title: gd IEL, IgG, PBS, biol rep 3

value: PBS

value: IgG


title: ctrl_inj_3, 24_hpi, biol_rep_3_1

status: Public on Oct 01 2024

type: SRA

city: Oklahoma

first: David

middle: J

last: Forsthoefel

state: OK

address: 825 NE 13th St

department: Genes and Human Disease Research Program

country: USA

institute: Oklahoma Medical Research Foundation

description:
C3_fq1
ctrl_inj_3, 24_hpi, biol_rep_3, fastq1
raw_counts_run1.txt

library_source: transcriptomic

data_processing:
Read quality was assessed with FastQC (v0.11.5) before and after trimming with BBDuk (v36.99) for paired end reads: k=13 ktrim=r mink=11 qtrim=rl trimq=10 minlength=35 tbo tpe.
Reads were mapped to the dd_Smed_v6 transcriptome restricted to 28,069 unique transcripts as in (Forsthoefel et al., eLife, 2020) using Bowtie2 (v2.3.1) for paired end reads, with "-a" multi-mapping and "--local" soft-clipping allowed.
Read summarization was conducted with the "featureCounts" utility in the Subread package (v1.6.3) (Liao et al., Nuc. Acids Res., 2019), using a custom ".SAF" file and options "-p -M -O -F SAF" to include multi-mapping and multi-overlapping reads.
Count matrices from both sequencing runs were summed in R, then differentially expressed transcripts were identified in EdgeR (edgeR_4.0.16) in R4.3.2. Transcripts with <1 cpm in 4/12 samples were removed. After recalcluation of library sizes, samples were normalized using the trimmed mean of M-values (TMM) method, and generalized linear model (GLM) common, trended, and tagwise dispersions were calculated. The negative binomial GLM was fitted with glmQLFit, followed by identification of differentially expressed transcripts with the GLM quasi-likelihood ratio test (glmQLFTest).
Assembly: Dresden S. mediterranea transcriptome dd_Smed_v6 (http://planmine.mpi-cbg.de/) (Brandl et al., Nuc. Acids Res., 2016)
Supplementary files format and content: Processed data are in a tab-delimited .txt file, wich includes geneID, transcript length, log2 Fold Change, logCPM, F-test, P value, and FDR-adjusted P value.

molecule: total RNA

organism: Schmidtea mediterranea

source_name: tail (postpharyngeal region excluding ~10% of tail tip)

growth_protocol: Asexual Schmidtea mediterranea (clonal line CIW4) were maintained in Montjuic water and fed with calf liver paste. Planarians were starved 7 days prior to injection experiments.

extract_protocol:
Total RNA was extracted from the tail (postpharyngeal region excluding ~10% of the posterior-most tail tip) of 5 planarian tail fragments per biological replicate using Trizol and Zymo RNA columns as described (Forsthoefel et al., eLife, 2020).
Total RNA for 4 biological replicates per condition was used for library generation from ~750-1000 ng/sample using the IDT xGen RNA library prep kit with NEB poly-A selection, and RNA sequencing (150 bp PE reads on an Illumina NovaSeq X Plus) with standard Illumina adapters. Two sequencing runs were conducted per sample.

treatment_protocol: Extracellular vesicles were isolated from planarian tissue fragments 12 hours after amputation. 12 hpa fragments were dissociated in CMF-B/collagenase, and strained through a 70 um mesh. Supernatant was sequentially centrifuged at 200 x g, 3000 x g, and 10,000 x g, precipitated with 10% PEG 10,000, then EVs were enriched using SBI SmartSEC Mini EV size exclusion chromatography columns. EVs were eluted in 90 ul IB buffer, and mixed with 10 ul 546-Alexa-conjugated 10,000 kD dextrans (5 mg/ml), for a final concentration of ~1 animals' EVs per 1 ul. EVs (or buffer only + dextrans) were injected into planarian tails (~1 animal's EVs per planarian). Animals were allowed to recover for 1 hour, then animals with low dextran content were removed from the experiment.

tag: clonal line

tag: tissue

tag: cell type

value: wild type

tag: treatment

value: buffer injection, 24 hpi


title: mGCCtrl_HMD201207001_AA17

city: Fukuoka

first: Tappei

last: Mishina

address: 744 Motooka Nishi-ku

country: Japan

institute: Kyushu University

library_source: transcriptomic single cell

data_processing:
Adaptor sequences and low quality bases were trimmed using Fastq-mcf v1.1.2 in the ea-utils package.
The RamDA-seq reads were mapped to the mouse genome (GRCm38) using Hisat2 v2.2.0.
The gene count table was obtained using the featureCounts v2.0.1 tool in the Subread package with the option ‘-t exon -g gene_id’ and the annotation gtf file from GENCODE (vM25).
We evaluated the quality control metrics and filtered out low quality samples based on the RNA integrity assessed by coverage profile along the gene body and the number of detected genes ≤ 8,000.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts or TPM values for each sample.

organism: Mus musculus

source_name: ovary

growth_protocol: mouse lines used for this study were maintained on a mixed genetic background

extract_protocol:
At postnatal day (PD) 7, ovaries from euthanized control mice (n=3) and from Wls cKO mice (n=8) were collected. Ovaries were treated with a CTK solution (consisting of 0.25% trypsin (Thermo), 0.1% collagenase type IV (Gibco), 20% KSR (Invitrogen) and 1 mM CaCl2 in PBS) for 30 min at 37°C, then further treated with Accutase (Nacalai) at 37°C for 15 min. The reaction was halted by adding L-15 medium with 0.1% penicillin-streptomycin and 5% FBS, and the cells were dissociated by pipetting. The cell suspension was filtered through 70 μm cell strainers, followed by centrifugation at 400 g for 5 min and resuspension in sorting buffer (7.5% BSA (Life Technologies) in PBS). Blocking was performed with rat IgG (5 mg/mL, I8015, Sigma-Aldrich) for 15 min on ice. Subsequently, cell surface staining was conducted using anti-ckit-APC (1:50, 105812, BioLegend) and anti-CD45-Alexa Fluor 488 (1:200, 103122, BioLegend) for 15 min on ice. After centrifugation at 400 g for 5 min, cells were resuspended in sorting buffer. Prior to single-cell sorting by flow cytometry, samples were passed through 40 μm cell strainers, and DAPI (1:10,000) was added. Control and Wls cKO samples were each sorted using MoFlo Astrios EQ with Summit v 6.3.0. software (Beckman Coulter) into 384-well plates containing 286 tdTomato-positive somatic cells and 95 ckit-positive oocytes. DAPI-positive dead cells and CD45-positive leukocytes were excluded.
Library preparation for RamDA-seq was performed according to a previously report. However, to reduce reagent costs and rRNA-derived sequencing reads, the method was modified as follows: To suppress rRNA-derived cDNA synthesis, 0.008 units/µl XRN-1 (NEB) was added to the genomic DNA digestion mix, and the reaction was performed at 30°C for 5 min. To reduce reagent costs, a liquid dispenser Mantis (Formulatrix) was used to perform the reaction up to second strand synthesis at 1/10 the reaction volume. After that, 2.5 μl 0.8 X Tagment DNA Buffer (Illumina) diluted with RNase-free water was added to 0.5 μl of the second strand synthesis products for dilution. Then, 0.5 μl Amplicon Tagment Mix (Illumina) was added to 1.5 μl of the diluted product, and tagmentation was performed at 55°C for 10 min. After that, the library was prepared using 1/10 the reaction volume according to the Nextera XT DNA Library Prep Kit (Illumina) procedure. Twelve PCR cycles were performed. Somatic and oocyte library products were collected separately in equal volumes of 1 μl/well. Subsequently, 50 μl of each sample was fractionated from the equal mixed library, purified with 1.2X AMPureXP (Beckman Coulter), and eluted with 25 μl TE. To prevent large discrepancies in the number of sequencing reads per cell between somatic and oocyte cells, purified libraries were mixed to ensure a constant average molar per cell type using the quantitative results from the Bioanalyzer Agilent High-Sensitivity DNA Kit and the ratio of the number of cells sorted (somatic cells: oocytes = 286:95). The pooled library of 2.3 pM was sequenced in single end read 76 cycles using NextSeq 500 High Output Kit v2.5.

value: ovary

tag: developmental stage

value: excluded by low quality

tag: subpopulation gc

tag: subpopulation oocyte

tag: genotype

value: Sf1-Cre;Wls flox/+;Ai9 (control)

tag: marker expression_tdtomato

tag: marker expression_kit-apc

tag: cell size_(fsc1_area)

tag: intron ratio


title: mGCCtrl_HMD201207001_AE13

value: pre-granulosa cells


title: mGCCtrl_HMD201207001_AK19


title: eWAT, IR 4A, replicate 3

city: New York

first: Eunhee

last: Choi

address: 630 West 168th Street

institute: Columbia University

data_processing:
Raw sequencing reads were quantified with Salmon v1.8.0 to obtain transcript abundance counts by mapping to mouse genome GRCm39 GENCODE v.M31. The resulting counts were summarized to the gene level using tximport v1.20.0.
Differential expression was analyzed using DESeq2 v1.32.0. Differentially expressed (DE) genes were defined by an absolute fold change > 1.5 and false discovery rate (FDR)-adjusted P value < 0.05 and visualized using Volcano plots.
The output of DESeq2 were scored and ranked by apeglm v1.14.0 using ranking metrics “−log10 P value multiplied by the sign of shrunken log2 fold-change”. The ranked gene list was then subjected to Gene Set Enrichment Analysis (GSEA) to identify the gene sets overrepresented at the top or bottom of the ranked list using pathway definition file “Mouse_GOBP_AllPathways_no_GO_iea_November_17_2022_symbol.gmt” downloaded from http://baderlab.org/GeneSets. Only ontologies with more than 15 genes and less than 200 genes were considered.
The top ranked pathways were manually curated to remove the repetitive pathways and visualized using dot plots.
The leading-edge genes enriched in the identified pathways were visualized using pheatmap v1.0.12.
Assembly: mouse genome GRCm39 GENCODE v.M31
Supplementary files format and content: tab-delimited text file for salmon counts
Supplementary files format and content: tab-delimited text file for DESeq2 normalized counts by rld
Supplementary files format and content: Differential expression analysis results by DESeq2

source_name: eWAT

extract_protocol:
Total RNA was extracted from liver and adipose tissues using TRIzol (Invitrogen) RNeasy mini kit (Qiagen).
All samples were prepared simultaneously to avoid bias related to batched library preparation. Library preparation and RNA sequencing were performed by the Columbia Genome Center. In brief, mRNA was isolated using poly-A tail pulldown and cDNA libraries constructed using TruSeq Stranded mRNA Library Prep Kit (Illumina).
RNA-seq, Libraries were sequenced using Illumina NovaSeq 6000 at Columbia Genome Center. Samples were multiplexed in each lane, yielding approximately 20 million 100 bp paired-end reads for each sample.

value: eWAT

tag: Sex

value: male

tag: age

value: 2 months

value: IR 4A


title: eWAT, WT, replicate 2

value: WT


title: H1299_C25

city: shanghai

first: Zhenyu

last: Shao

state: --- Select a state ---

address: Yueyang Road 320

department: Center for Excellence in Molecular Cell Science

country: China

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

library_source: genomic

data_processing:
For data processing, raw data were trimmed by Trim Galore with default settings. Then, the clean data were mapped to Hg38 human reference genome using Bismark (v0.20.1) with the parameters -X 2000 --score_min L,0,-0.6. Duplicates were removed using Picard (v2.22.4). Bigwig files were generated using bedGraphToBigWig (v4) and visualized in Integrative Genomics Viewer (IGV). CGmapTools (v0.1.2) was used for DMR calling, for which only the CpG sites with at least 3×coverage were kept. DMRs were defined by a dynamic fragment strategy: the length (the maximal distance between two adjacent common cytosines is 100 bp, and the maximal DMR size is 1000 bp), methylation level difference (at least 25% absolute methylation level difference), P value (less than 0.05) and CpG number (at least 6 CpG sites) were considered. All the annotated information was downloaded from the UCSC Genome Browser (Hg38). Promoters were defined as ± 2.5 kb from the TSS (Transcription Start Site).
Assembly: Hg38
Supplementary files format and content: bedgraph files for 5mC level

molecule: genomic DNA

organism: Homo sapiens

source_name: cell line

growth_protocol: NCI-H1299 cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total DNA was extracted from cells using Phenol-chloroform DNA extraction protocol.
Briefly, 200-1000 ng genomic DNA was used for WGBS library construction. DNA was sonicated to ~250 bp fragments with the Diagenode Bioruptor Pico. Then DNA was subjected to end-repair, A-tailing, and ligation using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607) and methylated adaptor (Roche) according to the manufacturer’s instructions. DNA was purified with VAHTS DNA Clean Beads. Subsequently, library was bisulfite modified using QIAGEN EpiTect Fast DNA Bisulfite Kit (59824) and amplified with KAPA2G Robust HotStart PCR Kits with dNTPs (Sigma-Aldrich). Library was finally subjected to 150 bp paired-end sequencing using the Illumina Novaseq6000 instrument.

