title: Chronic_MitoQ_Rep4

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

data_processing:
Raw fastq files generated were quality inspected using the FastQC (available at: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC (Ewels et al., 2016) tools. For reference mapping (BDGP6), the nf-core RNA-Seq Seq pipeline (version 3.10.1; available at https://nf-co.re/rnaseq) was used in conjunction with select parameters (--outFilterMultimapNmax 500, --winAnchorMultimapNmax 500, --clip_r1 12, --clip_r2 12). To enumerate counts for known genes, the featureCounts tool was used (Liao et al., 2014). To enumerate counts for transposable elements (TEs), the TEcount tool was used (Jin et al., 2015).  Counts output were than row concatted and saved as a tab-deliminated text file named "enumerated_counts.txt".
Assembly: BDGP6
Supplementary files format and content: tab-delimited text files describes enumerated expression per linrary in raw counts

organism: Drosophila melanogaster

source_name: head

growth_protocol: Wild-type male Drosophila melanogaster flies were grown from larval stage to pupa stage into adults (10 days-old).

extract_protocol:
For extraction and isolation of RNA, 13-21 male flies were euthanized per treatment condition without the use of CO2 sedation by flash freezing in liquid nitrogen. Fly heads from those euthanized were recovered by vortexing to separate heads from bodies and subsequently passing the heads and bodies through two sieves (with the upper sieve retaining the bodies and the lower sieve retaining the heads). Groups of heads were then homogenized in Lysis Binding Mix (from MagMAX mirVana Total RNA Isolation Kit; Thermo Fisher Scientific, Washington, DC; #A27828) using Navy Eppendorf RNA Lysis Kits (Next Advance, Troy, NY; #NAVYE5-RNA) and a Bullet Blender Storm 24 (Next Advance, Troy, NY; #4116-BBY24M). RNA was then isolated from these homogenates using the MagMAX mirVana Total RNA Isolation Kit per the manufacturer’s instructions in conjunction with the KingFisher Apex Purification System with 96 Deep-Well head (Thermo Fisher Scientific, Washington, DC; #5400930).
For library construction, the quality of RNA was first assessed by TapeStation 2200 (Agilent Technologies, Santa Clara, CA) and NanoDrop (Thermo Fisher Scientific, Washington, DC). cDNA libraries were generated from 500 ng of total RNA using NEBNext Ultra II Directional Poly-A RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA; #E7760). cDNA library quality and quantity were assessed by TapeStation 2200 and Qubit (Thermo Fisher Scientific, Washington, DC). cDNA libraries were then sequenced on a NextSeq 2000 machine using NextSeq 2000 P3 reagents (Illumina, San Diego, CA).

treatment_protocol: Flies were treated with either vehicle (DMSO), vehicle and 2-AAPA, or vehicle and MitoQ acutely (24 hrs prior to RNA extraction and isolation ) or chronically (10 days).

value: head

value: Wild-type

value: chronic MitoQ (100 uM)

value: 10 days-old

tag: number heads


title: Chronic_MitoQ_Rep6

status: Public on Aug 22 2024

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: genotype

tag: treatment

tag: time


title: ICO1DMsiELF3D12

city: Nijmegen

first: Haoyu

last: Wu

address: Mr. van Houtenstraat, 24

country: Netherlands

institute: Radboud University

data_processing:
Paired-end reads were aligned to human genome (hg38) using STAR-2.7.6a with the default settings.
To have comparable sequencing depth from each sample, subsampling was applied to the datasets according to the amount of reads from the sample with lowest sequencing depth using SAMtools 1.7.
The number of mapped fragments was quantified at gene level using featureCount 2.0.1 with the following parameters, -p -g gene_name, based on Gencode annotation (v30).
The R package DEseq2 1.26.0 was used for differential gene expression analysis and for principal components analysis (PCA). Genes with less than 2 fragments were removed from the differential gene expression analysis. All the differentially expressed genes are determined according to adj-P<0.05.
Genome_build: hg38

organism: Homo sapiens

source_name: ICO

growth_protocol: Liver organoids were obtained from Erasmus university medical center and Radboud university medical center. Liver organoids were cultured and differentiated towards hepatocyte-like cells as published before. Briefly, liver organoids were cultured in Basement Membrane Extract (BME, Trevigen, 3533-010-02) and the expansion medium was refreshed every 3 days. For the hepatocyte differentiation, the organoids were first cultured in expansion medium supplemented with BMP7 (PEPROTECH, 120-03P) for 5 days, and then switched to differentiation medium for more than 10 days. To obtain single cells, BME was removed by 10-fold dilution in cold DMEM/F-12 (Thermo, 12634-010). The liver organoids were then digested using 0.05% Trypsin-EDTA (Thermo, 25300-054) until 80-90% of the cells were single cells. Trypsin was removed and cells were collected for further use.

extract_protocol:
For selection of pericentral cell population cells were stained in PBS containing 1% BSA with SLCO1B3 antibody (NBP2-36492AF700) at 1:33 dilution for a minimum of 30 min. After the incubation, cells were washed three times and used for bulk sorting. 500,000 cells were sorted into15ml tubes for RNA isolation using Becton Dickinson Aria with a 130 µm nozzle. RNA samples were isolated using the same kit following the manufacturer’s recommendations. 100-300 ng of RNA was used for cDNA synthesis using iScript cDNA Synthesis Kit (Bio-Rad, 1708891) following the online manual.
100 to 250 ng of total RNA was used for library construction using KAPA RNA Hyper + RiboErase HMR kit (Roche, 08098140702) following the manual. After the library construction, libraries were quantified on the bio-analyzer using DNA high-sensitivity kit (Agilent, 5067-4626), and sequenced paired-end (2 x 38bp) on the Illumina NextSeq 500 platform.

treatment_protocol: siRNA knockdown

tag: cell type

value: ICO

value: day 12 in diiferentiation medium


title: M6_rep2

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, feature counting and aggregation was done using Cell Ranger 6.1.2.
Assembly: Rnor_6
Supplementary files format and content: Supplementary files format and content: tsv files and matrix files

organism: Rattus norvegicus

source_name: mammary gland

extract_protocol:
Mammary glands were collected freshly and digested in digestion medium containing 2 mg/mL collagenase type IV, 2 mg/mL hyaluronidase and 2 mg/mL BSA in DMEM/F12 medium, at 37 ºC for 1 to 2 hours, then viable single cells were submitted to Translational Immunogenomics Lab core in Dana-Farber cancer institute for library construction.
The scRNA-seq libraries were prepared according to the Chromium Next GEM Single Cell 5’ HT v2 protocol (10x Genomics). Quality control for amplified cDNA libraries and final sequencing libraries were performed using Bioanalyzer High Sensitivity DNA Kit (Agilent). The pooled libraries were sequenced on Illumina NovaSeq S4 platform.

treatment_protocol: For midkine treatment, rat recombinant midkine was injected intraperitoneally 3 times/week at 300 ug/kg for four consecutive weeks. All rats were sacrificed immediately after the final dose, and mammary tissues were collected for scRNA sequencing.

value: mammary gland

tag: age

value: 6 months


title: SB620

city: New York

first: Sydney

middle: B

last: Blattman

state: NY

address: 1150 St. Nicholas Ave

institute: Columbia University

description:
PETRI-seq; metG* bioreactor timepoints (undiluted/stationary, 20 minutes - 2 hours after dilution)
Barcoded cDNA

data_processing:
Barcode demultiplexing with cutadapt 1.18
UMIs extracted with UMI-tools version 0.5.5
Reads aligned with bwa version 0.7.17
Features called with featureCounts version 1.6.3
Final matrix generated by collapsing reads by UMI with a custom script in python 2.7.15
Assembly: Genbank U00096

organism: Escherichia coli

extract_protocol:
in situ RT and ligations followed by cell lysis with detergent and proteinase K
Double-stranded cDNA was made by second strand synthesis. Libraries were tagmented and amplified using the Nextera XT kit

treatment_protocol: after chemostat exponential growth; cells taken 2 (t1), 2.7 (t2), 3.7 (t3), or 5.1 (t4) hours after OD600=0.1; sequenced in stationary phase or 20 minutes-2 hours after dilution into fresh media

value: metG


title: M6_rep4

description: 10x Genomics


title: Chronic_MitoQ_Rep5


title: M12_rep1

description: 10x Genomics

value: 12 months


title: ICO1DMConD8

value: day 8 in diiferentiation medium

value: control siRNA


title: KAPA_BR_O

city: Cleveland

first: Hyunmin

last: Kim

state: Ohio

address: 0900 Euclid Ave.

institute: Case Western Reserve University

library_source: genomic

data_processing:
trim fastq using fastp with Qxyg option
map the trimmed reads to galGal6 genome
extract mapped alignments in bed format using bedtools
Assembly: galGal6
Supplementary files format and content: bed coordinates and mapping read sequences

molecule: genomic DNA

organism: Brachylophosaurus canadensis

source_name: osteocytes

extract_protocol:
Tyrannosaurus rex (MOR1125) and Brachylophosaurus canadensis (MOR 2598) were prepared and analyzed in separate laboratories from the extant material, with separate buffers, reagents and instruments, by investigators wearing all protective lab garb (coats, hair covers, masks, gloves, etc.) and following aseptic procedures. Samples were prepared in the BioGard hood. Cortical bone fragments from each dinosaur were subjected to demineralization by incubation in 0.5 M EDTA (pH 8.0). Debris remaining from demineralization was filtered through a 40 µm cell strainer (BD Falcon 352340), and filtrate was centrifuged and washed with E-pure water to collect cells. Vessels were isolated from debris trapped within the cell strainer and washed. Both cells and vessels were incubated with the iron chelator pyridoxal isonicotinoyl hydrazone (PIH) in solution (5 mM PIH in 50 mM NaOH) (1,2,3) to remove iron, and then were prepared with "Protocol for preparing non-mammalian samples for Omni-C sequencing and do novo genome reconstruction— 2/22/2021, adopted by Berkley Gryder from Dovetail protocol used in the DNA zoo project" beginning at step 3, as above.
KAPA HyperPlus Kit protocol (Roche 07962401001)

value: osteocytes


title: Chronic_MitoQ_Rep3


title: ICO1EM

value: expansion medium

value: no


title: SB621


title: M12_rep3

description: 10x Genomics


title: SB605

description:
PETRI-seq; metG* stationary phase and 2 minutes, 2 hours, and 4 hours after dilution
Barcoded cDNA

treatment_protocol: after overnight growth (metG3_20201018_1), diluted into fresh media, grown for 2 minutes (metG4_20201018_1), 2 hours (metG5_20201018_1), or 4 hours (metG6_20201018_1)


