniquely mapped to the transcriptome and intersecting an exon at least 50% were considered for UMI counting.
Before quantification, the UMI sequences would be corrected for sequencing errors, and valid barcodes were identified based on the EmptyDrops method.The cell by gene matrices were produced via UMI counting and cell barcodes calling.
The cell by gene matrices for each sample were individually imported to Seurat  for downstream analysis.
Quality control, removing doublets, empty droplets, and cells with higher mitochondrial containment, was performed by utilizing the Seurat (v. 4.3.0) package in R with the thresholds calculated by scuttle::isOutlier function
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: matrix files

extract_protocol:
At 3, 6, and 11 dpf, zebrafish larvae were anesthetized in the E3 medium, and brain tissues were isolated within 30 min. 1500-2000 brain tissues were isolated from the above zebrafish at the corresponding time point and incubated at 37? with tissue digestion solution containing 2 mg/L of papain for about 25 min. Then the tissues were incubated with DMEM containing 5% fetal bovine serum (FBS) to terminate the digestion. Cell suspensions were centrifugated at 500 g for 30 min at 4? and resuspended with DMEM medium containing 5% FBS. Then cell suspensions were filtered through 70 ?m, 40 ?m cell strainer to prepare single cell suspensions. All filtration procedures were performed on ice to preserve cell viability. eGFP positive cells were sorted by FACS aril III and collected with DMEM medium containing 5% FBS.
Cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Upon dissolution of the Gel Bead in a GEM, primers containing (i) an Illumina® R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded, full-length cDNAs were then reverse-transcribed from poly-adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full-length, barcoded cDNAs were then amplified by PCR to generate sufficient mass for library construction. R1 (read 1 primer sequence) were added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produced Illumina-ready sequencing libraries. A Single Cell 3’ Library comprised standard Illumina paired-end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI were encoded in Read 1, while Read 2 was used to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read. Read 1 and Read 2 were standard Illumina® sequencing primer sites used in paired-end sequencing.

value: endothelial cells

tag: age


title: Batch2, 5 day, young intact, central brain

description:
Library name: Batch2-Young_int
Batch2-Young_int


title: A549 cells,RNAseq_ADAR_OE_nonSFTSV,rep2

description:
Library name: sample43
EXC2


title: 20-week SN Grin2a WT Sample 7

description: Library name: grin2a_20w-SN-WT7


title: Batch1, 40 day, young intact, central brain

description:
Library name: Batch1-Old_int
Batch1-Old_int


title: BMDMs from C57BL/6 mice cultured with M-CSF, naive rep1

city: New York

first: BiNGS

last: Core

address: 3 E 101st St

institute: Icahn School of Medicine at Mount Sinai

description: Library name: naive1

library_source: genomic

data_processing:
Reads were first evaluated for their quality using FastQC (v0.11.8)
Reads were trimmed for adapter sequences using Trim Galore! (v0.6.6)
Reads were aligned to the mouse genome reference GRCm38.p6 using Bowtie2 (version 2.2.8) with end-to-end mode, --sensitive and -X 2000 parameters
Reads aligned to mtDNA and noncanonical chromosome were removed.Picard (v2.2.4) was used to remove duplicated reads
Post-filtering bam file for samples from the same experimental condition were merged using the merge function from Samtools (v1.11), followed by peak calling using MACS (v2.1.0) with parameters --nomodel --nolambda –keepdup all –slocal 10000
Peak summits were extended +/- 200bp, and quantification of reads in peaks was performed using BEDTools multicov (v2.29.2)..Coverage tracks were generated from bam files using deepTools (v3.2.1) bamCoverage with parameters –normalizeUsingRPKM –binsize 10
Bigwig files were further normalized using the normalization factor calculated by DESeq2 using total counts in peak regions. Bigwigs from the same condition were merged together and uploaded to UCSC genome browser for visualization.
Assembly: GRCm38.p6 (mouse)
Supplementary files format and content: bigwig files
Supplementary files format and content: narrowPeak files containing peak coordinates

molecule: genomic DNA

source_name: bone marrow

growth_protocol: Isolated monocytes were seeded at a concentration of 5 x 105 monocytes/mL (1 x 105 monocytes in 200mL of media) in 96-well plates (Corning Inc., Corning, NY). Cell culture media for all conditions was Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS), 1% Penicillin/Streptomycin (P/S), 1% HEPES, 1% sodium pyruvate, 1% MEM non-essential amino acids (Thermo Fisher Scientific, Waltham, MA), 0.001% 2-mercaptoethanol (Sigma-Aldrich, St. Louis, MO), and 30 ng/mL recombinant murine M-CSF (PeproTech, Cranbury, NJ). For cryopreservation experiments, bone marrow cells were preserved in FBS containing 10% dimethyl sulfoxide (Sigma-Aldrich) and stored in liquid nitrogen for 24h

extract_protocol:
5 × 10⁴ viable BMDMs were lysed in buffer (10 mM PIPES pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl₂, 0.1% TritonX-100) at 4°C for 5 min, nuclei were pelleted, resuspended in transposase reaction buffer with Tn5 (1 μL per 5 × 10⁴ cells), incubated at 37°C for 30 min, treated with 0.1% SDS at 40°C for 30 min to stop the reaction, and DNA was isolated using KAPA Pure beads (SPRI beads) with concentrations measured by Qubit® fluorometer (Thermo Fisher Scientific).
For DNA library preparation, qPCR with i5 and i7 primers was performed using NEXTERA barcoding, followed by incubation with 0.5× SPRI beads (discarded), then 1.8× SPRI beads; beads were washed twice with 70% ethanol, eluted with EB buffer, measured using a Qubit® fluorometer, and library size and quality were assessed using an Agilent 2100 Bioanalyzer HS.

treatment_protocol: For naive BMDM, monocytes were culture with media for 6 days, changing the media on day 3. For activated BMDM, monocytes were cultured with media for 6 days, changing the media on day 3, and BMDM were stimulated with 10 ng/mL of LPS from Salmonella enterica serotype abortus equi (Sigma-Aldrich) for 6h. For trained BMDM, monocytes were cultured on day 0 with 10 µg/mL of β-glucan from Saccharomyces cerevisiae (InvivoGen, San Diego, CA) or Candida albicans as previously described. On day 3 the media was changed and, after 3 days of resting, trained BMDM were re-stimulated with LPS for 6h. Supernatants were collected on day 0 (unstimulated), day 3 before washing (stimulus 1), day 6 before washing (resting) and 6h after LPS stimulation (stimulus 2) and stored at -80ºC, while BMDM were recovered using a cell scraper (Corning Inc., Corning, NY) and processed for downstream applications.

value: bone marrow

value: Bone marrow-derived macrophages (BMDM)

value: Naive


title: 20-week SN Grin2a -/-  Sample 9

description: Library name: grin2a_20w-SN-KO9

value: Grin2a -/-


title: 6dpf, replicate 1, scRNA-seq


city: Solna

first: Joakim

middle: S

last: Dahlin

address: CMM, Visionsgatan 18

department: Department of Medicine, Solna

country: Sweden

institute: Karolinska Institutet

description:
Library name: DonorD1_MACS_basophils_Gene_Expression_Long_read
FLT-seq from 10X genomics cDNA

data_processing:
Illumina data was processed using cellranger count (Cellranger Pipeline 5.0.1 with the option include-introns for sample Donor B sorted basophils and Cellranger Pipeline 7.0.1 for the rest of the samples with default parameters)
Long-read data was processed using epi2me-labs/wf-single-cell
Assembly: GRCh38
Supplementary files format and content: count tables 10X Genomics .h5
Supplementary files format and content: count tables ONT .tsv
Library strategy: CITE-seq

source_name: peripheral blood

extract_protocol:
The isolated cells from each sample were used for GEM generation, barcoding, cleanup, cDNA amplification according to the protocol provided from 10x Genomics Chromium Next GEM Single Cell 3' Reagent kit v3.1 with feature barcode technology.
Illumina library construction was done using the protocol and reagents from the 10x Genomics Chromium Next GEM Single Cell 3' Reagent kit v3.1 with feature barcode technology. Long-read libraries were generated using a modified FLT-seq protocol (Tian et al, 2021, Genome Biology).

value: peripheral blood

tag: dataset number

value: CCR3 enriched low-density leukocytes

tag: library type

value: mRNA


title: A549 cells,RNAseq_ADAR_OE_nonSFTSV,rep1

description:
Library name: sample42
EXC1


title: A549 cells,RNAseq_ADAR_nonOE_SFTSV,rep3

description:
Library name: sample41
CONE3


title: 3dpf, replicate 1, scRNA-seq


title: 20-week SN Grin2a -/-  Sample 8

description: Library name: grin2a_20w-SN-KO8


title: 20-week SN Grin2a WT Sample 6

description: Library name: grin2a_20w-SN-WT6


title: 20-week SN Grin2a -/-  Sample 6

description: Library name: grin2a_20w-SN-KO6


title: A549 cells,RNAseq_ADAR_nonOE_SFTSV,rep2

description:
Library name: sample40
CONE2


title: A549 cells,RNAseq_ADAR_nonOE_SFTSV,rep1

description:
Library name: sample39
CONE1


title: Batch1, 40 day, young ablated, central brain

description:
Library name: Batch1-Old_abl
Batch1-Old_abl

value: Central brain

value: ablated


title: NB_PDLTMA06-10_5K_with_v1_segmentation

type: other

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

hyb_protocol: A total of 5001 + 480  genes were included in the analysis of this dataset. For the dual slide, the probe hybridization mix recipe: 94.5uL Probe Hyb Buffer B, 52.5uL Xenium 5K Hu PTP Panel Probes, 5.25uL 3X 6ZAAWG, 2.63uL 6X 6ZX7JP, 2.63uL 6X 43R3RN. Probe hybridization occurred at 50°C for 16 hours (Bio-Rad DNA Engine Tetrad 2). For the ligation steps use Xenium Ligation Buffer (10X Genomics, 2000391) from the V1 chemistry kit instead of Ligation Buffer B (10X Genomics, 2001233) from the Prime chemistry kit. Finalized slides were stored in PBS-T in the dark at 4°C for ≤5 days until being loaded onto the Xenium Analyzer instrument. Stepwise Xenium FFPE preparation guidelines and buffer recipes can be found in 10X Genomics Demonstrated Protocol CG000760.

scan_protocol: Xenium Analyzer is fully automated. The user marks regions for analysis by manually selecting sample location on an initial low-resolution image. After loading consumable reagents and slides, internal sample and liquid handling mechanics control experiment progression. Data collection occurs in cycles of fluorescently labeled probe binding, image acquisition, and probe stripping. Localized points of fluorescence intensity detected during the rounds of imaging are then defined as potential RNA puncta. Each gene on the panel has a unique fluorescence pattern across the image channels. Puncta that match a specific pattern are then decoded and labeled according to the gene ID. All image FOVs (4240 x 2960 pixels) and associated detected transcripts are computationally stitched together via the DAPI-stained image. All data in this paper were collected on instrument software version 3.4.1.0 and onboard analysis version xenium-3.3.0.1. Detailed instructions on instrument operation and consumable preparation can be found in 10X Genomics’ Demonstrated Protocol CG000584.

data_processing: All processing was done on instrument with the Xenium Analyzer

molecule: other

source_name: Lung

label_protocol: Deparaffinization and decrosslinking was performed to make subcellular RNA targets accessible (10X Genomics Demonstrated Protocol CG000578).