treatment_protocol: Cells were treated with DMSO or C271 for 4 days.

value: cell line

tag: cell line

value: NSCLC


title: gd IEL, IgG, PBS, biol rep 2

first: Matthew

last: Fischer

state: New York

address: 1470 Madison Ave

department: Pathology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Partek Flow pipline (v11.0.23.1004), PGS7.21.1119
Sequence reads were aligned to mm39 using STAR (2.7.8a)
Aligned reads were filtered with a maximum <=100 reads and quantified to PartekE/M annotation model (Ensembl Transcripts release 104)
Read count normalization was performed with Median ratio followed by DESeq2 using Partek Flow
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for all samples
Supplementary files format and content: tab-delimited text file includes Median ratio (for DESeq2 only) normalized counts for all samples

source_name: small intestine

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using SMART-Seq HT kit following the manufacturer's protocols

treatment_protocol:
Mice were i.p. injected with either 200 ug UC7-13D5 or Armenian Hamster IgG Antibody 48 and 24 hours prior to IEL isolation.
Mice from both antibody treatment groups were treated with PBS or 1 ug IFNa i.v. 5 hours prior to IEL isolation

value: small intestine

value: gd intraepithelial lymphocyte


title: eWAT, WT, replicate 3


title: H1299_TDGKO

value: TDG KO


title: Liver, IR 4A, replicate 5

source_name: Liver

value: Liver


title: eWAT, WT, replicate 1


title: eWAT, WT, replicate 5


title: H1299_C50


title: gd IEL, IgG, IFNa, biol rep 4

value: IFNa

value: IgG


title: H1299_DMSO

value: DMSO


title: gd IEL, IgG, PBS, biol rep 1

value: PBS


title: Liver, IR 4A, replicate 4


title: mGCCtrl_HMD201207001_CN13

value: ovary

value: granulosa cells

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: mGCCtrl_HMD201207001_BA12

value: excluded by low quality


title: mGCCtrl_HMD201207001_CF17


title: gd IEL, IgG, IFNa, biol rep 3


title: MM_MDS_3

city: Jinan

first: jingjing

last: wang

address: No. 440 Jiyan Road, Huaiyin District, Jinan City, Shandong Province

institute: Shandong First Medical University and Shandong Academy of Medical Sciences

description: GEXSCOPE

data_processing:
Raw data from sequencing were processed using an internal pipeline to generate gene expression matrixes.
CeleScope v1.15.0 (Singleron Biotechnologies) were applied to process raw reads and remove doublets (cells with double amounts of UMIs) by keeping only cells with <10,000 UMI reads, and filter out cells with high percentages of mitochondrial genes (>10%).
Briefly, Barcodes and UMIs were extracted from R1 reads and corrected. Adapter sequences and poly A tails were trimmed from R2 reads. Later, Reads were mapped to the reference genome GRCh38 by STAR (v2.6.1a).
UMI counts and gene counts per cell were obtained using FeatureCounts (v1.6.2) to generate expression matrix. Analysis was performed in R (v4.1.3) using the package Seurat (v4.1.1).
The package ggplot2 (v3.3.6) was used to generate figures. To correct for any batch effect the samples were integrated by harmony (https://github.com/immunogenomics/harmony).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow

extract_protocol:
BM cells were isolated from bone marrow aspirates by Ficoll gradient separation of the mononuclear cell fraction. Isolated mononuclear cells were resuspended in 90% fetal bovine serum (FBS) with 10% dimethyl sulfoxide and stored at -80 °C.
scRNA-seq was performed on viably thawed BM samples and then loaded onto a microfluidic chip and scRNA-seq libraries generation were performed following the manufacturer’s instructions (Singleron GEXSCOPE Single Cell RNAseq Library Kit, Singleron Biotechnologies).

treatment_protocol: Ficoll

value: bone marrow

value: bone marrow cells


title: gd IEL, IgG, IFNa, biol rep 2

value: WT


title: Liver, IR 4A, replicate 3

value: male

value: 2 months

value: IR 4A


title: MM_MDS_4

description: GEXSCOPE


title: mGCCtrl_HMD201207001_CJ15

value: interstitial cells


title: MM_MDS_2

description: GEXSCOPE


title: mGCCtrl_HMD201207001_CJ23


title: MM_MDS_1

description: GEXSCOPE


title: mGCCtrl_HMD201207001_BG14


title: Liver, IR 4A, replicate 1


title: GSC, H3K18la, ChIP

city: Hangzhou

first: Rongxuan

last: Zhu

address: No. 268 Kaixuan Road

institute: Zhejiang University

description: GSC_H3K18la_PTM BIO Inc

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. 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 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Human primary GBM cells (3565)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a ultrasonicator (Covaris).
DNA fragments were end-repaired, 3’A-tail added, and ligated to Illumina sequencing adapters. Libraries were amplified and post amplification libraries were size selected at 100-300bp in length using Agencourt AMPure XP beads from Beckman Coulter.

value: Human primary GBM cells (3565)

tag: antibody


title: mGCCtrl_HMD201207001_CB05


title: GSC, KAT2A, ChIP


title: EV_inj_1, 24_hpi, biol_rep_1_1

description:
E1_fq1
EV_inj_1, 24_hpi, biol_rep_1, fastq1
raw_counts_run1.txt

value: tail (postpharyngeal region excluding ~10% of tail tip)

value: wild type

value: EV injection, 24 hpi


title: TfebWT_MSUc_rep2

city: La Jolla

first: Christopher

last: Glass

state: CA

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego

data_processing:
RNA-Seq analysis  FASTQ sequencing files were mapped to the mm10 using STAR with default parameters. Biological and technical replicates were used in all experiments. Quantification of transcripts was performed using the analyzeRepeats.pl of HOMER with the following parameters -condenseGenes -count exons -noadj. Principal Component Analysis (PCA) and correlation analyses were obtained based on the Transcripts Per kilobase Million (TPM) on all genes of all samples and TPM for each transcript was calculated using the analyzeRepeats.pl tool of HOMER with the parameters -condenseGenes -count exons -tpm. Differential expression analysis was generated using getDiffExpression.pl tool of HOMER (Heinz et al. 2010) with default parameters: FDR <0.05 and log2fold change >1 or < (-1) for cells treated with PBS or MSUc and FDR <0.05 for treatment with other chemicals. Pathway analyses of differentially expressed genes were performed using Metascape (Zhou et al. 2019).    ChIP-Seq analysis  ChIP-Seq analysis was performed as described previously (Cobo, Tanaka, et al. 2022; Seidman et al. 2020). Briefly, ChIP-Seq peaks for TFEB, TFEC, BHLHE40, BHLHE41, DOT1L and DNMT3A replicates were obtained using HOMER with parameters –L 0 –C 0 –fdr 0.9 –minDist 200 –size 200. Only peaks with IDR <0.05 were considered for downstream analyses. The merged tag directories from all replicates from each experimental conditions were used for visualization in the UCSC Browser (Kent et al. 2002). Peaks were annotated with the nearest gene to analyse the overlap between conditions. For H3K27ac and H3K4me3 differential peaks, H3K27ac and H3K4me3 ChIP-Seq peaks were centred to regions of open chromatin using the annotatePeak.pl tool of HOMER an ATAC-Seq peak file of BMDM treated with PBS or MSUc. Differential peaks were calculated using the getDiffExpression.pl tool of HOMER with default parameters. A list of the IDR peaks for TFEB, TFEC, BHLHE40, BHLHE41, DOT1L, DNMT3A, H3K27ac, H3K4me3 and H3K79me3 as well as the differential peaks after treatment with MSUc can be found in GEO under the accession number (GSE). To generate a histogram of the intensity of a given ChIP-Seq over a subset of differential peaks or regions using the annotatePeaks.pl tool of HOMER with the parameters -size 6000 -hist 25. To identify DNA motifs in differential peak or regions over background sequences, the findMotifGenome.pl tool of HOMER was used with default parameters and random genomic sequences as background (Heinz et al. 2010). In the figures, de novo motifs are displayed unless otherwise indicated.
In silico promoter analysis of differentially expressed genes was performed using the findMotifs.pl tool of Homer searching for motifs of length 8 and 10 and from -2000 to +500 bp relative to the TSS, using 4 threads.
Assembly: mm10
Supplementary files format and content: The list of Transcripts Per Million reads (TPM) and differential peak files are provided in fastq.gz

source_name: Bone Marrow

growth_protocol: Flushed bone marrow from both femurs and tibias of C57BL/6, Tfeb-Tg, Bhlhe40-/- and Bhlhe41-/- mice were cultured in DMEM medium supplemented with 10% de-complemented FBS, Penicillin-Streptomycin 100 U/mL and 16 ng/mL of recombinant murine M-CSF (Peprotech, #315-02). Fresh M-CSF was added 72h after seeding. Ampkα1-/-  BMDM were generated as explained elsewhere (Wang et al. 2016). Briefly, bone marrows from 7-week-old to 8-week-old Ampkα1-/- and congenic WT mice were cultured in complete Roswell Park Memorial Institute (RPMI) media containing 10% fetal bovine serum (FBS), penicillin (100 U/mL) and streptomycin (100 μg/mL) in the presence of 5 ng/mL of MCSF (R&D Systems).