title: ICO1DMsiELF3D8


title: ICO1-DM_1544

data_processing:
Barcode information was extracted from read 1 and added to the ID of paired read 2 using UMI-tools 1.1.0. The barcoded reads containing unique molecular identifier (UMIs, 1-8bp) and cell barcode (9-16bp) were not used for mapping. Only the paired read 2 were aligned to a modified human genome (hg38) containing 92 ERCC spike-in sequences using STAR-2.7.6a with default settings. After mapping, featureCount 2.0.1 was used to assign the reads to genes. The number of UMIs per gene was counted for each cell and the gene-cell count tables were generated using UMI-tools 1.1.0 with the following parameters, --per-gene, --per-cell. For the downstream analysis, Seurat 3.2.3 was applied for data filtering, batch correction, normalization, clustering, visualization and differentially expressed gene analysis. Briefly, Seurat objects were created per donor using gene-cell matrices. Genes detected (UMIs > 0) in at least 5 cells were kept. Cells that are with less than 1000 UMIs or more than 50% of mitochondrial gene expression (mt%) were removed. UMI counts were then log2 transformed and normalized to sequencing depth per cell, and number of total UMIs and mt% were regressed out during the scaling to correct for sequencing depth and mt%.
For scRNA-seq data analysis within PHHs or ICOs, to minimize the batch effect, Seurat objects from different donors were integrated using the functions FindIntegrationAnchors and IntegrateData. Next, Top 2000 variable genes were found and used for PCA analysis with the setting, npcs=50. Seurat function FindNeighbors, FindClusters, and RunUMAP were used to construct a Shared Nearest Neighbor (SNN) Graph, identify clusters of cells based on the SNN graph, and finally to reduce the dimension for the visualization. Finally, differentially expressed genes from each cluster were identified, and the significant ones were used for pathway analysis via Enrichr web tool.
For integration analysis of PHHs and ICOs, PHH and ICO Seurat objects were merged using Seurat merge function. To compare ICOs to PHHs only, non-hepatocyte cluster in the PHHs dataset was not included in the integration. Then the newly merged Seurat object was first scaled with regressing out the number of total UMIs, mt% and biological replicates, and then used for further analysis following the same procedure as mentioned before.
For correlation analysis of zonally-expressed genes between human and mouse hepatocyte, we used a set of 94 genes previously identified to be expressed in both human and mouse. Average expression levels of each gene were calculated for all the 4 hepatocyte clusters (from this study) and then scaled and centered by z-scores. Same analysis was applied for nine layers of mouse hepatocytes. Pearson correlation was calculated to compare the 4 human hepatocyte clusters with the nine layers of mouse hepatocytes.
SCENIC R version was used for gene regulatory network analysis. Briefly, raw gene-cell count matrix was extracted from “RNA” assay in Seurat object and used as input for SCENIC. The matrix was log 2 transformed, and co-expression network was calculated using runGenie3 with default setting. To predict the transcription factor regulons, hg19-tss-centered-10kb-7species.mc9nr.feather motif database from RcisTarget was used. Regulons were created with the following parameters, minGenes = 20, coexMethod="top5perTarget". The Area Under the recovery Curve (AUC) scores were generated per cells and imported into Seurat for downstream analysis and visualization.
Genome_build: hg38

growth_protocol: Liver organoids were obtained from Erasmus university medical center and Radboud university medical center. Liver organoids were cultured and differentiated towards hepatocyte-like cells as published before (8, 18). Briefly, liver organoids were cultured in Basement Membrane Extract (BME, Trevigen, 3533-010-02) and the expansion medium was refreshed every 3 days. For the hepatocyte differentiation, the organoids were first cultured in expansion medium supplemented with BMP7 (PEPROTECH, 120-03P) for 5 days, and then switched to differentiation medium for more than 10 days. To obtain single cells, BME was removed by 10-fold dilution in cold DMEM/F-12 (Thermo, 12634-010). The liver organoids were then digested using 0.05% Trypsin-EDTA (Thermo, 25300-054) until 80-90% of the cells were single cells. Trypsin was removed and cells were collected for further use.

extract_protocol:
For single cell sorting, cells were washed one time with cold PBS containing 1% BSA, and then sorted using BDFACSMelody with a 100 µm nozzle into a 384-well plate containing 100 nl unique Cel-seq primer solution and 5 µl of mineral oil (Sigma, M5310).
Single-cell RNA libraries were constructed according to the mCEL-seq2 protocol . Briefly, 100 nL lysis buffer (0.2% Triton X-100, 2mM dNTPs, 1:50.000 ERCC ExFold RNA spike-in (Thermo, 4456739)) was added per well using the Nanodrop Ns-2 Stage (BioNex). For the in vitro reverse transcription reaction, SuperScript™ II Reverse Transcriptase (Invitrogen, 18064-14) was used with the following the protocol, 4 ⁰C for 5 min; 25 ⁰C for 10 min; 42 ⁰C for 60 min; 70 ⁰C for 10 min. Next, 960 nL second-strand reaction mix containing E. coli DNA ligase (NEB, M0205L), E. coli DNA polymerase I (NEB, M0209L) and Random hexamer (sigma, 11034731001) were added per well for second-strand synthesis following the protocol, 16 ⁰C for 2 hrs. All the cDNA from one 384-well plate was pooled. In vitro transcription was performed using the MEGAscript™ T7 Transcription Kit (Invitrogen, AMB 1334-5) by incubating the reaction at 37 ⁰C for 14 hrs. The amplified RNA was fragmented and used for cDNA synthesis using Superscript II and the random octamer primer. Libraries were amplified for 9 cycles for the hepatocyte libraries and 8 cycles for the liver organoid libraries using Phusion® High-Fidelity PCR Master Mix (NEB, M0531S) with the Nextflex primers, and quantified on the bio-analyzer using DNA high-sensitivity kit (Agilent, 5067-4626). Barcoded libraries were sequenced on an Illumina NextSeq 500 with 38bp paired-end reads at a depth of about 25 million reads per plates.

treatment_protocol: no treatment

tag: plate index


title: Chronic_MitoQ_Rep2


title: SB591


title: M3_rep3

description: 10x Genomics

value: 3 months


title: SB623d

extract_protocol:
in situ RT and ligations followed by cell lysis with detergent and proteinase K
Double-stranded cDNA was made by second strand synthesis. Libraries were tagmented and amplified using the Nextera XT kit. rRNA was depleted using GenScript Cas9 and partial probe set


title: Chronic_2AAPA_Rep7

value: chronic 2-AAPA (10 uM)


title: M6_rep1

description: 10x Genomics


title: SB572

description:
PETRI-seq; metG* 2 hours and 4 hours after dilution from overnight
Barcoded cDNA

treatment_protocol: after overnight growth, diluted into fresh media, grown for 2 (metG1_20200926) or 4 (metG2_20200926) hours


title: ICO1DMConD12


title: M3_rep2

description: 10x Genomics


title: M3_rep4

description: 10x Genomics


title: SB588


title: PHH7-1B3posi

source_name: PHH

value: PHH

value: SLCO1B3 stained

value: FACS SLCO1B3 positive pupolation


title: SB563


title: Chronic_2AAPA_Rep6

value: head

value: Wild-type

value: 10 days-old


title: PHH7-1B3nega

value: FACS SLCO1B3 negative pupolation


title: M3_rep1

description: 10x Genomics

value: mammary gland


title: SB562

value: metG


title: Chronic_2AAPA_Rep5


title: Chronic_MitoQ_Rep1

value: chronic MitoQ (100 uM)


title: PHH6-rep2-1B3posi

description:
independent experiment 2
Zonal_1B6_RNAseq_Rcount.csv


title: PHH6-rep2-1B3nega

description:
independent experiment 2
Zonal_1B5_RNAseq_Rcount.csv


title: Chronic_2AAPA_Rep3


title: scATAC-seq_M22_rep1

description: 10x Genomics

library_source: genomic single cell

data_processing:
Raw sequencing data were converted to fastq format using cellranger atac mkfastq (10x Genomics, v.2.0.0). scATAC-seq reads were aligned to the rat Rnor_6 reference genome and quantified using cellranger count (10x Genomics, v.2.0.0).
Assembly: Rnor_6
Supplementary files format and content: tsv files, csv files and bed files

extract_protocol:
Mammary glands were collected freshly and digested in digestion medium containing 2 mg/mL collagenase type IV, 2 mg/mL hyaluronidase and 2 mg/mL BSA in DMEM/F12 medium, at 37 ºC for 1 to 2 hours, then viable single cells were submitted to Center for library construction.
Libraries were constructed using the 10X Genomics ATAC-seq kits v2 by Functional Cancer Epigentics in Dana-Farber cancer institute.

value: 22 months


title: scATAC-seq_M22_rep2

description: 10x Genomics


title: SB556


title: scATAC-seq_M12_rep2

description: 10x Genomics

value: 12 months


title: Non-treated bshC:Tn cells replicate 2

city: Fresno

first: Mamta

last: Rawat

state: CA

address: 2555 E. San Ramon Ave. MS S/B 73

department: Biology

institute: California State University, Fresno

description:
BshC8
TMM_CPM.txt
SAUSA300_processed.xlsx

data_processing:
Reads were mapped to the reference genome for S. aureus (RefSeq GCA_000013465.1) using Rsubread version 2.4.0.
EdgeR was used to normalize gene expression using trimmed means of M-values (TMM) and to identify differentially expressed genes and statistical analysis
Only mapped reads equal to or greater than 10 counts per million reads, and a cut-off of p-value < 0.05 were considered for further analysis.
Assembly: RefSeq GCA_000013465.1
Supplementary files format and content: TMM_CPM.txt contains the raw counts for each set of aligned reads for each individual sample.
Supplementary files format and content: SAUSA300_processed.xlsx contains an excel file containing the gene ID, gene description, log2FC of the bshC mutant compared to the wildtype strain, and p-value.

organism: Staphylococcus aureus

source_name: whole bacterial cell

growth_protocol: S. aureus was grown in TSB and collected at mid-logarithmic phase (OD600 0.4 - 0.6) grown while shaken at 37C

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen), according to manufacturer instructions with the following exception: samples were lysed by bead-beating using a BeadBlaster 24 (Benchmark Scientific). To remove ribosomal RNAs, high-quality total RNA was processed using Illumina’s Ribo-Zero Bacteria kit (Illumina, San Diego, CA).
cDNA libraries were generated with rRNA depleted mRNA using the KAPA RNA Hyper Plus Kit (Roche, Indianapolis, IN) following the manufacturer’s instructions

treatment_protocol: No treatments were applied, rather a comparison between the wildtype and transposon mutated strain were compared.