growth_protocol: A 5um section of each archived lung FFPE block was H&E stained and presented to a physician who identified areas of interest. TMA block was designed in a 3x6 pattern of  3mm cores, respectively. Sample cores were punched and placed manually using a “Quick-Ray Manual Tissue Microarrayer Full Set”, custom square punch, and assembled inverted using double-sided tape as an anchor. Paraffin (VWR 76548-194) was then poured to fill the cassette and allowed to solidify. Once complete, TMA blocks were stored at 4°C.

extract_protocol: Sectioning was performed at 5um on a Leica RM2135 with a water float temperature of 38°C. Sections were placed on Xenium slides (10X Genomics) and left to dry overnight. Slides were baked the next day for 3 hours at 42°C, then stored in a sealed dessicator at room temperature for up to a month.

treatment_protocol: All protocol workstations and equipment were cleaned using RNase Away (RPI 147002) followed by 70% Isopropanol. All reagents, including water, were molecular grade nuclease-free.

value: Lung


title: A549 cells,RNAseq_ADAR_nonOE_nonSFTSV,rep2

description:
Library name: sample37
CONC2

value: A549 cells


title: 20-week SN Grin2a WT Sample 4

description: Library name: grin2a_20w-SN-WT4


title: A549 cells,RNAseq_ADAR_nonOE_nonSFTSV,rep1

description:
Library name: sample36
CONC1


title: Batch1, 5 day, young intact, central brain

description:
Library name: Batch1-Young_int
Batch1-Young_int


title: 20-week SN Grin2a WT Sample 1

description: Library name: grin2a_20w-SN-WT1


title: NB_PDLTMA6-9


title: 20-week SN Grin2a WT Sample 2

description: Library name: grin2a_20w-SN-WT2


title: ZmNRL1-OE 48h_N+ rep1

city: Guangzhou

first: Chunyan

last: Zheng

address: Wushan Street

institute: South China Agricultural University

data_processing:
Basecalls performed using bcl2fastq v2.19.1
Sequence raw reads were trimmed for adaptor/low-quality sequence using trim_galore (v.1.18).
Clean data were aligned to the B73_ RefGen_v4 genome assembly using HISAT2 program (v.2.2.1) with default parameters.
Read counts extraction and normalization were performed using FeatureCounts software (v.2.0.1).
Assembly: B73 RefGen_v4
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files includes FPKM values for each Sample

organism: Zea mays

extract_protocol:
RNA was harvested using RNAprep Pure kit (TIANGEN, Beijing, China). 2 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit following manufacture's protocols.

value: Root

value: ZmNRL1-OE, overexpression

value: N+


title: zmnrl-m 48h_N+ rep3

value: zmnrl1-m, mutant


title: ZmNRL1-OE 48h_N+ rep3


title: ZmNRL1-OE 48h_N+ rep2


title: A549 cells,RNAseq_ADAR_nonOE_nonSFTSV,rep3

description:
Library name: sample38
CONC3


title: Batch1, 5 day, young ablated, central brain

description:
Library name: Batch1-Young_abl
Batch1-Young_abl


title: PDLTMA6-10-v1


title: zmnrl-m 48h_N+ rep2


title: zmnrl-m 48h_N+ rep1


title: A549 cells,RNAseq_ADAR_KD_SFTSV,rep2

description:
Library name: sample34
1206B3E2


title: 20-week SN Grin2a WT Sample 5

description: Library name: grin2a_20w-SN-WT5

value: Substantia Nigra

value: Grin2a WT


title: 20-week SN Grin2a +/-  Sample 6

description: Library name: grin2a_20w-SN-HT6

value: Grin2a +/-


title: A549 cells,RNAseq_ADAR_KD_SFTSV,rep1

description:
Library name: sample33
1206B3E1


title: PDLTMA06-11_5K


title: PDLTMA06-10_5K


title: PD16, Amitrole 50mg/kg bw/day, 86_20-24

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

description:
Library name: PD16_Ami_high_86_20-24
BRB-seq

data_processing:
Quality control and preprocessing of data were performed by GenomEast (France).
The first read contains 16 bases that must have a quality score higher than 10. The first 6 bp correspond to a unique sample-specific barcode and the following 10 bp to a unique molecular identifier (UMI).
The second reads were aligned to the Rattus niorvegicus reference transcriptome from the UCSC website (release rn6) using BWA version 0.7.4.4 with the parameter “-l 24”
Assembly: rn6
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: testis

growth_protocol: The dams, and their litters, were housed in semi-transparent polysulfone (PSU) cages of 15 x 27 x 43 cm (PSU) (Techniplast S.p.A, Buguggiate, Italy) in ventilated cabinets (ScanTainers, Scanbur, Karlslunde, Denmark) with ScanClime (Scanbur, Karlslunde, Denmark) controlled environment: 55 ± 5% humidity, 21 ± 1°C, air-change 50 times/hr, reversed light/dark cycles (light form 9 PM to 9 AM, dark form 9 AM to 9 PM). The animals had ad libitum access to water (acidified, in PSU bottles from Techniplast) and soy and alfalfa-free Altromin 1314 feed (Altromin GmbH, Lage, Germany). The diet contained 1.52 mg/kg iodine and 0.26 mg/kg selenium.

extract_protocol:
Testis were dissected and frozen in liquid nitrogen. Samples were stored at –80 ˚C until further analysis. Total RNA isolation was performed using a RNeasy Micro Kit following manufacturer’s protocol with the DNase step included (Qiagen, Germany). RNA quantity, quality, and purity was determined by a combination of a Nano-drop-1000 spectrophotometer (ND-1000, Fisher Scientific) and an Agilent 2100 Bioanalyzer System (Agilent Technologies, CA, USA). Samples with RNA integrity (RIN)-score > 6.8 were used. RNA samples were diluted to 25 ng/µL, and stored at -80 ˚C.
The sequencing libraries were built by tagmentation using 50 ng of ds cDNA with the Illumina Nextera XT Kit (Illumina, #FC-131-1024) following the manufacturer’s recommendations. Library strategy: Bulk RNA Barcoding and sequencing (BRB-seq)

treatment_protocol: Time-mated nulliparous Sprague-Dawley rat dams (Crl:CD(SD) bred by Charles River Europe and distributed by SCANBUR, Denmark) arrived on gestation day (GD) 3 and were exposed to test compounds from GD7 to pup day (PD) 22. The day of expected birth (GD23) was designated as PD1. The test compounds were methimazole, also known as thiamazole, (MMI) (CAS no: 60-56-0, Sigma-Aldrich 301507-5G, batch: WXBC9951 V, purity 99.0 %) and 3-Amino-1H-1,2,4-triazole (amitrole or Ami) (CAS no: 61-82-5, Sigma-Aldrich 8144950100, batch: S7075495 925, purity 99.7 %). Administration of test compounds took place once daily by oral gavage to animals pseudo-randomly divided into 5 groups: control (vehicle, corn oil, Sigma-Aldrich), 8 mg/kg bodyweight/day (mg/kg/d) MMI, 16 mg/kg/d MMI, 25 mg/kg/d amitrole and 50 mg/kg/d amitrole. Exposure was performed at aconstant volume of 2 mL/kg/d.

value: testis

tag: developmental stage

tag: strain

value: Amitrole 50mg/kg bw/day


title: 20-week SN Grin2a +/-  Sample 3

description: Library name: grin2a_20w-SN-HT3


title: PD16, Amitrole 50mg/kg bw/day, 85_20-24

description:
Library name: PD16_Ami_high_85_20-24
BRB-seq

value: Sprague-Dawley rat dams (Crl:CD(SD) bred by Charles River


title: 20-week SN Grin2a +/-  Sample 5

description: Library name: grin2a_20w-SN-HT5


title: PD16, Amitrole 50mg/kg bw/day, 83_20-24

description:
Library name: PD16_Ami_high_83_20-24
BRB-seq


title: B73 48h_N+ rep3


title: A549 cells,RNAseq_ADAR_nonKD_SFTSV,rep3

description:
Library name: sample32
1206BCE3


title: A549 cells,RNAseq_ADAR_KD_SFTSV,rep3

description:
Library name: sample35
1206B3E3


title: B73 48h_N+ rep2


title: B73 48h_N+ rep1


title: PD16, Amitrole 50mg/kg bw/day, 40_20-24

description:
Library name: PD16_Ami_high_40_20-24
BRB-seq


title: PD16, Amitrole 50mg/kg bw/day, 84_20-24

description:
Library name: PD16_Ami_high_84_20-24
BRB-seq


title: A549 cells,RNAseq_ADAR_nonKD_SFTSV,rep1

description:
Library name: sample30
1206BCE1


description:
Library name: DonorC_MACS_basophils_Gene_Expression_Long_read
FLT-seq from 10X genomics cDNA

value: peripheral blood


title: 20-week SN Grin2a +/-  Sample 1

description: Library name: grin2a_20w-SN-HT1


title: A549 cells,RNAseq_ADAR_nonKD_SFTSV,rep2

description:
Library name: sample31
1206BCE2


title: 20-week SN Grin2a +/-  Sample 2

description: Library name: grin2a_20w-SN-HT2


title: ZmNRL1-OE 48h_N- rep2

value: N-


title: ZmNRL1-OE 48h_N- rep3


title: TB

city: Shanghai

first: Siyi

last: Shen

address: 320 Yueyang Road

institute: Shanghai Institution of Nutrition and Health, Chinese Academy of Sciences

description:
Library name: Sample 1
10x Genomics

data_processing:
The FASTQ files were processed and aligned to mm10 reference genome using Cell Ranger software (v7.0.1) from 10x Genomics, with unique molecular identifier (UMI) counts summarized for each barcode.
Assembly: mm10
Supplementary files format and content: CellRanger Outputs including matrix.mtx, features.tsv and barcodes.tsv

source_name: thyroid

extract_protocol:
Thyroid tissues were minced into pieces and digested in HBSS containing 1 mg/mL Collagenase Type I (Sigma) and 1 mg/mL Collagenase Type II (Worthington) at 37℃ for 1 h. Live cells were sorted by FACS.
Single cell gel beads in emulsion (GEMs) generation, barcoding, post GEM-RT cleanup, cDNA amplification, and cDNA library construction were performed using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics), according to the manufacturer’s protocol. The libraries were sequenced on Illumina Nova 6000 PE150.

treatment_protocol: To induce Cre recombination in adult transgenic mice, 100 μg of tamoxifen (TAM) per gram of body weight was intraperitoneally injected. 5-7 months after TAM-induced recombination, thyroid tissues from TPO-CreERT2; BRAFV600E; Rosa26tdTomato/+ (TB) mice and TPO-CreERT2; BRAFV600E; Trp53f/f; Rosa26tdTomato/+ (TBP) mice were collected for scRNA-seq.

value: thyroid

value: tamoxifen-injection


title: A549 cells,RNAseq_ADAR_KD_nonSFTSV,rep3

description:
Library name: sample29
1206B3C3


title: PD16, Amitrole 50mg/kg bw/day, 39_20-24

description:
Library name: PD16_Ami_high_39_20-24
BRB-seq


title: PD16, Amitrole 50mg/kg bw/day, 37_20-24

description:
Library name: PD16_Ami_high_37_20-24
BRB-seq


title: zmnrl-m 48h_N- rep3


title: ZmNRL1-OE 48h_N- rep1


title: TBP

description:
Library name: Sample 2
10x Genomics

value: TPO-CreERT2; BRAFV600E; Trp53f/f; Rosa26tdTomato/+


title: A549 cells,RNAseq_ADAR_nonKD_nonSFTSV,rep3

description:
Library name: sample26
1206BCC3


title: PD16, Amitrole 50mg/kg bw/day, 38_20-24

description:
Library name: PD16_Ami_high_38_20-24
BRB-seq


title: PD16, Amitrole 50mg/kg bw/day, 19_20-24

description:
Library name: PD16_Ami_high_19_20-24
BRB-seq


title: A549 cells,RNAseq_ADAR_nonKD_nonSFTSV,rep1

description:
Library name: sample24
1206BCC1


title: 4-week PFC WT snRNA-seq Sample 1

description:
Library name: P28-PFC-WT1
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10, including introns
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Prefrontal Cortex

extract_protocol:
Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe).
Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer’s protocol.