extract_protocol:
It was performed as described elsewhere (Cobo, Cheng, et al. 2022; Cobo, Tanaka, et al. 2022). Briefly, BMDM were lysed in Trizol (ThermoFisher, #15596026) and RNA was isolation and DNase treatment were carried out using RNA MicroPrep kit (Zymoresearch, #11-33MB).
RNA-Seq library preparation  It was performed as described elsewhere (Cobo, Cheng, et al. 2022; Cobo, Tanaka, et al. 2022). Briefly, BMDM were lysed in Trizol (ThermoFisher, #15596026) and RNA was isolation and DNase treatment were carried out using RNA MicroPrep kit (Zymoresearch, #11-33MB). 500 ng-1 μg of RNA was incubated with Oligo d(T) magnetic beads (NEB, #S1419S) to enrich for poly-A tailed transcripts and then fragmented by incubating for 9 min at 94º in 2X Superscript III first-strand buffer containing 10 mM DTT (Invitrogen, #P2325). Reverse transcription (RT) of fragmented RNA was performed at 25ºC for 10 min followed by 50ºC for 50 min. RT product was purified with RNAClean XP (Beckman Coulter, #A63987) and the solution of RNA-cDNA complexes was then added to a mix containing 1.5 μl of 10X Blue Buffer (Enzymatics, #B0110-L), 1.1 μl of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 μl of 5 U/ml RNAseH (Enzymatics, #Y9220L), 1 μl of 10 U/ml DNA polymerase I (Enzymatics, #P7050L), 0.15 μl of 1% Tween 20 and 1.05 μl of nuclease free water; and incubated at 16ºC overnight. Next day, the resulting DNA was purified using 28 μl of SpeedbBead Magnetic Carboxylate (GE Health- care, #651521050 50250) diluted in 20%PEG8000:2.5M NaCl to a final 13% PEG concentration. After two washes owith 80% etOH, air dry and eluted, the purified DNA was end-repaired by blunting followed by A-tailing and adapter ligation using NOVA (BIOO-NextFlex adapters. Libraries were amplified by PCR for 13 cycles using Solexa 1GA and Solexa 1GB primers (AATGATACGGCGACCACCGA and CAAGCAGAAGACGGCATACGA, respectively), purified using 1 μl of SpeedbBead Magnetic Carboxylate. Eluted libraries were quantified using a Qubit dsDNA HS Assay Kit and sequenced on NovaSeq SP100 (Illumina, San Diego, California).  ChIP-Seq library preparation  Chromatin immunoprecipitation (ChIP) was performed as described elsewhere (Seidman et al. 2020; Gosselin et al. 2017). Briefly, MDM or BMDM were fixed with 1% formaldehyde for H3K27ac, H3K4me3 and H3K79me3 or doubly fixed with 3 mM Disuccinimidyl-glutarate -DSG- (Proteochem, #C1104) in PBS for 30 min at room temperature and then with 1% formaldehyde (ThermoFisher, #28906) for 10 min at room temperature for TFEB, TFEC, BHLHE40, BHLHE41, DOT1L and DNMT3A. Fixation was then quenched upon adding glycine to final concentration of 125 mM. Cells were then washed with 0.01%Triton X-100:PBS, scraped and pelleted by centrifugation at 3000 rpm for 10 min at 4ºC and snap frozen for storage at -80ºC. For ChIP experiments, fixed cells were thawed and permeabilised in 1 mL of chilled buffer containing 10 mM HEPES/KOH pH7.9, 85 mM KCl, 1 mM EDTA, 0.2% IGEPAL CA-630 (Sigma-Aldrich, #I8896), 1X protease inhibitor cocktail (Sigma, #11836145001) and 1 mM PMSF for 10 min on ice. After that cells were spun down and lysed in 130 μl of either LB3 lysis buffer containing 10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1 X protease inhibitor cocktail for H3K27ac, H3K4me3 and H3K79me3 or lysis buffer containing 20 mM Tris/HCl pH7.5, 1 mM EDTA, 0.5 mM EGTA, 0.1% SDS, 0.4% Sodium Deoxycholate, 1% NP-40, 0.5 mM DTT, 1x protease inhibitor cocktail and 1 mM PMSF. Chromatin was sheared by sonication in a 96 microTUBE Rack (Covaris, #500282) using a Covaris E220 for 25 cycles with the following settings: time, 60 s; duty, 5.0; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0. Sonicated lysates were spun down at 10,000 rpm for 10 min at 4ºC and one percent of the sonicated lysate was kept as ChIP input for analysis. In all buffers, DTT, protease inhibitor and PMSF were added freshly. Sonicated lysates were incubated with a mix consisting of Protein G Dynabeads (Invitrogen, #10003D) and TFEB antibody cocktail (Abcam, #ab2636 plus CST, #37785), TFE3 antibody cocktail (Abcam, #196681 plus Abcam, #93808), BHLHE40 (Novus Biologicals, #NBP100-1800), DOT1L (CST, #D1W4Z), DNMT3A cocktail (Abcam, #ab2850 plus Diagenode, #C15410085), H3K27ac (ActiveMotifs, #AB_2793305), H3K4me3 (Millipore, #04-745), or H3K79me3 (Diagenode, #C15410068),  was added to the sonicated material and incubated overnight on a rotator at 4ºC. Next day, immunocomplexes were placed on a magnet and bead complexes were washed with 100 μl of chilled buffers. For H3K27ac, H3K4me3 and H3K79me3 ChIP, beads were washed four times each with wash buffer I containing 20 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, wash buffer III containing 10 mM Tris/HCl pH 7.4, 250 mM LiCl, 1% Triton X-100, 0.7% Na-Deoxycholate, 1 mM EDTA and twice with ice-cold TET containing 10 mM Tris/HClpH7.5, 1 mM EDTA, 0.2% Tween-20. For TFEB, TFEC, BHLHE40, BHLHE41, DOT1L and DNMT3A ChIP beads were washed as it follows: 3 times lysis buffer, 6 times with wash buffer containing 10 mM Tris/HCl pH7.5, 250 mM LiCl, 1 mM EDTA, 0.7% Na-Deoxycholate and 1% NP-40 alternative; 3 times with TET buffer containing 10 mM Tris/HCl pH 8.0, 1 mM EDTA, 0.2% Tween 20; and 1 time with IDTE buffer containing 10 mM Tris/HCl pH 8.0 and 0.1 mM EDTA. Bead complexes were resuspended in 25 mL of TT buffer containing 10 mM Tris/HCl pH 8.0, 0.05% Tween 20. ChIP libraries for sequencing were prepared on beads using NEBNext Ultra II Library kit (NEB, #E7645L) by reducing 50% the reaction volume as previously described (Heinz et al. 2015; Sakai et al. 2019). Reverse crosslinking was performed by adding 33.5 μl of a mix containing 4 μl 10% SDS, 3 μl 0.5 M EDTA, 1.6 μl 0.2M EGTA, 1 μl 10 mg/ml Proteinase K (Biolabs, #P8107 S), 1 μl 10 mg/ml RNase A, 4.5 μl 5M NaCl and 18.4 μl nuclease free water and incubating at 55C for 1h followed by 75ºC for 30 min. After removing the dynabeads, libraries were cleaned by adding  2 μl of SpeadBeads in 124 μl of 20% PEG 8000/ 1.5M NaCl and washed twice with 100 μl of 80% etOH, air dry and eluted in 13 μl of buffer containing 10 mM Tris/HCl pH 8.0 and 0.05% Tween 20. Libraries were amplified by PC for 14 cycles using NEBNext Ultra II PCR master mix using Solexa 1GA and Solexa 1GB primers. After that, libraries were size selected 200-500 bp upon running in 10% TBE acrylamide gels (ThermoFisher, #EC62752BOX) and sequenced using a NovaSeq SP100.

treatment_protocol: On day six after seeding, BMDM were scrapped out and plated one day prior treatment with Metformin (MP Biomedicals, #151691), 125 mM A769662 (Sigma, # SML2578), or since day 0 with 1 μM SGC0946 (Selleckchem, #S7079). BMDM were then treated with control PBS or 250 μg/mL of MSUc, calcium pyrophosphate dihydrate crystals, silica nanoparticles (Invivogen, #tlrl-sio-2), or aluminum hydroxide salt (Invivogen, #tlrl-aloh) at various timepoints as explained in the text and Figure legends.

value: Bone Marrow

value: Bone Marrow-derived macrophages

value: MSUc


title: TfebWT_MSUc_rep3

value: PBS


title: GSC, ACSS2, ChIP


title: TfebWT_PBS_rep1


title: Liver, WT, replicate 4

value: Liver


title: mGCCtrl_HMD201207001_CP15

value: ovary

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: TfebWT_PBS_rep2


title: Liver, IR 4A, replicate 2


title: U87, KAT2A, ChIP

source_name: Human GBM cell line U87 MG

value: Human GBM cell line U87 MG


title: Liver, WT, replicate 1

value: WT


title: TfebTg_PBS_rep3

value: Tfeb-Tg


title: TfebWT_MSUc_rep1


title: mOCCtrl_HMD201207001_DJ20

value: excluded by low quality


title: Liver, WT, replicate 2

value: male

value: 2 months


title: U87, ACSS2, ChIP


title: TfebTg_PBS_rep2


title: gd IEL, IgG, IFNa, biol rep 1

value: small intestine

value: gd intraepithelial lymphocyte

value: IFNa

value: IgG


title: mOCCtrl_HMD201207001_DH02

value: oocytes


title: mGCCtrl_HMD201207001_AM03

value: granulosa cells


title: 4F2A cell, CX-5461, DAY2_1 [ATAC]

city: Harbin

first: Yuchen

last: Sun

state: Heilongjiang

address: Baojian road 157

department: Department of histology and embryology

institute: Harbin Medical University

data_processing:
Sequenceweretrimmedbycutadapt-4.3.
Trimmedsequencereadsweremappedtomm10bybowtie2.
Removing PCR duplication by picard.
callpeak by macs2 (--shift -100 --extsize 200 --nomodel).
Assembly: mm10

source_name: 4F2A cell

extract_protocol:
ATAC-seqwasperformedbyHyperactiveATAC-seqLibraryPrepKitforIllumina(TD711,Vazyme).Inbrief,atotalof50000cellswerewashedtwicewith50ulofTWbufferandresuspendedin50ullysisbuffer(RSbuffer,11%NP40,10%Tween,1%Digitonin).
ATAC-seq was performed by Hyperactive ATAC-seq Library Prep Kit for Illumina (TD711, Vazyme).  The suspension was then centrifuged for 10min at 500g at 4℃, followed by adding 50ul transposition reaction mix (TWbuffer, 10%Tween, 1% digitonin, ddH2O, 5*TTBL, TTE mix V50) and then incubated at 37℃ for 30min. 5μl stop buffer was added to stop reaction. DNA was isolated by ATAC DNA Extract Beads. ATAC library was subjected to 17 cycles of amplification with TruePrep Index Kit V2 for Illumina (TD202, Vazyme). ATAC library was purified by ATAC DNA Clean Beads and measured using Qbit 4 fluorometer. Library integrity was checked by gel electrophoresis. Finally, the ATAC libraries were sequenced on Illumina NovaSeq 6000 platform to generate 150 bp paired-end reads at BerryGenomics Corporation.

treatment_protocol: Dox, DMSO, and CX-5461wereaddedinD0.

value: 4F2A cell

value: mef

tag: time

value: Treat


title: TfebTg_PBS_rep1

value: Bone Marrow

value: Bone Marrow-derived macrophages

value: PBS


title: Liver, WT, replicate 3

value: Liver

value: WT


title: TfebTg_MSUc_rep3

value: Tfeb-Tg

value: MSUc


title: mGCCtrl_HMD201207001_BK18

value: ovary

value: interstitial cells

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: 4F2A cell, CX-5461, DAY2_2 [ATAC]


title: mGCCtrl_HMD201207001_AG15


title: 4F2A cell, DMSO, DAY2_2 [ATAC]

value: Contrl

value: DMSO, DOX


title: TfebTg_MSUc_rep1


title: mGCCtrl_HMD201207001_CH13


title: 4F2A cell, DMSO, DAY2_1 [ATAC]


title: U87, H3K18la, ChIP

description: U87_H3K18la_PTM BIO Inc

value: Human GBM cell line U87 MG


title: mGCCtrl_HMD201207001_CB07

value: early theca cells


title: Liver, WT, replicate 5

value: male

value: 2 months


title: 4F2A cell, CX-5461, DAY2_3

data_processing:
SequenceweretrimmedbyTrimmomatic-0.39.
Trimmedsequencereadsweremappedtomm10byhista2.
ReadcountextractionwereperformedusingfeatureCounts.
AnalysisbyR.
Assembly: mm10
Supplementary files format and content: ACommaSeparatedValues(CSV)fileincludeTPMvaluesforeachSample

extract_protocol:
DOX wasaddedinD0,DMSO or CX-5461 was added in D0 for only 1 hour, the total RNA of 4F2A MEFs was harvested by TRIzol in Day2. Each group was prepared with two parallel replicates.  All the samples were sent to  BMKCloud Corporation (www.biocloud.net) by using NovaSeq 6000 for RNA sequencing.
thetotalRNAwasextractedaccordingtotheinstructionmanualoftheTRlzolReagent(Lifetechnologies,California,USA).RNAconcentrationandpuritywasmeasuredusingNanoDrop2000(ThermoFisherScientific,Wilmington,DE).RNAintegritywasassessedusingtheRNANano6000AssayKitoftheAgilentBioanalyzer2100system(AgilentTechnologies,CA,USA).Atotalamountof1μgRNApersamplewasusedasinputmaterialfortheRNAsamplepreparations.SequencinglibrariesweregeneratedusingHieffNGSUltimaDual-modemRNALibraryPrepKitforIllumina(YeasenBiotechnology(Shanghai)Co.,Ltd.)followingmanufacturer’srecommendationsandindexcodeswereaddedtoattributesequencestoeachsample.Briefly,mRNAwaspurifiedfromtotalRNAusingpoly-Toligo-attachedmagneticbeads.FirststrandcDNAwassynthesizedandsecondstrandcDNAsynthesiswassubsequentlyperformed.Remainingoverhangswereconvertedintobluntendsviaexonuclease/polymeraseactivities.Afteradenylationof3’endsofDNAfragments,NEBNextAdaptorwithhairpinloopstructurewereligatedtoprepareforhybridization.ThelibraryfragmentswerepurifiedwithAMPureXPsystem(BeckmanCoulter,Beverly,USA).Then3μlUSEREnzyme(NEB,USA)wasusedwithsize-selected,adaptor-ligatedcDNAat37°Cfor15minfollowedby5minat95°CbeforePCR.ThenPCRwasperformedwithPhusionHigh-FidelityDNApolymerase,UniversalPCRprimersandIndex(X)Primer.Atlast,PCRproductswerepurified(AMPureXPsystem)andlibraryqualitywasassessedontheAgilentBioanalyzer2100system.ThelibrariesweresequencedonIlluminaNovaSeq6000platformtogenerate150bppaired-endreads,accordingtothemanufacturer’sinstructions.Therawreadswerefurtherprocessedwithabioinformaticpipelinetool,BMKCloud(www.biocloud.net)onlineplatform.Rawdata(rawreads)offastqformatwerefirstlyprocessedthroughin-houseperlscripts.Inthisstep,cleandata(cleanreads)wereobtainedbyremovingreadscontainingadapter,readscontainingploy-Nandlowqualityreadsfromrawdata.Atthesametime,Q20,Q30,GC-contentandsequenceduplicationlevelofthecleandatawerecalculated.Allthedownstreamanalyseswerebasedoncleandatawithhighquality.