tag: strain

value: whole bacterial cell

tag: growth condition

value: 37C, shaken, logarithmic growth


title: Chronic_2AAPA_Rep2


title: PHH6-rep1-1B3nega

description:
independent experiment 1
Zonal_1B3_RNAseq_Rcount.csv


title: Chronic_2AAPA_Rep1


title: PHH6-rep1-1B3posi

description:
independent experiment 1
Zonal_1B4_RNAseq_Rcount.csv


title: PHH5-ATAC

data_processing:
For ATAC-seq data analysis, pair-end reads were mapped to human genome reference (hg38) using BWA 0.7.17-r1188 mem  with default settings. Next, duplicates and reads with mapping quality lower than 30 were removed using samtools 1.7.
Open chromatin profile tracks were generated using deeptools 3.5.0  bamCoverage function with the following setting, --normalizeUsing CPM.
For peak calling, MACS2 v2.2.7.1 was used with the following settings, -g hs, --nomodel. Overlapping and unique peak sets between biological replicates or different samples were identified using homer mergePeaks function with the parameter, -d given. To minimize the donor variation and get most confident peak sets, only the peaks presented from both biological replicates were used for further analysis.
For spearman correlation analysis, ATAC peaks were first merged from all the samples, and the ATAC signal was quantified in all peaks from each sample using bedtools v2.29.2 multicov function. The peak-sample count table was either imported into DEseq2 1.26.0 for making the PCA plot following the online tutorial, or CPM normalized for spearman correlation analysis using rcorr function from R package Hmisc 4.4-2.
For motif analysis, GimmeMotifs v0.15.1 was applied using 200bp around peak summit regions as input with the following settings, -s 0, -b gc. For differentially enriched motif analysis, the unique peak sets from each sample were merged. Then normalized read coverage was quantified (as CPM) in each peak region (200bp around summit point) for each sample. After log2 transformation, the matrixes were imported into GimmeMotifs, and maelstrom function was used with the default settings.
Genome_build: hg38

extract_protocol:
25000 cells were sorted into a 1.5ml tube containing PBS with 5% BSA.
25000 cells were washed once with cold PBS, and then resuspended in Tn5 reaction mix (12.5 µl 2x TD buffer (homemade), 1.25µl Tn5 enzyme (homemade), 0.5 µl Digitonin (Promega, G9441), and 11 µl H2O). Cells were incubated in the thermo mixer at 37 ⁰C, 800 rpm for 20 min. After the incubation, reaction cleanup was performed using QIAGEN MinElute Reaction Cleanup Kit (28204). The purified tagmented DNA samples were barcoded with Nextera Index Kit primers and amplified via PCR followed by a AMpureXP bead (Agencourt, A63882) size selection. Briefly, after first 5 PCR cycles, 5ul of PCR reaction was used for qPCR to determine the number of additional cycles needed. After amplification, PCR reaction was cleaned up with 0.65x AMpureXP beads followed by 1.8x SPRI beads to select DNA fragments from 150 to 600 bp. Finally, libraries were quantified on the bio-analyzer using DNA high-sensitivity kit, and sequenced on an Illumina NextSeq 500 with 38bp paired-end reads at a depth of about 20 million reads per sample.

value: no


title: Chronic_DMSO_Rep7

value: chronic DMSO (0.2%)


title: scATAC-seq_M12_rep1

description: 10x Genomics


title: Non-treated bshC:Tn cells replicate 1

description:
BshC7
TMM_CPM.txt
SAUSA300_processed.xlsx


title: PHH4-ATAC


title: scATAC-seq_M6_rep2

description: 10x Genomics

value: 6 months


title: Non-treated wildtype cells replicate 1

description:
WT1
TMM_CPM.txt
SAUSA300_processed.xlsx

value: wild-type


title: Non-treated wildtype cells replicate 2

description:
WT2
TMM_CPM.txt
SAUSA300_processed.xlsx


title: scATAC-seq_M6_rep1

description: 10x Genomics


title: Chronic_2AAPA_Rep4

value: chronic 2-AAPA (10 uM)


title: Chronic_DMSO_Rep6


title: treat-D

city: Beijing

first: Rui

last: Liang

address: Tsinghua  University, Haidian  District

country: China

institute: Tsinghua university

description: treat-D

data_processing:
lllumina Casava1.7 sottware used for basecalling
Assembly: mm9
Supplementary files format and content: genes.fpkm_table.xls

source_name: kidney

growth_protocol: HEK-293T cells  were cultured in high-glucose DMEM supplemented with 10% FBS, and cells grown at 37°C in a 5% CO2humidified atmosphere (≥95%).

extract_protocol:
Total cellular RNA was extracted from the infected cells with TRIzol reagent (Invitrogen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: The mock PCAGGS and PCAGGS-EP152R plasmids were transfected into HEK-293T cells, and the cells were harvested 24 hours

value: kidney

tag: cell line

value: human embryonic kidney 300 cells

value: wild type

value: EP152R transfection


title: ICO2-EM-ATAC

value: expansion medium

value: ICO


title: Chronic_DMSO_Rep5

value: head

value: Wild-type

value: 10 days-old


title: scATAC-seq_M3_rep2

description: 10x Genomics

value: mammary gland

value: 3 months


title: scATAC-seq_M3_rep1

description: 10x Genomics


title: Chronic_DMSO_Rep4


title: ICO2-DM-ATAC

value: differnetiation medium


title: ICO1-EM-ATAC


title: treat-B

description: treat-B

value: human embryonic kidney 298 cells


title: ICO1-DM-ATAC


title: treat-A

description: treat-A

value: human embryonic kidney 297 cells


title: OM, Recovery, Replicate 1

city: Pittsburgh

first: Ulka

last: Sachdev-Ost

address: 300 Halket Street Suite 5414

institute: University of Pittsburgh School of Medicine

description: 10X Genomics

data_processing:
Raw reads were processed using the 10X mm10 reference genome with Cell Ranger (v6.1) to generate raw UMI count tables
Assembly: The mouse reference genome (mm10) was downloaded from 10X Genomics (https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz)
Supplementary files format and content: h5

organism: Mus musculus

source_name: Oral mucosa

extract_protocol:
Maxilla were disassociated manually and then strained using a 100µm cell strainer. Tissues was further digested with collagenase type 1 (0.2mg/ml, Worthington Lakewood, NJ) for 1 hour at 37°C. Cells were washed, collected by centrifugation, and resuspended in incubation buffer (0.5% BSA in PBS).
Viable CD45+ cells were isolated via flow cytometry as described above. The isolated cells were prepared in a single cell suspension and library preparation was performed using the Chromium Single Cell 3’ Reagent Version 2 Kit (10X Genomics). Each sample was loaded and run on separate lanes. Droplets were subjected to reverse transcription and then cDNA amplified.

value: Oral mucosa

value: 16 weeks

value: Immune cells (Cd45+)

value: Periodontal Disease Recovery


title: Chronic_DMSO_Rep2

value: chronic DMSO (0.2%)


title: OM, Recovery, Replicate 2

description: 10X Genomics


title: RAW264.7-dox-Cas9, sgERH, IFNgamma, biol rep 3

city: Vienna

first: Gijs

middle: A.

last: Versteeg

address: Dr. -Bohrgasse 9

department: Department of Microbiology

country: Austria

institute: Max Perutz Labs, University of Vienna

data_processing:
For RNA-seq analysis, quality control was done with fastqc (v0.11.8) and pre-processing (adapter and quality trimming) with fastp (v0.20.1). Cell-line specific 3’-ends were determined with 3-GAmES (https://github.com/poojabhat1690/3-GAmES) using mouse (GRCm38) RefSeq and Ensembl annotations. QuantSeq reads were quantified with SlamDunk (v0.3.4, Neumann et al., 2019 ) using the counting Windows output from 3-GAmES and 3’-end read counts were collapsed per gene.
Assembly: Mus musculus GRCm38 (mm10)
Supplementary files format and content: tab-delimited .csv files including count values

molecule: polyA RNA

source_name: Abelson murine leukemia virus-induced tumor

growth_protocol: RAW264.7 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM; Sigma-Aldrich, D6429)  supplemented with  10% FBS (Sigma-Aldrich, F7524) and 1% penicillin/streptomycin (Sigma-Aldrich, P4333)

extract_protocol:
Total RNA was isolated using Trizol (Invitrongen, 15596018).
3’ mRNA sequencing libraries were generated according to manufacturer’s recommendations (QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina and PCR Add-on Kit for Illumina, Lexogen).

treatment_protocol:
Cas9 induced knockouts were generated by 5 days of doxycycline (Sigma-Aldrich,D9891) treatment (500 ng/mL).
Stimulation of immune pathways was done by treating the cells with 10 ng/mL IFNγ (gift from G. Adolf, Boehringer Ingelheim, Vienna), 50 ng/mL IL-1beta (Peprotech, 211-11b), or non-treated (negative control) for 4 hours.

value: Macrophage-like

value: sgERH

value: IFNgamma

value: 5 days dox


title: RAW264.7-dox-Cas9, sgERH, IFNgamma, biol rep 2

value: Abelson murine leukemia virus-induced tumor


title: control-3

value: kidney

value: human embryonic kidney 295 cells

value: wild type

value: PCAGGS transfection


title: control-4

value: human embryonic kidney 296 cells


title: Chronic_DMSO_Rep1

value: head

value: Wild-type

value: 10 days-old


title: Acute_MitoQ_Rep7

value: acute MitoQ (100 uM)


title: Acute_MitoQ_Rep5


title: OM, Disease, Replicate 3

description: 10X Genomics

value: Oral mucosa

value: 16 weeks

value: Immune cells (Cd45+)

value: Periodontal Disease Induced


title: RAW264.7-dox-Cas9, sgERH, IL-1beta, biol rep 3

value: Macrophage-like

value: sgERH


title: control-2

value: human embryonic kidney 294 cells


title: RAW264.7-dox-Cas9, sgERH, IFNgamma, biol rep 1

value: Abelson murine leukemia virus-induced tumor

value: IFNgamma

value: 5 days dox


title: OM, Control, Replicate 3

description: 10X Genomics

value: Healthy Controls


title: Acute_MitoQ_Rep6


title: OM, Recovery, Replicate 3

description: 10X Genomics

value: Periodontal Disease Recovery


title: OM, Disease, Replicate 2

description: 10X Genomics


title: control-1

value: kidney

value: human embryonic kidney 293 cells

value: wild type

value: PCAGGS transfection


title: OM, Control, Replicate 2

description: 10X Genomics


title: RAW264.7-dox-Cas9, sgERH, IL-1beta, biol rep 2


title: OM, Disease, Replicate 1

description: 10X Genomics


title: RAW264.7-dox-Cas9, sgERH, IL-1beta, biol rep 1


title: Acute_MitoQ_Rep3

value: head

value: Wild-type

value: acute MitoQ (100 uM)

value: 10 days-old


title: hlh-30 ko rep2

city: Shanghai

first: Hongru

last: Lin

state: Shanghai

address: Siping road 1239

department: life and science technology

institute: Tongji university

data_processing:
hisat2
featureCounts
DESeq2
clusterProfiler
Assembly: ALLPaths-LG

organism: Caenorhabditis elegans

source_name: Whole nematode

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: adult 1 day

value: Whole nematode

value: hlh-30 ko


title: Chronic_DMSO_Rep3

value: chronic DMSO (0.2%)


title: Acute_MitoQ_Rep4


title: RAW264.7-dox-Cas9, sgERH, non-treated, biol rep 2

value: Macrophage-like

value: sgERH

value: non-treated


title: hlh-30 ko rep1

description: GMC101 mut_1


title: treat-C

description: treat-C

value: human embryonic kidney 299 cells

value: EP152R transfection


title: Acute_MitoQ_Rep1


title: hlh-30 overexpression rep2

value: hlh-30 overexpression


title: OM, Control, Replicate 1

description: 10X Genomics

value: Oral mucosa

value: 16 weeks

value: Immune cells (Cd45+)

value: Healthy Controls


title: RAW264.7-dox-Cas9, sgERH, non-treated, biol rep 3

value: Abelson murine leukemia virus-induced tumor

value: 5 days dox


title: Acute_MitoQ_Rep2

value: head

value: Wild-type

value: acute MitoQ (100 uM)


title: wt rep2

value: Whole nematode

value: WT


title: Mid5

data_processing:
VIPER pipeline (https://github.com/hanfeisun/viper-rnaseq/blob/master/cfce/README_CFCE.md) was used for alignment, assembly and gene counting.
Assembly: rn6
Supplementary files format and content: csv files including raw counts for each gene and each sample

source_name: mammary tumor

extract_protocol:
A small piece of tumors were cut and grinded. Then RNA was harvested using RNeasy Micro Kit. 3000 ng RNA of each sample was submitted for the construction of sequencing libraries by GENEWIZ.
Libraries preparation with poly(A) selection and 150-bp paired-end sequencing on an Illumina HiSeq platform were performed by GENEWIZ.