value: Prefrontal Cortex

value: WT


title: zmnrl-m 48h_N- rep1

value: Root


title: 4-week PFC WT snRNA-seq Sample 3

description:
Library name: P28-PFC-WT3
10x Genomics


title: A549 cells,RNAseq_ADAR_KD_nonSFTSV,rep1

description:
Library name: sample27
1206B3C1

value: A549 cells


title: B73 48h_N- rep3


title: 4-week PFC WT snRNA-seq Sample 2

description:
Library name: P28-PFC-WT2
10x Genomics


title: PD16, Amitrole 50mg/kg bw/day, 17_20-24

description:
Library name: PD16_Ami_high_17_20-24
BRB-seq


title: A549 cells,RNAseq_ADAR_nonKD_nonSFTSV,rep2

description:
Library name: sample25
1206BCC2


title: A549 cells,RNAseq_ADAR_KD_nonSFTSV,rep2

description:
Library name: sample28
1206B3C2


title: zmnrl-m 48h_N- rep2


title: PD16, Amitrole 50mg/kg bw/day, 20_20-24

description:
Library name: PD16_Ami_high_20_20-24
BRB-seq


title: 4-week PFC Grin2b +/- snRNA-seq Sample 3

description:
Library name: P28-PFC-HT3
10x Genomics

value: Grin2b +/-


title: 4-week TH WT snRNA-seq Sample 4

description:
Library name: P28-TH-WT4
10x Genomics

source_name: Thalamus

value: Thalamus


title: PD16, Amitrole 50mg/kg bw/day, 18_20-24

description:
Library name: PD16_Ami_high_18_20-24
BRB-seq


title: 4-week PFC Grin2b +/- snRNA-seq Sample 2

description:
Library name: P28-PFC-HT2
10x Genomics


title: A549 cells,miRNA_ADAR_OE_nonSFTSV,rep3

description:
Library name: sample20
SREXC3


title: A549 cells,miRNA_ADAR_OE_SFTSV,rep3

description:
Library name: sample23
SREXE3


title: A549 cells,miRNA_ADAR_OE_SFTSV,rep2

description:
Library name: sample22
SREXE2


title: 4-week PFC Grin2b +/- snRNA-seq Sample 1

description:
Library name: P28-PFC-HT1
10x Genomics


title: DOR09

city: Nanning

first: Fengxia

last: Liu

address: No. 3 Longyuan Road

institute: Reproductive Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China

description: Library name: Sample 19

data_processing:
After passing the library check, the different libraries were sequenced in Illumina after pooling them according to the effective concentration and the target sequencing output data volume, yielding 150bp paired-end reads. The basic principle of sequencing is to synthesize and sequence at the same time. Four types of fluorescently labeled dNTPs, DNA polymerase, and junction primers were added to the sequencing flow cell for amplification. When extending the complementary strand of each sequencing cluster, each fluorescently labeled dNTP added emits corresponding fluorescence, and the sequencer captures the fluorescence signals, and converts the light signals into sequencing peaks through computer software, so as to obtain the sequence information of the fragment to be tested.
The reference genome and its annotation files were downloaded from a specified website. HISAT was used to build an index, and clean reads were aligned to the reference genome.
Assembly: NOT PROVIDED
Supplementary files format and content: The table includes the normalized values (FPKM) of RNA for each sample.

source_name: blood

extract_protocol:
RNA was were extracted by Trizol method；
1) By utilizing the structural characteristic that most eukaryotic mRNAs carry a polyA tail, mRNAs with polyA tails were enriched by Oligo(dT) magnetic beads; 2) The purified mRNAs were cleaved into small fragments with fragmentation buffer at a suitable temperature; 3) First-strand cDNAs were produced by reverse transcription using a random hexamer primer; 4) Second-strand cDNAs are synthesized (strand-specific library: dUTPs were used instead of dTTPs in the second-strand synthesis to incorporate dUTPs in the second-strand cDNAs, while the high-fidelity DNA polymerase used in this method could not amplify uracil-containing DNA templates, thus realizing the strand-specificity), while simultaneously performing end repair and dA-Tailing; 5) Sequencing adapter ligation was performed, followed by DNA magnetic bead purification and fragment selection after ligation was completed to yield a library with 250-350 bp insert fragments; 6) The ligated products were amplified by PCR and purified again using DNA magnetic beads, where the products were solubilized with nuclear-free water; 7) After the initial library was constructed, a Qubit fluorescence quantifier was used for concentration detection, followed by a Qsep400 high-throughput biofragment analyzer for fragment size detection，Finally, the effective concentration of the library was accurately quantified using Q-PCR;

value: blood

tag: sample group

value: patients with diminished ovarian reserve (DOR)


title: 4-week TH WT snRNA-seq Sample 3

description:
Library name: P28-TH-WT3
10x Genomics


title: PD16, Amitrole 25mg/kg bw/day, 35_20-24

description:
Library name: PD16_Ami_low_35_20-24
BRB-seq

value: Amitrole 25mg/kg bw/day


title: B73 48h_N- rep1


title: 4-week TH WT snRNA-seq Sample 1

description:
Library name: P28-TH-WT1
10x Genomics


title: A549 cells,miRNA_ADAR_OE_nonSFTSV,rep2

description:
Library name: sample19
SREXC2


title: DOR10

description: Library name: Sample 20


title: PD16, Amitrole 25mg/kg bw/day, 79_20-24

description:
Library name: PD16_Ami_low_79_20-24
BRB-seq

value: testis


title: A549 cells,miRNA_ADAR_nonOE_SFTSV,rep1

description:
Library name: sample16
SRCONE2


title: A549 cells,miRNA_ADAR_OE_nonSFTSV,rep1

description:
Library name: sample18
SREXC1


title: A549 cells,miRNA_ADAR_OE_SFTSV,rep1

description:
Library name: sample21
SREXE1


title: 4-week TH WT snRNA-seq Sample 2

description:
Library name: P28-TH-WT2
10x Genomics


title: PD16, Amitrole 25mg/kg bw/day, 78_20-24

description:
Library name: PD16_Ami_low_78_20-24
BRB-seq


title: B73 48h_N- rep2


title: PD16, Amitrole 25mg/kg bw/day, 80_20-24

description:
Library name: PD16_Ami_low_80_20-24
BRB-seq


title: A549 cells,miRNA_ADAR_nonOE_SFTSV,rep2

description:
Library name: sample17
SRCONE3


title: PD16, Amitrole 25mg/kg bw/day, 36_20-24

description:
Library name: PD16_Ami_low_36_20-24
BRB-seq


title: DOR07

description: Library name: Sample 17


title: PD16, Amitrole 25mg/kg bw/day, 34_20-24

description:
Library name: PD16_Ami_low_34_20-24
BRB-seq


title: A549 cells,miRNA_ADAR_nonOE_nonSFTSV,rep2

description:
Library name: sample14
SRCONC2


title: 4-week TH Grin2b +/- snRNA-seq Sample 4

description:
Library name: P28-TH-HT4
10x Genomics


title: DOR08

description: Library name: Sample 18


title: PD16, Amitrole 25mg/kg bw/day, 33_20-24

description:
Library name: PD16_Ami_low_33_20-24
BRB-seq


title: DOR06

description: Library name: Sample 16


title: DOR02

description: Library name: Sample 12


title: 4-week TH Grin2b +/- snRNA-seq Sample 2

description:
Library name: P28-TH-HT2
10x Genomics


title: DOR05

description: Library name: Sample 15


title: DOR04

description: Library name: Sample 14


title: PD16, Amitrole 25mg/kg bw/day, 16_20-24

description:
Library name: PD16_Ami_low_16_20-24
BRB-seq


title: NOR10

description: Library name: Sample 10

value: normal ovarian reserve (NOR)