value: 4F2A cell

value: mef

value: Treat


title: 4F2A cell, CX-5461, DAY2_2


title: TFEBChIP_PBS_rep3

value: Bone Marrow

value: Bone Marrow-derived macrophages

value: PBS


title: TfebTg_MSUc_rep2

value: Tfeb-Tg


title: mOCCtrl_HMD201207001_DN08

value: oocytes


title: Cal33 CDX pTEADi, rep1

first: Kuniaki

last: Sato

address: 3855 Health Sciences Dr Room 2345

department: Moores Cancer Center

institute: University of California San Diego

data_processing:
The raw reads were filtered to remove low quality reads and adapters. The filtering process is as follows: (1) Remove reads containing adapters. (2) Remove reads containing N > 10% (N represents the base cannot be determined). (3) Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
The filtered sequenced reads were aligned to the human reference genome hg38 using STAR v2.7.9a with Gencode v38 annotations.
Read count data for each gene was calculated usng RSEM v1.3.1.
Assembly: hg38
Supplementary files format and content: tab-deliminated text files containing read count data of each gene. Gene names are represented as Ensembl Gene IDs.

source_name: xenograft tumor

extract_protocol:
The extraction of RNA from the xenograft tumors were performed using a QIAGEN RNAeasy Mini Kit.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: xenograft tumor

value: Head and neck squamous cell carcinoma

value: pTEADi (DOX+)


title: Cal33 CDX Control, rep1

value: Control (DOX-)


title: TFEBChIP_PBS_rep2

value: WT


title: 4F2A cell, DMSO, DAY2_3

value: Contrl

value: DMSO, DOX


title: Cal33 CDX Control, rep2


title: Cal33 CDX Control, rep3


title: Cal33 CDX pTEADi, rep3


title: mOCCtrl_HMD201207001_DP02

value: ovary

value: excluded by low quality

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: Cal33 CDX Vehicle, rep3

value: Vehicle


title: TFEBChIP_PBS_rep1


title: 4F2A cell, DMSO, DAY2_2

value: 4F2A cell

value: mef


title: Cal33 CDX Vehicle, rep2


title: mGCCtrl_HMD201207001_BE12

value: granulosa cells


title: mOCCtrl_HMD201207001_DD02


title: WT_D42_4

city: NEWCASTLE UPON TYNE

last: Young

address: Centre For Life

country: United Kingdom

institute: Newcastle University

data_processing:
Kallisto was used for pseudo-alignment and quantification, against the mouse GRCh38 (release 92) transcriptome.
Mapped transcripts were converted to a gene level using Tximport.
DESeq2 was used to calculate P-values and log2 fold-changes (logFC), using the Benjamini-Hochberg method to adjust for multiple testing.
Assembly: Mouse GRCh38 (release 92)

source_name: cartilage

extract_protocol:
RNA was extracted from the cells using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific), following the manufacturer’s protocol to isolate total RNA.
The sequencing library was prepared using theNEB_low_input_RNA kit following the manufacturer’s protocol. Barcoding was with the NEBNext_Multiplex Oligos for Illumina_(96 Unique Dual Index Primer Pairs)

treatment_protocol: The destabilisation of the medial meniscus (DMM) surgical model was performed on C57Bl/6J male mice (25-30 g; bred inhouse from Charles River, UK) at 11-weeks of age. mice were given a pre-operative analgesic (buprenorphine), anaesthetised (isoflurane) and had their left knee medial meniscus destabilized by transecting the medial meniscus tibial ligament (MMTL) with a needle blade.  The surgical wound was closed with Reflex 7mm wound clips which were removed seven days post-surgery. The day after surgery animals were given two doses of buprenorphine subcutaneously ~8 hours apart. Six weeks post-surgery, mice were euthanised, by cervical dislocation. Naive mice (DO) were untreated controls.

value: cartilage

value: chondrocyte

value: wild-type control

value: Surgery


title: TFEBChIP_MSUc_rep2

value: Bone Marrow

value: Bone Marrow-derived macrophages

value: MSUc


title: WT_D42_3


title: TFEBChIP_MSUc_rep1

value: WT


title: Cal33 CDX smTEADi, rep3

value: xenograft tumor

value: Head and neck squamous cell carcinoma


title: mGCCtrl_HMD201207001_CF13

value: ovary

value: pre-granulosa cells


title: mOCCtrl_HMD201207001_DJ06

value: oocytes

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: WT_D42_1


title: mGCCtrl_HMD201207001_CL07


title: WT_D42_2


title: Tfe3WT_Silica_rep2

value: Silica


title: Cal33 CDX smTEADi, rep2


title: mOCCtrl_HMD201207001_DL16

value: excluded by low quality


title: Tfe3WT_Silica_rep3


title: Cal33 CDX smTEADi, rep1


title: WT_D0_4

value: Naïve


title: Tfe3WT_Silica_rep1


title: human CD34+CD38low cells, 78c_24h_donor67

city: Bethesda

first: Jianyi

last: Ding

state: MD

address: 9000 Rockville Pike

department: CMTB

institute: NHLBI, NIH

data_processing:
The mRNA sequencing data was processed using default parameter with RNA-seek workflow (https://github.com/OpenOmics/RNA-seek)
Preprocessing of the raw sequencing reads to remove low quality bases, adapters, and shorter reads using Cutadapt (v1.18)
Alignment to human hg38 reference genome (GRCh38, Gencode Release 30) using STAR (v.2.7.6a) aligner in two-pass mapping mode
Gene expression counts were estimated from number of reads mapping to each annotated gene using RSEM (v.1.3.0). The expression data were transformed to log2-counts per million (logCPM) and then filtered to remove genes with < 0.5 CPM in at least one sample.
The filtered gene expression count was normalized using TMM (Trimmed Mean of M-values) method. Differential expression analysis of 78c-treated samples (n = 3) relative to the DMSO vehicle controls (n = 3) was then performed using DESeq2 while blocking on donor-specific variation in gene expression.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: mobilized pheripheral blood human CD34+ cells

growth_protocol: Human CD34+CD38low hematopoietic stem and progenitor cells isolated from mobilized peripheral blood CD34+ cells and cultured for 24 hours in the presence of cytokines (SCF, FLT3, and TPO) with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) as per the manufacturer’s protocol
The sequencing libraries were constructed from 800 ng of total RNA using the Illumina Stranded mRNA library prep kit (#20040534, Illumina) following the manufacturer instruction.

treatment_protocol: Cells were treated with either 5 μM of the CD38 inhibitor 78c or a DMSO vehicle control

value: human hematopoietic stem and progenitor cells


title: mGCCtrl_HMD201207001_BE18

value: interstitial cells


title: Tfe3WT_PBS_rep3

value: PBS


title: mGCCtrl_HMD201207001_BC18

value: ovarian surface epithelial cells


title: WT_D0_3

value: cartilage

value: chondrocyte

value: wild-type control


title: Tfe3WT_PBS_rep2

value: Bone Marrow

value: Bone Marrow-derived macrophages


title: WT_D0_2


title: human CD34+CD38low cells, 78c_24h_donor66

value: mobilized pheripheral blood human CD34+ cells

value: WT


title: mOCCtrl_HMD201207001_DN20

value: ovary


title: Tfe3WT_PBS_rep1


title: Cal33 CDX Vehicle, rep1

value: xenograft tumor

value: Head and neck squamous cell carcinoma

value: Vehicle


title: WT_D0_1


title: mOCCtrl_HMD201207001_DF04

value: oocytes

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: human CD34+CD38low cells, DMSO_24h_donor67

value: human hematopoietic stem and progenitor cells

value: DMSO


title: Tfe3WT_MSUc_rep3

value: MSUc


title: mGCCtrl_HMD201207001_AK23

value: granulosa cells


title: iWAT-6, KO

city: Gainesville

first: Zhiyong

last: Cheng

state: Florida

address: 572 Newell Drive

department: Food Science and Human Nutrition

institute: University of Florida

data_processing:
Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling)
Remove reads containing adaptors
Remove reads containing N > 10% (N represents base that could not be determined)
The Qscore (Quality value) of over 50% bases of the read is <= 5.
STAR software to alignment for RNA-seq sequencing data analysis
Assembly: mm10

source_name: inguinal adipose

extract_protocol:
Qiagen RNeasy mini kit
NEBNext® UltraTM RNA Library Prep Kit

value: inguinal adipose

value: FoxO1 knockout


title: iWAT-5, KO


title: human CD34+CD38low cells, DMSO_24h_donor55


title: mGCCtrl_HMD201207001_AG21

value: early theca cells


title: Tfe3WT_MSUc_rep2

value: Bone Marrow


title: mGCCtrl_HMD201207001_AC03


title: human CD34+CD38low cells, DMSO_24h_donor66


title: Cal33 CDX pTEADi, rep2

value: pTEADi (DOX+)


title: gWAT-6, KO

source_name: gonadal adipose

value: gonadal adipose


title: Tfe3WT_MSUc_rep1

value: Bone Marrow-derived macrophages


title: mGCCtrl_HMD201207001_CP11

value: ovary

value: interstitial cells


title: gWAT-5, KO


title: Tfe3WT_CPPD_rep3

value: CPPDc


title: Tfe3WT_CPPD_rep2


title: human CD34+CD38low cells, 78c_24h_donor55

value: mobilized pheripheral blood human CD34+ cells

value: WT


title: DOR2

city: Beijing

first: Qinyign

address: 9 Dongdan Santiao, Dongcheng District

institute: Peking Union Medical College

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include readcount values for each Sample ...

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: granulosa cell

tag: condition

value: diminished ovarian reserve (DOR)


title: mOCCtrl_HMD201207001_DD06

tag: tissue

value: oocytes

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: iWAT-4, KO


title: DOR3

tag: cell type


title: iWAT-3, KO


title: DOR1


title: mGCCtrl_HMD201207001_AE03


title: Tfe3WT_CPPD_rep1

tag: treatment


title: NOR3

value: normal ovarian reserve (NOR)


title: gWAT-4, KO


title: mOCCtrl_HMD201207001_DH06

tag: developmental stage


title: NOR2


title: Tfe3KO_Silica_rep3

value: Silica


title: Tfe3KO_Silica_rep2


title: mGCCtrl_HMD201207001_BK22

value: granulosa cells

tag: subpopulation gc


title: Tfe3KO_Silica_rep1


title: iWAT-2, KO

value: inguinal adipose

value: FoxO1 knockout


title: NOR1


title: mGCCtrl_HMD201207001_CL23

value: pre-granulosa cells

tag: subpopulation oocyte


title: Tfe3KO_PBS_rep3

value: Bone Marrow

tag: genotype

value: PBS


title: mGCCtrl_HMD201207001_AC01

value: ovary

value: early theca cells

tag: marker expression_tdtomato


title: bone marrow organoid day 16

city: Chicago

first: Peng

last: Ji

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

data_processing:
Data was demultiplexed and counted using Cell Ranger
Assembly: hg38
Supplementary files format and content: Tab separated values files and matrix files

source_name: bone marrow organoid

extract_protocol:
Ten organoids were collected into a 15 mL Falcon tube and centrifuged at 100 × g for 5 minutes at room temperature. After discarding the supernatant, the organoids were washed twice with 5 mL of MACS buffer. Following the washes, the organoids were incubated at 37ºC with collagenase to facilitate tissue dissociation. The dissociated organoids were then resuspended in 5 mL of PBS and filtered through a 40 µm cell strainer. The resulting single-cell suspension was subsequently used for single-cell library construction.
10X Genomics NEXT GEM Kit V2, 10X genomics Library Construction kit

value: bone marrow organoid

value: human iPSCs

value: organoid

value: Wildtype


title: Tfe3KO_PBS_rep2

value: Bone Marrow-derived macrophages


title: Mesenchymal stem/stromal cells treated with 100 ng/mL Pam2CSK4 for 24 hours

city: Seoul

first: Joo Youn

last: Oh

state: Korea, Republic of

address: 103 Daehakro, Jongrogu, Yeongondong

department: Ophthalmology

country: South Korea

institute: Seoul National University College of Medicine

description: 10x Genomics

data_processing:
Sample demultiplexing, barcode processing and UMI counting were performed using the 10x Genomics pipeline Cell Ranger (https://support.10xgenomics.com). Raw base call files generated by Illumina sequencers were demultiplexed into reads in FASTQ format using the bcl2fastq software developed by Illumina (https://github.com/brwnj/bcl2fastq). The raw reads were trimmed from the 3’ end to obtain the recommended number of cycles for read pairs (Read1: 28 bp; Read2: 90 bp). The reads of each library were then processed separately using the “cellranger count” pipeline to generate a gene-barcode matrix for each library. During this step, the reads were aligned to a human reference genome (version: hg19), and cell barcodes and UMIs associated with the aligned reads were corrected and filtered. scRNA-seq expression data were analyzed with Seurat for PCA, clustering, t-SNE and UMAP.
Assembly: hg19
Supplementary files format and content: tap-separated values files, matrix files

source_name: Bone marrow

growth_protocol: Primary human bone marrow-derived MSCs were obtained from the Center for the Preparation and Distribution of Adult Stem Cells at the Institute for Regenerative Medicine, Texas A&M University, which provided standardized preparations of MSCs enriched for early progenitor cells under the auspices of an NIH/NCRR grant (P40 RR 17447-06). Passage 2 MSCs were expanded in complete culture media composed of α-MEM (Gibco/Thermo Fisher Scientific, Waltham, MA) supplemented with 17% (vol/vol) fetal bovine serum (Gibco), 1% penicillin-streptomycin (Lonza, Walkersville, MD) and 2 mM L-glutamine (Lonza) at 37°C in a 5% CO2 incubator.