treatment_protocol: Fischer rats were treated with midkine protein at 300 ug/kg 3 times/ week for two weeks and followed by a single intraperitoneal injection (i.p.) of 50 mg/kg N-nitroso N-methylurea (NMU). Then, rats were treated with midkine protein for another two weeks with same injection frequency, followed by another single NMU injection. Rats were checked three times/ week, and tumor growth was monitored using caliper measurements. Maximum tumor size burden allowed for rats is 4 cm and this was not exceeded in any of the experiments. All the remaining rats were sacrificed upon the last tumor in midkine treatment group reached the size limit.

value: mammary tumor

value: Fischer

value: rat midkine recombinant protein


title: hlh-30 overexpression rep1


title: RAW264.7-dox-Cas9, sgERH, non-treated, biol rep 1

value: Macrophage-like

value: sgERH

value: non-treated


title: Mid6


title: hlh_30_Male_3

city: Daejeon

first: Seung-Jae

middle: V

last: Lee

address: 291 Daehak-ro

department: Biological Sciences

country: South Korea

institute: KAIST

data_processing:
Sequencing pairs were aligned to the C. elegans genome WBcel235 (ce11) and Ensembl transcriptome (release 104) by using STAR (v.2.7.0e). Aligned pairs on genes or transcripts were quantified by using RSEM (v.1.3.1). Detailed parameters of alignment and quantification were calculated by following guidelines of ENCODE long RNA-Seq processing pipeline.
Assembly: WBcel235 (ce11)
Supplementary files format and content: txt files with read counts were generated by using RSEM (v.1.3.1)

source_name: Whole body

growth_protocol: All strains were maintained on E. coli OP50-seeded nematode growth media (NGM) plates at 20°C. Males were generated by heat shock at 37°C for 1 h  of L4 stage larval WT or mutant worms. Male worms were maintained by crossing between hermaphrodites and males.

extract_protocol:
Total RNAs were extracted from prefertile adult to day 1 adult WT and hlh-30(tm1978) hermaphrodites and males, three times independently. Synchronized hermaphrodites were harvested using S-basal buffer. Males were picked and harvested using S-basal buffer every day. One set of total RNA of males was extracted from the samples collected for about 20 days. Total RNA was isolated using RNAiso plus following the manufacturer’s instructions.
cDNA library was prepared for paired-end RNA seq using Illumina NovaSeq 6000 platform.

value: Whole body

tag: developmental stage

value: Prefertile adult to day 1 adult

tag: Sex

value: Male


title: RAW264.7-dox-Cas9, sgROSA, IFNgamma, biol rep 1

value: sgROSA

value: IFNgamma


title: Acute_2AAPA_Rep3

value: acute 2-AAPA (10 uM)

value: 10 days-old


title: hlh_30_Male_2


title: Acute_2AAPA_Rep5

value: head

value: Wild-type


title: RAW264.7-dox-Cas9, sgROSA, IL-1beta, biol rep 3

value: Abelson murine leukemia virus-induced tumor

value: 5 days dox


title: Mid4-3

value: mammary tumor


title: Acute_2AAPA_Rep6


title: wt rep1

value: Whole nematode

value: WT


title: RAW264.7-dox-Cas9, sgROSA, IFNgamma, biol rep 2

value: Macrophage-like


title: Mid3-2

value: Fischer

value: rat midkine recombinant protein


title: RAW264.7-dox-Cas9, sgROSA, IFNgamma, biol rep 3


title: RAW264.7-dox-Cas9, sgROSA, IL-1beta, biol rep 2


title: Mid3-1


title: Mid4-2


title: Mid4-1


title: RAW264.7-dox-Cas9, sgROSA, IL-1beta, biol rep 1


title: Acute_2AAPA_Rep2


title: Mid2


title: hlh_30_Male_1

value: Whole body


title: RAW264.7-dox-Cas9, sgROSA, non-treated, biol rep 3

value: non-treated


title: Mid1


title: hlh_30_Her_1

value: Prefertile adult to day 1 adult

value: Hermaphrodite


title: hlh_30_Her_3


title: Acute_2AAPA_Rep1


title: hlh_30_Her_2


title: WT_Male_3

value: wild type

value: Male


title: Veh6

value: vehicle


title: Acute_2AAPA_Rep4

value: head

value: acute 2-AAPA (10 uM)

value: 10 days-old


title: WT_Male_2


title: Acute_DMSO_Rep4

value: Wild-type

value: acute DMSO (0.2%)


title: RAW264.7-dox-Cas9, sgROSA, non-treated, biol rep 1

value: Abelson murine leukemia virus-induced tumor

value: sgROSA

value: 5 days dox


title: Veh5

value: mammary tumor

value: Fischer


title: WT_Male_1

value: Whole body


title: Veh4


title: mouse_G9a_mKO_H3K9me2_rep2

first: Qingyuan

last: Sun

state: Beijing

address: Beichen West Rd., Chaoyang

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
The raw reads were processed by Trimmomatic (version 0.38) to cut adapters and to trim low quality reads with the minimal length 90bp and minimal quality of bases 20.
Clean reads were mapped to the mouse mm10 genome by Bowtie2 with parameters as described previously and the default parameters in zygote ChIP sequencing data.
High quality unique mapping was performed by Samtools with MAPQ more than 30 and self-coded Perl scripts.
The duplication reads were removed by Picard to obtain the non-redundant reads.
SNP split was utilized to split the maternal and paternal reads alignment with the allele-specific C57BL6 and PWK mm10 genome.
SICER was utilized to call peaks (windows 200, Gap 600, q value 1e-5) with SICER.sh module and the differential peaks were found with SICER-df.sh module
Genome_build: mm10
Supplementary_files_format_and_content: bw files were used to check the distribution of reads in the genome

source_name: GV oocytes

extract_protocol:
Samples were collected in Nuclei Extraction Buffer directly and sheared by micrococcal nuclease (MNase) at 25°C for 5 min. Then the samples were the was incubated with H3K9me2 or CTCF antibody overnight with rotation under constant rotation on a rotator at 4°C. The next day, 10ul Dyna beads Protein A (Thermo Fisher Scientific) was added to each sample and incubated 2 hours up to overnight at 4 °C. Subsequently, the beads were washed twice with low salt wash buffer, twice high salt wash buffer. For each sample, 100 ul eluiton buffer were added to resuspend beads and incubated at 65℃ for 2h to elute DNA from the beads. The DNA was purified by phenol:chloroform:isoamyl alcohol method.
Then samples were subjected to CUT&RUN  or STAR-seq library preparation. ULI-NChIP library was generated using the KAPA Hyper Prep Kit according to the manufacture’s protocol. Paired-end 150-bp sequencing was performed on a HiSeq2500.

value: C57BL/6 J

tag: tissue/cell type

value: GV oocytes

tag: antibody

value: abcam ab1220


title: Acute_DMSO_Rep3

extract_protocol:
For extraction and isolation of RNA, 13-21 male flies were euthanized per treatment condition without the use of CO2 sedation by flash freezing in liquid nitrogen. Fly heads from those euthanized were recovered by vortexing to separate heads from bodies and subsequently passing the heads and bodies through two sieves (with the upper sieve retaining the bodies and the lower sieve retaining the heads). Groups of heads were then homogenized in Lysis Binding Mix (from MagMAX mirVana Total RNA Isolation Kit; Thermo Fisher Scientific, Washington, DC; #A27828) using Navy Eppendorf RNA Lysis Kits (Next Advance, Troy, NY; #NAVYE5-RNA) and a Bullet Blender Storm 24 (Next Advance, Troy, NY; #4116-BBY24M). RNA was then isolated from these homogenates using the MagMAX mirVana Total RNA Isolation Kit per the manufacturer’s instructions in conjunction with the KingFisher Apex Purification System with 96 Deep-Well head (Thermo Fisher Scientific, Washington, DC; #5400930).
For library construction, the quality of RNA was first assessed by TapeStation 2200 (Agilent Technologies, Santa Clara, CA) and NanoDrop (Thermo Fisher Scientific, Washington, DC). cDNA libraries were generated from 500 ng of total RNA using NEBNext Ultra II Directional Poly-A RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA; #E7760). cDNA library quality and quantity were assessed by TapeStation 2200 and Qubit (Thermo Fisher Scientific, Washington, DC). cDNA libraries were then sequenced on a NextSeq 2000 machine using NextSeq 2000 P3 reagents (Illumina, San Diego, CA).