title: A549 cells,miRNA_ADAR_nonOE_nonSFTSV,rep3

description:
Library name: sample15
SRCONC3


title: 4-week TH Grin2b +/- snRNA-seq Sample 3

description:
Library name: P28-TH-HT3
10x Genomics


title: DOR03

description: Library name: Sample 13


title: PD16, Amitrole 25mg/kg bw/day, 15_20-24

description:
Library name: PD16_Ami_low_15_20-24
BRB-seq

value: Sprague-Dawley rat dams (Crl:CD(SD) bred by Charles River


title: A549 cells,miRNA_ADAR_KD_SFTSV,rep1

description:
Library name: sample10
SRA3E1


title: 4-week STR WT snRNA-seq Sample 5

description:
Library name: P28-STR-WT5
10x Genomics

source_name: Striatum

value: Striatum


title: 4-week TH Grin2b +/- snRNA-seq Sample 1

description:
Library name: P28-TH-HT1
10x Genomics


title: PD16, Amitrole 25mg/kg bw/day, 14_20-24

description:
Library name: PD16_Ami_low_14_20-24
BRB-seq


title: 4-week STR WT snRNA-seq Sample 4

description:
Library name: P28-STR-WT4
10x Genomics


title: A549 cells,miRNA_ADAR_KD_SFTSV,rep3

description:
Library name: sample12
SRA3E3


title: A549 cells,miRNA_ADAR_nonKD_SFTSV,rep2

description:
Library name: sample8
SRACE2


title: 4-week STR WT snRNA-seq Sample 3

description:
Library name: P28-STR-WT3
10x Genomics


title: DOR01

description: Library name: Sample 11


title: NOR08

description: Library name: Sample 8


title: 4-week STR Grin2b +/- snRNA-seq Sample 4

description:
Library name: P28-STR-HET4
10x Genomics


title: A549 cells,miRNA_ADAR_KD_SFTSV,rep2

description:
Library name: sample11
SRA3E2


title: NOR07

description: Library name: Sample 7


title: PD16, Methimazole 16mg/kg bw/day, 30_20-24

description:
Library name: PD16_MMI_high_30_20-24
BRB-seq

value: Methimazole 16mg/kg bw/day


title: PD16, Methimazole 16mg/kg bw/day, 75_20-24

description:
Library name: PD16_MMI_high_75_20-24
BRB-seq


title: 4-week STR WT snRNA-seq Sample 2

description:
Library name: P28-STR-WT2
10x Genomics


title: 4-week STR WT snRNA-seq Sample 1

description:
Library name: P28-STR-WT1
10x Genomics


title: PD16, Amitrole 25mg/kg bw/day, 13_20-24

description:
Library name: PD16_Ami_low_13_20-24
BRB-seq


title: A549 cells,miRNA_ADAR_nonOE_nonSFTSV,rep1

description:
Library name: sample13
SRCONC1


title: PD16, Methimazole 16mg/kg bw/day, 29_20-24

description:
Library name: PD16_MMI_high_29_20-24
BRB-seq


title: NOR05

description: Library name: Sample 5


title: PD16, Methimazole 16mg/kg bw/day, 12_20-24

description:
Library name: PD16_MMI_high_12_20-24
BRB-seq


title: NOR09

description: Library name: Sample 9


title: 4-week STR Grin2b +/- snRNA-seq Sample 3

description:
Library name: P28-STR-HET3
10x Genomics


title: PD16, Methimazole 16mg/kg bw/day, 32_20-24

description:
Library name: PD16_MMI_high_32_20-24
BRB-seq


title: A549 cells,miRNA_ADAR_nonKD_SFTSV,rep3

description:
Library name: sample9
SRACE3


title: PD16, Methimazole 16mg/kg bw/day, 11_20-24

description:
Library name: PD16_MMI_high_11_20-24
BRB-seq


title: PD16, Methimazole 16mg/kg bw/day, 31_20-24

description:
Library name: PD16_MMI_high_31_20-24
BRB-seq


title: PD16, Methimazole 16mg/kg bw/day, 73_20-24

description:
Library name: PD16_MMI_high_73_20-24
BRB-seq


title: 4-week STR Grin2b +/- snRNA-seq Sample 5

description:
Library name: P28-STR-HET5
10x Genomics


title: A549 cells,miRNA_ADAR_nonKD_SFTSV,rep1

description:
Library name: sample7
SRACE1


title: A549 cells,miRNA_ADAR_KD_nonSFTSV,rep3

description:
Library name: sample6
SRA3C3


title: NOR06

description: Library name: Sample 6


title: A549 cells,miRNA_ADAR_KD_nonSFTSV,rep2

description:
Library name: sample5
SRA3C2


title: PD16, Methimazole 16mg/kg bw/day, 10_20-24

description:
Library name: PD16_MMI_high_10_20-24
BRB-seq


title: 4-week HP WT snRNA-seq Sample 3

description:
Library name: P28-HP-WT3
10x Genomics

source_name: Hippocampus

value: Hippocampus


title: 4-week HP WT snRNA-seq Sample 2

description:
Library name: P28-HP-WT2
10x Genomics


title: 4-week STR Grin2b +/- snRNA-seq Sample 2

description:
Library name: P28-STR-HET2
10x Genomics


title: 4-week STR Grin2b +/- snRNA-seq Sample 1

description:
Library name: P28-STR-HET1
10x Genomics


title: PD16, Methimazole 8mg/kg bw/day, 66_20-24

description:
Library name: PD16_MMI_low_66_20-24
BRB-seq

value: Methimazole 8mg/kg bw/day


title: NOR04

description: Library name: Sample 4


title: 4-week HP WT snRNA-seq Sample 1

description:
Library name: P28-HP-WT1
10x Genomics


title: 4-week HP WT snRNA-seq Sample 4

description:
Library name: P28-HP-WT4
10x Genomics


title: A549 cells,miRNA_ADAR_KD_nonSFTSV,rep1

description:
Library name: sample4
SRA3C1


title: A549 cells,miRNA_ADAR_nonKD_nonSFTSV,rep3

description:
Library name: sample3
SRACC3


title: NOR02

description: Library name: Sample 2


title: NOR03

description: Library name: Sample 3


title: PD16, Methimazole 16mg/kg bw/day, 9_20-24

description:
Library name: PD16_MMI_high_9_20-24
BRB-seq


title: A549 cells,miRNA_ADAR_nonKD_nonSFTSV,rep2

description:
Library name: sample2
SRACC2


title: GB2, Input

city: Bronx

first: Jorge

middle: Eduardo

last: Fajardo

state: NY

address: 1301 Morris Park Avenu

department: Computational and Systems Biology

institute: Albert Einstein College of Medicine

description: Library name: GB2, Input

data_processing:
Basecalls were performed using bcl2fastq v2.20 for Novaseq output.
ChIP-seq reads were aligned to the UCSC hg38 genome using bwa (v0.7.12) Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 200 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called using MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the wigToBigWig (v4) software. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: glioma stem cells were maintained in Neural basal A medium supplimented with EGF/FGF, glutamax, heparin, vitamin B27 and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: glioma stem cells

tag: chip antibody


title: NOR01

description: Library name: Sample 1


title: Kpy_PBS_rep1

city: HANGZHOU

first: xiaohan

last: song

address: No.1 XIANGSHAN ROAD

institute: University of the Chinese Academy of Sciences Hangzhou Institute for Advanced Study

description:
Library name: Sample 11
Kpy_PBS_rep1

data_processing:
Sequencing quality was evaluated by FastQC (v0.11.9).  All reads were mapped to hg38 using Bowtie2 (v2.4.4). Peaks were called using MACS version (v3.0.0b1). Peaks were annotated to nearest genes (ChIPseeker v1.34.1).
Assembly: hg38
Supplementary files format and content: TSS_reads_2000_BT_anno_short.csv (CUT&Tag, including sequencing read counts at transcription start site (TSS) regions for samples 1-12)
Library strategy: CUT&Tag

source_name: HEK293T cells

growth_protocol: HEK293T cells were maintained in DMEM supplemented containing 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were cultured in an incubator containing 5% CO2 at 37 oC with suitable humidity.

extract_protocol:
DNA was extracted from 100,000 cells using the NovoNGS® CUT&Tag 4.0 High-Sensitivity Kit (for Illumina®) (N259-YH01, Novoprotein), following the manufacturer's instructions. For each sample, 1 μg of anti-pan Kpy, anti-pan Kac, or anti-pan Kla antibody was used, respectively.
In situ tagmentation with pA-Tn5

treatment_protocol: HEK293T cells were treated with or without 20 mM oxamate for 24 h

value: HEK293T cells

value: human embryonic kidney cells


title: PD16, Methimazole 8mg/kg bw/day, 65_20-24

description:
Library name: PD16_MMI_low_65_20-24
BRB-seq


title: A549 cells,miRNA_ADAR_nonKD_nonSFTSV,rep1

description:
Library name: sample1
SRACC1


title: Kla_PBS_rep2

description:
Library name: Sample 10
Kla_PBS_rep2

value: WT


title: GB2, sicontrol, H3K9me3 ChIP

description: Library name: GB2, sicontrol, H3K9me3 ChIP

value: anti-H3K9me3 from Active Motif


title: PD16, Methimazole 8mg/kg bw/day, 63_20-24

description:
Library name: PD16_MMI_low_63_20-24
BRB-seq


title: 4-week HP Grin2b +/- snRNA-seq Sample 2

description:
Library name: P28-HP-HT2
10x Genomics

value: Grin2b +/-


title: 4-week HP Grin2b +/- snRNA-seq Sample 4

description:
Library name: P28-HP-HT4
10x Genomics


title: GB2, siHDAC7, H3K9me3 ChIP

description: Library name: GB2, siHDAC7, H3K9me3 ChIP


title: Kpy_PBS_rep2

description:
Library name: Sample 12
Kpy_PBS_rep2


title: PD16, Methimazole 8mg/kg bw/day, 64_20-24

description:
Library name: PD16_MMI_low_64_20-24
BRB-seq


title: Kac_PBS_rep2

description:
Library name: Sample 8
Kac_PBS_rep2


title: SKOV3 cSKOV3 cells, CUL4B, CUT&Tagells, control2

city: Chongqing

first: Xin

last: Yin

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing medical university

data_processing:
Base-Calling was performed by CASAVA version 1.4
The high quality reads were mapped to the Human genome 19 of Ensembl by using Bowtie(version 0.12.8) with the default parameter.
Data were filtered using the following specification:A Perl program was used to filter of low quality sequences from raw sequencing data. The quality of each base was checked from the first base of each read. Once a low-quality base (quality<10) was  found,  it was removed together with following sequences. For paired-end reads, if one read was less than 30 bases after the trimming of low quality bases, the whole paired-end reads were  removed.
The expression peaks were detected by MACS (Model-based Analysis for ChIP-Seq) using the parameter
Assembly: hg19
Supplementary files format and content: narrowPeak

growth_protocol: SKOV3 epithelial cells were maintained in Mc5a supplemented with 10% fetal bovine serum (FBS) and antibody in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
10 ng of ChIP DNA was end polished with T4 DNA polymerase and kinase. An 'A' base was added to the polished DNA fragments, followed by the Qiaquick column clean up. Solexa adaptors were ligated to the ChIP DNA fragments and enriched by 15 cycles of PCR amplification. 200-300 bp size fractions were selectively isolated from the 1% agarose gel and eluted by the Qiagen gel extraction kit. The extracted DNA was quantified by picogreen assay and subjected to HiSeq2000 sequencing according to the manufacturer‘s instructions.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For a ChIP assay, approximately 1 x 10^6 cells were used.The chromatin DNA precipitated by antibodies against GATA4 and CUL4B. The DNA was obtained using Cleavage Under Targets and Tagmentation (CUT&Tag) kit.

value: CUL4B (Proteintech)

value: epithelial cells


title: 4-week HP Grin2b +/- snRNA-seq Sample 3

description:
Library name: P28-HP-HT3
10x Genomics


title: Kac_PBS_rep1

description:
Library name: Sample 7
Kac_PBS_rep1


title: PD16, Methimazole 8mg/kg bw/day, 27_20-24

description:
Library name: PD16_MMI_low_27_20-24
BRB-seq


title: 4-week HP Grin2b +/- snRNA-seq Sample 1

description:
Library name: P28-HP-HT1
10x Genomics


title: Kla_PBS_rep1

description:
Library name: Sample 9
Kla_PBS_rep1


title: PD16, Methimazole 8mg/kg bw/day, 28_20-24

description:
Library name: PD16_MMI_low_28_20-24
BRB-seq


title: Kpy_Oxamate_rep2

description:
Library name: Sample 6
Kpy_Oxamate_rep2

value: oxamate treated


title: 2-week SN Grin2b WT Sample 3

description: Library name: grin2b_P14-SN-WT3

data_processing:
Reads were aligned to RefSeq M25/GRCm38.p6 and gene and isoform level expression values were estimated using RSEM v1.3.0
Assembly: RefSeq M25/
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

value: Substantia Nigra

value: Grin2b WT


title: 2-week SN Grin2b WT Sample 5

description: Library name: grin2b_P14-SN-WT5


title: PD16, Methimazole 8mg/kg bw/day, 26_20-24

description:
Library name: PD16_MMI_low_26_20-24
BRB-seq

value: testis


title: Kpy_Oxamate_rep1

description:
Library name: Sample 5
Kpy_Oxamate_rep1


title: SKOV3 cells, GATA4, CUT&Tag

value: GATA4 (Proteintech)


title: Control1

first: Yi

last: Sun

address: Zhizaoju Road 639

department: Department of Interventional Therapy, Multidisciplinary Team of Vascular Anomalies

institute: Shanghai Ninth People’s hospital, Shanghai Jiao Tong University, Shanghai, PR China

data_processing:
Reads were processed using the Cell Ranger 2.1.0 pipeline with default and recommended parameters.    FASTQs generated from Illumina sequencing output were aligned to the mouse genome, version GRCm38, using the STAR algorithm.    Next, gene barcode matrices were generated for each individual sample by counting UMIs and filtering noncell-associated barcodes.    Finally, we generated a gene-barcode matrix containing the barcoded cells and gene expression counts.    This output was then imported into the Seurat (v2.3.0) R toolkit for quality control and downstream analysis of our single-cell RNAseq data.    All functions were run with default parameters unless specified otherwise.    We excluded cells with fewer than 200 or more than 6000 detected genes (where each gene had to have at least one UMI aligned in at least three cells).    The expression of mitochondrial genes was calculated using the PercentageFeatureSet function of the seurat package.    To remove low-activity cells, cells with more than 10% expression of mitochondrial genes were excluded.    The normalized data (NormalizeData function in Seurat package) were used to extract a subset of variable genes.    Variable genes were identified while controlling for the strong relationship between variability and average expression.    Next, we integrated data from different samples after identifying ‘anchors’ between datasets using FindIntegrationAnchors and IntegrateData in the seurat package.    Then, we performed principal component analysis (PCA) and reduced the data to the top 30 PCA components after scaling the data.    We visualized the clusters on a 2D map produced with t-distributed stochastic neighbor embedding (t-SNE).
Assembly: hg38
Supplementary files format and content: Cell Ranger output files