extract_protocol:
Cell suspensions were loaded with the reverse transcription master mix onto 10x Genomics Single Cell Chip G, where cells were partitioned into the GEMs along with gel beads coated with oligonucleotides. These oligonucleotides facilitated mRNA capture inside the droplets by 30 bp oligo-dT after cell lysis and provided barcodes to index cells (16 bp) as well as transcripts (12 bp UMI). Following reverse transcription, cDNAs with both barcodes were amplified, and libraries were compiled using the Single Cell 3’ Reagent Kit for each sample.
Following reverse transcription, cDNAs with both barcodes were amplified, and libraries were compiled using the Single Cell 3’ Reagent Kit for each sample. The libraries were then sequenced on an Illumina NovaSeq 6000 System ((Illumina, San Diego, CA) in the 2 × 150 bp paired-end mode.

treatment_protocol: MSCs were treated with 100 ng/mL Pam2CSK4 (InvivoGen) for 24 hours. Pam2CSK4-treated MSCs and untreated MSCs were subjected to scRNA-seq.

value: Bone marrow

value: 100 ng/mL Pam2CSK4 for 24 hours


title: gWAT-2, KO

value: gonadal adipose


title: mOCCtrl_HMD201207001_DJ08

source_name: ovary

value: excluded by low quality

value: Sf1-Cre;Wls flox/+;Ai9 (control)

tag: marker expression_kit-apc


title: gWAT-1, KO


title: Tfe3KO_MSUc_rep3

value: MSUc


title: mGCCtrl_HMD201207001_BG20

tag: cell size_(fsc1_area)


title: 36550_PDGF_BB_treated ATAC

city: Indianapolis

first: Yue

last: Wang

address: 975 W. Walnut street

department: Medical Genetics

institute: Indiana University

data_processing:
Illumina adapter sequences and low-quality base calls were trimmed off the paired-end reads with Trim Galore v0.4.3.
The resulting high-quality reads were aligned to the human reference genome hg38 using bowtie2.
Duplicate reads were discarded with Picard.
Reads mapped to mitochondrial DNA together with low mapping quality reads were excluded from further analysis.
Peaks were called using MACS2 2.1.2, pyDNase was used to retrieve cleavage event falling in the merged peak. Differential accessibility analysis on the counts was performed using edgeR (v3.26.8)
Assembly: hg38
Supplementary files format and content: merged open chromatin region

source_name: mesenchymal stem cells

growth_protocol: The MSC cells were grown in a humidified chamber maintained at 37°C and 5% CO2, utilizing MSCBMTM Basal Media (PT-3238) and MSCGMTM SingleQuots Supplement Kit (PT-4105) obtained from Lonza. Media was changed every three days.

extract_protocol:
Cells were re-suspended in cold PBS according to ATAC-seq protocol (Buenrostro et al., 2013). Briefly, collected cells were lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) and the nuclei were pelleted and resuspended in Tn5 enzyme and transposase buffer (Illumina Nextera® DNA library preparation kit, cat# FC-121-1030). The Nextera libraries were amplified using the Nextera® PCR master mix and KAPA biosystems HiFi hotstart readymix (cat # NC0295239) successively. AMPure XP beads (Beckman Coulter cat# A63881) were used to purify the transposed DNA and the amplified PCR products. All libraries were sequenced on a 100 cycle paired-end run on an Illumina NOVAseq instrument.
The Nextera libraries were amplified using the Nextera® PCR master mix and KAPA biosystems HiFi hotstart readymix (cat # NC0295239) successively. AMPure XP beads (Beckman Coulter cat# A63881) were used to purify the transposed DNA and the amplified PCR products. All libraries were sequenced on a 100 cycle paired-end run on an Illumina NOVAseq instrument.

treatment_protocol: MSCs were cultured in media supplemented with 10 ng/ml PDGF-BB (Invitrogen) for 48 hours as the treated sample, while the control sample was cultivated without PDGF-BB.

value: mesenchymal stem cells

value: WT

value: 10 ng/ml PDGF-BB (Invitrogen) for 48 h


title: 36550_control ATAC

value: none; control


title: Tfe3KO_MSUc_rep2

value: Bone Marrow


title: Mesenchymal stem/stromal cells

description: 10x Genomics


title: iWAT-6, control

value: inguinal adipose

value: floxed FoxO1


title: mGCCtrl_HMD201207001_BE16

data_processing:
Adaptor sequences and low quality bases were trimmed using Fastq-mcf v1.1.2 in the ea-utils package.
The RamDA-seq reads were mapped to the mouse genome (GRCm38) using Hisat2 v2.2.0.
The gene count table was obtained using the featureCounts v2.0.1 tool in the Subread package with the option ‘-t exon -g gene_id’ and the annotation gtf file from GENCODE (vM25).
We evaluated the quality control metrics and filtered out low quality samples based on the RNA integrity assessed by coverage profile along the gene body and the number of detected genes ≤ 8,000.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts or TPM values for each sample.

extract_protocol:
At postnatal day (PD) 7, ovaries from euthanized control mice (n=3) and from Wls cKO mice (n=8) were collected. Ovaries were treated with a CTK solution (consisting of 0.25% trypsin (Thermo), 0.1% collagenase type IV (Gibco), 20% KSR (Invitrogen) and 1 mM CaCl2 in PBS) for 30 min at 37°C, then further treated with Accutase (Nacalai) at 37°C for 15 min. The reaction was halted by adding L-15 medium with 0.1% penicillin-streptomycin and 5% FBS, and the cells were dissociated by pipetting. The cell suspension was filtered through 70 μm cell strainers, followed by centrifugation at 400 g for 5 min and resuspension in sorting buffer (7.5% BSA (Life Technologies) in PBS). Blocking was performed with rat IgG (5 mg/mL, I8015, Sigma-Aldrich) for 15 min on ice. Subsequently, cell surface staining was conducted using anti-ckit-APC (1:50, 105812, BioLegend) and anti-CD45-Alexa Fluor 488 (1:200, 103122, BioLegend) for 15 min on ice. After centrifugation at 400 g for 5 min, cells were resuspended in sorting buffer. Prior to single-cell sorting by flow cytometry, samples were passed through 40 μm cell strainers, and DAPI (1:10,000) was added. Control and Wls cKO samples were each sorted using MoFlo Astrios EQ with Summit v 6.3.0. software (Beckman Coulter) into 384-well plates containing 286 tdTomato-positive somatic cells and 95 ckit-positive oocytes. DAPI-positive dead cells and CD45-positive leukocytes were excluded.
Library preparation for RamDA-seq was performed according to a previously report. However, to reduce reagent costs and rRNA-derived sequencing reads, the method was modified as follows: To suppress rRNA-derived cDNA synthesis, 0.008 units/µl XRN-1 (NEB) was added to the genomic DNA digestion mix, and the reaction was performed at 30°C for 5 min. To reduce reagent costs, a liquid dispenser Mantis (Formulatrix) was used to perform the reaction up to second strand synthesis at 1/10 the reaction volume. After that, 2.5 μl 0.8 X Tagment DNA Buffer (Illumina) diluted with RNase-free water was added to 0.5 μl of the second strand synthesis products for dilution. Then, 0.5 μl Amplicon Tagment Mix (Illumina) was added to 1.5 μl of the diluted product, and tagmentation was performed at 55°C for 10 min. After that, the library was prepared using 1/10 the reaction volume according to the Nextera XT DNA Library Prep Kit (Illumina) procedure. Twelve PCR cycles were performed. Somatic and oocyte library products were collected separately in equal volumes of 1 μl/well. Subsequently, 50 μl of each sample was fractionated from the equal mixed library, purified with 1.2X AMPureXP (Beckman Coulter), and eluted with 25 μl TE. To prevent large discrepancies in the number of sequencing reads per cell between somatic and oocyte cells, purified libraries were mixed to ensure a constant average molar per cell type using the quantitative results from the Bioanalyzer Agilent High-Sensitivity DNA Kit and the ratio of the number of cells sorted (somatic cells: oocytes = 286:95). The pooled library of 2.3 pM was sequenced in single end read 76 cycles using NextSeq 500 High Output Kit v2.5.

value: ovary

value: ovarian surface epithelial cells

tag: intron ratio


title: iWAT-5, control


title: 36461_PDGF_BB_treated ATAC


title: Tfe3KO_PBS_rep1

value: PBS


title: gWAT-6, control


title: mOCCtrl_HMD201207001_DP06

value: oocytes


title: Tfe3KO_MSUc_rep1

value: Bone Marrow-derived macrophages


title: 36461_control ATAC


title: mGCCtrl_HMD201207001_AE17

value: interstitial cells


title: gWAT-3, KO

value: gonadal adipose

value: FoxO1 knockout


title: Tfe3KO_CPPD_rep3

value: CPPDc


title: mGCCtrl_HMD201207001_AE19

value: early theca cells

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: gWAT-5, control


title: iWAT-1, KO


title: 36015_PDGF_BB_treated ATAC

value: mesenchymal stem cells

value: WT


title: Tfe3KO_CPPD_rep2


title: iWAT-4, control


title: 36015_control ATAC

value: none; control


title: iWAT-3, control


title: mGCCtrl_HMD201207001_AI03

value: granulosa cells


title: Tfe3KO_CPPD_rep1

value: Bone Marrow


title: TFE3ChIP_PBS_rep2


title: gWAT-4, control

value: floxed FoxO1


title: gWAT-3, control


title: mGCCtrl_HMD201207001_CP21

value: ovary


title: mGCCtrl_HMD201207001_CB01

value: pre-granulosa cells


title: 36650_control

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the mouse genome using STAR (v2.5.3a) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to UCSC hg38 genes using featureCounts (from subread v2.0.1) with the following parameters: “-s2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 3 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using likelihood ratio test method in edgeR (v3.38.4).
Assembly: hg38
Supplementary files format and content: raw counts

extract_protocol:
Total RNA was extracted from cells using the Qiagen RNeasy Mini kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using KAPA mRNA Hyperprep Kit (KK8581), Dual Index, following manufacturer's protocols.


title: 36650_PDGF_BB_treated


title: TFE3ChIP_PBS_rep1

value: PBS


title: mOCCtrl_HMD201207001_DB02

value: oocytes


title: 36461_PDGF_BB_treated


title: TFE3ChIP_MSUc_rep1

value: Bone Marrow-derived macrophages

value: MSUc


title: mGCCtrl_HMD201207001_BI02


title: 36461_control


title: PBS_5h_rep2


title: iWAT-1, control

value: inguinal adipose


title: mGCCtrl_HMD201207001_CH17


title: 36015_PDGF_BB_treated


title: PBS_5h_rep1


title: gWAT-2, control

value: gonadal adipose


title: PBS_30m_rep2


title: mGCCtrl_HMD201207001_CL13

value: ovarian surface epithelial cells


title: 36015_control


title: PBS_30m_rep1


title: mGCCtrl_HMD201207001_AI11


title: GBM6_X

first: Jinquan

last: Cai

address: Xuefu Road

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger software v3.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest).
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: GBM tumor tissue

extract_protocol:
For single-cell suspension preparation, tumour specimens were washed by PBS and mechanically cut into small pieces using sterile surgical scissors, and then digested into single cell suspensions using Brain Tumour Dissociation Kit (P) (Miltenyi Biotec, Bergisch Gladbach, Germany) according to the manufacturer’s protocols. Dead Cell Remove Kit (Miltenyi Biotec, Bergisch Gladbach, Germany) was used to remove non-vital cells from single cell suspensions.
Single-cell RNA libraries were constructed using Chromium Next GEM Single Cell 5’ V2 GEM, Library & Gel Bead Kit (10Genomics) following the manufacturer’s protocols.

value: GBM tumor tissue

value: tumor cell


title: mGCCtrl_HMD201207001_BA10

address: 744 Motooka Nishi-ku

value: interstitial cells

value: Sf1-Cre;Wls flox/+;Ai9 (control)


title: PBS_2h_rep2

value: WT


title: GBM5_L


title: PBS_2h_rep1


title: Tbx18_stroke

city: Ottawa

first: Jing

state: Ontario

address: 501 smyth road

country: Canada

institute: University of Ottawa

description: 10x Genomics library of cells from the cerebral cortex

data_processing:
Raw sequencing reads were processed using CellRanger v7.0.0. The GRCm38 build of the mouse genome was used for both. Except for explicitly setting --expect-cells=5000, default parameters were used for all samples.
Assembly: mm10
Supplementary files format and content: Cell metadata table: Various metadata (sample ID, cluster, etc) for each cell contained in the UMI count matrix. UMI count matrix: Matrix containing UMI counts for all cells passing quality control filters.

