title: nCATS of HoxB Del/Del(i9-13)Ins(CBS5-10) ESC

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

institute: EPFL

data_processing:
Base calling was computed with Guppy version 5.0.16+b9fcd7b from Oxford Nanopore (--flowcell FLO-MIN106 --kit SQK-LSK109 –fast5_out).
Mapping was performed on mm10 or on the in silico mutant genome using minimap2 version 2.28 (Li, 2018) (-ax splice).
Non primary alignments were removed with samtools version 1.16.1 (Danecek et al, 2021) and coverage was generated by BEDTools version 2.30.0 (Quinlan & Hall, 2010).
Assembly: mm10 and mm10_HoxB_deli9-13insCBS5-10_del
Supplementary files format and content: *bw = coverage file
Library strategy: nCATS

source_name: mESC

extract_protocol: nCATS was performed as in (Bolt et al, 2022) with a pool of 4 guides and a pool of 8 guides

value: mESC

value: HoxB Del/Del(i9-13):Ins(CBS5-10)


title: 05__T15smarcb1A2

status: Public on Jul 18 2024

type: SRA

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

country: Germany

library_source: transcriptomic

data_processing:
Raw FASTQ files were obtained and, after explorative quality control with FastQC (v0.11.8) and MultiQC (v1.7), we used Salmon (v0.14.1) for pseudo-alignment and quantification of the samples to the mouse transcriptome (downloaded from Ensembl, release 94). Default parameters were used.
Further analyses were performed in R. We employed the Bioconductor package tximport (v1.10.1) to summarize transcript-level estimates computed by Salmon for a gene-level analysis.
To find differentially expressed genes, we used the package DESeq2 (v1.22.2) and tested for SMARCB1 re-expression versus control conditions.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw_gene_counts_matrix.txt contains tab-separated raw counts for each gene and each sample

molecule: total RNA

organism: Mus musculus

source_name: T15 cell line

growth_protocol: All cells were maintained at 37°C and 5% CO2 in  RPMI 1640 medium with 10% FBS, 1% HEPES 1M, 1% penicillin/streptomycin (10,000 U/ml), sodium pyruvate (100 nM), l-glutamine (200 nM) and 0.1% β-mercaptoethanol (50 nM; all from Gibco).

extract_protocol:
Total RNA was isolated using RNeasy mini Kit (Qiagen) as specified by the manufacturer.
Sequencing libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs), following the manufacturer's guidelines.

treatment_protocol: For T15-Smarcb1 re-expression, T15 cells were lentivirally transduced with a control (Smarcb1-) or Smarcb1 expression plasmid pInd20. After antibiotic selection (G418) and Doxycyclin induction (0.5 µg/µl) (72 h) total RNA was extracted and sequenced. For T15-SAHA: T15 cells were treated with SAHA (1 µM final concentration) or vehicle twice in 72 h. Afterwards, RNA was isolated and sequenced.

tag: cell line

tag: treatment group


title: MA_PC3M_siJMJD6_HS_3

city: Chicago

first: Marc

middle: L

last: Mendillo

state: IL

address: 303 East Superior Street Simpson Querrey, 7th Floo

department: Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University

data_processing:
RNA-seq: Sequence quality was assessed with FastQC v0.11.2, Fastq files were trimmed using bbduk from BBTools v35.92 according to Lexogen QuantSeq manufacturer parameters, mapped to hg38 using STAR v2.6.0 and gene annotations from Ensembl 78. HTSeq was used to count uniquely mapped reads.
Assembly: hg38
Supplementary files format and content: htseq counts tables provide counts of uniquely mapped RNAseq reads

organism: Homo sapiens

growth_protocol: Cells were grown at 37°C and 5% CO2

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit according to supplied protocol.
Libraries were prepared from 100 ng RNA using the Lexogen QuantSeq FWD kit for Illumina sequencing , according to supplied protocol.

treatment_protocol: Cells were transfected with siNT or siJMJD6 for 72h, then were treated with DMSO or MG132 for 4h or heat shocked for 1h

tag: cell type

value: Prostate cancer cells

tag: genotype

tag: treatment

value: Heat shock 42C (1h), 2h Recovery


title: 06__T15smarcb1A3


title: OE- 5DAF_Re1

city: Shanghai

first: Ma

last: Bin

state: Shanghai

address: Fenglin 300 Road, Shanghai, China

country: China

institute: National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Assembly: RGAP_V7.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Oryza sativa

source_name: rice leaves

growth_protocol: All rice plants were normally grown in paddy field.

extract_protocol:
Total RNA were extracted using RNeasy Plant Mini Kit (Cat 74904, Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissues

value: flag leaf at grain filling stage

value: overexpression

tag: ture name


title: MA_PC3M_siJMJD6_HS_2


title: 04__T15smarcb1A1


title: OE- 5DAF_Re3


title: shGFP-control-rep-2

city: Oxford

first: Irina

last: Chelysheva

address: Roosevelt Dr

department: NDM

country: United Kingdom

institute: University of Oxford

data_processing:
Sequence reads were trimmed for adaptor sequence using Cutadapt
Sequencing data was aligned against the whole human (Homo sapiens) genome build GRCh38 using STAR (version 2.7.3a)
Gene features were counted using HTSeq (version 0.11.1), using human gene annotation general transfer format version GRCh38.92
Genes with low counts across most libraries, Ribosomal RNA (rRNA), sex chromosome genes, mitochondrial RNA and haemoglobin genes were removed
Assembly: GRCh38
Supplementary files format and content: txt file containing read counts per gene for each sample

source_name: Hela

growth_protocol: Stably integrated inducible shRNA Hela cells, expressing shRNA for TIRR or GFP as a control, were cultured in DMEM containing 1% L-glutamine, and 10% FBS at 37°C with 5% CO2

extract_protocol:
Total RNA was extracted by scrapping from plates using RNA lysis reagent from the Monarch Total RNA Miniprep Kit. RNA was eluted in water and quantified using an Implen NanoPhotometer N60.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DoDouble strand breaks were induced using Ionising Radiation (IR) using a Gravatom or by Etoposide - Eto (5-10μM). TIRR knockdown was induced using doxycycline for 48 hours, before inducing damage using IR (10Gy) or Eto (5-10μM). RNA was collected before andafter DNA damage,inducedby IR and followed by 1 hour incubation,or by Eto incubation for 2 hours.

value: Hela

value: shGFP

value: control


title: Ko1- 5DAF_Re3

value: mutant


title: DEX_TNF_IL1_IFN_3

city: Ulju-gun

first: Wonhyo

last: Lee

state: Ulsan

address: Unist-gil 50

department: Biological Sciences

country: South Korea

institute: UNIST

library_source: genomic

data_processing:
Raw fastq file is trimmed by skewer to get eliminate adaptor sequence of TN5
trimmed fastq file is aligned on Hg19 reference genome by bowtie 2 software
Homer software constructed Tag directories based on aligned bam files
Homer software transformed Tag directories to bedgraph
Assembly: hg19
Supplementary files format and content: bedgraph.gz

molecule: genomic DNA

source_name: Peripheral Blood

extract_protocol:
Nuclei are isolated by Lysis buffer(10 mM Tris-HCL, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP40)
ATAC-seq library was constructed by using illumina Tag DNA Enzyme & Buffer kit.

tag: tissue

value: Peripheral Blood

value: Cd14+ Monocyte

value: TNF, Il1b, IFNa, Dexamethasone


title: Control 1

city: Hyderabad

first: Nitesh

middle: Kumar

last: Singh

state: Telangana

address: Habsiguda

department: Bioinformatics

country: India

institute: Center for Cellular and Molecular Biology

data_processing:
Illumina adapters and low-quality reads were removed from raw sequencing reads using cutadapt Martin . Reads with quality scores less than 20 and smaller than 36 bp were discarded. The processed reads were then mapped to the Mycobacterium tuberculosis H37RV, downloaded from https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycobacterium_tuberculosis/reference/GCF_000195955.2_ASM19595v2/, using hisat2 with default parameters  . Uniquely aligned reads were counted using featureCounts of Subread package . There were 4008 genes in the gtf file, downloaded from https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycobacterium_tuberculosis/reference/GCF_000195955.2_ASM19595v2/, for which we had count information. Genes with total read count less than 10 across all the samples were removed, and the rest were used for further analysis. Differential gene expression analysis was performed using DESeq2 . Genes with adjusted p-value < 0.05 and absolute log2 Fold change > 1 were considered differentially expressed. For PCA plot and heat map, the raw read counts were rlog normalized, available with the DESeq2 package.
Assembly: Mycobacterium tuberculosis H37Rv
Supplementary files format and content: tab-delimited text files includes count data for each Sample

organism: Mycobacterium tuberculosis H37Rv

source_name: Mycobacterium tuberculosis H37Rv

growth_protocol: Mtb strains were grown in Middlebrook 7H9 liquid medium (BD Biosciences) supplemented with 10% ADC (albumin, dextrose, NaCl, catalase), 0.2% glycerol and 0.05% Tween-80.  For oxidative stress-related experiments, 7H9 medium was supplemented with ADS (ADC without catalase). H37Rv was either left untreated, or treated with 50 micromolar of CHP for 6 h for oxidative stress, resuspended in PBS for 7 days for starvation, 0.1% SDS for surfactant stress for 3 h, resuspended in pH 5.5 media for acidic stress for 2 days or were treated with sodium nitrate in pH 5.5 for 2 days for nitrosative stress. Comparative gene expression profiling analysis of RNA-seq data for H37Rv, RvDcysM, RvDcysK2 with and without oxidative stress. H37Rv, RvDcysM, , RvDcysK2 were either left untreated or treated with 50 micromolar CHP for 6 hours.

extract_protocol: Total RNA was isolated from two-three biological replicates of indicated Mtb strains, and their concentrations were checked by Qubit (ThermoFischer Scientific) followed by quality assessment through Agilent 2100 BioAnalyzer (Agilent RNA 6000 Nano Kit). All samples were processed at the same time and same set of control (Rv) triplicates were used for the comparative analysis. Samples with RIN values > 7 were processed for RNA sequencing at CSIR-Centre for Cellular and Molecular Biology, India, using the Illumina NovaSeq 6000 Platform with a read length of 100 bp, generating 20 million paired-end reads per sample.

value: Mycobacterium tuberculosis H37Rv

value: Control

value: Untreated


title: Ko1- 5DAF_Re2


title: DEX_TNF_IL1_IFN_2


title: MA_PC3M_siJMJD6_HS_1


title: OE- 5DAF_Re2


title: DEX_TNF_IL1_IFN_1


title: Ko1- 5DAF_Re1


title: MA_PC3M_siNT_HS_2

value: siNT


title: shGFP-control-rep-1


title: WT- 5DAF_Re2

value: wild type

value: WT


title: MA_PC3M_siNT_HS_3

value: Prostate cancer cells


title: DEX_TNF_IL1b_3

value: TNF, IL1b, Dexamethasone


title: MA_PC3M_siNT_HS_1

value: Heat shock 42C (1h), 2h Recovery


title: WT- 5DAF_Re1

value: flag leaf at grain filling stage


title: WT- 5DAF_Re3


title: DEX_TNF_IL1b_2


title: DEX_TNF_IL1b_1


title: MA_PC3M_siNT_3

value: Basal


title: MA_PC3M_siNT_2


title: shGFP-IR-rep-1

value: Hela

value: shGFP

value: IR


title: MA_PC3M_siNT_1


title: DEX_IFNa_2

value: Peripheral Blood

value: IFNa, Dexamethasone


title: MA_PC3M_dH1B_MG132

value: HSF1 KO


title: tmk4-Input_rep1

city: Changsha

first: Chongsheng

last: He

state: Hunan

address: 27 Tianma road

institute: Hunan university

description: m6A-seq tmk4 Input replicate 1

data_processing:
Adapters were removed from reads with the AdapterRemoval tool.
Reads were then mapped against the Arabidopsis (TAIR10) with STAR (v 2.5.3a).
Peak calling was done with R package MeRIPtools. The overlap of peaks from two biological replicates were used to generate the final peak list.
Assembly: tir10
Supplementary files format and content: peak excel files

organism: Arabidopsis thaliana

source_name: 15-day-old seedlings

growth_protocol: All plants were grown on 1/2-strength Murashige and Skoog (MS) medium (1/2 MS) with 0.8% sucrose under long-day conditions (16 hr light/8 hr dark) at 21ºC ±2ºC.