source_name: skin and soft tissue

extract_protocol:
Tissues were transported in sterile culture dishes with 10 ml 1x Dulbecco's phosphate-buffered saline (DPBS; Thermo Fisher, Cat. no. 14190144) on ice to remove the residual tissue storage solution and then minced on ice. We used dissociation enzyme 0.25% Trypsin (Thermo Fisher, Cat. no. 25200-072) and 10 µg/mL lDNase I (Sigma, Cat. no. 11284932001) dissolved in PBS with 5% fetal bovine serum (FBS; Thermo Fisher, Cat. no. SV30087.02) to digest the tissues. eAVM tissues were dissociated at 37 ℃ with a shaking speed of 50 r.p.m for approximately 40 min. We repeatedly collected the dissociated cells at intervals of 20 min to increase cell yield and viability. Cell suspensions were filtered using a 40 µm nylon cell strainer, and red blood cells were removed by 1X Red Blood Cell Lysis Solution (Thermo Fisher, Cat. no. 00-4333-57). Dissociated cells were washed with 1x DPBS containing 2% FBS. Cells were stained with 0.4% Trypan blue (Thermo Fisher, Cat. no. 14190144) to check the viability on a Countess® II Automated Cell Counter (Thermo Fisher).
Beads with unique molecular identifiers (UMIs) and cell barcodes were loaded close to saturation so that each cell was paired with a bead in a gel beads-in-emulsion (GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’ end (that is, the 3’ end of a messenger RNA transcript) with UMI and a cell label indicating its cell of origin. Briefly, 10× beads were then subjected to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures, including library construction, were performed according to the standard manufacturer’s protocol (CG000206 RevD). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on a NovaSeq6000 (Illumina) using 2x150 chemistry.

value: skin and soft tissue

tag: condition

value: Control


title: 2-week SN Grin2b WT Sample 2

description: Library name: grin2b_P14-SN-WT2


title: 2-week SN Grin2b WT Sample 1

description: Library name: grin2b_P14-SN-WT1


title: Control2


title: Kla_Oxamate_rep2

description:
Library name: Sample 4
Kla_Oxamate_rep2


title: eAVM9

value: eAVM


title: PD16, Methimazole 8mg/kg bw/day, 8_20-24

description:
Library name: PD16_MMI_low_8_20-24
BRB-seq

value: Sprague-Dawley rat dams (Crl:CD(SD) bred by Charles River

value: Methimazole 8mg/kg bw/day


title: 2-week SN Grin2b +/- Sample 4

description: Library name: grin2b_P14-SN-HT4


title: PD16, Methimazole 8mg/kg bw/day, 25_20-24

description:
Library name: PD16_MMI_low_25_20-24
BRB-seq


title: Kac_Oxamate_rep2

description:
Library name: Sample 2
Kac_Oxamate_rep2

value: HEK293T cells


title: 2-week SN Grin2b +/- Sample 5

description: Library name: grin2b_P14-SN-HT5


title: Kla_Oxamate_rep1

description:
Library name: Sample 3
Kla_Oxamate_rep1

value: human embryonic kidney cells


title: PD16, Methimazole 8mg/kg bw/day, 7_20-24

description:
Library name: PD16_MMI_low_7_20-24
BRB-seq


title: PD16, Vehicle (corn oil), 59_20-24

description:
Library name: PD16_ctrl_59_20-24
BRB-seq

value: Vehicle (corn oil)


title: Kac_Oxamate_rep1

description:
Library name: Sample 1
Kac_Oxamate_rep1

value: WT


title: eAVM7


title: eAVM8


title: PD16, Vehicle (corn oil), 60_20-24

description:
Library name: PD16_ctrl_60_20-24
BRB-seq


title: PD16, Vehicle (corn oil), 58_20-24

description:
Library name: PD16_ctrl_58_20-24
BRB-seq


title: eAVM6


title: eAVM5


title: 2-week SN Grin2b +/- Sample 3

description: Library name: grin2b_P14-SN-HT3

value: Grin2b +/-


title: eAVM4


title: 2-week SN Grin2b +/- Sample 2

description: Library name: grin2b_P14-SN-HT2


title: PD16, Vehicle (corn oil), 57_20-24

description:
Library name: PD16_ctrl_57_20-24
BRB-seq


title: 2-week SN Grin2b +/- Sample 1

description: Library name: grin2b_P14-SN-HT1


title: PAH_tolerant_+PAH_RNA

city: Saint Paul

first: Caren

last: Weinhouse

state: Minnesota

address: 1988 Fitch Ave

institute: Oregon H

description:
Library name: RPERSE_RNA_seq
Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Reference Guide

data_processing:
Raw RNA-seq reads were aligned to our de novo Kings Creek Fundulus heteroclitus reference genome using STAR, configured for a stranded RNA-seq protocol
Assembly: de novo genome assembly (PRJNA1381666/SAMN54117932)
Supplementary files format and content: RNA-seq: sample.gtf, sample.stringtie.abundance.tsv

organism: Fundulus heteroclitus

source_name: embryo

extract_protocol:
Total RNA was extracted using a Qiagen RNEasy Blood and Tissue Minikit
Total RNA was prepped following the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus manufacturers protocol. https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/illumina_prep/RNA/illumina-stranded-total-rna-prep-reference-guide-1000000124514-02.pdf

value: embryo

value: PAH exposed


title: eAVM3


title: PAH_sensitive_+PAH_RNA

description:
Library name: KCERSE_RNA_seq
Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Reference Guide


title: 4-week SN Grin2b WT Sample 5

description: Library name: grin2b_P28-SN-WT5


title: PD16, Vehicle (corn oil), 23_20-24

description:
Library name: PD16_ctrl_23_20-24
BRB-seq


title: eAVM2


title: PD16, Vehicle (corn oil), 24_20-24

description:
Library name: PD16_ctrl_24_20-24
BRB-seq


title: 4-week SN Grin2b WT Sample 2

description: Library name: grin2b_P28-SN-WT2


title: PAH_sensitive_control_RNA

description:
Library name: KCClean_RNA_seq
Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Reference Guide


title: PD16, Vehicle (corn oil), 22_20-24

description:
Library name: PD16_ctrl_22_20-24
BRB-seq


title: 4-week SN Grin2b WT Sample 3

description: Library name: grin2b_P28-SN-WT3


title: eAVM1


title: siCT1 2 INPUT

city: Boston

first: Kashish

last: Chetal

address: 55 Fruit St

department: Molecular biology

institute: MGH

description: Library name: siCT1_2_INPUT

data_processing:
Sequencing reads were aligned against the hg19 reference genome using BWA (PMID: 20080505). Alignments were filtered for uniquely mapped reads and duplicates were removed.
ChIP over Input ratio coverage tracks were generated using deepTools (PMID: 27079975).
Peaks were called using HOMER (PMID: 20513432) with default parameters.
Assembly: hg19
Supplementary files format and content: bigwig

source_name: RPE

extract_protocol:
Cells were fixed with 1% formaldehyde for 13 minutes. After quenching and cell lysis, chromatin was sonicated using a Q800R3 sonicator (QSonica).
ChIP-seq libraries were prepared using the Illumina TruSeq ChIP Library Preparation Kit Set A and B with associated index barcode adapters. 1 ng or 30µL of DNA was used as starting material for input and ip samples. Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were cleaned up using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity D1000 DNA Kit.

value: RPE

value: Retinal pigment epithelial

value: siRNA Knockdown

value: Chromatin


title: siKDM5A 36 INPUT

description: Library name: siKDM5A_36_INPUT


title: 4-week SN Grin2b WT Sample 1

description: Library name: grin2b_P28-SN-WT1

value: Substantia Nigra

value: Grin2b WT


title: PD16, Vehicle (corn oil), 21_20-24

description:
Library name: PD16_ctrl_21_20-24
BRB-seq

value: testis


title: GSC R83 cells, GNAO1 OE, rep3

first: Guoyu

last: Chen

address: Xuhui District Yueyang Road 320

institute: PICB

data_processing:
raw sequencing reads were mapped to hg38/gencode v38 using hisat2
raw read counts were quantified using featureCounts
differential expression analysis were done by DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts for each sample

source_name: GSC R83

growth_protocol: GSC R83 cells were from ATCC (Manassas, VA, USA), and were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin and streptomycin with 5% CO2 at 37C. Human GNAO1 coding regions were cloned into a pLVX-Puro Vector (Clontech) with Flag tag. GSC R83 overexpression GNAO1 Cells are sorted by flow cytometry and continued culture.

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen) and 1 μg was used for synthesis of first-strand cDNA with Maxima First Strand cDNA Synthesis Kit (Takara). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prey Kit following manufacturer's protocols.

value: GSC R83

value: Glioma cells

value: GNAO3 overexpression


title: GSC R83 cells, GNAO1 OE, rep1

value: GNAO1 overexpression


title: PAH_tolerant_control_RNA

description:
Library name: RPClean_RNA_seq
Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Reference Guide

value: Control


title: PD16, Vehicle (corn oil), 4_20-24

description:
Library name: PD16_ctrl_4_20-24
BRB-seq

value: Sprague-Dawley rat dams (Crl:CD(SD) bred by Charles River

value: Vehicle (corn oil)


title: GSC R83 cells, WT, rep3

value: WT


title: PD16, Vehicle (corn oil), 3_20-24

description:
Library name: PD16_ctrl_3_20-24
BRB-seq


title: 4-week SN Grin2b +/- Sample 4

description: Library name: grin2b_P28-SN-HT4

extract_protocol:
RNA libraries for RNA-seq were prepared using an Illumina TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions.
RNA-seq

value: Grin2b +/-


title: siKDM5A 34 INPUT

description: Library name: siKDM5A_34_INPUT


title: siCT1 2 H3K4me3

description: Library name: siCT1_2_H3K4me3


title: 4-week SN Grin2b +/- Sample 3

description: Library name: grin2b_P28-SN-HT3


title: GD21, Amitrole 50mg/kg bw/day, 90_20-24

description:
Library name: GD21_Ami_high_90_20-24
BRB-seq

value: Amitrole 50mg/kg bw/day


title: siCT1 1 H3K4me3

description: Library name: siCT1_1_H3K4me3

value: RPE


title: GSC R83 cells, WT, rep1


title: GSC R83 cells, WT, rep2


title: GD21, Amitrole 50mg/kg bw/day, 88_20-24

description:
Library name: GD21_Ami_high_88_20-24
BRB-seq


title: 4-week SN Grin2b +/- Sample 1

description: Library name: grin2b_P28-SN-HT1


title: GD21, Amitrole 50mg/kg bw/day, 89_20-24

description:
Library name: GD21_Ami_high_89_20-24
BRB-seq


title: siKDM5A 36 H3K4me3

description: Library name: siKDM5A_36_H3K4me3

value: Retinal pigment epithelial


title: 4-week SN Grin2b +/- Sample 5

description: Library name: grin2b_P28-SN-HT5


title: 4-week SN Grin2b +/- Sample 2

description: Library name: grin2b_P28-SN-HT2


title: GSC R83 cells, GNAO1 OE, rep2

value: GNAO2 overexpression


title: siCT1 1 INPUT

description: Library name: siCT1_1_INPUT

value: siRNA Knockdown

value: Chromatin


title: 12-week SN Grin2b WT Sample 5

description: Library name: grin2b_12w-SN-WT5

value: Substantia Nigra

value: Grin2b WT


title: GD21, Amitrole 50mg/kg bw/day, 87_20-24

description:
Library name: GD21_Ami_high_87_20-24
BRB-seq

value: testis


title: 12-week SN Grin2b WT Sample 4

description: Library name: grin2b_12w-SN-WT4


title: GD21, Amitrole 50mg/kg bw/day, 55_20-24

description:
Library name: GD21_Ami_high_55_20-24
BRB-seq


title: siKDM5A 34 H3K4me3

description: Library name: siKDM5A_34_H3K4me3


title: Patient B1, recovered health status after respiratory infection, mRNA

city: Budapest

first: Zsolt

last: Ronai

address: Ulloi u. 26.