source_name: Brain, cerebral cortex

extract_protocol:
Extract intake or damged cortical tissue before digestion followed by FACS
cDNA synthesis and library construction was performed using the 10x Genomics Single Cell 3' Reagent Kit v3

treatment_protocol: We performed scRNA-seq using ET-1/L-NAME stroke-injured cerebral cortical tissues isolated from two pericyte lineage tracing mice (NG2-Cre-ERT2/Ai14-flx and Tbx18-CreERT2/Ai14-flx) that received intracerebral injections of ET-1/L-NAME (or saline) 3 days prior to scRNA-seq. Both transgenic mice were also treated with tamoxifen 7 days before injury to enable lineage tracing of Tbx18-Ai14+ and NG2-Ai14+ cells. Three groups of Tbx18-Ai14+ and NG2-Ai14+ cells from 1) no injury (naïve), 2) physical injury (saline), and 3) ischemic injury (ET-1/L-NAME) were Fluorescence-activated Cell (FAC) sorted for tdT (Ai14)+/DAPI- live cells to perform scRNA-seq.

value: Brain, cerebral cortex

value: 3-4 months old

value: Ischemic stroke


title: iWAT-2, control

value: floxed FoxO1


title: GBM4_W


title: GBM3_Y


title: nullOB4

first: David

source_name: Bone

treatment_protocol: Osteoblasts were plated in osteogenic growth media (complete α-MEM supplemented with 2 mM β-glycerophosphate (BGP) and 50 µg/mL L-ascorbic acid (both Sigma-Aldrich)) for 18 days.  BMMs were plated in complete α-MEM, supplemented either with 30 ng/mL M-CSF and 50 ng/mL RANK-L to stimulate osteoclastogenesis (samples labelled osteoclasts) or 30 ng/mL M-CSF only (samples labelled BMMs) and stimulated for 5 days

value: Bone

value: Osteoblasts


title: Tbx18_naive

value: Naive

value: 10x Genomics library of cells from the cerebral cortex


title: PBS_1h_rep1

value: Bone Marrow

value: Bone Marrow-derived macrophages

value: PBS


title: PBS_1h_rep2


title: nullOB2


title: nullOB3


title: Ng2_stroke


title: GBM1_L


title: PBS_10m_rep2


title: nullOB6


title: WTOB6

value: wild-type control


title: 72kd_r4_fadu

city: Heidelberg

first: Rebecca

middle: Emma

last: Wagner

address: Inf 280 im Neuenheimer Feld

department: Cell Biology and Tumor Biology

country: Germany

institute: DKFZ

data_processing:
Reads were aligned to the hs37d5 reference genome using STAR aligner
FeatureCounts was used for gene specific quantification fo reads on the appropriate gene annotation
Raw gene count values were then used as input for a differential gene expression analysis using DESeq2 within R
Assembly: hs37d5

source_name: FaDu

growth_protocol: Keratinocytes were cultured with KBM-Gold (Lonza) medium  supplemented with 0.06mM CaCl and the essential growth factors supplied. FaDu cells were cultured with EMEM supplemented with 10% FBS and pen/strep. SCC25 cells were cultured in DMEM/F12 HEPES with 10% FBS and pen/strep. All cells were kept at 37 with 5% CO2

extract_protocol:
Total RNA was extracted using Trizol reagent, following manufacturer's instructions. DNA was purified using spin columns following manufacturer's instructions.
Total RNA from keratinocytes was rRNA depleted and RNA-sequencing libraries were prepped using NEB Ultra II directional kit (NEB). Total RNA from FaDu cells was used to prepare libraries using TruSeq stranded total RNA kit (Illumina). RNA from SCC25 cells and clones was used to generate RNA-sequencing libraries using stranded total RNA prep with Ribo-zero plus kit (Illumina). SLAM-sequencing libraries were prepared using Quant-seq 3' mRNA library prep kit (Lexogen). Libraries were prepared from purified DNA using the SimpleChIP, ChIP-seq DNA library prep kit for illumina (CST).

treatment_protocol: SRSF2 depletion was achieved by transfecting an siRNA pool using Lipofectamine RNAiMax

value: FaDu

value: siRNA transfection


title: gWAT-1, control

value: gonadal adipose


title: Tbx18_nonstroke

value: Physical injury


title: 72kd_r3_fadu


title: nullOB1


title: Ng2_nonstroke


title: Ng2_naive


title: MSUc_5h_rep2

value: WT

value: MSUc


title: nullOB5


title: PBS_10m_rep1


title: 72kd_r2_fadu


title: WTOB5


title: 150-40-mJ-cm2-96-hr_R1

last: Meier

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.23.0
Alignment was performed using STAR v2.7.10a
Gene counts were performed with qCount in the QuasR R package v1.34.0
Normalization was performed with DESeq2 v1.36.1
Assembly: GRCm39
Supplementary files format and content: Tab-separated count matrix

source_name: Dorsal skin, 40 mJ/cm2 96 hr

extract_protocol:
Total RNA was extracted using RNeasy Fibrous Tissue Kits (Qiagen Inc., cat #: 74704) according to the manufacturer’s instructions (with 700 µL of the mixed lysate transferred to a RNeasy Mini column and repeated until all lysate had been used). During the procedure, Qiagen’s On-Column RNase-free DNase was used to eliminate possible DNA contamination.
Library preparation for next-generation sequencing was conducted on randomized RNA samples using the TruSeq-stranded mRNA kit (Illumina, San Diego, California) according to the sample preparation guide. The input RNA for library preparation was 300 ng per sample. A dual index scheme was used to multiplex samples for sequencing, which were pooled and sequenced on high output flow cells using an Illumina NextSeq® 500. Single-end sequencing was performed with a read length of 75 bp. A sequencing depth ~40 million reads per sample was achieved.

value: Dorsal skin

value: 40 mJ/cm2

value: 96 hr


title: WTOB4

value: Bone


title: 149-40-mJ-cm2-96-hr_R1


title: 72kd_r5_fadu


title: 72kd_r1_fadu


title: MSUc_5h_rep1

data_processing:
RNA-Seq analysis  FASTQ sequencing files were mapped to the mm10 using STAR with default parameters. Biological and technical replicates were used in all experiments. Quantification of transcripts was performed using the analyzeRepeats.pl of HOMER with the following parameters -condenseGenes -count exons -noadj. Principal Component Analysis (PCA) and correlation analyses were obtained based on the Transcripts Per kilobase Million (TPM) on all genes of all samples and TPM for each transcript was calculated using the analyzeRepeats.pl tool of HOMER with the parameters -condenseGenes -count exons -tpm. Differential expression analysis was generated using getDiffExpression.pl tool of HOMER (Heinz et al. 2010) with default parameters: FDR <0.05 and log2fold change >1 or < (-1) for cells treated with PBS or MSUc and FDR <0.05 for treatment with other chemicals. Pathway analyses of differentially expressed genes were performed using Metascape (Zhou et al. 2019).    ChIP-Seq analysis  ChIP-Seq analysis was performed as described previously (Cobo, Tanaka, et al. 2022; Seidman et al. 2020). Briefly, ChIP-Seq peaks for TFEB, TFEC, BHLHE40, BHLHE41, DOT1L and DNMT3A replicates were obtained using HOMER with parameters –L 0 –C 0 –fdr 0.9 –minDist 200 –size 200. Only peaks with IDR <0.05 were considered for downstream analyses. The merged tag directories from all replicates from each experimental conditions were used for visualization in the UCSC Browser (Kent et al. 2002). Peaks were annotated with the nearest gene to analyse the overlap between conditions. For H3K27ac and H3K4me3 differential peaks, H3K27ac and H3K4me3 ChIP-Seq peaks were centred to regions of open chromatin using the annotatePeak.pl tool of HOMER an ATAC-Seq peak file of BMDM treated with PBS or MSUc. Differential peaks were calculated using the getDiffExpression.pl tool of HOMER with default parameters. A list of the IDR peaks for TFEB, TFEC, BHLHE40, BHLHE41, DOT1L, DNMT3A, H3K27ac, H3K4me3 and H3K79me3 as well as the differential peaks after treatment with MSUc can be found in GEO under the accession number (GSE). To generate a histogram of the intensity of a given ChIP-Seq over a subset of differential peaks or regions using the annotatePeaks.pl tool of HOMER with the parameters -size 6000 -hist 25. To identify DNA motifs in differential peak or regions over background sequences, the findMotifGenome.pl tool of HOMER was used with default parameters and random genomic sequences as background (Heinz et al. 2010). In the figures, de novo motifs are displayed unless otherwise indicated.
In silico promoter analysis of differentially expressed genes was performed using the findMotifs.pl tool of Homer searching for motifs of length 8 and 10 and from -2000 to +500 bp relative to the TSS, using 4 threads.
Assembly: mm10
Supplementary files format and content: The list of Transcripts Per Million reads (TPM) and differential peak files are provided in fastq.gz