title: Veh3


title: WT_Her_3

value: wild type

value: Prefertile adult to day 1 adult

value: Hermaphrodite


title: mouse_G9a_mKO_H3K9me2_rep1


title: Acute_DMSO_Rep1

value: head


title: Veh2-2

value: vehicle


title: Acute_DMSO_Rep6

value: 10 days-old


title: Stiff3

status: Public on Aug 21 2024

city: Regensburg

first: Xin

last: Lu

address: Universitätsstraße 31

country: Germany

institute: University of Regensburg

data_processing:
After demultiplexing, raw FASTQ data were given to an in-house mRNA analysis pipeline. BBDuk was used to trim the raw sequence data from soft, 3D matrigel and 3D alginate stiff, deleting any residual adapter sequences and low-quality bases at the ends of each read.
BioBloom Tools was used to decontaminate reads from the genomes Mus musculus (mm38), Escherichia coli (BL21), Mycoplasma pneumoniae (M129), Sphingobium sp. (SYK-6), Bradyrhizobium japonicum (USDA 110), Pichia pastoris (GS115), Malessia globosa (CBS 7966), Aspergillus fumigatus (Af293), and a set of viral genomes (RefSeq, 5k+ genomes).
All reads that did not map exclusively to the transcriptome of hg38 (GENCODE version 27, GRCh38.p10) were labeled as potentially contaminated and were removed from further processing. FastQC was used to evaluate sequence quality per sample before as well as after trimming and decontamination. In addition, all samples were examined as a collective with MultiQC.
Following that, the cleaned sample reads were aligned to the hg38 reference genome using STAR. Using featureCounts from Subread, uniquely mapping reads were counted per gene and per sample8. Further quality criteria were evaluated, including library complexity (using Preseq) and the genomic origin of the reads and the 5'-3'-bias (both using QualiMap). The final counts table of 9 samples were utilized for differential expression analysis.
All the subsequent steps after count tables were performed in R programming language. Matrix table containing gene counts were visualized using Principle Component Analysis (PCA) and t-distributed stochastic neighbor embedding (t-SNE) clustering techniques. For PCA, raw counts were scaled and prcomp function from stats package was employed. tSNE plots were constructed using Rtsne 0.1512. Subsequent steps including Quality Control (QC) analysis, filtering, normalization, feature selection, scaling, regression of unwanted variables and differential expression for the RNAseq count were performed using Seurat package. Default parameters were taken for all used functions unless otherwise mentioned. Normalization was done using ‘log.normalize’ method with a scale factor of 1e-6 to obtain logCPM count values and 2000 most variable genes were used for feature selection. Only mitochondrial genes were regressed out during scaling, cell cycle associated genes did not have an effect on the cell-to-cell clustering. “DESeq2” method was applied to do differential expression analysis between the three groups, soft, stiff and matrigel and in addition testing of genes were limited to a logFoldChange (logFC) cutoff of 1. Further, the differentially expressed genes were manually filtered for an adjusted p-value of 0.05. Finally, volcano plots were constructed using EnhancedVolcano.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Cells retrieved from 3D stiff alginate hydrogels

growth_protocol: MDA-MB-231 cells were normally grown in glucose Dulbecco’s Modified Eagle’s Medium (D6046; Sigma-Aldrich) with 10% v/v fetal bovine serum (S0615, Sigma-Aldrich) and 1% penicillin/streptomycin (Gibco), incubated in a 5% CO2 environment at 37 °C and passaged every 3-5 days. Cells were then encapsulated in 3D covalently-crosslinked alginate hydrogels with two different stiffness (stiff vs soft) and 3D Matrigel for 5 days. Cells were then retrieved from the hydrogel, the lysates collected until further processing.

extract_protocol:
Samples were resuspended in 5 µl 1X NEBNext Cell Lysis Buffer of the NEBNext Single Cell/Low Input RNA Library Prep Kit (NEB, E6420). After 5 min incubation at RT, 2.5X RNA XP Clean Up Beads (Beckman Coulter, A63987) were added to the sample by pipetting up and down. Then, samples were incubated for 5 min at RT, the beads were pelleted on a magnet, the supernatant was removed, the samples were washed twice with 80% ethanol while remaining on the magnet, and finally the beads were resuspended in 8 µl nuclease-free water. The reverse transcription was conducted according to the manual of the NEBNext Single Cell/Low Input RNA Library Prep Kit in the presence of the beads
The lysates were thawed on ice and the RNA precipitated by adding 0.1 volume 3 M sodium acetate (pH 5.5) and 2.5 volumes 100% cold ethanol. After Incubation at − 80 °C for 30 min, the RNA was recovered by centrifugation at 16,000×g for 30 min at 4 °C. The RNA pellet was washed with 1 mL 80% cold ethanol, centrifuged at 16,000×g for 5 min at 4 °C, the ethanol solution carefully removed by aspiration and the RNA pellet dried. The pellet was resuspended in 5 µl 1X NEBNext Cell Lysis Buffer of the NEBNext Single Cell/Low Input RNA Library Prep Kit (NEB, E6420). After 5 min incubation at RT, 2.5X RNA XP Clean Up Beads (Beckman Coulter, A63987) were added to the sample by pipetting up and down. Then, samples were incubated 5 min at RT, the beads were pelleted on a magnet, the supernatant was removed, the samples were washed twice with 80% ethanol while remaining on the magnet, and finally the beads were resuspended in 8 µl nuclease-free water. The reverse transcription was conducted as described in the manual of the NEBNext Single Cell/Low Input RNA Library Prep Kit in the presence of the beads.

treatment_protocol: For inhibition experiments, the following small molecule and inhibitors were used: MEK/ERK inhibitor PD98059 (10 mM, Focus Biomolecules), JNKinhibitor SP600125 (10 mM, Focus Biomolecules) and PI3K/Akt inhibitor LY294002 (10 mM, Focus Biomolecules). The inhibitors were mixed with culture medium and refreshed every 2-3 days. To knock down FHL2, MDA-MB-231 cells were transfected with two different FHL2-targeting small interfering RNA (Silencer siRNA, Invitrogen) or non-targeting siRNA (Stealth RNAi negative control, Invitrogen) using Lipofectamine RNAiMAX Reagent (Invitrogen), diluted in Opti-MEM reduced serum medium (Gibco) for a final concentration of 10-20 nM. Cells were transfected 2-3 days before encapsulation following manufacturer’s instructions. To assess MDA-MB-231 response to chemotherapy, Paclitaxel (Tokyo Chemical Industry) was diluted at 0.01, 0.1 and 0.5 mM and added to the culture medium after 3-5 days post-encapsulation, for a drug treatment of 2 days. The highest concentration tested contained around 1% (v/v) of DMSO, which was used as vehicle medium and didn’t show any negative effect on cell viability.

value: MDA-MB-231 WT

value: Breast mammary gland


title: mouse_G9a_Ctrl_H3K9me2_rep2


title: WT_Her_1


title: WT_Her_2


title: Stiff2


title: RAW264.7-dox-Cas9, sgROSA, non-treated, biol rep 2

value: Abelson murine leukemia virus-induced tumor

value: Macrophage-like

value: non-treated


title: mouse_G9a_Ctrl_H3K9me2_rep1


title: Acute_DMSO_Rep5

data_processing:
Raw fastq files generated were quality inspected using the FastQC (available at: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC (Ewels et al., 2016) tools. For reference mapping (BDGP6), the nf-core RNA-Seq Seq pipeline (version 3.10.1; available at https://nf-co.re/rnaseq) was used in conjunction with select parameters (--outFilterMultimapNmax 500, --winAnchorMultimapNmax 500, --clip_r1 12, --clip_r2 12). To enumerate counts for known genes, the featureCounts tool was used (Liao et al., 2014). To enumerate counts for transposable elements (TEs), the TEcount tool was used (Jin et al., 2015).  Counts output were than row concatted and saved as a tab-deliminated text file named "enumerated_counts.txt".
Assembly: BDGP6
Supplementary files format and content: tab-delimited text files describes enumerated expression per linrary in raw counts

value: Wild-type

value: acute DMSO (0.2%)


title: Soft3

source_name: Cells retrieved from 3D soft alginate hydrogels


title: Stiff1


title: Acute_DMSO_Rep7


title: Soft2


title: Matrigel3

source_name: Cells retrieved from 3D Matrigel


title: Acute_DMSO_Rep2


title: Matrigel2


title: Matrigel1


title: GES_EH4_miRasd1

city: Bristol

first: Ghadir

last: ElSamad

address: Whitson St.

country: United Kingdom

institute: University of Bristol

data_processing:
Original .fastq files were inspected using FastQC. As all samples passed initial QC no further trimming was applied
.fastq were aligned to the rat reference genome (Rn6) using RNA-STAR mapper
Reads were counted using featureCounts at a gene level
Differential expression analysis was performed using DEseq2
Assembly: Rn6
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: KD

growth_protocol: Male Sparague Dawley rats weighing 250–300 g (Envigo) were maintained under a 12:12 light-dark cycle at a constant temperature of 21-22°C and a relative humidity of 40%-50% with ad libitum access to food and water

extract_protocol:
SON samples were collected using a 1-mm micropunch (Fine Scientific Tools) from 100 um brain coronal sections in a cryostat. RNA from individual SONs was extracted with RNeasy Mini Kit (74106, Qiagen) according to manufacturer's instructions and eluted in a final volume of 30 ul.
Poly(A) enriched mRNA libraries were prepared and tested for quality by High Sensitivity D100 ScreenTape on Agilent 2100 Bioanalyzer. All libraries were uniquely indexed with specific adaptors ligated and normalised across to 2mM concentration. This allows libraries to be pooled and run together on the flow cell.

treatment_protocol: Rats were left to acclimitize for 1 week. miCtl and miRASD1 AAV virus were delivered  stereotaxically to the SON.

value: Hypothalamic supraoptic nucleus

value: Sprague Dawley

value: male

value: KD


title: GES_EH11_miRasd1


title: HBGsgRNA_oVK230

city: Memphis

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl

department: Department of Hematology

institute: St Jude Children's Research Hospital

description: sgRNA-sequencing

library_source: other

data_processing:
Paired-end reads were merged using FLASH with an expected fragment length of 100bp. Scaffold specific primer (3’-end) was trimmed using cutadapt (v4.1) and read with length than 20bp were removed. The percentage of target gRNA and full length product (target gRNA + scaffold sequence) were based on an exact string match. Merged reads were aligned to the expected full length product using bowtie2 to identify indels in the gRNA sequencing data.
Supplementary files format and content: csv

molecule: other

organism: synthetic construct

source_name: synthetic construct

extract_protocol:
Commercially synthesized sgRNA by Synthego
Pooled index library 2.2 nM (+10% Phix) was sequenced on MiSeq (Illumina) with a MiSeq v.2 micro kit using paired-end sequencing with 101-8-8-101 cycles.

value: synthetic construct


title: HBGsgRNA_oVK231 (Additional Primer)

description: sgRNA-sequencing


title: GES_EH2_miRasd1


title: GES_EH3_miRasd1


title: GES_EH12_miRasd1


title: GES_EH1_miRasd1


title: GES_EH12_miCtl

source_name: Control

value: Control


title: Veh2-1

value: mammary tumor

value: Fischer


title: GES_EH11_miCtl


title: GES_EH8_miCtl


title: GES_EH2_miCtl


title: GES_EH3_miCtl


title: GES_EH1_miCtl


title: Soft1


title: Tumor methylation  V8

type: genomic

city: Toronto

first: Vikas

last: Patil

state: Ontario

address: 610 University Ave.

country: Canada

institute: Princess Margaret Cancer Center

description: Tumor methylation

hyb_protocol: Samples were fragmented, amplified and hybridized to the Illumina Infinium MethylationEPIC BeadChip (850K) as per standard Illumina protocols.