extract_protocol:
Seedlings were homogenized in liquid nitrogen, and RNA was harvested using Trizol reagent. PolyA mRNA was isolated by oligodT beads and further fragmented. The m6A containing RNA was isolated with antibody.
RNA libraries were prepared for sequencing using standard Illumina protocols. m6A-seq libraries were prepared according to Shen, L. et al., Developmental Cell, 2016. Briefly, RNA was converted to final cDNA libraries in accordance with a dUTP dependent strand-specific library preparation. Libraries were sequenced on the Illumina Nova 6000 platform as single-end 150 bp reads at the OE Biotech (Shanghai, China) following the vendor's recommended protocol.

value: 15-day-old seedlings

value: 50 µM NAA treated for 3 h


title: tmk4-m6A_rep2

description: m6A-seq tmk4 IP replicate 2


title: tmk4-Input_rep2

description: m6A-seq tmk4 Input replicate 2


title: tmk4-m6A_rep1

description: m6A-seq tmk4 IP replicate 1


title: MA_PC3M_dH1A_MG132


title: DEX_IFNa_1

value: Cd14+ Monocyte


title: DEX_CTL_3

value: Dexamethasone


title: fip373A-Input_rep2

description: m6A-seq 35S:FIP373A Input replicate 2

data_processing:
Adapters were removed from reads with the AdapterRemoval tool.
Reads were then mapped against the Arabidopsis (TAIR10) with STAR (v 2.5.3a).
Peak calling was done with R package MeRIPtools. The overlap of peaks from two biological replicates were used to generate the final peak list.
Assembly: tir10
Supplementary files format and content: peak excel files
Library strategy: m6A-seq


title: MA_PC3M_X2_siJMJD6_MG132


title: DEX_CTL_2


title: DEX_IFNa_3


title: fip373A-Input_rep1

description: m6A-seq 35S:FIP373A Input replicate 1


title: DEX_CTL_1


title: MA_PC3M_X2_NT_MG132

value: siNT


title: NT_TNF_IL1_IFN_3

value: TNF, Il1b, IFNa


title: MA_PC3M_X1_NT_MG132

value: Prostate cancer cells


title: fip373A-m6A_rep2

description: m6A-seq 35S:FIP373A IP replicate 2


title: fip373A-m6A_rep1

description: m6A-seq 35S:FIP373A IP replicate 1


title: NT_TNF_IL1_IFN_2


title: MA_PC3M_X2_NT_DMSO

value: DMSO


title: NT_TNF_IL1_IFN_1


title: fip37-Input_rep2

description: m6A-seq 35S:FIP37 Input replicate 2


title: F_GCPTH80_3369

type: RNA

city: San Francisco

first: Cristal

last: Yee

state: CA

address: 35 Medical Center Way, 923A

department: Orthopaedic Surgery Department

institute: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO

description: RNA isolated from humeri of mice treated with either placebo or prednisolone (2.1mg/kg/d) with saline or rat PTH 1-34 (80µg/kg) for 21 days

source_name: GC and PTH 1-34 treated mouse bones

label_protocol: Total 400ng of RNA per sample was used to measure direct mRNA counts using an automated Nanostring nCounter Mx system with a custom probe set for 94 mouse skeletal genes in the UCSF CCMBM Skeletal Biology and Biomechanics Core.

growth_protocol: Mice housed at the University of California, San Francisco Laboratory Animal Resource Center (LARC) facility with 67°-74°F, 30-70% humidity, a 12-hr light/dark cycle, and free access to water and irradiated standard chow (LabDiet 5058-PicoLab Rodent Diet 20).

extract_protocol: RNA was extracted from humeri after removal of epiphysis and bone marrow to assess transcriptotomic profiles of osteocyte-enriched cortical bone. The dissected bones were flash frozen in liquid nitrogen and homogenized in QIAzol Lysis Reagent (Qiagen cat#79306), and total RNA was extracted using the RNeasy mini kit (Qiagen cat#74106) according to the manufacturer's instructions.

treatment_protocol: Mice were randomly assisgned for subcutaneous implantation with recommended placebo pellets (Innovative Research of America, cat# NG-111) or slow-releasing prednisolone (GC) pellets (2.1 mg/kg/d, 90-day release, cat# NG-151) for 21 days. Throughout the 21-day treatment, mice received subcutaneous injections (5 day/week) of either vehicle (2% heat-inactivated FBS, 1mM HCl, 150mM NaCl) or rat parathyroid hormone 1-34 (80µg/kg; Bachem Cat# H-5460), prior to euthanasia following LARC standard procedure using carbone dioxide inhalation at 16 weeks of age.

tag: Sex

value: female

tag: age

tag: strain

value: FVB mice

tag: experimental group

value: GC + PTH 1-34

value: humeri bone


title: fip37-Input_rep1

description: m6A-seq 35S:FIP37 Input replicate 1


title: F_GCPTH80_3345


title: MA_PC3M_X1_siJMJD6_MG132


title: PC3M, siJMJD6, HS, Input, biol rep 2

data_processing:
Reads were aligned to hg38 using Bowtie v0.12.9. Peaks were called relative to siJMJD6 samples using MACS v1.4.2
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes and quenched for 5 mins.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Cells were transfected with siNT or siJMJD6 for 72h and then heat shocked at 42C for 1

value: Prostate cancer cell line

value: Heat shock 42C (1h), 2h Recovery


title: fip37-m6A_rep2

description: m6A-seq 35S:FIP37 IP replicate 2


title: NT_TNF_IL1b_3

value: Peripheral Blood

value: TNF, IL1b


title: F_GCPTH80_3370


title: PC3M, siJMJD6, HS, Input, biol rep 1


title: NT_TNF_IL1b_1


title: PC3M, siJMJD6, HS, HSF1 ChIP, biol rep 2


title: NT_TNF_IL1b_2


title: MA_PC3M_X1_NT_DMSO


title: fip37 NAA-RNAseq_rep3

description:
RNA-seq NAA treated fip37 mutant replicate 3
RPKMs.csv

data_processing:
Adapters were removed from reads with the AdapterRemoval tool.
Reads were then mapped against the Arabidopsis (TAIR10) with STAR (v 2.5.3a).
Peak calling was done with MACS2. The overlap of peaks from two biological replicates were used to generate the final peak list.
Reads Per Kilobase per Million mapped reads (RPKM) were calculated in R. In short, the number of reads falling in the each gene were counted and normalized by the length of genes and by the size of the library.
Genome_build: tir10
Supplementary_files_format_and_content: m6A-seq:  peak .txt files
Supplementary_files_format_and_content: m6A-seq:  bigwig files were generated using bedGraphToBigWig; Scores represent Reads Per 10 Million mapped reads (RP10M); Scores of Input were subtracted from that of IP.
Supplementary_files_format_and_content: RNA-seq: comma separated text file includes RPKM values for each Sample

extract_protocol:
Seedlings were homogenized in liquid nitrogen, and RNA was harvested using Trizol reagent. PolyA mRNA was isolated by oligodT beads and further fragmented. The m6A containing RNA was isolated with antibody.
RNA libraries were prepared for sequencing using standard Illumina protocols. m6A-seq libraries were prepared according to Shen, L. et al., Developmental Cell, 2016. Briefly, RNA was converted to final cDNA libraries in accordance with a dUTP dependent strand-specific library preparation. Libraries were sequenced on the Illumina Novaseq 6000 platform as single-end 150 bp reads at the OE Biotech (Shanghai, China) following the vendor's recommended protocol.

treatment_protocol: 15-day-old seedlings were treated with mock or 50 µM NAA for 3 h.

tag: rip antibody

value: treated with 50 µM NAA for 3 h

value: fip37 LEC1:FIP37


title: F_PTH80_3348


title: NT_IFNa_3

value: IFNa


title: Colon8

city: Xiamen

first: Shuqin

last: Li

state: Fujian Province

address: Xiang'an south rd, Xiang'an district

department: Life Science

institute: Xiamen University

data_processing:
The sequencing data was obtained after filtering low-quality sequences using a standard procedure. Alignment was performed using the RNA-seq pipeline in MIXCR. The CDR3 ratio was calculated based on read counts associated with each CDR3.
Assembly: mm10
Supplementary files format and content: Comma-delimited csv files include each CDR3 count values and frequency.

source_name: colon

extract_protocol:
Tregs (CD45+CD3+CD4+CD25+) were sort-purified from normal colons or tumors from WT and ApcMin/+ mice, respectively. Cells were collected into tubes with lysis buffer and ribonuclease inhibitor. Total RNA was extracted and reverse transcribed into cDNA using the Smart-Seq2 protocol.
In order to remove contamination from primers from the previous step, VAHTS DNA Clean Beads (Vazyme, N411) were used to purify the products after each round of PCR. A two-round nested PCR was then performed using primers specific for TCRα and TCRβ. For the first round of PCR, 4.4 μL of reverse-transcribed product was used as a template, and the TCRα primer (5’-ctggttgctccaggcaatgg-3’) and TCRβ primer (5’-tgtaggcctgagggtccgt-3’) were used to specifically amplify TCRα and TCRβ. Subsequently, all product was used in the second round of PCR and the primers (TCRα: 5’- agtcaaagtcggtgaacaggca-3’, TCRβ: 5’-ggccaagcacacgagggta-3’) were used. The amplicons were purified using VAHTS DNA Clean Beads and subjected to paired-end sequencing (2 × 150 bp) on an Illumina platform (NovaSeq X Plus-PE150) according to standard protocols.

value: colon

value: regulatory T cell

value: WT

value: male

value: 16 weeks old


title: Tumor5

value: Apc Min/+


title: Colon6


title: Tumor2


title: Colon3


title: Colon4


title: Tumor4


title: Colon7


title: Colon1


title: Colon2


title: PC3M, siJMJD6, HS, HSF1 ChIP, biol rep 1


title: Tumor3


title: Colon5


title: F_GCPTH80_3323

value: female


title: Tumor6


title: Tumor1


title: fip37-m6A_rep1

description: m6A-seq 35S:FIP37 IP replicate 1

value: 15-day-old seedlings


title: NT_IFNa_2

value: Cd14+ Monocyte


title: fip37 NAA-RNAseq_rep2

description:
RNA-seq NAA treated fip37 mutant replicate 2
RPKMs.csv


title: F_PTH80_3286

value: FVB mice

value: humeri bone


title: PC3M, siNT, HS, Input, biol rep 2

value: Prostate cancer cell line

value: siNT

value: Heat shock 42C (1h), 2h Recovery


title: fip37 NAA-RNAseq_rep1

description:
RNA-seq NAA treated fip37 mutant replicate 1
RPKMs.csv

value: treated with 50 µM NAA for 3 h


title: NT_IFNa_1

value: Peripheral Blood


title: F_PTH80_3374


title: PC3M, siNT, HS, Input, biol rep 1


title: shGFP-IR-rep-2

value: Hela

value: shGFP

value: IR


title: fip37 mock-RNAseq_rep3

description:
RNA-seq mock treated fip37 mutant replicate 3
RPKMs.csv

value: treated with mock for 3 h

value: fip37 LEC1:FIP37


title: NT_CTL_3


title: fip37 mock-RNAseq_rep2

description:
RNA-seq mock treated fip37 mutant replicate 2
RPKMs.csv


title: PC3M, siJMJD6, Basal, Input, biol rep 2

value: Basal


title: NT_CTL_1


title: PC3M, siNT, HS, HSF1 ChIP, biol rep 2


title: PC3M, siJMJD6, Basal, Input, biol rep 1


title: F_GC_3375

value: GC- prednisolone (2.1 mg/kg/d)


title: WT NAA-RNAseq_rep2

description:
RNA-seq NAA treated WT replicate 2
RPKMs.csv

value: wild type


title: F_PTH80_3325

value: female


title: Donor2_Mock_1

city: Philadelphia

first: Marco

last: Ruella

state: PA

address: 3400 Civic Center Blvd.