source_name: Bone Marrow

extract_protocol:
It was performed as described elsewhere (Cobo, Cheng, et al. 2022; Cobo, Tanaka, et al. 2022). Briefly, BMDM were lysed in Trizol (ThermoFisher, #15596026) and RNA was isolation and DNase treatment were carried out using RNA MicroPrep kit (Zymoresearch, #11-33MB).
RNA-Seq library preparation  It was performed as described elsewhere (Cobo, Cheng, et al. 2022; Cobo, Tanaka, et al. 2022). Briefly, BMDM were lysed in Trizol (ThermoFisher, #15596026) and RNA was isolation and DNase treatment were carried out using RNA MicroPrep kit (Zymoresearch, #11-33MB). 500 ng-1 μg of RNA was incubated with Oligo d(T) magnetic beads (NEB, #S1419S) to enrich for poly-A tailed transcripts and then fragmented by incubating for 9 min at 94º in 2X Superscript III first-strand buffer containing 10 mM DTT (Invitrogen, #P2325). Reverse transcription (RT) of fragmented RNA was performed at 25ºC for 10 min followed by 50ºC for 50 min. RT product was purified with RNAClean XP (Beckman Coulter, #A63987) and the solution of RNA-cDNA complexes was then added to a mix containing 1.5 μl of 10X Blue Buffer (Enzymatics, #B0110-L), 1.1 μl of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 μl of 5 U/ml RNAseH (Enzymatics, #Y9220L), 1 μl of 10 U/ml DNA polymerase I (Enzymatics, #P7050L), 0.15 μl of 1% Tween 20 and 1.05 μl of nuclease free water; and incubated at 16ºC overnight. Next day, the resulting DNA was purified using 28 μl of SpeedbBead Magnetic Carboxylate (GE Health- care, #651521050 50250) diluted in 20%PEG8000:2.5M NaCl to a final 13% PEG concentration. After two washes owith 80% etOH, air dry and eluted, the purified DNA was end-repaired by blunting followed by A-tailing and adapter ligation using NOVA (BIOO-NextFlex adapters. Libraries were amplified by PCR for 13 cycles using Solexa 1GA and Solexa 1GB primers (AATGATACGGCGACCACCGA and CAAGCAGAAGACGGCATACGA, respectively), purified using 1 μl of SpeedbBead Magnetic Carboxylate. Eluted libraries were quantified using a Qubit dsDNA HS Assay Kit and sequenced on NovaSeq SP100 (Illumina, San Diego, California).  ChIP-Seq library preparation  Chromatin immunoprecipitation (ChIP) was performed as described elsewhere (Seidman et al. 2020; Gosselin et al. 2017). Briefly, MDM or BMDM were fixed with 1% formaldehyde for H3K27ac, H3K4me3 and H3K79me3 or doubly fixed with 3 mM Disuccinimidyl-glutarate -DSG- (Proteochem, #C1104) in PBS for 30 min at room temperature and then with 1% formaldehyde (ThermoFisher, #28906) for 10 min at room temperature for TFEB, TFEC, BHLHE40, BHLHE41, DOT1L and DNMT3A. Fixation was then quenched upon adding glycine to final concentration of 125 mM. Cells were then washed with 0.01%Triton X-100:PBS, scraped and pelleted by centrifugation at 3000 rpm for 10 min at 4ºC and snap frozen for storage at -80ºC. For ChIP experiments, fixed cells were thawed and permeabilised in 1 mL of chilled buffer containing 10 mM HEPES/KOH pH7.9, 85 mM KCl, 1 mM EDTA, 0.2% IGEPAL CA-630 (Sigma-Aldrich, #I8896), 1X protease inhibitor cocktail (Sigma, #11836145001) and 1 mM PMSF for 10 min on ice. After that cells were spun down and lysed in 130 μl of either LB3 lysis buffer containing 10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1 X protease inhibitor cocktail for H3K27ac, H3K4me3 and H3K79me3 or lysis buffer containing 20 mM Tris/HCl pH7.5, 1 mM EDTA, 0.5 mM EGTA, 0.1% SDS, 0.4% Sodium Deoxycholate, 1% NP-40, 0.5 mM DTT, 1x protease inhibitor cocktail and 1 mM PMSF. Chromatin was sheared by sonication in a 96 microTUBE Rack (Covaris, #500282) using a Covaris E220 for 25 cycles with the following settings: time, 60 s; duty, 5.0; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0. Sonicated lysates were spun down at 10,000 rpm for 10 min at 4ºC and one percent of the sonicated lysate was kept as ChIP input for analysis. In all buffers, DTT, protease inhibitor and PMSF were added freshly. Sonicated lysates were incubated with a mix consisting of Protein G Dynabeads (Invitrogen, #10003D) and TFEB antibody cocktail (Abcam, #ab2636 plus CST, #37785), TFE3 antibody cocktail (Abcam, #196681 plus Abcam, #93808), BHLHE40 (Novus Biologicals, #NBP100-1800), DOT1L (CST, #D1W4Z), DNMT3A cocktail (Abcam, #ab2850 plus Diagenode, #C15410085), H3K27ac (ActiveMotifs, #AB_2793305), H3K4me3 (Millipore, #04-745), or H3K79me3 (Diagenode, #C15410068),  was added to the sonicated material and incubated overnight on a rotator at 4ºC. Next day, immunocomplexes were placed on a magnet and bead complexes were washed with 100 μl of chilled buffers. For H3K27ac, H3K4me3 and H3K79me3 ChIP, beads were washed four times each with wash buffer I containing 20 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, wash buffer III containing 10 mM Tris/HCl pH 7.4, 250 mM LiCl, 1% Triton X-100, 0.7% Na-Deoxycholate, 1 mM EDTA and twice with ice-cold TET containing 10 mM Tris/HClpH7.5, 1 mM EDTA, 0.2% Tween-20. For TFEB, TFEC, BHLHE40, BHLHE41, DOT1L and DNMT3A ChIP beads were washed as it follows: 3 times lysis buffer, 6 times with wash buffer containing 10 mM Tris/HCl pH7.5, 250 mM LiCl, 1 mM EDTA, 0.7% Na-Deoxycholate and 1% NP-40 alternative; 3 times with TET buffer containing 10 mM Tris/HCl pH 8.0, 1 mM EDTA, 0.2% Tween 20; and 1 time with IDTE buffer containing 10 mM Tris/HCl pH 8.0 and 0.1 mM EDTA. Bead complexes were resuspended in 25 mL of TT buffer containing 10 mM Tris/HCl pH 8.0, 0.05% Tween 20. ChIP libraries for sequencing were prepared on beads using NEBNext Ultra II Library kit (NEB, #E7645L) by reducing 50% the reaction volume as previously described (Heinz et al. 2015; Sakai et al. 2019). Reverse crosslinking was performed by adding 33.5 μl of a mix containing 4 μl 10% SDS, 3 μl 0.5 M EDTA, 1.6 μl 0.2M EGTA, 1 μl 10 mg/ml Proteinase K (Biolabs, #P8107 S), 1 μl 10 mg/ml RNase A, 4.5 μl 5M NaCl and 18.4 μl nuclease free water and incubating at 55C for 1h followed by 75ºC for 30 min. After removing the dynabeads, libraries were cleaned by adding  2 μl of SpeadBeads in 124 μl of 20% PEG 8000/ 1.5M NaCl and washed twice with 100 μl of 80% etOH, air dry and eluted in 13 μl of buffer containing 10 mM Tris/HCl pH 8.0 and 0.05% Tween 20. Libraries were amplified by PC for 14 cycles using NEBNext Ultra II PCR master mix using Solexa 1GA and Solexa 1GB primers. After that, libraries were size selected 200-500 bp upon running in 10% TBE acrylamide gels (ThermoFisher, #EC62752BOX) and sequenced using a NovaSeq SP100.


title: WTOB3

value: Osteoblasts


title: MSUc_30m_rep1


title: WTOB2


title: MSUc_30m_rep2


title: MSUc_2h_rep2


title: repeat_148-40-mJ-cm2-96-hr_R1


title: 145-20-mJ-cm2-96-hr_R1

source_name: Dorsal skin, 20 mJ/cm2 96 hr

value: 20 mJ/cm2


title: MSUc_2h_rep1


title: nullOC6

value: Osteoclasts


title: 144-20-mJ-cm2-96-hr_R1


title: 4399, FFPE, TNBC, liver metastasis

city: Darlinghurst

first: Taopeng

state: New South Wales

address: 384 Victoria St

department: Cancer ecosystem

country: Australia

institute: Garvan institute of medical research

data_processing:
spaceranger v2.0.0
Assembly: hg38 & FFPE Visium probe set v2.0
Supplementary files format and content: default spaceranger V2 ouptuts
Library strategy: Spatial Transcriptomics

source_name: Breast cancer liver metastasis

extract_protocol: 10X Genomics FFPE Visium CytAssist workflow

value: Breast cancer liver metastasis


title: WTOB1


title: Ovary_230303, FFPE, single-nucleus, snPATHO-seq workflow

data_processing:
Demultiplexing and reads alignment were performed using Cell Ranger v7.0.1 or v2023.0415.0 as documented in https://www.biorxiv.org/content/10.1101/2023.12.07.570700v1.
raw count matrix generated using 10X Genomics cellranger v7.0.1
filtered count matrix gnerated using cellbender v0.2.0
Assembly: hg38
Supplementary files format and content: Unfiltered counts in .h5 format generated by 10X Genomics cellranger (v2023.0415.0 / v7.0.1)
Supplementary files format and content: 10X Genomics cellranger v3 format .h5 files for counts filtered using cellranger v7.0.1 (PBMC data) or cellbender v2.0.0 (all other data)

molecule: nuclear RNA

source_name: Ovary

extract_protocol:
Samples were processed for 3' or Flex chemistry (10x Genomics) using establihsed protocols as mentioned in https://www.biorxiv.org/content/10.1101/2023.12.07.570700v1.
libraries were prepared accoridng to the manufacturer's instructions (3' V3.1 chemistry & Flex chemistry, 10x Genomics).

value: Ovary

tag: sample type

value: FFPE sample

tag: workflow

value: snPATHO-seq workflow

tag: library protocol

value: 10X Genomics FLEX


title: 4066, FFPE, HER2 amplified, primary breast cancer

source_name: Primary human breast cancer

value: Primary human breast cancer


title: MSUc_1h_rep2

value: Bone Marrow

value: Bone Marrow-derived macrophages


title: nullOC5


title: MSUc_1h_rep1

value: WT


title: nullOC4


title: Colon_213641, FFPE, single-nucleus, snPATHO-seq workflow

source_name: Colon

value: Colon


title: 141-20-mJ-cm2-96-hr_S68_R1_001

first: Matthew

value: Dorsal skin


title: Endometrium_220952, FFPE, single-nucleus, snPATHO-seq workflow

source_name: Endometrium

value: Endometrium


title: 4411, FFPE, Luminal, liver metastasis


title: nullOC3


title: melanoma_7167A, FFPE, single-cell, scFFPE workflow

data_processing:
Demultiplexing and reads alignment were performed using Cell Ranger v7.0.1 or v2023.0415.0 as documented in https://www.biorxiv.org/content/10.1101/2023.12.07.570700v1.
raw count matrix generated using 10X Genomics cellranger v2023.0415.0
filtered count matrix gnerated using cellbender v0.2.0
Assembly: hg38
Supplementary files format and content: Unfiltered counts in .h5 format generated by 10X Genomics cellranger (v2023.0415.0 / v7.0.1)
Supplementary files format and content: 10X Genomics cellranger v3 format .h5 files for counts filtered using cellranger v7.0.1 (PBMC data) or cellbender v2.0.0 (all other data)

source_name: Skin

value: Skin

value: 10X scFFPE workflow


title: 146-40-mJ-cm2-96-hr_S69_R1_001

value: 40 mJ/cm2

value: 96 hr


title: melanoma_7167A, FFPE, single-nucleus, snPATHO-seq workflow


title: 140_S59-10-mJ-cm2-96-hr_R1

source_name: Dorsal skin, 10 mJ/cm2 96 hr

value: 10 mJ/cm2


title: nullOC1

data_processing:
Kallisto was used for pseudo-alignment and quantification, against the mouse GRCh38 (release 92) transcriptome.
Mapped transcripts were converted to a gene level using Tximport.
DESeq2 was used to calculate P-values and log2 fold-changes (logFC), using the Benjamini-Hochberg method to adjust for multiple testing.
Assembly: Mouse GRCh38 (release 92)

value: Osteoclasts


title: 143-20-mJ-cm2-96-hr_R1

value: 20 mJ/cm2


title: 137-10-mJ-cm2-96-hr_S62_R1_001


title: Particles_PBS_rep3

description: ExposuretoParticles.txt

value: Vehicle


title: 138-10-mJ-cm2-96-hr_S65_R1_001


title: WTOC6

value: wild-type control


title: Particles_Silica_rep1

description: ExposuretoParticles.txt

value: Silica


title: WTOC5


title: lung_cancer_20011329LC, FFPE, single-nucleus, snPATHO-seq workflow

source_name: Lung

value: Lung

value: FFPE sample

value: snPATHO-seq workflow

value: 10X Genomics FLEX


title: lung_cancer_20011329LC, FFPE, single-cell, scFFPE workflow


title: Particles_PBS_rep2

description: ExposuretoParticles.txt

value: Bone Marrow

value: Bone Marrow-derived macrophages

value: WT


title: MSUc_10m_rep2

value: MSUc


title: 135-5-mJ-cm2-96-hr_R1

source_name: Dorsal skin, 5 mJ/cm2 96 hr

value: Dorsal skin

value: 5 mJ/cm2


title: 134-5-mJ-cm2-96-hr_R1

value: 96 hr


title: lung_20011329NL, FFPE, single-nucleus, snPATHO-seq workflow


title: MSUc_10m_rep1


title: Particles_MSUc_rep3

description: ExposuretoParticles.txt


title: nullOC2


title: liver_8754A, FFPE, single-cell, scFFPE workflow

source_name: Liver

value: Liver

value: 10X scFFPE workflow


title: 139-10-mJ-cm2-96-hr_R1

value: 10 mJ/cm2


title: Particles_Silica_rep2

description: ExposuretoParticles.txt


title: WTOC2

value: Osteoclasts


title: 131-5-mJ-cm2-96-hr_S61_R1_001


title: Particles_MSUc_rep2

description: ExposuretoParticles.txt


title: liver_8754A, FFPE, single-nucleus, snPATHO-seq workflow


title: lung_20011329NL, FFPE, single-cell, scFFPE workflow


title: nullBMM6

value: Bone Marrow Macrophages


title: Kidney_1305272B, FFPE, single-cell, scFFPE workflow

source_name: Kidney

value: Kidney


title: Particles_MSUc_rep1

description: ExposuretoParticles.txt


title: WTOC4

value: wild-type control


title: 130-Sham-96-hr_R1

source_name: Dorsal skin, Sham 96 hr

value: Sham


title: 133-5-mJ-cm2-96-hr_R1


title: Particles_PBS_rep1

description: ExposuretoParticles.txt

value: Vehicle


title: WTOC3


title: Kidney_1305272B, FFPE, single-nucleus, snPATHO-seq workflow

value: FFPE sample

value: snPATHO-seq workflow

value: 10X Genomics FLEX


title: nullBMM5

value: Bone Marrow


title: Particles_CPPD_rep2

description: ExposuretoParticles.txt

value: Bone Marrow-derived macrophages

value: WT

value: CPPDc


title: 127-Sham-96-hr_S64_R1_001

value: Dorsal skin

value: 96 hr


title: 128-Sham-96-hr_R1


title: Glioblastoma_1773A, FFPE, single-cell, scFFPE workflow

source_name: Brain

value: Brain

value: 10X scFFPE workflow


title: 129-Sham-96-hr_R1


title: Glioblastoma_1773A, FFPE, single-nucleus, snPATHO-seq workflow


title: nullBMM3


title: Particles_Alum_rep3

description: ExposuretoParticles.txt

value: Aluminum particles


title: 126-Sham-96-hr_S60_R1_001


title: WTOC1

value: Osteoclasts


title: nullBMM2

value: Bone Marrow Macrophages


title: 125-40-mJ-cm2-72-hr_R1

source_name: Dorsal skin, 40 mJ/cm2 72 hr

value: 40 mJ/cm2

value: 72 hr


title: Particles_CPPD_rep1

description: ExposuretoParticles.txt


title: Particles_CPPD_rep3

description: ExposuretoParticles.txt


title: Particles_Alum_rep2

description: ExposuretoParticles.txt


title: nullBMM1


title: Particles_Alum_rep1

description: ExposuretoParticles.txt


title: Endocervical_Adenocarcinoma_6707, FFPE, single-nucleus, snPATHO-seq workflow