department: Molecular Biology

country: Hungary

institute: Semmelweis University

description: Library name: SZ374mes

data_processing:
Trimmed sequence sets (FASTQ-formatted) were aligned to the genome sequences using HISAT2 with default parameters.
The aligned reads were collected in bam files and were aligned according to genomic coordinates using the SAMTOOLS program package before further use.
The function featureCounts (Rsubread R package) were used for counting reads for each gene.
Assembly: GRCH38 genome sequence version 39
Supplementary files format and content: tab delimited text file contains raw counts for each sample in case of both mRNA and miRNA datasets

source_name: 47-year-old male patient, day 6

extract_protocol:
RNAs from blood samples were isolated with TRIzol protocol and Tempus™ Spin RNA Isolation Kit according to the manufacturers’ instructions (TRIzol™ Reagent User Guide1 – ThermoFisher Scientific, Inc., Waltham, MA, USA; Tempus Blood RNA Tube and Tempus Spin RNA Isolation Kit User Guide2 ThermoFisher Scientific, Inc., Waltham, MA, USA). RNA concentration, quality and RNA integrity number (RIN) of each sample were measured using Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA, USA) instruments using Eukaryotic Total RNA Nano Kit (RNA 6000) (Agilent Technologies, Inc., Santa Clara, CA, USA) according to manufacturer’s protocol.
RNA-Seq libraries were prepared from total RNA using Ultra II RNA Sample Prep kit (New England BioLabs, Inc., Ipswich, MA, USA) according to the manufacturer’s protocol. Briefly, poly-A RNAs were captured by oligo-dT conjugated magnetic beads then the mRNAs were eluted and fragmented at 94-Celsius degree. First strand cDNA was generated by random priming reverse transcription and after second strand synthesis step double stranded cDNA was generated. After repairing ends, A-tailing and adapter ligation steps adapter ligated fragments were amplified in enrichment PCR and finally sequencing libraries were generated.

value: blood

tag: gender

value: male


title: GD21, Amitrole 50mg/kg bw/day, 56_20-24

description:
Library name: GD21_Ami_high_56_20-24
BRB-seq


title: 12-week SN Grin2b WT Sample 3

description: Library name: grin2b_12w-SN-WT3

source_name: Substantia Nigra


title: Patient B1, improving health status after sepsis originating from respiratory infection, mRNA

description: Library name: SZ373mes

source_name: 47-year-old male patient, day 3


title: p53MDM2_99_6hr

type: RNA

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

hyb_protocol: Hybridized to Human GeneChipTM Human Gene 1.0 ST Arrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment. RMA was used to normalize and fit log2 transformed expression values.

label: biotin

source_name: purified AML cells from PBMCs

label_protocol: Biotinylated cDNA were prepared according to the Nugen WT-Pico Ovation kit protocol from 10 ng total RNA (WT-Pico Ovation RNA Amplification System Manual, 2007, NuGEN). Subsequently cDNA is made double stranded fragmented and end-labeled following manufacturers standard protocol (NuGEN encore end-labeling module).

growth_protocol: Mononuclear cells from blood or marrow from AML patients were isolated by Ficoll gradient centrifugation (GE Healthcare), aliquoted into FCS with 10% DMSO, and cryopreserved in liquid nitrogen. For purification of AML blasts using negative selection, cryopreserved PBMCs were washed and recovered by centrifugation and then treated with anti-human CD3 (Miltenyi Biotec #130-050-101), anti-human CD14 microbeads (if blasts were negative for CD14 expression; Miltenyi Biotec #130-050-201), anti-human CD19 (if blasts were negative for CD19 expression; Miltenyi Biotec #130-050-301) and anti-human CD235a (Miltenyi Biotec #130-050-501) per manufacturer’s recommendations. Cell suspensions were run through Miltenyi MACS separation LS columns (#130-042-401) to negatively enrich for AML blasts.  All blast preps were analyzed by cytospins for purity. This schema resulted in greater than 90%-95% blast purity.

extract_protocol: RNA was extracted using the Trizol reagent. RNA was further purified using the RNeasy kit (Qiagen 74104) and the integrity analyzed using the bioanalyzer platform (Agilent).

treatment_protocol: Blasts enriched to >90% purity were incubated in serum-supplemented RPMI medium at 2.5x105 cells in 100 µl final volume in the presence of 0.625-20µM of the MDM2 inhibitor MI-219

value: f

tag: mdm2 inhibitor sensitivity

value: Resistant

tag: time point (h)

tag: aml type

value: de novo


title: p53MDM2_99_u


title: Patient B1, severe sepsis originating from respiratory infection, mRNA

description: Library name: SZ372mes

source_name: 47-year-old male patient, day 0

tag: tissue


title: p53MDM2_98_6hr

value: m


title: p53MDM2_99_2hr


title: 12-week SN Grin2b WT Sample 1

first: Ally

last: Nicolella

address: 75 Ames St

institute: Broad Institute

description: Library name: grin2b_12w-SN-WT1


title: Patient B5, recovered health status after urogenital infection, mRNA

description: Library name: SZ357mes

source_name: 64-year-old female patient, day 1

value: female


title: 12-week SN Grin2b +/- Sample 5

description: Library name: grin2b_12w-SN-HT5

value: Grin2b +/-


title: Patient B5, severe sepsis originating from urogenital infection, mRNA

description: Library name: SZ356mes

source_name: 64-year-old female patient, day 0


title: GD21, Amitrole 25mg/kg bw/day, 54_20-24

description:
Library name: GD21_Ami_low_54_20-24
BRB-seq

source_name: testis

value: Sprague-Dawley rat dams (Crl:CD(SD) bred by Charles River

value: Amitrole 25mg/kg bw/day


title: p53MDM2_98_u


title: GD21, Amitrole 25mg/kg bw/day, 82_20-24

description:
Library name: GD21_Ami_low_82_20-24
BRB-seq


title: 12-week SN Grin2b +/- Sample 4

description: Library name: grin2b_12w-SN-HT4


title: GD21, Amitrole 25mg/kg bw/day, 53_20-24

description:
Library name: GD21_Ami_low_53_20-24
BRB-seq


title: Patient B4, improving health status after sepsis originating from urogenital infection, mRNA

description: Library name: SZ351mes

source_name: 72-year-old female patient, day 1


title: GD21, Amitrole 25mg/kg bw/day, 81_20-24

description:
Library name: GD21_Ami_low_81_20-24
BRB-seq


title: Patient B4, recovered health status after urogenital infection, mRNA

description: Library name: SZ352mes

source_name: 72-year-old female patient, day 2


title: p53MDM2_98_2hr


title: 12-week SN Grin2b +/- Sample 3

description: Library name: grin2b_12w-SN-HT3


title: GD21, Amitrole 25mg/kg bw/day, 52_20-24

description:
Library name: GD21_Ami_low_52_20-24
BRB-seq


title: GD21, Amitrole 25mg/kg bw/day, 51_20-24

description:
Library name: GD21_Ami_low_51_20-24
BRB-seq


title: 12-week SN Grin2b WT Sample 2

description: Library name: grin2b_12w-SN-WT2


title: Patient B4, severe sepsis originating from urogenital infection, mRNA

description: Library name: SZ350mes

source_name: 72-year-old female patient, day 0


title: 12-week SN Grin2b +/- Sample 2

description: Library name: grin2b_12w-SN-HT2


title: 12-week SN Grin2b +/- Sample 1

description: Library name: grin2b_12w-SN-HT1


title: p53MDM2_90_6hr

value: Sensitive


title: p53MDM2_90_2hr


title: GD21, Methimazole 16mg/kg bw/day, 71_20-24

description:
Library name: GD21_MMI_high_71_20-24
BRB-seq

value: Methimazole 16mg/kg bw/day


title: Patient B3, recovered health status after respiratory infection, mRNA

description: Library name: SZ347mes

source_name: 52-year-old male patient, day 9


title: GD21, Methimazole 16mg/kg bw/day, 72_20-24

description:
Library name: GD21_MMI_high_72_20-24
BRB-seq


title: p53MDM2_9_u


title: GD21, Methimazole 16mg/kg bw/day, 50_20-24

description:
Library name: GD21_MMI_high_50_20-24
BRB-seq


title: p53MDM2_90_u


title: 20-week SN Grin2b WT Sample 5

description: Library name: grin2b_20w-SN-WT5


title: p53MDM2_9_6hr


title: 20-week SN Grin2b WT Sample 4

description: Library name: grin2b_20w-SN-WT4


title: Patient B3, improving health status after sepsis originating from respiratory infection, mRNA

description: Library name: SZ345mes

source_name: 52-year-old male patient, day 5


title: 20-week SN Grin2b WT Sample 2

description: Library name: grin2b_20w-SN-WT2


title: GD21, Methimazole 16mg/kg bw/day, 49_20-24

description:
Library name: GD21_MMI_high_49_20-24
BRB-seq


title: 20-week SN Grin2b WT Sample 3

description: Library name: grin2b_20w-SN-WT3


title: p53MDM2_9_2hr


title: Patient B3, severe sepsis originating from respiratory infection, mRNA

description: Library name: SZ341mes

source_name: 52-year-old male patient, day 0


title: Patient B2, recovered health status after urogenital infection, mRNA

description: Library name: SZ340mes

source_name: 83-year-old female patient, day 4


title: Patient B2, improving health status after sepsis originating from urogenital infection, mRNA