institute: University of Pennsylvania

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases using Trimmomatic (version 0.36)
Trimmed samples  were aligned with the hg19 reference genome and  annotated  using Spliced Transcripts Alignment to a Reference (STAR; version 2.6.0c)
Gene expression quantification analysis was performed for all samples using STAR and featureCounts (version 1.6.1).
Assembly: hg19
Supplementary files format and content: Tab-separated value file includes raw counts for each sample

source_name: Primary T cell

extract_protocol: none provided

value: Primary T cell

value: Donor 2

value: electroporated without RNP complex


title: PC3M, siNT, HS HSF1 ChIP, biol rep 1

value: Prostate cancer cell line


title: NT_CTL_2

value: Cd14+ Monocyte


title: F_GC_3352

value: FVB mice

value: humeri bone


title: PC3M, siJMJD6, Basal, HSF1 ChIP, biol rep 2


title: Donor2_CD5KO_2

value: electroporated with RNP complex


title: PC3M, siJMJD6, Basal, HSF1 ChIP, biol rep 1


title: F_GC_3344


title: WT NAA-RNAseq_rep1

description:
RNA-seq NAA treated WT replicate 1
RPKMs.csv

value: treated with 50 µM NAA for 3 h


title: WT mock-RNAseq_rep3

description:
RNA-seq mock treated WT replicate 3
RPKMs.csv


title: PC3M, siNT, Basal, Input, biol rep 2

value: siNT


title: F_Ctrl_3350

value: Control


title: F_Ctrl_3377


title: F_Ctrl_3284


title: fip37 mock-RNAseq_rep1

description:
RNA-seq mock treated fip37 mutant replicate 1
RPKMs.csv

value: treated with mock for 3 h


title: F_Ctrl_3291


title: Donor2_Mock_2


title: WT NAA-RNAseq_rep3

description:
RNA-seq NAA treated WT replicate 3
RPKMs.csv


title: Donor1_Mock_2

value: Donor 1


title: WT mock-RNAseq_rep1

description:
RNA-seq mock treated WT replicate 1
RPKMs.csv


title: PC3M, siNT, Basal, Input, biol rep 1

value: Basal


title: F_GC_3328

value: GC- prednisolone (2.1 mg/kg/d)


title: Donor1_Mock_1


title: PC3M, siNT, Basal, HSF1 ChIP, biol rep 2


title: Donor1_CD5KO_2


title: M_GCPTH80_3363

value: male

value: GC + PTH 1-34


title: PC3M, siNT, Basal, HSF1 ChIP, biol rep 1


title: Colony, PDA medium,DPI treatment, 4 days + H2O2 treatment, 4 days [S3-2]

city: Lanzhou

first: jie

last: li

state: Gansu

address: No. 1, yingmen village

institute: Gansu Agricultural University

data_processing:
Data quality inspection and filtering.Use Trimmomatic software (v0.33) to remove reads with sequencing adapters* (adapter), remove reads with N (indeterminate bases) content greater than 10%, and low-quality bases (Q≤20) with content greater than 50% Reads. Finally get Clean data (clean reads),
Reference sequence alignment. Statistical sequencing data availability through HISAT2 software and reference genomes
Expression level analysis.Using RSEM, the comparison results of bowtie2 are called for statistics, and the number of Reads that each sample is compared to each transcript is obtained, and FPKM conversion is performed on it, and then the expression levels of genes and transcripts are obtained.
Differential gene screening.Gene differential expression analysis was performed according to the read count data obtained in the gene expression level analysis. The standard of differential gene screening is generally: |log2(FoldChange)| > 1 & padj < 0.05.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Fusarium solani

source_name: colony

growth_protocol: PDA medium was used to activate and culture at 25℃ for 8 days before use, and then transfer a small amount of colony to the PDA medium to culture in the same condition. After the second culture, the 5mm plug was taken out and used as inoculation material in this study.

extract_protocol:
Trizol ® kit method be used to extract total RNA of S1, S2 and S3 strains and remove the genomic DNA.
mRNA with PolyA tail was enriched by oligo (DT) magnetic beads, the library constructed by the common NEB library.

treatment_protocol: S1 was inoculated with PDA medium. S2 was S1 + 40µmol/L DPI. S3 was S2 cultured to the 4th day and added 5ml 0.0012% H2O2 solution to each dish.

value: colony

value: wild type

tag: time

value: Day 4+4


title: Colony, PDA medium,DPI treatment, 4 days + H2O2 treatment, 4 days [S3-3]


title: M_GCPTH80_3341


title: Colony, PDA medium,DPI treatment, 4 days + H2O2 treatment, 4 days [S3-1]


title: GFP+Eto

growth_protocol: Hela cells with integrated inducible TIRR-GFP or GFP only (as a control for background) were cultured in DMEM containing 1% L-glutamine, and 10% FBS at 37°C with 5% CO2. Drugs were added to cell culture media as indicated: Doxycycline (1μg/ml, 16-48 hours), Etoposide (5-10μM, 2 hours).

extract_protocol:
RNA was extracted using Trizol and the Monarch Total RNA Miniprep kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hela cells with integrated inducible TIRR-GFP or GFP only (as a control for background) were plated and 24 hours later, induced with 1 μg/ml doxycycline overnight to induce expression of TIRR-GFP or GFP. Cells were washed three times in cold PBS and cross-linked at 254nm at 0.15 J/cm2.

value: Hela

value: GFP

value: Eto


title: 5_0AF7_01D6SUNY_LNCaP-Rescue-1_Abi1_hs_i82.fastq.gz

city: Syracuse

first: Leszek

last: Kotula

state: New York

address: 750 East Adams Str

department: Urology

institute: Upstate Medical University

data_processing:
Base calls were made using bcl2fastq2 (v2.20)
Reads were aligned to the human genome (hg38) using BWA (0.7.12)
Duplicate reads, non-uniquely mapped reads, and reads with more than 2 mismatches were filtered out
MACS (v2.1.0) peak calling was performed (with narrow setting)
peak counts were quantified for each sample, with closest gene using Ensembl108
Assembly: hg38
Supplementary files format and content: matrix file with peak counts for each of the seven samples

source_name: LNCaP

growth_protocol: Adherent cultures were grown in DMEM at 37C with 5% CO2

extract_protocol:
ChIP immunopreciptiation of DNA
Standard Illumina ChIP-Seq library method, with single-end 1 x 75 bp sequencing

value: LNCaP

value: Humanprostatecarcinoma

tag: chip antibody

value: Abi1 (MBL International, # D147-3)


title: M_GCPTH80_3298

value: FVB mice

value: humeri bone


title: 6_0AF6_01D6SUNY_LNCaP-KO-1_Abi1_hs_i81.fastq.gz


title: M_GCPTH80_3307


title: Donor2_CD5KO_1

value: Primary T cell

value: Donor 2

value: electroporated with RNP complex


title: GFP-Eto

value: Control


title: WT mock-RNAseq_rep2

description:
RNA-seq mock treated WT replicate 2
RPKMs.csv

value: treated with mock for 3 h


title: Colony, PDA medium,DPI treatment, 8 days [S2-3]

value: DPI

value: Day 8


title: M_PTH80_3338

value: male


title: 4_09XE_01D6SUNY_LNCaP-Abi1-KO-2_AR_hs_i44.fastq.gz

value: AR (SCBT, #SC-816)


title: Colony, PDA medium,DPI treatment, 8 days [S2-2]

value: colony

value: wild type


title: 3_09XD_01D6SUNY_LNCaP-Abi1-KO-1_AR_hs_i43.fastq.gz


title: Colony, PDA medium, 8 days [S1-3]

value: control


title: TIRR-Eto2

value: Hela

value: TIRR-GFP


title: M_PTH80_3360


title: TIRR+Eto1

value: Eto


title: Colony, PDA medium,DPI treatment, 8 days [S2-1]


title: 2_09XC_01D6SUNY_LNCaP-Rescue-2_AR_hs_i40.fastq.gz

value: LNCaP

value: Humanprostatecarcinoma


title: 1_09XB_01D6SUNY_LNCaP-Rescue-1_AR_hs_i96.fastq.gz


title: M_GC_3362

value: FVB mice

value: GC- prednisolone (2.1 mg/kg/d)

value: humeri bone


title: TIRR-Eto1

value: Control


title: M_PTH80_3306


title: β-asarone treatment-3

city: Jinan

first: jianhua

last: zhang

address: gongyebei street No. 23788

institute: Shandong Academy of Agricultural Sciences

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/ , version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination (command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
After removed the low quality bases and undetermined bases, we used HISAT2 software (https://daehwankimlab.github.io/hisat2/ , version:hisat2-2.0.4) to map reads to the genome (for example: Homo sapiens Ensembl v96), (command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/ , version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml , version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]), (command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2 (http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html), and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Assembly: GCA_014465815.1
Supplementary files format and content: Comma-separated text file includes FPKM values for each Sample.

organism: Laodelphax striatellus

source_name: whole body

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesize U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

value: whole body

value: WT

value: treat with beta-asarone


title: Colony, PDA medium, 8 days [S1-1]

value: Day 8


title: M_PTH80_3318

value: male


title: SW620 cells, shMMP-9, rep3

city: Los Angeles

first: Yonghwan

last: Shin

address: 1450 Biggy St

department: Biochemistry and Molecular Medicine

institute: University of Southern California

data_processing:
Partek Flow
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partek Flow
Trimmed sequence reads were mapped to hg38 - GENCODE Genes - release 40 using Partek Flow
Read count extraction and normalization were performed using Partek Flow
Assembly: hg38
Supplementary files format and content: Processed data-humanMMP-9.txt (raw read counts table)

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

value: Colon cancer

value: MMP-9 Knockdown


title: Right kidney, Unilateral nephrectomised, 24h, rep2, snRNAseq

city: Bedford Park

first: Jonathan

last: Gleadle

state: SA

address: 3D226 Renal Lab, Flinders Medical Centre, Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

description:
Unx78
Unx78

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using the Alevin-fry pipeline with the mouse reference genome (mm10) splice reference and index for pseudo-alignment and gene quantification was carried out using Alevin-fry's quant mode. The resulting gene expression matrix was imported into Seurat for single-cell RNA sequencing data analysis. Seurat was used for quality control, filtering out low-quality cells and potential doublets. The filtered data were then SCTransform normalized and to regress out percentage of mitochondria and ribosomal transcript per cell. Principal component analysis (PCA) was performed on the variable genes, followed by unsupervised clustering using the Louvain algorithm. Harmony was used to remove the influence of batch effects11 and Uniform Manifold Approximation and Projection (UMAP) was employed for dimensionality reduction and visualization of the clusters. Differential gene expression analysis was performed on individual clusters using Seurat's FindMarkers function. The results were used to identify marker genes and characterize the cell types present in the kidney tissue.
mm10
csv files; meta data and information for each nucleus labelled by sample name followed by cell barcode.
csv files; raw gene counts from Alevin-fry pipeline output for each nucleus labelled by sample name followed by cell barcode.