source_name: Endocervical tissue

value: Endocervical tissue


title: Colon_1328A, FFPE, single-cell, scFFPE workflow

value: Colon

value: FFPE sample


title: WTBMM6

source_name: Bone Marrow

value: wild-type control


title: Colon_1328A, FFPE, single-nucleus, snPATHO-seq workflow

value: snPATHO-seq workflow

value: 10X Genomics FLEX


title: 122-40-mJ-cm2-72-hr_S63_R1_001


title: WTBMM5

value: Bone Marrow


title: MITFChIP_PBS_rep2

description: Used for visualization

value: Bone Marrow-derived macrophages

value: WT

value: PBS


title: 4411, snap frozen, single-nucleus, 3' workflow

value: Breast cancer liver metastasis

value: snap frozen sample

value: 10X 3p workflow

value: 10X Genomics 3' v3.1


title: 123-40-mJ-cm2-72-hr_R1

value: Dorsal skin


title: 124-40-mJ-cm2-72-hr_R1

value: 40 mJ/cm2


title: 121-40-mJ-cm2-72-hr_S59_R1_001

value: 72 hr


title: WTBMM4

value: Bone Marrow Macrophages


title: Endocervical_Adenocarcinoma_6707, FFPE, single-cell, scFFPE workflow

value: Endocervical tissue

value: 10X scFFPE workflow


title: 120-20-mJ-cm2-72-hr_R1

source_name: Dorsal skin, 20 mJ/cm2 72 hr

value: 20 mJ/cm2


title: WTBMM3

value: wild-type control


title: 4411, snap frozen, single-nucleus, FLEX workflow

source_name: Breast cancer liver metastasis

value: 10X FLEX workflow

value: 10X Genomics FLEX


title: MITFChIP_PBS_rep1

description: Used for visualization

value: Bone Marrow

value: Bone Marrow-derived macrophages


title: MITFChIP_MSUc_rep2

description: Used for visualization

value: WT

value: MSUc


title: 4411, FFPE, single-cell, scFFPE workflow

value: Breast cancer liver metastasis

value: FFPE sample


title: MITFChIP_MSUc_rep1

description: Used for visualization


title: nullBMM4


title: 119-20-mJ-cm2-72-hr_R1


title: 4411, FFPE, single-nucleus, snPATHO-seq workflow

value: snPATHO-seq workflow


title: 118-20-mJ-cm2-72-hr_R1

value: Dorsal skin


title: Vehicle_PBS_rep3

description: Treatment_of_macrophages_with_Metformin.txt

value: PBS


title: WTBMM2


title: WTBMM1


title: 4399, snap frozen, single-nucleus, 3' workflow

value: snap frozen sample

value: 10X 3p workflow

value: 10X Genomics 3' v3.1


title: 117-20-mJ-cm2-72-hr_S56_R1_001

value: 72 hr


title: Vehicle_PBS_rep1


title: 116-20-mJ-cm2-72-hr_S53_R1_001

value: 20 mJ/cm2


title: P95H_28d_17457_mouse_bio_rep4

data_processing:
Reads were aligned to the GRCm38mm10 reference genome using STAR aligner
FeatureCounts was used for gene specific quantification fo reads on the appropriate gene annotation
Raw gene count values were then used as input for a differential gene expression analysis using DESeq2 within R
Assembly: Grcm38mm10
Supplementary files format and content: tab and delimited text file

source_name: back skin

extract_protocol:
RNA was extracted with Trizol following manufacturer's instructions
For SRSF2 knock out mice and controls RNA sequencing libraries were prepared using TruSeq Stranded Total RNA Gold library prep kit. For SRSF2 P95H mutant mice and controls RNA sequencing libraries were prepared using stranded Total RNA prep with Ribo-zero plus kit.

treatment_protocol: mouse back skin was treated topically every other day for a given period of time with 4-hydroxy tamoxifen

value: back skin

value: Cre positive

tag: srsf2 ko/mut

value: SRSF2 MUT

tag: tdtomato

value: wild type

value: 4-hydroxy tamoxifen

value: 28 days


title: 4066, snap frozen, single-nucleus, 3' workflow

source_name: Primary human breast cancer

value: Primary human breast cancer


title: Vehicle_MSUc_rep3

value: Bone Marrow

value: Bone Marrow-derived macrophages

value: WT

value: MSUc


title: P95H_28d_17454_mouse_bio_rep1

tag: time


title: 4399, snap frozen, single-nucleus, FLEX workflow

tag: tissue

value: Breast cancer liver metastasis

value: 10X FLEX workflow

value: 10X Genomics FLEX


title: Vehicle_MSUc_rep2

tag: cell type


title: P95H_28d_17455_mouse_bio_rep2

tag: treatment


title: 115-10-mJ-cm2-72-hr_R1

source_name: Dorsal skin, 10 mJ/cm2 72 hr

value: Dorsal skin

value: 10 mJ/cm2


title: 114-10-mJ-cm2-72-hr_R1

value: 72 hr


title: Vehicle_MSUc_rep1


title: P95H_28d_17456_mouse_bio_rep3

value: back skin


title: 4066, FFPE, single-cell, scFFPE workflow

value: FFPE sample

value: 10X scFFPE workflow


title: 112-10-mJ-cm2-72-hr_S20_R1_001


title: 4399, FFPE, single-cell, scFFPE workflow


title: 4066, FFPE, single-nucleus, snPATHO-seq workflow

value: snPATHO-seq workflow


title: CTR_28d_17458_mouse_bio_rep2

value: ctr

value: Cre negative

value: SRSF2 MUT

value: wild type

value: 4-hydroxy tamoxifen


title: Vehicle_PBS_rep2

value: Bone Marrow

value: Bone Marrow-derived macrophages

value: WT

value: PBS


title: CTR_28d_16706_mouse_bio_rep1

value: 28 days


title: Metformin_PBS_rep2


title: 111_2-10-mJ-cm2-72-hr_S52_R1_001

value: Dorsal skin


title: blood, AT-37

city: Napoli

first: Aannamaria

last: Carissimo

address: via Pietro Castellino

department: IAC

country: Italy

institute: CNR Italy

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in
fastq file through bcl2fastq
Trimming and cleaning with Trim Galore (v0.6.2)
Alignment was performed with Bowtie (v1.2.2)
The counts were determined with SAMtools (v1.9)
Assembly: hg19 (release 75) - miRBase (release 21)
Supplementary files format and content: tab-delimited text files including raw counts

source_name: BLOOD-CELLS

extract_protocol:
small RNAs was then extracted from PBMCs using the miRNeasy Kit (Qiagen, Germantown, MD, USA) according to the manufacturer′s instructions. 250 ng of total RNA was used for the construction of sequqncing libraries.
Libraries were prepared from 250 ng of total RNA using NEGEDIA smallRNAseq sequencing service (Next Generation Diagnostics srl) which included, library preparation, quality assessment and sequencing on a NovaSeq 6000 sequencing system using a single-end, 50 cycle strategy (Illumina Inc.).
NEGEDIA smallRNAseq

value: BLOOD-CELLS

tag: condition

value: AT


title: Metformin_PBS_rep1

address: 9500 Gilman Dr.


title: P95H_12d_16415_mouse_bio_rep2

value: back skin

value: Cre positive

value: 12 days


title: 110-5-mJ-cm2-72-hr_R1

source_name: Dorsal skin, 5 mJ/cm2 72 hr

value: 5 mJ/cm2

value: 72 hr


title: blood, AT-34


title: P95H_12d_16413_mouse_bio_rep1


title: 109_5-5-mJ-cm2-72-hr_R1


title: blood, AT-33


title: Metformin_MSUc_rep3


title: CTR_28d_17462_mouse_bio_rep4

value: ctr

value: Cre negative


title: blood, AT-32


title: Metformin_PBS_rep3


title: 4066, snap frozen, single-nucleus, FLEX workflow

value: Primary human breast cancer

value: snap frozen sample

value: 10X FLEX workflow

value: 10X Genomics FLEX


title: 108-5-mJ-cm2-72-hr_R1


title: Metformin_MSUc_rep2

value: Bone Marrow

value: Bone Marrow-derived macrophages

value: WT


title: 113-10-mJ-cm2-72-hr_R1

value: Dorsal skin

value: 10 mJ/cm2


title: CTR_12d_16581_mouse_bio_rep5

value: SRSF2 MUT

value: wild type

value: 4-hydroxy tamoxifen


title: 107-5-mJ-cm2-72-hr_S55_R1_001


title: H3K79me3_PBS_rep3

description: Used for visualization

value: PBS


title: Metformin_MSUc_rep1


title: blood, AT-31

value: BLOOD-CELLS

value: AT


title: CTR_12d_16578_mouse_bio_rep4

value: back skin

value: ctr

value: 12 days


title: blood, AT-30


title: CTR_12d_16412_mouse_bio_rep3

value: Cre negative


title: 106_2-5-mJ-cm2-72-hr_S51_R1_001

value: 5 mJ/cm2

value: 72 hr


title: 105-Sham-72-hr_R1

source_name: Dorsal skin, Sham 72 hr

value: Sham


title: blood, AT-28


title: CTR_12d_16411_mouse_bio_rep2


title: H3K79me3_PBS_rep2

description: Used for visualization

value: Bone Marrow

value: Bone Marrow-derived macrophages


title: H3K79me3_PBS_rep1

description: Used for visualization

value: WT


title: CTR_12d_16410_mouse_bio_rep1


title: 104_S23-Sham-72-hr_R1

value: Dorsal skin


title: H3K79me3_MSUc_rep2

description: Used for visualization

value: MSUc


title: blood, AT-27


title: blood, AT-25


title: 103-Sham-72-hr_R1


title: H3K79me3_MSUc_rep1

description: Used for visualization


title: blood, AT-23


title: 20_63_mouse_12d_bio_rep1

value: Cre positive

value: SRSF2 KO

value: heterozygous


title: 102-Sham-72-hr_S54_R1_001


title: input3_Histone

description: Regions_gained_by_MSUc_H3K4me3.txt & Regions_reduced_by_MSUc_H3K4me3.txt

value: input


title: 100-40-mJ-cm2-48-hr_R1

source_name: Dorsal skin, 40 mJ/cm2 48 hr

value: 40 mJ/cm2

value: 48 hr


title: 20_64_mouse_12d_bio_rep2

value: back skin

value: 4-hydroxy tamoxifen


title: 101-Sham-72-hr_S50_R1_001


title: input1_Histone


title: blood, CTR-48

value: BLOOD-CELLS

value: CTR


title: 20_61_mouse_10d_bio_rep2

value: wild type

value: 10 days


title: blood, CTR-47


title: input2_Histone

value: Bone Marrow


title: blood, CTR-46


title: H3K4me3_PBS_rep2

value: Bone Marrow-derived macrophages

value: PBS


title: blood, CTR-45


title: 98-40-mJ-cm2-48-hr_R1

value: Dorsal skin


title: H3K4me3_PBS_rep1

value: WT


title: 20_59_mouse_10d_bio_rep1

value: Cre positive

value: homozygous


title: 20_48_mouse_4d_bio_rep3

value: SRSF2 KO

value: 4 days


title: 97-40-mJ-cm2-48-hr_S47_R1_001

value: 40 mJ/cm2


title: blood, CTR-43


title: 99-40-mJ-cm2-48-hr_R1

value: 48 hr


title: H3K4me3_MSUc_rep2

value: MSUc


title: 20_66_mouse_12d_bio_rep3

value: back skin

value: heterozygous

value: 4-hydroxy tamoxifen

value: 12 days


title: 20_39_mouse_4d_bio_rep2

value: wild type


title: 96-40-mJ-cm2-48-hr_S44_R1_001


title: 20_58_mouse_10d_bio_rep3

value: 10 days


title: blood, CTR-41

value: BLOOD-CELLS

value: CTR


title: H3K4me3_MSUc_rep1

value: Bone Marrow

value: Bone Marrow-derived macrophages


title: blood, CTR-40


title: 95-20-mJ-cm2-48-hr_R1

source_name: Dorsal skin, 20 mJ/cm2 48 hr

value: Dorsal skin

value: 20 mJ/cm2


title: 20_36_mouse_4d_bio_rep1

value: Cre positive

value: SRSF2 KO

value: homozygous


title: H3K27ac_PBS_rep3

description: Regions_gained_by_MSUc_H3K27ac.txt & Regions_reduced_by_MSUc_H3K27ac.txt

value: WT

value: PBS


title: 20_62_mouse_CTR_bio_rep2

value: back skin

value: ctr

value: Cre negative


title: H3K27ac_PBS_rep2