description: Library name: SZ336mes

source_name: 83-year-old female patient, day 1


title: 20-week SN Grin2b WT Sample 1

description: Library name: grin2b_20w-SN-WT1


title: GD21, Methimazole 8mg/kg bw/day, 69_20-24

description:
Library name: GD21_MMI_low_69_20-24
BRB-seq

value: Methimazole 8mg/kg bw/day


title: GD21, Methimazole 16mg/kg bw/day, 47_20-24

description:
Library name: GD21_MMI_high_47_20-24
BRB-seq


title: GD21, Methimazole 16mg/kg bw/day, 48_20-24

description:
Library name: GD21_MMI_high_48_20-24
BRB-seq


title: GD21, Methimazole 8mg/kg bw/day, 70_20-24

description:
Library name: GD21_MMI_low_70_20-24
BRB-seq


title: 20-week SN Grin2b +/- Sample 5

description: Library name: grin2b_20w-SN-HT5


title: Patient B6, recovered health status after respiratory infection, mRNA

description: Library name: SZ334mes

source_name: 46-year-old female patient, day 14


title: 20-week SN Grin2b +/- Sample 4

description: Library name: grin2b_20w-SN-HT4


title: p53MDM2_86_6hr


title: p53MDM2_81_u


title: Patient B2, severe sepsis originating from urogenital infection, mRNA

description: Library name: SZ335mes

source_name: 83-year-old female patient, day 0


title: p53MDM2_86_2hr


title: p53MDM2_86_u


title: GD21, Methimazole 8mg/kg bw/day, 68_20-24

description:
Library name: GD21_MMI_low_68_20-24
BRB-seq


title: 20-week SN Grin2b +/- Sample 3

description: Library name: grin2b_20w-SN-HT3

source_name: Substantia Nigra


title: GD21, Methimazole 8mg/kg bw/day, 67_20-24

description:
Library name: GD21_MMI_low_67_20-24
BRB-seq


title: p53MDM2_81_6hr


title: GD21, Methimazole 8mg/kg bw/day, 46_20-24

description:
Library name: GD21_MMI_low_46_20-24
BRB-seq


title: MCF10A cells, BAP1 knockout, 2D culture, pool of clones 1 and 2 and biol reps 1 and 2, input

city: Lyon

first: Zdenko

last: Herceg

address: 25 avenue Tony Garnier CS 90627

department: EGM

institute: IARC

data_processing:
Reads were mapped to hg38 with BWA v0.7.17 and trimmed using Trim Galore v0.6.10.
Peak signals were called with MACS2, using the broad option, and then filtered using irreproducible discovery rate (IDR) within each condition. We considered duplicates for peak calling and read counting.
Differential analysis was performed with DiffBind v3.12.0. Read numbers per peak were normalized using the RLE method, and differential peaks were called using DESeq2.
Assembly: hg38
Supplementary files format and content: bw (BigWig) ; broadpeaks (bed file)

growth_protocol: MCF10A cells were maintained in DMEM/F12 medium supplemented with 5% fetal bovine serum (FBS), insulin (10 µg/mL), epidermal growth factor (20 ng/mL), hydrocortisone (500 ng/mL), cholera toxin (100ng/mL), and 1% penicillin/streptomycin, in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
1 million cells were fixed with 1% formaldehyde for 8 minutes, and sonicated for 8 cycles on a Bioruptor Pico (Diagenode). ChIP-seq against H2AK119ub1 (D27C4, Cell Signaling Technology) was performed with the iDeal ChIP-seq kit for histones (Diagenode) as per the manufacturer’s protocol.
Libraries were prepared using the TruSeq ChIP Sample Prep kit (Illumina) using 10ng of DNA as starting material for inputs and IP samples.

tag: cell line

tag: cell type

value: Non-tumorigenic mammary cells

value: BAP1 knockout, pool of clones


title: MCF10A cells, BAP1 knockout clone 2, 2D culture, biol rep 2, H2AK119ub1

value: H2AK119ub1 (D27C4, Cell Signaling Technology)

tag: genotype

value: BAP1 knockout, clone 2


title: 20-week SN Grin2b +/- Sample 2

description: Library name: grin2b_20w-SN-HT2

value: Substantia Nigra


title: p53MDM2_80_u


title: MCF10A cells, Cas9-expressing controls, 2D culture, pool of biol reps 1 and 2, input

value: Cas9-expressing control


title: 20-week SN Grin2b +/- Sample 1

description: Library name: grin2b_20w-SN-HT1


title: p53MDM2_81_2hr

value: f


title: GD21, Vehicle (corn oil), 62_20-24

description:
Library name: GD21_ctrl_62_20-24
BRB-seq

value: testis

tag: treatment

value: Vehicle (corn oil)


title: p53MDM2_80_2hr

value: m

value: Resistant

value: de novo

tag: age


title: MCF10A cells, BAP1 knockout clone 2, 2D culture, biol rep 1, H2AK119ub1


title: p53MDM2_80_6hr


title: GD21, Methimazole 8mg/kg bw/day, 45_20-24

description:
Library name: GD21_MMI_low_45_20-24
BRB-seq

value: Sprague-Dawley rat dams (Crl:CD(SD) bred by Charles River


title: SufuD159R_Mut_RNAseq_rep3

city: Cincinnati

first: Samantha

last: Brugmann

state: OH

address: 3333 Burnet Ave

department: Developmental Biology

institute: Cincinnati Children's Hospital

description: Library name: SufuD159R_Mut_RNAseq_rep3

data_processing:
A quality control check on the fastq files was performed using FastQC. Upon passing basic quality metrics, the reads were trimmed to remove adapters and low-quality reads using default parameters in Trimmomatic. The trimmed reads were then mapped to a reference genome GRCm39 using STAR. Transcript/gene abundance was determined using featureCounts and DEseq2.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: head

extract_protocol:
Total RNA was extracted by using RNAqueous-Micro Total RNA Isolation Kit (ThermoFisher).
150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high-sensitivity spectrofluorometric measurement was poly-A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit. Each sample was fitted with one of 96 adapters containing a different 8 base molecular barcode for high level multiplexing. After 15 cycles of PCR amplification, completed libraries were sequenced on an Illumina NovaSeqTM 6000, generating 20 million or more high quality 100 base long paired end reads per sample.

value: head


title: Patient B6, severe sepsis originating from respiratory infection, mRNA

description: Library name: SZ329mes

source_name: 46-year-old female patient, day 0

value: blood

value: female


title: SufuD159R_Mut_RNAseq_rep1

description: Library name: SufuD159R_Mut_RNAseq_rep1


title: Single-cell RNA-seq of CD4⁺CXCR5⁺PD-1⁺ T cells from tumor lymph node

city: Montreal

first: Saba

last: Mohammaei

address: 110 Pine Ave W

country: Canada

institute: IRCM

description:
Library name: Roquin_TumorLN
Sorted CD4⁺CXCR5⁺PD-1⁺ T cells from Roquin san/+ tumor lymph node; 10x Genomics

data_processing:
Data were processed using the Seurat R package (v3.0). Control and tumor samples were merged, and cells with >10% mitochondrial gene expression or <200 unique features were excluded. Data were log-normalized, and the top 2,000 variable genes were identified. Principal component analysis (PCA) was performed using these features, and the top 30 PCs were used to construct a Shared Nearest Neighbor (SNN) graph. Clustering was performed with the Modularity Optimizer (v1.3.0), and clusters were visualized using UMAP.
Assembly: GRCm38.p6 (mm10)
Supplementary files format and content: .rds containing Seurat object containing log-normalized expression matrix, and Rd

source_name: Tumor lymph node

extract_protocol:
Tumor or tumor-free lymph node (control) were isolated from Roquinsan/+ mice and stained to sort live CD4+CXCR5+PD-1+ T follicular helper-like cells (>95% purity). Sorted conventional and Tfh-like cells were mixed in a 1:10 ratio to have an internal control. A total of 13,500 cells from Roquinsan/+ mice were sent for library preparation using 10×Genomics platform: Chromium Next GEM Single Cell 39 GEM, Chromium Next GEM Chip G Single Cell Kit, Library & Gel Bead Kit v3.1, and Chromium i7 Multiplex Kit. Sequencing was conducted at Genome Quebec Core Facility using an Illumina NovaSeq 6000, utilizing a flow cell S1 PE28*91.
Libraries were generated at the Institut de Recherches Cliniques de Montreal Molecular Biology and Functional Genomics Core Facility using the following components from 10× Genomics: Chromium Next GEM Chip G Single Cell kit, Chromium Next GEM Single Cell 39 GEM, Library & Gel Bead kit v3.1, and Chromium i7 Multiplex Kit.

value: Tumor lymph node

value: T follicular helper-like cells

value: Roquin san/+


title: MCF10A cells, BAP1 knockout clone 1, 2D culture, biol rep 2, H2AK119ub1

value: Non-tumorigenic mammary cells

value: H2AK119ub1 (D27C4, Cell Signaling Technology)

value: BAP1 knockout, clone 1


title: MCF10A cells, Cas9-expressing controls, 2D culture, biol rep 1, H2AK119ub1

value: Cas9-expressing control


title: GD21, Vehicle (corn oil), 61_20-24

description:
Library name: GD21_ctrl_61_20-24
BRB-seq

data_processing:
Quality control and preprocessing of data were performed by GenomEast (France).
The first read contains 16 bases that must have a quality score higher than 10. The first 6 bp correspond to a unique sample-specific barcode and the following 10 bp to a unique molecular identifier (UMI).
The second reads were aligned to the Rattus niorvegicus reference transcriptome from the UCSC website (release rn6) using BWA version 0.7.4.4 with the parameter “-l 24”
Assembly: rn6
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Testis were dissected and frozen in liquid nitrogen. Samples were stored at –80 ˚C until further analysis. Total RNA isolation was performed using a RNeasy Micro Kit following manufacturer’s protocol with the DNase step included (Qiagen, Germany). RNA quantity, quality, and purity was determined by a combination of a Nano-drop-1000 spectrophotometer (ND-1000, Fisher Scientific) and an Agilent 2100 Bioanalyzer System (Agilent Technologies, CA, USA). Samples with RNA integrity (RIN)-score > 6.8 were used. RNA samples were diluted to 25 ng/µL, and stored at -80 ˚C.
The sequencing libraries were built by tagmentation using 50 ng of ds cDNA with the Illumina Nextera XT Kit (Illumina, #FC-131-1024) following the manufacturer’s recommendations. Library strategy: Bulk RNA Barcoding and sequencing (BRB-seq)


title: p53MDM2_8_u

source_name: purified AML cells from PBMCs

value: f

value: Sensitive


title: GD21, Vehicle (corn oil), 44_20-24

description:
Library name: GD21_ctrl_44_20-24
BRB-seq

value: testis

value: Vehicle (corn oil)


title: Single-cell RNA-seq of CD4⁺CXCR5⁺PD-1⁺ T cells from tumor-free lymph node

description:
Library name: Roquin_ControlLN
Sorted CD4⁺CXCR5⁺PD-1⁺ T cells from Roquin san/+ tumor-free lymph node; 10x Genomics

source_name: Tumor-free lymph node

value: Tumor-free lymph node


title: MCF10A cells, BAP1 knockout clone 1, 2D culture, biol rep 1, H2AK119ub1


title: SufuD159R_Mut_RNAseq_rep2

description: Library name: SufuD159R_Mut_RNAseq_rep2


title: p53MDM2_8_6hr

value: de novo


title: GD21, Vehicle (corn oil), 43_20-24

description:
Library name: GD21_ctrl_43_20-24
BRB-seq

source_name: testis

value: Sprague-Dawley rat dams (Crl:CD(SD) bred by Charles River


title: MCF10A cells, wildtype, 2D culture, biol rep 2, H2AK119ub1

value: Wildtype


title: MCF10A cells, BAP1 knockout clone 2, 3D culture, biol rep 2 [ATAC-seq]

description:
BAP1KO_Cl2.bed
BAP1KO_Cl2.bw

data_processing:
Reads were mapped to hg38 with BWA v0.7.17 and trimmed using Trim Galore v0.6.10.
Peak signals were called with MACS2, using the following options: –extsize 150 –shift 75, as well as –keep-duplicates 1, and then filtered using irreproducible discovery rate (IDR) within each condition. We considered the union of resulting peaks and called reads without considering duplicated ones.
Differential analysis was performed with DiffBind v3.12.0. Read numbers per peak were normalized using the RLE method, and differential peaks were called using DESeq2.
Assembly: hg38
Supplementary files format and content: BED (Browser Extensible Data) ; bw (bigWig)

growth_protocol: MCF10A cells were cultured in low attachment conditions to form mammospheres, and were maintained in DMEM/F12 medium supplemented with 5% fetal bovine serum (FBS), insulin (10 µg/mL), epidermal growth factor (20 ng/mL), hydrocortisone (500 ng/mL), cholera toxin (100ng/mL), and 1% penicillin/streptomycin, in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
A total of 50,000 viable cells were collected and a 45 minute transposition reaction was performed using the Tagment DNA TDE1 Enzyme (Illumina).
ATAC-seq libraries were prepared using the previously described Omni-ATAC protocol (Corces et al., Nature Methods 2017).