molecule: polyA RNA

source_name: cross sectional sample

extract_protocol:
Nuclei were isolated from a section of the kidney as per published protocol (Leiz et al., 2021). Briefly, kidney section was minced and homogenized in EZ lysis buffer. The homogenate was filtered through a 40 µm cell strainer and centrifuged to pellet the nuclei. The nuclei pellet was resuspended and layered onto a sucrose gradient and centrifuged to separate and remove any other cellular components and debris. The purified nuclei were resuspended in an appropriate volume of resuspension buffer. Single nuclei were then sorted based on DAPI fluorescence using a flow cytometer. The sorted nuclei were counted using a CellDrop FL Automated Cell Counter (DeNovix) to determine the concentration. The single nuclei suspension was loaded onto a Chromium Controller (10x Genomics) for single nuclei encapsulation, barcoding and cDNA synthesis.
Library preparation using the Chromium Single Cell 3' Reagent Kit v3 (10x Genomics) following the manufacturer's instructions. The prepared libraries were sequenced on an MGI FCL sequencer.

value: Right kidney

value: cross sectional sample

value: Unilateral nephrectomy

tag: time post_surgery

tag: gender

value: Male

tag: mouse id

tag: batch

value: 8-12 weeks

tag: library kit

value: 10x Genomics Chromium Next GEM v3.1, Library & Gel Bead Kit

tag: bp size


title: TIRR+Eto2

tag: cell line

value: Hela

tag: genotype

value: TIRR-GFP

tag: treatment

value: Eto


title: SW620 cells, shMMP-9, rep2

tag: cell type


title: β-asarone treatment-2

tag: tissue


title: SW620 cells, shMMP-9, rep1


title: Right kidney, Unilateral nephrectomised, 24h, rep1, snRNAseq

description:
Unx70
Unx70

tag: age


title: β-asarone treatment-1


title: M_GC_3315

tag: Sex

tag: strain

value: FVB mice

value: GC- prednisolone (2.1 mg/kg/d)

value: humeri bone


title: Donor1_CD5KO_1

value: Primary T cell

value: Donor 1

value: electroporated with RNP complex


title: Right kidney, Sham operated, 24h, rep2, snRNAseq

description:
Sham77
Sham77

value: Sham operation


title: M_GC_3316

value: male

tag: experimental group


title: 0_09XJ_01D6SUNY_LNCaP-Pooled_Input_hs_i45.fastq.gz

value: LNCaP

value: Humanprostatecarcinoma

value: None (input DNA)


title: SW620 cells, shControl, rep3

value: Colon cancer

value: WT


title: Right kidney, Sham operated, 24h, rep1, snRNAseq

description:
Sham71
Sham71

value: Right kidney

value: cross sectional sample

value: Male

value: 8-12 weeks

value: 10x Genomics Chromium Next GEM v3.1, Library & Gel Bead Kit


title: control-3

value: whole body

value: control


title: control-2


title: WT_immune

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Apc Min/+ mice or WT mice were treated with colon tumor tissue or normal colon tissue, tissues were minced into small fragments, which were treated with 1.5 mg/mL collagenase IV and 50 U/mL DNase I for 30 min at 37°C under agitation. Single cell suspensions were stained with fixable viability violet dye Zombie Red and α-CD45 mAbs (30-F11) (BioLegend) and sorted using BD Aria Fusion (BD Biosciences).
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: colon

value: immune cell

value: 16 weeks old


title: M_Ctrl_3358

value: FVB mice

value: Control

value: humeri bone


title: Colony, PDA medium, 8 days [S1-2]

value: colony

value: wild type

tag: time

value: Day 8


title: control-1

value: WT


title: SW620 cells, shControl, rep2

value: Colon cancer


title: M_GC_3339

value: male

value: GC- prednisolone (2.1 mg/kg/d)


title: M_Ctrl_3310


title: SW620 cells, shControl, rep1


title: M_Ctrl_3317


title: Tumor_immune

description: 10x Genomics

value: Apc Min/+


title: M_Ctrl_3303


title: Group6- High Ints6 - High U2 (replicate 3)

status: Public on Jul 17 2024

city: Logrono

first: María

last: de Toro

state: La Rioja

address: C/Piqueras 98

department: Genomics & Bioinformatics Core Facility

country: Spain

institute: Centro de Investigación Biomédica de La Rioja

data_processing:
Data quality analysis: FastQC v12.1
Data quality filtering and trimming: TrimGalore v0.6.4 (parameters min qual 25, min length 50)
rRNA removal: SortmeRNA (silva-euk-18s-id95, silva-euk-28s-id98 databases)
Trimmed & cleaned sequence reads were mapped to GRCh38 using HiSat2 (v2.1.0; parameters: rna-strandness RF, rest default)
Read count extraction performed with featureCounts (v2.0.0, parameters: t=gene, s=2 reversely stranded, p=fragment count, gene_id)
Assembly: GRCh38.105
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: colorectal biopsy sample

growth_protocol: biopsy samples

extract_protocol:
RNA was extracted by following the instructions of the QIAGEN RNeasy Kit
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit following manufacturer's protocols.

value: colorectal biopsy sample

tag: ints6 levels

value: high Ints6

tag: snrna processing

value: High U2


title: Group4-Low Ints6 - High U2 (replicate 1)

value: Low Ints6


title: Group3-High Ints6 - Normal U2 (replicate 3)

value: Normal U2


title: Group6- High Ints6 - High U2 (replicate 2)


title: Group4-Low Ints6 - High U2 (replicate 3)


title: Group3-High Ints6 - Normal U2 (replicate 2)


title: Group4-Low Ints6 - High U2 (replicate 2)


title: Group6- High Ints6 - High U2 (replicate 1)


title: Group2-Normal Ints6- Normal U2 (replicate 1)

value: normal Ints6


title: Group2-Normal Ints6- Normal U2 (replicate 3)


title: Group3-High Ints6 - Normal U2 (replicate 1)


title: Group2-Normal Ints6- Normal U2 (replicate 2)


title: ARL11 Adenoviral Transducted NHU-hTERT cells after 48 hours C

city: Houston

first: Bogdan

last: Czerniak

state: TX

address: 1515 Holcombe

department: Pathology

institute: UT MD Anderson Cancer Center

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalization in the Linear Model for Microarray Data (LIMMA)

label: biotin

source_name: human normal urothelial immortalized cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: NHU-hTERT cells transducted with empty and ARL11-adenovirus were grown in Keratinocyte-SFM medium.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: NHU-hTERT cells transducted with empty and ARL11-adenovirus were grown for 2 days before the harvest.

value: NHU-hTERT

tag: transduced

value: ARL11 Adenoviral


title: ARL11 Adenoviral Transducted NHU-hTERT cells after 48 hours A

description: replicate 1


title: Mouse LPAR6 plus  3 6752326031

description: replicate 3

source_name: Mouse MEFs

value: 129SV and C57BL/6 mix

tag: genotype/variation


title: NHU-hTERT cells with empty vector  Adeno B

description: replicate 2

value: empty vector


title: Mouse LPAR6 minus 2 6752326031

description: replicate 2


title: NHU-hTERT cells with Stable expression of ARL11 after 48 hours A

description: replicate 1

source_name: human normal urothelial limmortalized cells

growth_protocol: NHU-hTERT cells stably transfected with empty and ARL11-lenti viral vector were grown in Keratinocyte-SFM medium.

treatment_protocol: NHU-hTERT cells with empty vector and stable expression of ARL11 were starved for 2 days before the harvest.

tag: transfection

value: ARL11-lenti viral vector


title: Group1-Low Ints6-Normal U2 (replicate 2)


title: Group1-Low Ints6-Normal U2 (replicate 3)


title: Mouse LPAR6 minus 3 6752326031

description: replicate 3


title: infected 3n_replicate 6

city: Liběchov

first: Tomáš

last: Tichopád

address: Rumburská 89

country: Czech Republic

institute: ÚŽFG

data_processing:
bbduk trimming: ftm=5 ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=rl trimq=10 minlen=40, adapters are part of bbmap package
rRNA removal using bbduk k=21 and bbduk Rrna removal fasta
aligment to genome using STAR
feature counts in default mode for paired reads
Assembly: ensembl: Carassius_auratus.ASM336829v1.dna.toplevel.fa
Supplementary files format and content: raw output of feature counts

organism: Carassius gibelio

source_name: spleen

extract_protocol:
Total RNA was isolated from each individually preserved spleen using PureLink® RNA Mini Kit (Ambion) along with TRIzol™ Reagent (Invitrogen) and PureLink® DNase (Ambion). The quantity of extracted RNA was assessed using a NanoDrop 8000 spectrophotometer (Thermo Fisher Scientific). The quality and integrity of RNA were analyzed using RNA 6000 Nano Kit on a 2100 Bioanalyzer instrument (Agilent Technologies).
RNA samples with an acceptable RNA integrity number (RIN>7) were used for DNA library preparation. 500 ng of total RNA was used for mRNA enrichment using the Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Subsequently, NEBNextUltra II DirectionalRNA Library Prep Kit for Illumina, and Dual Index Primers Set 2 of NEBNextMultiplex Oligos for Illumina (New England Biolabs) were used for library preparation. The numbers of PCR cyclers used for enrichment and the beads ratio used for fragment size selection were modified according to the recommendations in the manufacturers´ protocol. The quantification of DNA libraries was performed on a Qubit 4 fluorometer (Invitrogen by Thermo Fisher Scientific) using Qubit dsDNA HS Assay Kit, and quality and size controls were performed on a 2100 Bioanalyzer with DNA 1000Kit (Agilent Technologies). Finally, amplicons (average size of 355 bp) were pooled in equimolar amounts.

value: spleen

value: infected


title: Control Sample (replicate 3)

source_name: healthy biopsy sample

value: healthy biopsy sample


title: Mouse LPAR6 plus 1 6752326031

description: replicate 1


title: NHU-hTERT cells with empty vector B

description: replicate 2


title: NHU-hTERT cells with Stable expression of ARL11 after 48 hours B

description: replicate 2


title: NHU-hTERT cells with empty vector A

description: replicate 1


title: Group1-Low Ints6-Normal U2 (replicate 1)


title: NHU-hTERT cells with Stable expression of ARL11 after 48 hours C

description: replicate 3


title: Control Sample (replicate 2)


title: Mouse LPAR6 minus 1 6752326031

description: replicate 1


title: infected 3n_replicate 5


title: Mouse LPAR6 plus 2 6752326031

description: replicate 2


title: NHU-hTERT cells with empty vector  Adeno A

description: replicate 1


title: infected 3n_replicate 3


title: PD4 response evaluation

city: FUKUI

first: Yosuke

last: Murata

address: 23-3 Matsuoka Shimoaizuki, Eiheiji-cho, Yoshida-gun

department: second Department of Internal Medicine

country: Japan

institute: University of Fukui

data_processing:
Local Run Manager RNA Amplicon Analysis Module (Illumina)
Normalization of read count information and identification of differentially expressed genes (DEGs) between baseline and treatment effect assessment was performed using the edgeR package,
Functional annotation was performed on the samples using the gene set enrichment analysis (GSEA) method
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes differential expression for each sample

source_name: blood

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen, Germany). Library construction commenced with 1–3 ng of RNA input.
AmpliSeq cDNA Synthesis for Illumina (Illumina, San Diego, CA, USA) was utilized for cDNA synthesis. For RNA library preparation, the AmpliSeq for Illumina custom RNA panel (Illumina), AmpliSeq library PLUS for Illumina (Illumina), and AmpliSeq CD indexes Set A for Illumina (Illumina) were employed, with the custom panel comprising 373 genes associated with cancer progression.