scan_protocol: Infinium MethylationEPIC

data_processing:
Normalization and background correction of raw IDAT files was performed using ssNoob in the Bioconductor package minfi (version minfi_1.36.0). Beta values were calculated for each probe across all samples after post-processing.
Average Beta or normalized (provide the normalization method) Normalized Beta using preprocessNoob
Unmethylated and methylated signal intensities

label: Cy3 and Cy5

source_name: Meningioma

label_protocol: Infinium MethylationEPIC

growth_protocol: not applicable

extract_protocol: Genomic DNA was extracted from formalin-fixed paraffin-embedded or fresh-frozen tumor specimens and 250-500ng of bisulfite-treated DNA (EZ DNA Methylation Kit, Zymo, California, USA) per sample was used to obtain genome-wide DNA methylation profiles using the Infinium MethylationEPIC array

treatment_protocol: not applicable

tag: sample type

value: Tumor methylation


title: Tumor methylation  V7

description: Tumor methylation


title: GES_EH8_miRasd1


title: Dissected Caenorhabditis elegans germline 3

city: Clayton

first: Sandeep

middle: Deveson

last: Gopal

state: Vic

address: 15 Innovation Walk,

department: Department of Anatomy and Developmental Biology

country: Australia

institute: Monash University

data_processing:
Raw fastq files were analysed using the RNAsik pipeline (Tsyganovet al., 2018) using STAR aligner (Dobinet al., 2013) to theCaenorhabditis elegans reference genome WBcel235.Reads were quantified using featureCounts (Liao,et al., 2014) producing the raw genes count matrix and various quality control metrics.
Assembly: Caenorhabditis elegans  WBcel235
Supplementary files format and content: raw gene counts, text file, tab separated

source_name: Germline

extract_protocol:
mRNA was isolated using RNAeasy Micro Kit (Qiagen)
Illumina sequencing libraries were constructed using 2.5ng DNA and Clontech SMART-SeqÒ v4 Ultra Low Input RNA Kit.

value: Germline

value: N2 (wild-type)