value: BAP1 knockout, clone 2


title: MCF10A cells, Cas9-expressing controls, 2D culture, biol rep 2, H2AK119ub1


title: p53MDM2_8_2hr


title: GD21, Vehicle (corn oil), 42_20-24

description:
Library name: GD21_ctrl_42_20-24
BRB-seq


title: SufuD159R_Het_RNAseq_rep2

description: Library name: SufuD159R_Het_RNAseq_rep2

value: head


title: p53MDM2_60_u

value: m


title: SufuD159R_Het_RNAseq_rep3

description: Library name: SufuD159R_Het_RNAseq_rep3


title: GD21, Vehicle (corn oil), 41_20-24

description:
Library name: GD21_ctrl_41_20-24
BRB-seq


title: MCF10A cells, wildtype, 2D culture, biol rep 1, H2AK119ub1


title: MCF10A cells, BAP1 knockout clone 2, 3D culture, biol rep 1 [ATAC-seq]

description:
BAP1KO_Cl2.bed
BAP1KO_Cl2.bw


title: p53MDM2_7_u

value: Resistant


title: bone, exercised, rep3

city: beijing

first: Chenchen

last: Li

address: 37 Xueyuan Road

institute: beihang university

description: Library name: Sample 6

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastp version 0.19.5；RNA-seq reads were aligned to the hg38 genome assembly using Hisat2 version 2.1.0 .
Gene abundance measurements were generationed and normalized  using Stringtie ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using edgeR package in R program version 3.4.3
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw fragment counts for each Sample

source_name: bone

extract_protocol:
Total RNA was extracted from cell using the RNeasy mini kit (Qiagen, Germany).  1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone

value: oeteocyte

value: WT

value: exercise


title: p53MDM2_60_6hr


title: bone, exercised, rep1

description: Library name: Sample 4


title: Sufu_WT_RNAseq_rep2

description: Library name: Sufu_WT_RNAseq_rep2

value: wild type


title: Sufu_WT_RNAseq_rep3

description: Library name: Sufu_WT_RNAseq_rep3


title: bone, exercised, rep2

description: Library name: Sample 5


title: SufuD159R_Het_RNAseq_rep1

description: Library name: SufuD159R_Het_RNAseq_rep1


title: p53MDM2_7_6hr


title: p53MDM2_60_2hr


title: MCF10A cells, BAP1 knockout clone 1, 3D culture, biol rep 1 [ATAC-seq]

description:
BAP1KO_Cl1.bed
BAP1KO_Cl1.bw

value: Non-tumorigenic mammary cells

value: BAP1 knockout, clone 1


title: Mouse Keratinocytes p63 alphaKO 11

city: Napoli

first: Dario

last: Antonini

address: Strada Vicinale Cupa Cintia, 21

country: Italy

institute: University of Naples "Federico II"

description: Library name: Sample 6

data_processing:
Alignment of the reads performed with RNA STAR
Measure of gene expression performed with HTSeq
Differential expression analysis was performed using edgeR5
Assembly: mm10
Supplementary files format and content: Tabular files of normalized counts contain gene symbol and normalized counts of each sample

source_name: Epidermal keratinocytes

growth_protocol: Epidermal cells were cultured for 5–6 days until full confluency in low-calcium medium (0.05 mM) supplemented with 4% chelated fetal bovine serum and 2.5 ng/mL EGF

extract_protocol:
Rneasy plus mini kit (Qiagen #74134)
3'DGE mRNA-seq digital mRNA- sequencing service (NEGEDIA)

value: Epidermal keratinocytes

value: Primary cells

value: p63 alphaKO


title: p53MDM2_7_2hr

value: de novo


title: MCF10A cells, Cas9-expressing controls, 3D culture, biol rep 2 [ATAC-seq]

description:
Cas9_Ctrl.bed
Cas9_Ctrl.bw

value: Cas9-expressing control


title: bone, control, rep3

description: Library name: Sample 3

value: no


title: p53MDM2_5_6hr

value: Sensitive


title: Sufu_WT_RNAseq_rep1

description: Library name: Sufu_WT_RNAseq_rep1

value: head


title: bone, control, rep1

description: Library name: Sample 1


title: p53MDM2_5_2hr

value: m


title: MCF10A cells, BAP1 knockout clone 1, 3D culture, biol rep 2 [ATAC-seq]

description:
BAP1KO_Cl1.bed
BAP1KO_Cl1.bw


title: MCF10A cells, Cas9-expressing controls, 3D culture, biol rep 1 [ATAC-seq]

description:
Cas9_Ctrl.bed
Cas9_Ctrl.bw


title: ILCs, HFD-KO-2

city: Gainesville

first: Liang

last: Zhou

address: 1945 SW 16th Ave

institute: University of Florida

description: Library name: HFD-KO-2

data_processing:
The alignment, quantification, and quality control were performed using the Cell Ranger Software and mouse transcriptome (mm10) (10X Genomics) with default parameters.
Assembly: Mouse mm10
Supplementary files format and content: Barcodes files, features files and matrix file.

source_name: Large intestine

extract_protocol:
Lamina propria cells from large intestine were isolated and sorted by flow cytometry
Chromium GEM-X Single Cell 3' Reagent Kits v4 was used for reverse transcription, cDNA amplification, and library construction of gene expression libraries (10x Genomics) according to the manufacturer.

treatment_protocol: High-fat diet treatment for 12 weeks

value: Large intestine

value: ILCs

value: Tfamf/f Rorc-cre

value: High-fat diet


title: Mouse Keratinocytes p63 alphaKO 10

description: Library name: Sample 5


title: p53MDM2_5_u


title: bone, control, rep2

description: Library name: Sample 2

value: bone

value: oeteocyte

value: WT


title: MCF10A cells, BAP1 knockout clone 2, 3D culture, biol rep 2

data_processing:
Reads were mapped to hg38 with STAR v2.7.3a and counted with HTSeq v0.12.4.
Differential expression analysis was performed with DESeq2 v1.38.3.
Assembly: hg38
Supplementary files format and content: rawcount.txt : HTseq Count output, tabular file

extract_protocol:
RNA was harvested using the AllPrep DNA/RNA Mini Kit (Qiagen). 1ug of total RNA was used for the construction of the sequencing libraries.
RNA libraries were prepared using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems) following the manufacturer's protocol.

value: Non-tumorigenic mammary cells

value: BAP1 knockout, clone 2


title: MCF10A cells, BAP1 knockout clone 2, 3D culture, biol rep 1


title: Mouse Keratinocytes p63 alphaKO 9

description: Library name: Sample 4

value: Epidermal keratinocytes

value: Primary cells


title: Mouse Keratinocytes wild type WT 15

description: Library name: Sample 3

value: wild type


title: ILCs, HFD-KO-1

description: Library name: HFD-KO-1


title: p53MDM2_36_u

value: Resistant

value: de novo


title: Mouse Keratinocytes wild type WT 14

description: Library name: Sample 2


title: Mouse Keratinocytes wild type WT 13

description: Library name: Sample 1


title: p53MDM2_36_6hr


title: MCF10A cells, BAP1 knockout clone 1, 3D culture, biol rep 1

value: BAP1 knockout, clone 1


title: ILCs, HFD-WT-2

description: Library name: HFD-WT-2

value: Tfamf/f


title: MCF10A cells, BAP1 knockout clone 1, 3D culture, biol rep 2


title: p53MDM2_35_u

value: m

value: Sensitive

value: secondary (MDS)


title: ILCs, HFD-WT-1

description: Library name: HFD-WT-1

value: Large intestine

value: ILCs


title: ILCs, CD-KO-2

description: Library name: CD-KO-2

value: Tfamf/f Rorc-cre

value: Control diet


title: p53MDM2_36_2hr


title: MCF10A cells, Cas9-expressing controls, 3D culture, biol rep 2

value: Cas9-expressing control


title: Mouse_Epidermis_p63alphaKO3

description: Library name: Mouse_Epidermis_p63alphaKO3_E4

data_processing:
Alignment of the reads performed with RNA STAR
Measure of gene expression performed with HTSeq
Differential expression analysis was performed using edgeR5
Assembly: mm10
Supplementary files format and content: Tabular files of normalized counts contain EnsemblGeneID, gene symbol and normalized counts of each sample

source_name: epidermis

value: epidermis

value: p63 alphaKO


title: Mouse_Epidermis_p63alphaKO2

description: Library name: Mouse_Epidermis_p63alphaKO2_E3


title: ILCs, CD-KO-1

description: Library name: CD-KO-1


title: p53MDM2_35_2hr


title: MCF10A cells, Cas9-expressing controls, 3D culture, biol rep 1

value: Non-tumorigenic mammary cells


title: ILCs, CD-WT-2

description: Library name: CD-WT-2


title: Mouse_Epidermis_p63alphaKO1

description: Library name: Mouse_Epidermis_p63alphaKO1_E2


title: p53MDM2_35_6hr


title: ILCs, CD-WT-1

description: Library name: CD-WT-1


title: p53MDM2_24_u

value: f


title: MCF10A cells, BAP1 knockout clone 2, 2D culture, biol rep 1

extract_protocol:
RNA was harvested using the AllPrep DNA/RNA Mini Kit (Qiagen). 2ug of total RNA was used for the construction of the sequencing libraries.
RNA libraries were prepared using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems) following the manufacturer's protocol.

value: BAP1 knockout, clone 2


title: MCF10A cells, BAP1 knockout clone 2, 2D culture, biol rep 2


title: p53MDM2_24_6hr


title: 811_Quad

city: Rochester

first: Chantal

last: McCabe

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description: Library name: 811_Quad

data_processing:
Data processing for FeatureCounts done with Galaxy using HISAT2 and FeatureCount Packages
Assembly: mm10
Supplementary files format and content: FeatureCounts in a tabular format

source_name: Quadricep

extract_protocol:
Tissues collected and homogenized in QIAZOL and totalRNA extracted via Qiagen's mRNeasy kit
Library construction via LibStrmRNA(MRNA)

treatment_protocol: Mice dosed with either Vehicle or AP over a 16-week timecourse (2x per week)

value: Quadricep

value: AP


title: Mouse_Epidermis_WT2

description: Library name: Mouse_Epidermis_WT2_E7

value: wild type


title: MCF10A cells, BAP1 knockout clone 1, 2D culture, biol rep 2

value: BAP1 knockout, clone 1


title: MCF10A cells, BAP1 knockout clone 1, 2D culture, biol rep 1


title: Mouse_Epidermis_WT1

description: Library name: Mouse_Epidermis_WT1_E6


title: p53MDM2_24_2hr

value: de novo


title: 736_Quad

description: Library name: 736_Quad

value: Vehicle


title: p53MDM2_162_u

value: m

value: Sensitive


title: Mouse_Epidermis_WT3

description: Library name: Mouse_Epidermis_WT3_E8