treatment_protocol: Atezolizumab Plus Bevacizumab was administered following the IMbrave 150 protocol schedule. Adjustments to the dosage or discontinuation of Atezo+Bev were made to manage adverse events. Treatment response was evaluated using dynamic computed tomography or gadolinium ethoxybenzyl magnetic resonance imaging (Gd-EOB-MRI) at 8–12 weeks after the initial administration.

value: blood

value: M

tag: etiology

value: HBV

tag: bclc stage

value: C


title: ARL11 Adenoviral Transducted NHU-hTERT cells after 48 hours B

description: replicate 2


title: PD4 pretreatment

value: Atezolizumab+Bevacizumab


title: infected 2n_replicate 6


title: infected 3n_replicate 2


title: infected 3n_replicate 1


title: infected 2n_replicate 4


title: Control Sample (replicate 1)


title: infected 2n_replicate 3


title: PD2 pretreatment

value: F

value: HCV


title: PD3 pretreatment

value: Al


title: PD3 response evaluation


title: control 3n_replicate 4

value: control


title: infected 2n_replicate 5


title: SD2 response evaluation


title: PD2 response evaluation


title: control 2n_replicate 5


title: control 2n_replicate 3


title: SD2 pretreatment


title: SD1 response evaluation

value: B


title: control 3n_replicate 6


title: SD3 response evaluation


title: PD1 response evaluation


title: PD1 pretreatment


title: infected 2n_replicate 1


title: NHU-hTERT cells with empty vector C

description: replicate 3

value: NHU-hTERT


title: control 3n_replicate 1


title: PR3 pretreatment


title: control 2n_replicate 2


title: PR2 response evaluation


title: control 2n_replicate 1


title: SD1 pretreatment


title: PR2 pretreatment


title: SD3 pretreatment


title: BXPC-3 cells, si-LINC01133, sample 3

city: Nanjing

first: Zhihong

last: Zhang

state: Jiangsu

address: Guangzhou Road 300

institute: Jiangsu Province Hospital

data_processing:
Sequencing-derived raw image files were processed by BGISEQ-500 basecalling Software for base-calling with default parameters.
SOAPnuke (https://github.com/BGI‐flexlab/SOAPnuke) was used to filter the sequencing data.
Bowtie2 (https://bowtie‐bio.sourceforge.net/bowtie2/index.shtml) was used to align the clean reads to the reference gene set.
The data mining and figure presentation process were  done by the BGI in-house customized data mining system Dr.Tom.
Assembly: GRCh38
Supplementary files format and content: TXT file with read counts of each samples.

growth_protocol: BXPC-3 was cultured in RPMI 1640 medium. The medium was added with 10% fetal bovine serum and 1% penicillin and streptomycin.

extract_protocol:
Total RNA from BXPC-3 was extracted using TRIzol reagent. Reverse transcription was performed using PrimeScriptTM RT reagent Kit with gDNA Eraser.
Library was constructed following BGI mRNA Library Preparation protocol.

treatment_protocol: Si-LINC01133 was transfected to BXPC-3 cells together with Lipofectamine 3 000 (Invitrogen Co., Ltd) according to the manufacturer’s instructions.

tag: cell line

value: pancreatic adenocarcinoma


title: BXPC-3 cells, si-LINC01133, sample 1


title: PR3 response evaluation


title: PR1 pretreatment


title: BXPC-3 cells, si-LINC01133, sample 2


title: PR1 response evaluation


title: BXPC-3 cells, negative control, sample 3


title: control 3n_replicate 5


title: TNF_Rat29

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

institute: Cleveland State University

data_processing:
FASTQ files were generated by CASAVA.
The gene expected read counts and TPMs were estimated by RSEM (v1.2.3)
TPMs were median-by-ratio normalized
Assembly: GRCh38 (Human); mRatBN7.2 (Rat)
Supplementary files format and content: ExpectedCounts.txt.gz: Text file, mapping read counts
Supplementary files format and content: MedianNorm_TPMs.txt.gz: text file, normalized TPM values

organism: Rattus norvegicus

source_name: Medial Collateral Ligament (MCL)

extract_protocol:
MSCs were grown to confluence in 75-cm2 filter cap cell culture flasks, washed with PBS, and the media was replaced with StemPro MSC serum-free media (SFM) CTS (Gibco Life Technologies, Gaithersburg, MD). Cells were incubated 18-24 hours upon which the conditioned culture media (CM) was collected and exosomes were isolated by differential ultracentrifugation essentially as previously described.21  The CM was centrifuged using a Beckman Coulter Allegra® X-15R centrifuge (2000 g at 4°C for 20 minutes) to remove any detached cells, apoptotic bodies, and cell debris. Clarified supernatant CM was then centrifuged in a Beckman Coulter Optima™ L-80XP Ultracentrifuge (100,000 g at 4°C for 2 hours) with a SW 28 rotor to pellet exosomes. The supernatant was carefully removed, and exosome pellets were re-suspended in PBS and pooled. Exosomes were characterized using a Thermo NanoDrop spectrophotometer for protein and RNA concentration. Particle diameter and concentration were evaluated via IZON qNano Nanoparticle Characterization instrument (Zen-bio Inc, Research Triangle Park, NC).
Total RNAs were isolated from Human MSCs and MSCs-derived exosomes, as well as rat medial collateral ligaments (MCLs) (post-injury day 14) using trizol (ThermoFisher #15596018) and chloroform phase separations followed by the RNeasy mini protocol (Qiagen #74106) with optional on-column Dnase digestion (Qiagen #79254). One hundred nanograms of total RNA were used to prepare sequencing libraries using the LM-Seq (Ligation Mediated Sequencing) protocol
mRNA-seq: RNAs were selected using the NEB Next Poly A+ Isolation Kit (NEB #E7490S/L).  Poly A+ fractions were eluted, primed, and fragmented for 7 minutes at 85°C.  First stand cDNA synthesis was performed using SmartScribe Reverse Transcriptase (Takara Bio USA #639538), and RNA was removed.  cDNA fragments were purified with Ampure XP beads (Beckman Coulter #A63881). The 5’ adapter was ligated, and 18 cycles of amplification were performed. These final indexed cDNA libraries were quantified, normalized, multiplexed, and run as single-end reads on the HiSeq 3000; small RNA-seq: Total RNAs were isolated using trizol (ThermoFisher #15596018) and chloroform phase separations followed by the RNeasy mini protocol (Qiagen #74106) with optional on-column DNase digestion (Qiagen #79254). One hundred nanograms of total RNA was used to prepare sequencing libraries using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB #E7560S). The 3’ adapter was ligated and the reverse transcription primer hybridized.  The 5’ adapter was ligated and cDNA synthesis was performed using ProtoScript II Reverse Transcriptase.  PCR amplification was performed with 15 cycles and purified with Qiaquick PCR Purification Kit (Qiagen # 28106).  cDNA libraries were then size-selected using AMpure XP beads (Beckman Coulter #A63881).

value: Medial Collateral Ligament (MCL)

value: TNF-α-preconditioned MSCs


title: BXPC-3 cells, negative control, sample 2


title: SUM159_spheroid

city: Athens

first: Spyros

last: Foutadakis

address: Soranou

country: Greece

institute: Biomedical Research Foundation Academy of Athens

description:
BD Single-Cell multiplexing Kit SampleTag04_hs
BD Single-Cell multiplexing Kit SampleTag06_hs
BD Single-Cell multiplexing Kit SampleTag08_hs

data_processing:
FASTQ files obtained from sequencing were provided to the Seven Bridges Genomics platform for further analyses.
The quality-filtered R1 reads were analyzed to identify the cell label sequence (CL), Molecular Identifier sequence (UMI), and poly-dT tail sequence.
Then putative cell information were combined together with RSEC-adjusted molecules to generate a single-cell expression matrix.
Assembly: hg38
Supplementary files format and content: Count matrix files in mtx format
Supplementary files format and content: Barcodes and features in tsv format

growth_protocol: SUM159 cells were cultured in Ham's medium  supplemented with 5% fetal bovine serum, 1% penicillin/streptomycin, 5 μg/mL insulin and 1 μg/mL hydrocortisone in a humidified atmosphere of 5% CO2 at 37 °C.

extract_protocol:
The different cell populations were labelled with the BD Single-Cell Multiplexing Kit (BD Biosciences),  following the manufacturer's protocol. Cell viability and numbers were  evaluated by the BD Rhapsody scanner, and samples with high viability (> 85%) were used for sequencing. Approximately 15000 cells for the attached SUM159 were pooled together and another 15000 cells for the speroid and loaded in 2 BD Rhapsody cartridges.
The BD Rhapsody protocol was followed for library construction

treatment_protocol: SUM159 attached cells were made resistant to paclitaxel or doxorubicin by long term treatment with escalating doses

tag: genotype

value: Wt

value: SampleTag4:untreated, SampleTag6:paclitaxel treated, Sample Tag8:doxorubicin treated


title: BXPC-3 cells, negative control, sample 1


title: SUM159_attached

description:
BD Single-Cell multiplexing Kit SampleTag01_hs
BD Single-Cell multiplexing Kit SampleTag02_hs
BD Single-Cell multiplexing Kit SampleTag03_hs

tag: treatment

value: SampleTag1:untreated, SampleTag2:paclitaxel resistant, Sample Tag3:doxorubicin resistant


title: TNF_Rat28

tag: cell type


title: CV0985 venom gland ATACseq

city: Arlington

first: Siddharth

last: Gopalan

address: 501 S. Nedderman Dr, Life Sciences Building RM 337

department: Biology

institute: University of Texas at Arlington

data_processing:
Broadly, ATAC-seq steps followed methods previously published (Perry et al., 2022; GSM5183958)
Assembly: UTA_CroVir_3.0 (GCA_003400415.2)
Supplementary files format and content: All sample files except for CV1084 (which was of lower quality, and excluded from the study), bigwig (.bw) are provided. These files allow one to visualize chromatin accessibility peaks mapped across the reference genome build.

organism: Crotalus concolor

source_name: venom gland

extract_protocol:
Venom gland samples were extracted, snap frozen with liquid nitrogen, and sent to Active Motif for ATAC-seq data generation.
ATAC-seq libraries were prepared by Active Motif (Carlsbad, CA). ATAC-seq libraries were sequenced on an Illumina NextSeq500 using 42 bp paired-end reads.

tag: tissue

value: venom gland


title: TNF_Rat26


title: TNF_Rat27


title: T2D_Participant_6_w52

type: genomic

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

hyb_protocol: The bisulfite treatment and hybridisation was carried out by Eurofins Genomics GmbH

scan_protocol: iscan, carried out by Eurofins Genomics GmbH

data_processing:
ChAMP package v2.24.0 in R environment
combat normalised beta methylation values

label: Cy3 and Cy5

source_name: skeletal muscle

label_protocol: Labeling was carried out by Eurofins Genomics GmbH

extract_protocol: Invisorb® Genomic DNA Kit II according to the manufacturer’s protocol was used

treatment_protocol: Genomic DNA was extracted from frozen muscle biopsies.