title: Dissected Caenorhabditis elegans germline 1


title: Dissected Caenorhabditis elegans germline 2


title: Tumor methylation  V9

description: Tumor methylation


title: Tumor methylation  V6

description: Tumor methylation


title: Tumor methylation  V5

description: Tumor methylation


title: Tumor methylation  V14

description: Tumor methylation


title: Tumor methylation  V13

description: Tumor methylation


title: Tumor methylation  V1

description: Tumor methylation


title: Tumor methylation  V12

description: Tumor methylation


title: Tumor methylation  V4

description: Tumor methylation


title: Tumor methylation  VB9

description: Tumor methylation


title: Tumor methylation  VB8

description: Tumor methylation


title: Tumor methylation  V2

description: Tumor methylation


title: Tumor methylation  V3

description: Tumor methylation


title: GES_EH4_miCtl


title: Tumor methylation  V15

description: Tumor methylation


title: Tumor methylation  V11

description: Tumor methylation


title: Tumor methylation  VB43

description: Tumor methylation


title: Tumor methylation  VB47

description: Tumor methylation


title: Tumor methylation  VB4

description: Tumor methylation


title: Tumor methylation  VB40

description: Tumor methylation


title: Tumor methylation  VB45

description: Tumor methylation


title: Tumor methylation  VB44

description: Tumor methylation


title: Tumor methylation  VB46

description: Tumor methylation


title: Tumor methylation  VB37

description: Tumor methylation


title: Tumor methylation  VB7

description: Tumor methylation


title: Tumor methylation  VB34

description: Tumor methylation


title: Tumor methylation  VB42

description: Tumor methylation


title: Tumor methylation  VB35

description: Tumor methylation


title: Tumor methylation  VB39

description: Tumor methylation


title: Tumor methylation  VB30

description: Tumor methylation


title: Tumor methylation  VB38

description: Tumor methylation


title: Tumor methylation  VB5

description: Tumor methylation


title: Tumor methylation  VB36

description: Tumor methylation


title: Tumor methylation  V10

description: Tumor methylation


title: Tumor methylation  VB28

description: Tumor methylation


title: Tumor methylation  VB33

description: Tumor methylation


title: Tumor methylation  VB31

description: Tumor methylation


title: Tumor methylation  VB29

description: Tumor methylation


title: Tumor methylation  VB3

description: Tumor methylation


title: Tumor methylation  VB6

description: Tumor methylation


title: Tumor methylation  VB27

description: Tumor methylation


title: Tumor methylation  VB26

description: Tumor methylation


title: Tumor methylation  VB16

description: Tumor methylation


title: Tumor methylation  VB17

description: Tumor methylation


title: Tumor methylation  VB15

description: Tumor methylation


title: Tumor methylation  VB14

description: Tumor methylation


title: Tumor methylation  VB11

description: Tumor methylation


title: Tumor methylation  VB23

description: Tumor methylation


title: Tumor methylation  VB19

description: Tumor methylation


title: Tumor methylation  VB22

description: Tumor methylation


title: Tumor methylation  UHN259

description: Tumor methylation


title: Tumor methylation  VB12

description: Tumor methylation


title: Tumor methylation  VB24

description: Tumor methylation


title: Tumor methylation  VB25

description: Tumor methylation


title: Tumor methylation  VB32

description: Tumor methylation


title: Tumor methylation  VB10

description: Tumor methylation


title: Tumor methylation  VB20

description: Tumor methylation


title: Tumor methylation  VB13

description: Tumor methylation


title: Tumor methylation  UHN254

description: Tumor methylation


title: Tumor methylation  VB21

description: Tumor methylation


title: Tumor methylation  VB1

description: Tumor methylation


title: Tumor methylation  UHN252

description: Tumor methylation


title: Tumor methylation  VB2

description: Tumor methylation


title: Tumor methylation  VB18

description: Tumor methylation


title: Tumor methylation  UHN256

description: Tumor methylation


title: Tumor methylation  UHN253

description: Tumor methylation


title: Tumor methylation  UHN257

description: Tumor methylation


title: Tumor methylation  UHN251

description: Tumor methylation


title: Tumor methylation  UHN258

description: Tumor methylation


title: Tumor methylation  UHN249

description: Tumor methylation


title: Tumor methylation  UHN250

description: Tumor methylation


title: Tumor methylation  UHN248

description: Tumor methylation


title: Tumor methylation  UHN243

description: Tumor methylation


title: Tumor methylation  UHN246

description: Tumor methylation


title: Tumor methylation  UHN247

description: Tumor methylation


title: Tumor methylation  UHN245

description: Tumor methylation


title: Tumor methylation  UHN236

description: Tumor methylation


title: Tumor methylation  UHN255

description: Tumor methylation


title: Tumor methylation  UHN242

description: Tumor methylation


title: Tumor methylation  UHN244

description: Tumor methylation


title: Tumor methylation  UHN238

description: Tumor methylation


title: Tumor methylation  UHN237

description: Tumor methylation


title: Tumor methylation  UHN241

description: Tumor methylation


title: Tumor methylation  UHN231

description: Tumor methylation


title: Tumor methylation  UHN235

description: Tumor methylation


title: Tumor methylation  UHN234

description: Tumor methylation


title: Tumor methylation  UHN229

description: Tumor methylation


title: Tumor methylation  UHN227

description: Tumor methylation


title: Tumor methylation  UHN233

description: Tumor methylation


title: Tumor methylation  UHN228

description: Tumor methylation


title: Tumor methylation  UHN232

description: Tumor methylation


title: Tumor methylation  VB41

description: Tumor methylation


title: Tumor methylation  UHN230

description: Tumor methylation


title: Tumor methylation  UHN225

description: Tumor methylation


title: Tumor methylation  UHN222

description: Tumor methylation


title: Tumor methylation  UHN240

description: Tumor methylation


title: Tumor methylation  UHN218

description: Tumor methylation


title: Tumor methylation  UHN223

description: Tumor methylation


title: Tumor methylation  UHN219

description: Tumor methylation


title: Tumor methylation  UHN217

description: Tumor methylation


title: Tumor methylation  UHN239

description: Tumor methylation


title: Tumor methylation  UHN220

description: Tumor methylation


title: Tumor methylation  UHN224

description: Tumor methylation


title: Tumor methylation  UHN216

description: Tumor methylation


title: Tumor methylation  UHN214

description: Tumor methylation


title: Tumor methylation  UHN211

description: Tumor methylation


title: Tumor methylation  UHN213

description: Tumor methylation


title: Tumor methylation  UHN209

description: Tumor methylation


title: Tumor methylation  UHN208

description: Tumor methylation


title: Tumor methylation  UHN207

description: Tumor methylation


title: Tumor methylation  UHN226

description: Tumor methylation


title: Tumor methylation  UHN210

description: Tumor methylation


title: Tumor methylation  UHN206

description: Tumor methylation


title: Tumor methylation  UHN204

description: Tumor methylation


title: Tumor methylation  UHN200

description: Tumor methylation


title: Tumor methylation  UHN203

description: Tumor methylation


title: Tumor methylation  UHN199

description: Tumor methylation


title: Tumor methylation  UHN201

description: Tumor methylation


title: Tumor methylation  UHN198

description: Tumor methylation


title: Tumor methylation  UHN197

description: Tumor methylation


title: Tumor methylation  UHN195

description: Tumor methylation


title: Tumor methylation  UHN196

description: Tumor methylation


title: Tumor methylation  UHN215

description: Tumor methylation


title: Tumor methylation  UHN192

description: Tumor methylation


title: Tumor methylation  UHN191

description: Tumor methylation


title: Tumor methylation  UHN189

description: Tumor methylation


title: Tumor methylation  UHN194

description: Tumor methylation


title: Tumor methylation  UHN188

description: Tumor methylation


title: Tumor methylation  UHN186

description: Tumor methylation


title: Tumor methylation  UHN187

description: Tumor methylation


title: Tumor methylation  UHN184

description: Tumor methylation


title: Tumor methylation  UHN185

description: Tumor methylation


title: Tumor methylation  UHN178

description: Tumor methylation


title: Tumor methylation  UHN183

description: Tumor methylation


title: Tumor methylation  UHN176

description: Tumor methylation


title: Tumor methylation  UHN202

description: Tumor methylation


title: Tumor methylation  UHN180

description: Tumor methylation


title: Tumor methylation  UHN181

description: Tumor methylation


title: Tumor methylation  UHN182

description: Tumor methylation


title: Tumor methylation  UHN177

description: Tumor methylation


title: Tumor methylation  UHN175

description: Tumor methylation


title: Tumor methylation  UHN179

description: Tumor methylation


title: Tumor methylation  UHN174

description: Tumor methylation


title: Tumor methylation  UHN172

description: Tumor methylation


title: Tumor methylation  UHN221

description: Tumor methylation


title: Tumor methylation  UHN193

description: Tumor methylation


title: Tumor methylation  UHN190

description: Tumor methylation


title: Tumor methylation  UHN212

description: Tumor methylation


title: Tumor methylation  UHN171

description: Tumor methylation


title: Tumor methylation  UHN169

description: Tumor methylation


title: Tumor methylation  UHN168

description: Tumor methylation


title: Tumor methylation  UHN163

description: Tumor methylation


title: Tumor methylation  UHN161

description: Tumor methylation


title: Tumor methylation  UHN164

description: Tumor methylation


title: Tumor methylation  UHN160

description: Tumor methylation


title: Tumor methylation  TB9

description: Tumor methylation


title: Tumor methylation  UHN167

description: Tumor methylation


title: Tumor methylation  TB68

description: Tumor methylation


title: Tumor methylation  TB67

description: Tumor methylation


title: Tumor methylation  UHN173

description: Tumor methylation


title: Tumor methylation  UHN205

description: Tumor methylation


title: Tumor methylation  TB63

description: Tumor methylation


title: Tumor methylation  TB66

description: Tumor methylation


title: Tumor methylation  TB61

description: Tumor methylation


title: Tumor methylation  TB65

description: Tumor methylation


title: Tumor methylation  TB59

description: Tumor methylation


title: Tumor methylation  TB62

description: Tumor methylation


title: Tumor methylation  TB57

description: Tumor methylation


title: Tumor methylation  TB60

description: Tumor methylation


title: Tumor methylation  TB56

description: Tumor methylation


title: Tumor methylation  TB52

description: Tumor methylation


title: Tumor methylation  TB54

description: Tumor methylation


title: Tumor methylation  UHN170

description: Tumor methylation


title: Tumor methylation  TB49

description: Tumor methylation


title: Tumor methylation  TB58

description: Tumor methylation


title: Tumor methylation  TB45

description: Tumor methylation


title: Tumor methylation  TB47

description: Tumor methylation


title: Tumor methylation  TB44

description: Tumor methylation


title: Tumor methylation  TB37

description: Tumor methylation


title: Tumor methylation  TB17

description: Tumor methylation


title: Tumor methylation  TB12

description: Tumor methylation


title: Tumor methylation  TB32

description: Tumor methylation


title: Tumor methylation  TB19

description: Tumor methylation


title: Tumor methylation  TB100

description: Tumor methylation


title: Tumor methylation  TB97

description: Tumor methylation


title: Tumor methylation  TB98

description: Tumor methylation


title: Tumor methylation  TB95

description: Tumor methylation


title: Tumor methylation  TB93

description: Tumor methylation


title: Tumor methylation  TB92

description: Tumor methylation


title: Tumor methylation  TB53

description: Tumor methylation


title: Tumor methylation  TB90

description: Tumor methylation


title: Tumor methylation  TB91

description: Tumor methylation


title: Tumor methylation  TB96

description: Tumor methylation


title: Tumor methylation  TB85

description: Tumor methylation


title: Tumor methylation  TB89

description: Tumor methylation


title: Tumor methylation  TB87

description: Tumor methylation


title: Tumor methylation  TB83

description: Tumor methylation


title: Tumor methylation  TB80

description: Tumor methylation


title: Tumor methylation  TB82

description: Tumor methylation


title: Tumor methylation  TB81

description: Tumor methylation


title: Tumor methylation  TB86

description: Tumor methylation


title: Tumor methylation  TB8

description: Tumor methylation


title: Tumor methylation  TB77

description: Tumor methylation


title: Tumor methylation  TB78

description: Tumor methylation


title: Tumor methylation  TB79

description: Tumor methylation


title: Tumor methylation  TB99

description: Tumor methylation


title: Tumor methylation  TB75

description: Tumor methylation


title: Tumor methylation  TB71

description: Tumor methylation


title: Tumor methylation  TB76

description: Tumor methylation


title: Tumor methylation  TB69

description: Tumor methylation


title: Tumor methylation  TB64

description: Tumor methylation


title: Tumor methylation  TB94

description: Tumor methylation


title: Tumor methylation  TB55

description: Tumor methylation


title: Tumor methylation  TB50

description: Tumor methylation


title: Tumor methylation  TB51

description: Tumor methylation


title: Tumor methylation  TB46

description: Tumor methylation


title: Tumor methylation  TB84

description: Tumor methylation


title: Tumor methylation  TB41

description: Tumor methylation


title: Tumor methylation  TB42

description: Tumor methylation


title: Tumor methylation  TB48

description: Tumor methylation


title: Tumor methylation  TB43

description: Tumor methylation


title: Tumor methylation  TB4

description: Tumor methylation


title: Tumor methylation  TB40

description: Tumor methylation


title: Tumor methylation  TB39

description: Tumor methylation


title: Tumor methylation  TB38

description: Tumor methylation


title: Tumor methylation  TB31

description: Tumor methylation


title: Tumor methylation  TB3

description: Tumor methylation


title: Tumor methylation  TB28

description: Tumor methylation


title: Tumor methylation  TB36

description: Tumor methylation


title: Tumor methylation  TB27

description: Tumor methylation


title: Tumor methylation  TB34

description: Tumor methylation


title: Tumor methylation  TB26

description: Tumor methylation


title: Tumor methylation  TB24

description: Tumor methylation


title: Tumor methylation  TB25

description: Tumor methylation


title: Tumor methylation  TB22

description: Tumor methylation


title: Tumor methylation  TB21

description: Tumor methylation


title: Tumor methylation  TB102

description: Tumor methylation


title: Tumor methylation  TB104

description: Tumor methylation


title: Tumor methylation  TB103

description: Tumor methylation


title: Tumor methylation  TB14

description: Tumor methylation


title: Tumor methylation  TB2

description: Tumor methylation


title: Tumor methylation  TB105

description: Tumor methylation


title: Tumor methylation  TB15

description: Tumor methylation


title: Tumor methylation  TB101

description: Tumor methylation


title: Tumor methylation  TB10

description: Tumor methylation


title: Tumor methylation  TB1

description: Tumor methylation


title: Tumor methylation  FH177

description: Tumor methylation


title: Tumor methylation  FH176

description: Tumor methylation


title: Tumor methylation  FH173

description: Tumor methylation


title: Tumor methylation  FH172

description: Tumor methylation


title: Tumor methylation  FH174

description: Tumor methylation


title: Tumor methylation  FH170

description: Tumor methylation


title: Tumor methylation  FH175

description: Tumor methylation


title: Tumor methylation  FH167

description: Tumor methylation


title: Tumor methylation  FH169

description: Tumor methylation


title: Tumor methylation  FH171

description: Tumor methylation


title: Tumor methylation  FH165

description: Tumor methylation


title: Tumor methylation  FH164

description: Tumor methylation


title: Tumor methylation  FH162

description: Tumor methylation