value: skeletal muscle

value: female

tag: timepoint

value: 52 weeks post metabolic surgery

tag: group

value: Obese diabetic


title: T2D_Participant_11_w52

tag: Sex


title: T2D_Participant_8_w52


title: T2D_Participant_12_w52


title: T2D_Participant_10_w52

value: male


title: T2D_Participant_9_w52


title: PBS_Rat25

value: PBS


title: T2D_Participant_7_w52


title: T2D_Participant_4_w52


title: T2D_Participant_5_w52


title: T2D_Participant_13_w52


title: PBS_Rat23


title: T2D_Participant_3_w52


title: PBS_Rat22


title: T2D_Participant_2_w52


title: Intact_Rat40

value: No treatment


title: T2D_Participant_1_w52


title: Intact_Rat39


title: Intact_Rat38

value: Exosomes


title: T2D_Participant_10_w0

value: Before metabolic surgery


title: T2D_Participant_11_w0


title: Exo_Rat33


title: Exo_Rat32


title: T2D_Participant_9_w0


title: T2D_Participant_7_w0


title: T2D_Participant_8_w0


title: PBS_Rat24


title: T2D_Participant_5_w0


title: Exo_Rat30


title: Exo_Rat31


title: T2D_Participant_4_w0


title: T2D_Participant_6_w0


title: CRX_Rat37

value: CRX-preconditioned MSCs


title: CRX_Rat36


title: Intact_Rat41


title: T2D_Participant_3_w0


title: CRX_Rat34


title: T2D_Participant_2_w0


title: T2D_Participant_1_w0


title: pMb_scr_rep2

city: Berlin

first: Paul-Lennard

last: Mendez

address: Thielallee 63

department: Institute for Chemistry and Biochemistry

institute: Freie Universität Berlin

data_processing:
FASTQ files were mapped to GRcm38p6 with STAR (v. 2.7.2.b) with standard settings.
Mapped reads were counted using featureCounts (v 2.0.1) and GRcm38p6 using the following flags: "-p" "-M" "-O" "-T" "24" "-F" "GTF"
Batch correction on count matrices was performed with ComBat_seq from the R sva package (3.35.2).
Differential gene analyis of batch corrected counts was performed with DeSeq2 (1.40.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts matrices
Supplementary files format and content: tab-delimited text files include adjusted, normalized counts

source_name: muscle

growth_protocol: Cells were maintained under culture conditions at 37°C, 5% CO2, and 95% RH. For C2C12 cells, 150,000 cells were seeded in 2 ml of antibiotic-free C2C12 proliferation medium (high glucose DMEM with stable L-glutamine, supplemented with 10% FCS) in a 6 cm dish. The following day, 50 nM Septin9 siRNA or non-targeting siRNA was mixed with Lipofectamine iMax in Opti-MEM™ and incubated for 20 minutes. The cells were washed once with PBS, and 1.7 ml of Opti-MEM™ was added. Subsequently, 300 µl of the transfection mix was added dropwise to the cells (calculated for a total of 4 ml transfection medium), effectively increasing the siRNA concentration to 100 nM for the first 5 hours. After 5 hours, 2 ml of 20% FCS antibiotic-free medium was added. For primary myoblasts, cells were handled at recommended densities and always seeded on Matrigel-coated dishes. The cells were transfected with either Septin9 siRNA or non-targeting siRNA in 3.7 ml of full myoblast proliferation medium (high glucose DMEM with stable L-glutamine, supplemented with 20% FCS, 10% HS, 2.5 ng/ml recombinant human FGFb, and 0.5% chicken embryo extract) and 300 µl of Opti-MEM/siRNA mix.

extract_protocol:
Cellular RNA was isolated using the NucleoSpin RNA isolation kit (Macherey-Nagel, Düren, Germany) according to the manufacturer's instructions.
mRNA was isolated using polyA selection by a company-specific protocol of GENEWIZ (Azenta).

treatment_protocol: 24 h post-transfection (as described in the growth protocol), 140,000 C2C12 cells were seeded in 12-well plates in C2C12 proliferation medium. 48 h following the siRNA treatment, the proliferation medium was substituted with 1 ml of C2C12 differentiation medium for 12 h prior to sample collection. Primary myoblasts were reseeded 24 h post-transfection in 12-well plates in myoblast proliferation medium. Samples were collected 24 h later, 48 h following the siRNA treatment.

value: muscle

value: primary myoblasts

value: myoblasts

value: WT

value: proliferation


title: pMb_SEPT9KD_rep2

value: Septin 9 KD


title: T2D_Participant_12_w0


title: OB_Participant_13_w52

value: Obese non diabetic


title: pMb_scr_rep1


title: OB_Participant_12_w52

value: skeletal muscle


title: OB_Participant_11_w52

value: female


title: C2C12_scr_rep2

value: 12h myogneic differentiation


title: C2C12_SEPT9KD_rep2


title: OB_Participant_10_w52

value: 52 weeks post metabolic surgery


title: CRX_Rat35

value: Medial Collateral Ligament (MCL)


title: OB_Participant_9_w52


title: OB_Participant_7_w52


title: OB_Participant_8_w52


title: NHU-hTERT cells with empty vector  Adeno C

description: replicate 3

value: NHU-hTERT

value: empty vector


title: C2C12_scr_rep1


title: OB_Participant_4_w52


title: OB_Participant_6_w52


title: T2D_Participant_13_w0

value: male

value: Obese diabetic


title: OB_Participant_5_w52


title: pMb_SEPT9KD_rep1


title: S.aureus-3

city: Guangzhou

first: mingchao

last: Jin

state: Guangdong Province

address: No.1838 North of Guangzhou Avenue

department: Division of Orthopedics and Traumatology, Department of Orthopedics

institute: Nanfang Hospital, Southern Medical University

data_processing:
The resulting gene profiles were analyzed using limma package (3.54.0) to determine DEGs between S. aureus infected BMDMs and control ones. GO analysis of DEGs (p value < 0.05, and │Log2(fold change)│>1) was performed by clusterProfiler package (Version 4.7.1) in R platform (Version 4.2.3, https://www.r-project.org/). Terms with adjusted p values of < 0.05 were considered significant enrichment. Heatmap was plotted by pheatmap R package (version 1.0.12).
Assembly: GRCm38, mm10
Supplementary files format and content: count, fpkm

source_name: femora and tibiae

growth_protocol: BMDMs were prepared from C57BL/6 mice (8-10 weeks old) according to the protocols as described previously. Briefly, mice were euthanized by cervical dislocation, and the femora and tibiae were exposed carefully followed by flush of cells from bone marrow. After lysis of the red blood cells with ACK lysis buffer, bone marrow cells were cultured and differentiated in RPMI-1640 medium supplemented with 30% L929 conditioned medium, 10% fetal bovine serum and 1% penicillin/streptomycin for 7 days with medium refreshed every 3 days for differentiation into macrophages. On day 8 of differentiation, cells were treated for further analysis

extract_protocol:
BMDMs were washed with PBS, lysed in Trizol (9108, Takara, Japan), and sent for next-generation sequencing.
RNA was quality-assessed with Agilent 2100 (Agilent, USA) using RNA 6000 Nano kit (5067-1511, Agilent, USA), with RNA integrity number above 9 for library construction. The total RNA samples from three independent experiments were used for library construction according to the protocol of Illumina NovaSeq 6000 platform and then sequenced on a Thermal Cycler (Eastwin, Suzhou, China) using HighSensivity DNA assay Kit (5067-4626, Agilent, USA). The FASTq sequencing files were aligned to the mouse reference genome (GRCm38, mm10) using STAR aligner for further analysis.

treatment_protocol: On day 8, BMDMs in S.aureus-infected group were infected with S. aureus at MOI of 10 for 1 h, and then treated with 20 μg/mL lysostaphin and 50 μg/mL gentamicin to remove extracellular bacteria. After being washed with PBS for three times, Cells were then cultured for additional 12 h.

value: femora and tibiae

value: bone marrow-derived macrophages

value: macrophage

tag: agent


title: Control-3

value: Control


title: S.aureus-2


title: OB_Participant_1_w52


title: S.aureus-1


title: OB_Participant_2_w52


title: OB_Participant_13_w0

value: Before metabolic surgery


title: OB_Participant_3_w52


title: C2C12_SEPT9KD_rep1

value: muscle

value: myoblasts


title: F38

city: New York

first: David

middle: A.

last: Goukassian

state: NY

address: One Gustave L. Levy Place, Box 1014

department: Cardiovascular Research Institute

institute: Icahn School of Medicine at Mount Sinai

data_processing:
FastQC (version 0.11.9) was used for the quality assessment of raw sequencing reads (Q30% was greater than 94%). Next, we aligned the reads to the mouse reference genome (mm39) using the STAR aligner (version 2.7.8a) in gene count quantification mode and obtained raw gene counts. The GRCm39 release 110 GTF file was used for gene annotation.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: left ventricular tissue

extract_protocol:
Total RNA was extracted from LV tissues using the RNeasy Mini Kit (Qiagen, USA) according to the manufacturer’s protocol and stored at -80°C until further use.
A poly-A selected mRNA library was prepared using the NEBNextUltra™II RNA Library Prep Kit.

value: left ventricular tissue

tag: strain

tag: diet

value: Normal

tag: field

value: Gamma

tag: dose

value: 100 cGy


title: Control-2


title: F40

value: female


title: OB_Participant_10_w0

value: skeletal muscle

value: Obese non diabetic


title: F37


title: F36


title: OB_Participant_11_w0


title: F39


title: F35

value: Western

value: Sham

value: 0 cGy


title: OB_Participant_12_w0


title: OB_Participant_9_w0


title: F34


title: F33


title: OB_Participant_7_w0


title: OB_Participant_8_w0


title: OB_Participant_6_w0


title: OB_Participant_5_w0


title: F32


title: F31


title: Control-1

value: femora and tibiae


title: OB_Participant_3_w0


title: F28


title: OB_Participant_2_w0


title: F30


title: F27


title: OB_Participant_4_w0


title: F29


title: F24

value: Mix

value: 50 cGy


title: F26


title: F23


title: OB_Participant_1_w0


title: F22


title: F21


title: F18


title: F17


title: F16


title: F13


title: F14


title: F15


title: F25


title: F12


title: F20


title: F8


title: F9


title: F11


title: F6


title: F10


title: F19


title: F7


title: F5


title: F3


title: F4


title: F2


title: F1


title: M40

value: male


title: M39


title: DNAm postmortem brain s45

city: Munich

first: Natan

last: Yusupov

address: Kraepelinstr. 2-10

department: Dept. Genes and Environment

institute: Max Planck Institute of Psychiatry

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC v1.0 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Minfi pipline with stratified quantile normalization and subsequently beta-mixture quantile normalization.

label: Cy3, Cy5

source_name: postmortem brain

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from fresh-frozen postmorten brain samples according to standard procedures

tag: age

value: Female

tag: hemisphere

value: Right

tag: pmi

value: no

value: Current


title: DNAm postmortem brain s19

value: Male

value: Left


title: M37

value: left ventricular tissue

value: Normal

value: Gamma

value: 100 cGy


title: DNAm postmortem brain s79


title: DNAm postmortem brain s38

value: Ex-smoker


title: DNAm postmortem brain s73

value: Never


title: DNAm postmortem brain s75


title: M36


title: DNAm postmortem brain s42


title: DNAm postmortem brain s28


title: DNAm postmortem brain s81


title: M35

value: Western

value: Sham

value: 0 cGy


title: DNAm postmortem brain s11


title: DNAm postmortem brain s76


title: DNAm postmortem brain s30


title: M34


title: DNAm postmortem brain s29


title: DNAm postmortem brain s6


title: DNAm postmortem brain s90


title: DNAm postmortem brain s66


title: DNAm postmortem brain s22


title: M33


title: DNAm postmortem brain s24


title: DNAm postmortem brain s7


title: M31


title: DNAm postmortem brain s58


title: DNAm postmortem brain s5


title: M30


title: DNAm postmortem brain s31


title: DNAm postmortem brain s63


title: M32


title: M38


title: M29


title: M28


title: M27


title: M26


title: DNAm postmortem brain s2


title: M24

value: Mix

value: 50 cGy


title: M23

value: male


title: M22


title: M25


title: DNAm postmortem brain s40

value: Right


title: DNAm postmortem brain s47

value: Female

value: no


title: DNAm postmortem brain s68

value: Male

value: Current


title: M20

value: left ventricular tissue


title: M21

value: Normal


title: M19

value: Gamma


title: M18

value: 100 cGy


title: M16


title: M14


title: DNAm postmortem brain s3


title: M17


title: M13


title: M12


title: DNAm postmortem brain s10


title: M11


title: DNAm postmortem brain s52

value: Left


title: DNAm postmortem brain s77


title: M10


title: M15


title: DNAm postmortem brain s15


title: DNAm postmortem brain s20


title: DNAm postmortem brain s78

value: Never


title: DNAm postmortem brain s57


title: DNAm postmortem brain s13


title: DNAm postmortem brain s71


title: M6


title: DNAm postmortem brain s54


title: DNAm postmortem brain s53


title: M9


title: M7


title: M8


title: DNAm postmortem brain s49


title: DNAm postmortem brain s89

value: Ex-smoker


title: M5


title: DNAm postmortem brain s91


title: M4


title: M2


title: M3


title: M1


title: DNAm postmortem brain s1


title: DNAm postmortem brain s43


title: DNAm postmortem brain s55_2

value: yes


title: DNAm postmortem brain s46


title: DNAm postmortem brain s17


title: DNAm postmortem brain s74


title: posterior posterolateral cortical amygdala biological replicate 2

city: La Jolla

first: Cory

middle: Matthew

last: Root

address: 3119 Pacific Hall, 9500 Gilman Drive

institute: University of California, San Diego

description: 10X Single Cell 3' v3.1 Single Index

data_processing:
Fastq demultiplexing with CellRanger (v5.0.0)
Read alignment and single cell data parsing with CellRanger (v5.0.0)
Reads aligned to CellRanger 2020-A reference genome (mm10) and annotation (GENCODE vM23/Ensembl 98)
Empty droplets were called using the emptyDrops model from DropletUtils (v1.10.2), where droplets with less than 100 counts were used to profile ambient RNA and over 1000 were assumed non-empty
Minimal quality filtering for each barcode was performed by setting a floor of 1000 features per barcode for downstream inclusion to ensure the dataset is entirely composed of high-quality nuclei. Next, to remove highly likely multiplet barcodes, barcodes were filtered out if their count depth was more than 5 median absolute deviations above the median count depth. Barcodes were then removed if their proportion of ribosomal or mitochondrial reads was more than 5 interquartile ranges above the 75th percentile.
Heterotypic doublets were identified by creating simulated artificial doublets in scDblFinder (v1.4.1),
Assembly: mm10
Supplementary files format and content: Barcodes: Tab-separated values files containing cell barcodes and matrix files
Supplementary files format and content: Features: Tab separated values files containing the gene identities in the matrix
Supplementary files format and content: Matrix: raw barcode by feature matrix files giving counts for each combination

source_name: brain

extract_protocol:
All sacrifices were performed during the dark period of the light cycle. Animals were anesthetized via combined intraperitoneal injection of 150 mg/kg ketamine and 15 mg/kg xylazine. Once unconscious, mice animals were transcardially perfused with ice-cold, carbogen-bubbled (95% O2, 5% CO2), nuclease-free, 0.22 µm sterile-filtered artificial cerebrospinal fluid (ACSF) with a composition of 93 mM N-methyl-D-glucamine, 2.5 mM KCl, 1.2 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 5 mM sodium ascorbate, 2 mM thiourea, 3 mM sodium pyruvate, 13.2 mM trehalose, 12 mM N-acetyl-cysteine, 0.5 mM CaCl2, 10 mM MgSO4, and 93 mM HCl, at pH 7.3-7.4.(Tasic et al., 2018; Ting et al., 2014) Following transcardial perfusion, brains were immediately extracted and submerged into ice-cold carbogen-bubbled ACSF, with less than 5 minutes between the beginning of perfusion and final submersion after extraction. Brains were serially sectioned in ice-cold, carbogen-bubbled ACSF on a VT1000S vibratome (Leica) with polytetrafluoroethane-coated razor blades (Ted Pella) at 0.15 mm/sec and 100 Hz, dividing the whole cerebrum into 400 µm coronal slices. Target regions were microdissected from these slices under a stereomicroscope using a sterile blunt-end needle (22 gauge for CeA, ASt, and tail of striatum, 16 gauge for dorsal striatum). All regions were targeted using Paxinos and Franklin’s the Mouse Brain in Stereotaxic Coordinates as reference (Paxinos and Franklin, 2019). Extracted tissue samples were recovered in ice-cold, nuclease-free, 0.22 µm sterile-filtered cryoprotective nuclear storage buffer, composed of 0.32 M sucrose, 5 mM CaCl2, 3 mM magnesium acetate, 10 mM Trizma hydrochloride buffer (pH 8.0), 1 mM dithiothreitol, 0.02 U/µl SUPERase•In RNAse Inhibitor (Invitrogen), and 1X cOmplete Protease Inhibitor Cocktail with EDTA (Roche). Tissue was then snap frozen using a metal CoolRack M90 (Biocision) pre-chilled to -80˚C and stored at -80˚C until nuclear isolation. Cryopreserved tissue pieces were slow-thawed by incubation at 4˚C for 1 hour prior to isolation. Tissue pieces were then pooled and resuspended in nuclear isolation medium composed of 0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Trizma hydrochloride buffer (pH 7.4), 1 mM dithiothreitol, 0.04 U/µl RNasin Plus RNAse Inhibitor (Promega), 1X cOmplete Protease Inhibitor Cocktail with EDTA (Roche), and 0.1% Triton-X. The pooled tissue pieces in nuclear isolation medium were transferred to a 2 mL Dounce tissue grinder. Tissue was homogenized by 5 strokes from the loose pestle and 15 followed by the tight pestle, and the resulting homogenate was filtered through a 40 µm Flowmi cell strainer (Bel-Art) into a 1.5 ml Lo-Bind tube (Eppendorf). The homogenate was then centrifuged with a swinging bucket rotor at 4˚C and 1000 x g for 8 minutes. Nuclei were then washed with nuclear flow buffer composed of DPBS with 1% bovine serum albumin, 1 mM dithiothreitol, and 0.04 U/µl RNasin Plus RNAse Inhibitor (Promega) and centrifuged at 4˚C and 500 x g for 5 minutes, which was subsequently repeated. Nuclei were finally resuspended in nuclear flow buffer containing 3 µm DRAQ7 (Cell Signaling Technology) and again filtered through a 40 µm Flowmi cell strainer into a 5 ml round-bottom polystyrene tube. Each isolation took under 45 minutes to perform, from homogenization to final suspension.
Library construction was performed acording to manufacturers' instructions (10X Single Cell 3' v3.1 Single Index). GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip. RNA from nuclei in each droplet was reverse-transcribed to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with DynaBeads, PCR-amplified and appropriately-sized fragments were selected with SPRIselect reagents for subsequent library construction. During subsequent steps, Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: brain

tag: tissue region

value: 8 weeks old


title: DNAm postmortem brain s69


title: anterior posterolateral cortical amygdala biological replicate 3

description: 10X Single Cell 3' v3.1 Single Index


title: DNAm postmortem brain s55


title: anterior posterolateral cortical amygdala biological replicate 2

description: 10X Single Cell 3' v3.1 Single Index


title: anterior posterolateral cortical amygdala biological replicate 1 library 2

description: 10X Single Cell 3' v3.1 Single Index


title: DNAm postmortem brain s60


title: DNAm postmortem brain s27


title: MIN6 cell, chronic epinephrine 3

city: Chongqing

first: Bingpeng

last: Yao

state: -- Please Select --

address: Tiansheng Road 2

institute: southwest university

data_processing:
GCL Genomics Workbench v 11.0.1
Assembly: GRCm38

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

tag: cell line


title: anterior posterolateral cortical amygdala biological replicate 1 library 1

description: 10X Single Cell 3' v3.1 Single Index


title: posterior posterolateral cortical amygdala biological replicate 1

description: 10X Single Cell 3' v3.1 Single Index


title: MIN6 cell, chronic epinephrine 2


title: DNAm postmortem brain s12


title: DNAm postmortem brain s88


title: DNAm postmortem brain s82


title: DNAm postmortem brain s84_2


title: MIN6 cell, control 2


title: posterior posterolateral cortical amygdala biological replicate 3

description: 10X Single Cell 3' v3.1 Single Index


title: MIN6 cell, control 1


title: MIN6 cell, control 3


title: Cd11c-lineage

city: Salt Lake City

first: Monica

middle: L.

last: Vetter

state: UT

department: Neurobiology & Anatomy

institute: University of Utah

description: lineage

data_processing:
Illumina adapters were trimmed from reads with cutadapt v3.5, trimming after 6 matching bases and discarding trimmed reads shorter than 20 bases. Trimmed reads were aligned with STAR v2.7.9a in two pass mode to indexed genome GRCm39, created with splice junctions from Ensembl release 104 and a maximum overhang of 124 bases, to generate a BAM alignment file sorted by coordinates. Uniquely aligned fragment counts were assigned to Ensembl 104 transcripts from the alignment files with featureCounts v1.6.3.
edgeR v4.0.16 was used to calculate log fold changes and log CPM from read counts with the exactTest function.
Assembly: GRCm39
Supplementary files format and content: tab-deliminated file with fragment counts and fold change

source_name: retina

growth_protocol: FACs sorted cells from CD11c-Cre-gfp;Rosa-TDTom animals at P5.

extract_protocol:
Total RNA was prepared with the RNeasy Plus Kit (Qiagen 74034) and RNA Clean and Concentrator kit (Zymo R1013) and hybridized with NEBNext rRNA Depletion Kit v2 (E7400) to substantially diminish rRNA from the samples.
Stranded RNA sequencing libraries were prepared as described using the NEBNext Ultra II Directional RNA Library Prep Kit (Illumina E7760L). Purified libraries were qualified on an Agilent Technologies 4150 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583). The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 5 nM in preparation for Illumina sequence analysis.

treatment_protocol: One sample each of Cd11c lineage cells (GFP-TdTom+, 5441 cells) and Cd11c active cells (GFP+TdTom+, 4041 cells) were sorted from 8 retinas (4 female and 4 male).

value: retina

value: microglia

tag: genotype


title: MIN6 cell, chronic epinephrine 1


title: 10254-KV-0022_KO_Control

city: Nashville

first: Alyssa

last: Hasty

state: TN

address: 702 LIght Hall

department: Molecular Physiology and Biophysics

institute: Vanderbilt University

data_processing:
RNA sequencing reads were adapter-trimmed and quality-filtered using Trimgalore v0.6.7 (Krueger et al., 2023). An alignment reference was generated from the mm39 mouse genome and GENCODE comprehensive gene annotations (vM31), to which trimmed reads were aligned and counted using Spliced Transcripts Alignment to a Reference (STAR) v2.7.9a (Dobin et al., 2013) with the –quantMode GeneCounts parameter. About 30-50 million uniquely mapped reads were acquired per sample. DESeq2 package v1.36.0 (Love et al. 2014) was used to perform sample-level quality control, low count filtering, normalization and downstream differential gene expression analysis.
Assembly: mm39
Supplementary files format and content: tab-delimited text file containing raw counts for each sample
Supplementary files format and content: tab-delimited text file containing normalized counts for each sample

source_name: microglia from bilateral hippocampus

growth_protocol: All mice used in experiments were Slc11a2flfl;Cx3cr1Cre-ERT2+/- with either APP/PS1+ hemizygosity or WT as littermate controls, and were 129S;C57BL/6J mixed background. Mice were group-housed (2-5 per cage) by sex in transparent cages at 22-25°C under a 12 h light/dark cycle in a specific pathogen-free facility.

extract_protocol:
Bilateral hippocampi were isolated and minced in DMEM + 10% FBS + 1x pennicillin-streptomycin ("IMG media") before 30 min digestion in IMG media + Papain and DNase. Samples were triturated with pipettes of descending size every 5 min to break up tissue clumps and strained through 70 μm cell strainers. Single-cell suspension samples underwent Percoll gradient separation, followed by CD11b+ magnetic staining and sorting using a Miltenyi cell separation system. CD11b+ cell samples were collected, lysed in 350 μL lysis buffer and flash-frozen, and total RNA was extracted using RNeasy MicroKit (Qiagen).
Paired-end sequencing libraries were constructed using a standard mRNA NEBNext Poly(A) selection Library Prep Kit (Illumina). Library Quality Control analysis was performed by using Qubit and BioAnalyzer to determine the concentration and size bp. Samples were sequenced at multiplex Paired-End 150 bp using the Illumina NovaSeq 6000 sequencing platform.

treatment_protocol: To induce gene knockdown, 'KD' groups were adminstered a dose of 4 mg (maximum 200 μL volume) tamoxifen via oral gavage every day for five consecutive days at 5-6 months of age. 'Control' mice were given 200 μL corn oil. All mice were euthanized between 15-18 months of age for cell isolation.

value: microglia from bilateral hippocampus

value: KO

tag: treatment

value: Control


title: Cd11c-active

description: active

tag: cell type


title: 10254-KV-0023_KO_APP_PS1

tag: tissue


title: DNAm postmortem brain s83_2

value: Female

value: Right


title: DNAm postmortem brain s84

value: Male

value: no

value: Current


title: 10254-KV-0021_KO_APP_PS1


title: DNAm postmortem brain s23


title: DNAm postmortem brain s87


title: DNAm postmortem brain s41


title: DNAm postmortem brain s85


title: 10254-KV-0020_KO_APP_PS1


title: DNAm postmortem brain s21


title: 10254-KV-0018_KO_APP_PS1


title: DNAm postmortem brain s67_2


title: 10254-KV-0017_WT_APP_PS1

value: WT


title: DNAm postmortem brain s35


title: 10254-KV-0016_WT_APP_PS1


title: DNAm postmortem brain s61

value: Left


title: DNAm postmortem brain s86


title: 10254-KV-0015_WT_Control


title: DNAm postmortem brain s36


title: DNAm postmortem brain s18

value: Never


title: 10254-KV-0013_WT_APP_PS1


title: 10254-KV-0012_WT_Control


title: DNAm postmortem brain s14


title: 10254-KV-0019_KO_Control


title: DNAm postmortem brain s65


title: DNAm postmortem brain s62

value: Ex-smoker


title: 10254-KV-0009_WT_Control


title: DNAm postmortem brain s64


title: 10254-KV-0008_WT_Control


title: DNAm postmortem brain s56


title: 10254-KV-0011_WT_APP_PS1


title: 10254-KV-0007_WT_APP_PS1


title: DNAm postmortem brain s67


title: DNAm postmortem brain s9


title: DNAm postmortem brain s50


title: DNAmethylation_relapse5 [203986510139_R02C01]

city: Augsburg

first: Victoria

middle: Elisabeth

last: Fincke

address: Stenglinstraße 2

institute: Childens Cancer Center - University hospital Augsburg

description:
tumor RR 5
genomic DNA

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing:
Data was processed as described in Johann, Pascal D., et al. "Atypical teratoid/rhabdoid tumors are comprised of three epigenetic subgroups with distinct enhancer landscapes." Cancer cell 29.3 (2016): 379-393.
eMRTbetas.csv: normalized beta values

source_name: formalin-fixed paraffin-embedded tumor sample

label_protocol: standard protocol

extract_protocol: standard protocol

treatment_protocol: DNA was isolated from FFPE tumor samples, purification and bisulfite conversion were performed as described in:  Holdhof D, Johann PD, Spohn M, Bockmayr M, Safaei S, Joshi P, et al. Atypical teratoid/rhabdoid tumors (ATRTs) with SMARCA4 mutation are molecularly distinct from SMARCB1-deficient cases. Acta Neuropathologica. 2021;141(2):291-301.

value: extracranial malignanat rhabdoid tumor

tag: subgroup

tag: status (0=alive, 1=deceased)


title: 10254-KV-0010_WT_APP_PS1


title: DNAm postmortem brain s34

tag: Sex


title: DNAmethylation_relapse4 [203049640026_R03C01]

description:
tumor RR 4
genomic DNA


title: 10254-KV-0005_WT_APP_PS1


title: 10254-KV-0006_WT_Control


title: DNAm postmortem brain s26


title: DNAmethylation_relapse3 [201465960038_R03C01]

description:
tumor RR 3
genomic DNA


title: 10254-KV-0004_KO_APP_PS1


title: 10254-KV-0003_KO_Control


title: DNAmethylation_relapse2 [3998909037_R01C02]

description:
tumor RR 2
genomic DNA


title: DNAm postmortem brain s39


title: 10254-KV-0002_KO_Control


title: DNAmethylation_relapse1 [200325530093_R05C02]

description:
tumor RR 1
genomic DNA


title: DNAmethylation_patient80  [200848860184_R04C01]

description:
tumor sample 80
genomic DNA


title: DNAmethylation_patient9 [200925700161_R07C01]

description:
tumor sample 76
genomic DNA


title: 10254-KV-0001_KO_Control


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 168

city: Basel

first: Simona

last: Baghai Sain

address: Schanzenstrasse 44

department: Department of Biosystems Science and Engineering

country: Switzerland

institute: ETH Zurich

library_source: other

data_processing:
library strategy: Amplicon sequencing of genomic DNA
The raw sequencing data comprising the BCL files were demultiplexed into FASTQ files using the Illumina bcl2fastq program v2.20 with default options allowing one mismatch of the sample barcode sequences. The number of sgRNAs in each sample was counted by the count command from the MAGeCK package.
processed data files format and content: Count matrix of sgRNAs (represented by the gene symbol of their target gene). Gene symbols on rows, samples on columns.
Assembly: mm10

molecule: other

source_name: mouse epidermis

extract_protocol:
DMBA/TPA-induced tumors (which were not used for neither scRNA-seq nor spatial analysis) were minced and genomic DNA was extracted using the Qiagen DNeasy Blood and Tissue Kit.
The sgRNA region was amplified in a nested PCR. In PCR1, we used 12.5 µl KAPA HiFi HotStart ReadyMix (Roche, 07958935001), 0.75 µl forward primer (5‘ CTTGTGGAAAGGACGAAACACCG 3’, 10μM), 0.75 µl reverse primer (5‘ GTGTCTCAAGATCTAGTTACGCCAAGC 3’ 10μM), 1 µl of extracted genomic tumor DNA (with a concentration between 50-100 ng/μl) and 10 μl nuclease-free water for a total volume of 25 μl per tumor. PCR1 was performed using the following conditions: Initial denaturation at 98°C for 2:30 min, followed by 22 cycles of denaturation 98°C -– 20 s, annealing 62°C -– 30 s, extension 72°C -– 30 s. PCR1 products for each tumor were individually column-purified with a GenElute™ PCR Clean-Up Kit (Sigma-Aldrich NA1020-1KT). For PCR2, 1 μl of cleaned up PCR1 was used as template along with 0.75 μl forward barcoded i5 primer (see Supplementary Information Table 1, 10 μM), 0.75 μl reverse barcoded i7 primer (see table, 10 μM), 10 μl nuclease free-water, along with 12.5 μl of KAPA HiFi HotStart ReadyMix for a total volume of 25 μl. Eight different i5 and i7 primers allowed for a total of 64 different combinations. PCR2 was performed under following conditions: Initial denaturation at 95°C for 3 min, followed by 32 cycles of denaturation 98°C -– 30 s, annealing 62°C – 30 s, extension 72°C – 30 s. PCR2 products for a maximum of 64 individually barcoded tumor amplifications were pooled and cleaned up with Agencourt AMPure XP beads (Beckman Coulter, A63881) according to manufacturer’s instructions before sequencing.

treatment_protocol: DMBA/TPA chemical carcinogenesis: Two-stage cutaneous chemical carcinogenesis was performed as previously described by Filler et al. (2007). In brief: the back of 6-8 week old animals were shaved with electric hair clippers and treated once with 400 nmol 7,12-dimethylbenz[a]anthracene (DMBA)(Sigma-Aldrich D3254) per 100 µl (dissolved in acetone) application as an initiator mutagen. After a two-week rest period, 40 nmol 2-o-tetradecanoylphorbol-13-acetate (TPA)(Sigma-Aldrich 79346) dissolved in 100 µl 100% Ethanol was applied twice a week. Tumor formations were monitored regularly by visual inspection and mice were euthanized after 12 weeks of treatment or when tumors reached a cumulative length of 2cm.

value: mouse epidermis

value: DMBA/TPA carcinogenesis

value: JAX #026179, CD1 wildtype x Tg(B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J

value: 144 days post natal


title: DNAmethylation_patient8 [200925700161_R06C01]

description:
tumor sample 75
genomic DNA


title: DNAm postmortem brain s48


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 167


title: DNAmethylation_patient78 [205055470116_R02C01]

description:
tumor sample 73
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 166


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 165


title: DNAm postmortem brain s59


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 164


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 163


title: DNAmethylation_patient75 [205055470115_R06C01]

description:
tumor sample 70
genomic DNA


title: DNAm postmortem brain s51


title: DNAmethylation_patient74 [205055470115_R05C01]

description:
tumor sample 69
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 162


title: DNAmethylation_patient73 [205055470115_R04C01]

description:
tumor sample 68
genomic DNA


title: DNAmethylation_patient77 [205055470116_R01C01]

description:
tumor sample 72
genomic DNA


title: DNAm postmortem brain s83


title: DNAmethylation_patient72 [205055470115_R03C01]

description:
tumor sample 67
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 160


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 161


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 159


title: DNAm postmortem brain s8


title: DNAmethylation_patient71 [205055470115_R01C01]

description:
tumor sample 66
genomic DNA


title: 10254-KV-0014_WT_Control

value: microglia from bilateral hippocampus

value: microglia


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 158


title: DNAm postmortem brain s25


title: DNAm postmortem brain s4


title: DNAmethylation_patient7 [200925700161_R05C01]

description:
tumor sample 64
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 156


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 157


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 155


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 154


title: DNAmethylation_patient67 [205023290087_R04C01]

description:
tumor sample 61
genomic DNA


title: DNAmethylation_patient66 [205023290060_R01C01]

description:
tumor sample 60
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 153


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 152


title: DNAmethylation_patient64 [205023290054_R04C01]

description:
tumor sample 58
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 151


title: DNAmethylation_patient63 [205023290054_R02C01]

description:
tumor sample 57
genomic DNA


title: DNAmethylation_patient62 [205023290054_R01C01]

description:
tumor sample 56
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 149


title: DNAmethylation_patient76 [205055470115_R08C01]

description:
tumor sample 71
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 148


title: DNAmethylation_patient61 [205023290052_R08C01]

description:
tumor sample 55
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 147


title: DNAmethylation_patient60 [205023290052_R07C01]

description:
tumor sample 54
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 146


title: DNAmethylation_patient6 [200876170045_R07C01]

description:
tumor sample 53
genomic DNA


title: DNAmethylation_patient59 [205023290052_R06C01]

description:
tumor sample 52
genomic DNA


title: DNAm postmortem brain s92_2

value: yes


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 144


title: DNAmethylation_patient79 [205055470116_R04C01]

description:
tumor sample 74
genomic DNA


title: DNAm postmortem brain s33

value: Female


title: DNAm postmortem brain s72

value: Right


title: DNAmethylation_patient68 [205023290087_R05C01]

description:
tumor sample 62
genomic DNA


title: DNAm postmortem brain s16

value: Male


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 143


title: DNAmethylation_patient57 [205023290052_R04C01]

description:
tumor sample 50
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 142