title: Tumor methylation  FH161

description: Tumor methylation


title: Tumor methylation  FH163

description: Tumor methylation


title: Tumor methylation  FH166

description: Tumor methylation


title: Tumor methylation  FH157

description: Tumor methylation


title: Tumor methylation  FH158

description: Tumor methylation


title: Tumor methylation  FH159

description: Tumor methylation


title: Tumor methylation  FH155

description: Tumor methylation


title: Tumor methylation  FH151

description: Tumor methylation


title: Tumor methylation  FH152

description: Tumor methylation


title: Tumor methylation  FH149

description: Tumor methylation


title: Tumor methylation  FH150

description: Tumor methylation


title: Tumor methylation  FH154

description: Tumor methylation


title: Tumor methylation  FH146

description: Tumor methylation


title: Tumor methylation  FH147

description: Tumor methylation


title: Tumor methylation  FH143

description: Tumor methylation


title: Tumor methylation  FH142

description: Tumor methylation


title: Tumor methylation  FH145

description: Tumor methylation


title: Tumor methylation  FH141

description: Tumor methylation


title: Tumor methylation  FH140

description: Tumor methylation


title: Tumor methylation  FH137

description: Tumor methylation


title: Tumor methylation  FH135

description: Tumor methylation


title: Tumor methylation  FH132

description: Tumor methylation


title: Tumor methylation  FH160

description: Tumor methylation


title: Tumor methylation  FH138

description: Tumor methylation


title: Tumor methylation  FH133

description: Tumor methylation


title: Tumor methylation  FH131

description: Tumor methylation


title: Tumor methylation  FH139

description: Tumor methylation


title: Tumor methylation  FH134

description: Tumor methylation


title: Tumor methylation  FH153

description: Tumor methylation


title: Tumor methylation  FH130

description: Tumor methylation


title: Tumor methylation  FH156

description: Tumor methylation


title: Tumor methylation  FH129

description: Tumor methylation


title: Tumor methylation  FH128

description: Tumor methylation


title: Tumor methylation  FH127

description: Tumor methylation


title: Tumor methylation  FH148

description: Tumor methylation


title: Tumor methylation  FH125

description: Tumor methylation


title: Tumor methylation  FH124

description: Tumor methylation


title: Tumor methylation  FH144

description: Tumor methylation


title: Tumor methylation  FH123

description: Tumor methylation


title: Tumor methylation  FH121

description: Tumor methylation


title: Tumor methylation  FH122

description: Tumor methylation


title: Tumor methylation  FH120

description: Tumor methylation


title: Tumor methylation  FH118

description: Tumor methylation


title: Tumor methylation  FH117

description: Tumor methylation


title: Tumor methylation  FH116

description: Tumor methylation


title: Tumor methylation  FH115

description: Tumor methylation


title: Tumor methylation  FH114

description: Tumor methylation


title: Tumor methylation  FH113

description: Tumor methylation


title: Tumor methylation  FH112

description: Tumor methylation


title: Tumor methylation  FH108

description: Tumor methylation


title: Tumor methylation  FH107

description: Tumor methylation


title: Tumor methylation  FH110

description: Tumor methylation


title: Tumor methylation  FH106

description: Tumor methylation


title: Tumor methylation  FH109

description: Tumor methylation


title: Tumor methylation  FH105

description: Tumor methylation


title: Tumor methylation  FH126

description: Tumor methylation


title: Tumor methylation  FH103

description: Tumor methylation


title: Tumor methylation  FH98

description: Tumor methylation


title: Tumor methylation  FH102

description: Tumor methylation


title: Tumor methylation  FH97

description: Tumor methylation


title: Tumor methylation  FH101

description: Tumor methylation


title: Tumor methylation  FH100

description: Tumor methylation


title: Tumor methylation  FH99

description: Tumor methylation


title: Tumor methylation  FH94

description: Tumor methylation


title: Tumor methylation  FH92

description: Tumor methylation


title: Tumor methylation  FH91

description: Tumor methylation


title: Tumor methylation  FH119

description: Tumor methylation


title: Tumor methylation  FH93

description: Tumor methylation


title: Tumor methylation  FH90

description: Tumor methylation


title: Tumor methylation  FH86

description: Tumor methylation


title: Tumor methylation  FH85

description: Tumor methylation


title: Tumor methylation  FH84

description: Tumor methylation


title: Tumor methylation  FH87

description: Tumor methylation


title: Tumor methylation  FH88

description: Tumor methylation


title: Tumor methylation  FH82

description: Tumor methylation


title: Tumor methylation  FH111

description: Tumor methylation


title: Tumor methylation  FH81

description: Tumor methylation


title: Tumor methylation  FH80

description: Tumor methylation


title: Tumor methylation  FH77

description: Tumor methylation


title: Tumor methylation  FH79

description: Tumor methylation


title: Tumor methylation  FH74

description: Tumor methylation


title: Tumor methylation  FH73

description: Tumor methylation


title: Tumor methylation  FH95

description: Tumor methylation


title: Tumor methylation  FH72

description: Tumor methylation


title: Tumor methylation  FH71

description: Tumor methylation


title: Tumor methylation  FH70

description: Tumor methylation


title: Tumor methylation  FH69

description: Tumor methylation


title: Tumor methylation  FH67

description: Tumor methylation


title: Tumor methylation  FH64

description: Tumor methylation


title: Tumor methylation  FH68

description: Tumor methylation


title: Tumor methylation  FH61

description: Tumor methylation


title: Tumor methylation  FH62

description: Tumor methylation


title: Tumor methylation  FH63

description: Tumor methylation


title: Tumor methylation  FH55

description: Tumor methylation


title: Tumor methylation  FH54

description: Tumor methylation


title: Tumor methylation  FH56

description: Tumor methylation


title: Tumor methylation  FH59

description: Tumor methylation


title: Tumor methylation  FH57

description: Tumor methylation


title: Tumor methylation  FH52

description: Tumor methylation


title: Tumor methylation  FH76

description: Tumor methylation


title: Tumor methylation  FH53

description: Tumor methylation


title: Tumor methylation  FH49

description: Tumor methylation


title: Tumor methylation  FH47

description: Tumor methylation


title: Tumor methylation  FH51

description: Tumor methylation


title: Tumor methylation  FH45

description: Tumor methylation


title: Tumor methylation  FH65

description: Tumor methylation


title: Tumor methylation  FH66

description: Tumor methylation


title: Tumor methylation  FH43

description: Tumor methylation


title: Tumor methylation  FH44

description: Tumor methylation


title: Tumor methylation  FH60

description: Tumor methylation


title: Tumor methylation  FH58

description: Tumor methylation


title: Tumor methylation  FH39

description: Tumor methylation


title: Tumor methylation  FH40

description: Tumor methylation


title: Tumor methylation  FH36

description: Tumor methylation


title: Tumor methylation  FH41

description: Tumor methylation


title: Tumor methylation  FH34

description: Tumor methylation


title: Tumor methylation  FH37

description: Tumor methylation


title: Tumor methylation  FH38

description: Tumor methylation


title: Tumor methylation  FH30

description: Tumor methylation


title: Tumor methylation  FH33

description: Tumor methylation


title: Tumor methylation  FH31

description: Tumor methylation


title: Tumor methylation  FH104

description: Tumor methylation


title: Tumor methylation  FH29

description: Tumor methylation


title: Tumor methylation  FH27

description: Tumor methylation


title: Tumor methylation  FH32

description: Tumor methylation


title: Tumor methylation  FH35

description: Tumor methylation


title: Tumor methylation  FH50

description: Tumor methylation


title: Tumor methylation  FH48

description: Tumor methylation


title: Tumor methylation  FH28

description: Tumor methylation


title: Tumor methylation  FH22

description: Tumor methylation


title: Tumor methylation  FH24

description: Tumor methylation


title: Tumor methylation  FH46

description: Tumor methylation


title: Tumor methylation  FH25

description: Tumor methylation


title: Tumor methylation  FH23

description: Tumor methylation


title: Tumor methylation  FH20

description: Tumor methylation


title: Tumor methylation  FH21

description: Tumor methylation


title: Tumor methylation  FH17

description: Tumor methylation


title: Tumor methylation  FH19

description: Tumor methylation


title: Tumor methylation  FH18

description: Tumor methylation


title: Tumor methylation  FH15

description: Tumor methylation


title: Tumor methylation  FH13

description: Tumor methylation


title: Tumor methylation  FH14

description: Tumor methylation


title: Tumor methylation  FH26

description: Tumor methylation


title: Tumor methylation  FH11

description: Tumor methylation


title: Tumor methylation  FH9

description: Tumor methylation


title: Tumor methylation  FH12

description: Tumor methylation


title: Tumor methylation  FH7

description: Tumor methylation


title: Tumor methylation  FH16

description: Tumor methylation


title: Tumor methylation  FH5

description: Tumor methylation


title: Tumor methylation  FH3

description: Tumor methylation


title: Tumor methylation  FH8

description: Tumor methylation


title: Tumor methylation  FH89

description: Tumor methylation


title: Tumor methylation  FH96

description: Tumor methylation


title: Tumor methylation  FH2

description: Tumor methylation


title: Tumor methylation  FH78

description: Tumor methylation


title: Tumor methylation  FH168

description: Tumor methylation


title: Tumor methylation  FH83

description: Tumor methylation


title: Tumor methylation  FH42

description: Tumor methylation


title: Tumor methylation  FH75

description: Tumor methylation


title: Tumor methylation  FH6

description: Tumor methylation


title: Tumor methylation  UHN158

description: Tumor methylation


title: Tumor methylation  UHN159

description: Tumor methylation


title: Tumor methylation  UHN157

description: Tumor methylation


title: Tumor methylation  FH10

description: Tumor methylation


title: Tumor methylation  UHN153

description: Tumor methylation


title: Tumor methylation  FH136

description: Tumor methylation


title: Tumor methylation  UHN156

description: Tumor methylation


title: Tumor methylation  FH4

description: Tumor methylation


title: Tumor methylation  UHN151

description: Tumor methylation


title: Tumor methylation  FH1

description: Tumor methylation


title: Tumor methylation  UHN141

description: Tumor methylation


title: Tumor methylation  UHN155

description: Tumor methylation


title: Tumor methylation  UHN146

description: Tumor methylation


title: Tumor methylation  UHN143

description: Tumor methylation


title: Tumor methylation  UHN144

description: Tumor methylation


title: Tumor methylation  UHN137

description: Tumor methylation


title: Tumor methylation  UHN136

description: Tumor methylation


title: Tumor methylation  UHN134

description: Tumor methylation


title: Tumor methylation  UHN135

description: Tumor methylation


title: Tumor methylation  UHN133

description: Tumor methylation


title: Tumor methylation  UHN150

description: Tumor methylation


title: Tumor methylation  UHN129

description: Tumor methylation


title: Tumor methylation  UHN128

description: Tumor methylation


title: Tumor methylation  UHN130

description: Tumor methylation


title: Tumor methylation  UHN132

description: Tumor methylation


title: Tumor methylation  UHN124

description: Tumor methylation


title: Tumor methylation  UHN123

description: Tumor methylation


title: Tumor methylation  UHN131

description: Tumor methylation


title: Tumor methylation  UHN120

description: Tumor methylation


title: Tumor methylation  UHN118

description: Tumor methylation


title: Tumor methylation  UHN121

description: Tumor methylation


title: Tumor methylation  UHN119

description: Tumor methylation


title: Tumor methylation  UHN117

description: Tumor methylation


title: Tumor methylation  UHN116

description: Tumor methylation


title: Tumor methylation  UHN114

description: Tumor methylation


title: Tumor methylation  UHN112

description: Tumor methylation


title: Tumor methylation  UHN115

description: Tumor methylation


title: Tumor methylation  UHN113

description: Tumor methylation


title: Tumor methylation  UHN101

description: Tumor methylation


title: Tumor methylation  UHN106

description: Tumor methylation


title: Tumor methylation  UHN103

description: Tumor methylation


title: Tumor methylation  UHN110

description: Tumor methylation


title: Tumor methylation  UHN108

description: Tumor methylation


title: Tumor methylation  UHN100

description: Tumor methylation


title: Tumor methylation  UHN99

description: Tumor methylation


title: Tumor methylation  UHN107

description: Tumor methylation


title: Tumor methylation  UHN96

description: Tumor methylation


title: Tumor methylation  UHN92

description: Tumor methylation


title: Tumor methylation  UHN98

description: Tumor methylation


title: Tumor methylation  UHN93

description: Tumor methylation


title: Tumor methylation  UHN89

description: Tumor methylation


title: Tumor methylation  UHN127

description: Tumor methylation


title: Tumor methylation  UHN87

description: Tumor methylation


title: Tumor methylation  UHN125

description: Tumor methylation


title: Tumor methylation  UHN94

description: Tumor methylation


title: Tumor methylation  UHN88

description: Tumor methylation


title: Tumor methylation  UHN85

description: Tumor methylation


title: Tumor methylation  UHN82

description: Tumor methylation


title: Tumor methylation  UHN86

description: Tumor methylation


title: Tumor methylation  UHN84

description: Tumor methylation


title: Tumor methylation  UHN83

description: Tumor methylation


title: Tumor methylation  UHN79

description: Tumor methylation


title: Tumor methylation  UHN81

description: Tumor methylation


title: Tumor methylation  UHN77

description: Tumor methylation


title: Tumor methylation  UHN69

description: Tumor methylation


title: Tumor methylation  UHN74

description: Tumor methylation


title: Tumor methylation  UHN71

description: Tumor methylation


title: Tumor methylation  UHN68

description: Tumor methylation


title: Tumor methylation  UHN70

description: Tumor methylation


title: Tumor methylation  UHN72

description: Tumor methylation


title: Tumor methylation  UHN67

description: Tumor methylation


title: Tumor methylation  UHN60

description: Tumor methylation


title: Tumor methylation  UHN61

description: Tumor methylation


title: Tumor methylation  UHN65

description: Tumor methylation


title: Tumor methylation  UHN55

description: Tumor methylation


title: Tumor methylation  UHN58

description: Tumor methylation


title: Tumor methylation  UHN76

description: Tumor methylation


title: Tumor methylation  UHN53

description: Tumor methylation


title: Tumor methylation  UHN52

description: Tumor methylation


title: Tumor methylation  UHN51

description: Tumor methylation


title: Tumor methylation  UHN49

description: Tumor methylation


title: Tumor methylation  UHN59

description: Tumor methylation


title: Tumor methylation  UHN66

description: Tumor methylation


title: Tumor methylation  UHN47

description: Tumor methylation


title: Tumor methylation  UHN50

description: Tumor methylation


title: Tumor methylation  UHN73

description: Tumor methylation


title: Tumor methylation  UHN75

description: Tumor methylation


title: Tumor methylation  UHN54

description: Tumor methylation


title: Tumor methylation  UHN46

description: Tumor methylation


title: Tumor methylation  UHN44

description: Tumor methylation


title: Tumor methylation  UHN41

description: Tumor methylation


title: Tumor methylation  UHN38

description: Tumor methylation


title: Tumor methylation  UHN42

description: Tumor methylation


title: Tumor methylation  UHN37

description: Tumor methylation


title: Tumor methylation  UHN39

description: Tumor methylation


title: Tumor methylation  UHN35

description: Tumor methylation


title: Tumor methylation  UHN33

description: Tumor methylation


title: Tumor methylation  UHN56

description: Tumor methylation


title: Tumor methylation  UHN31

description: Tumor methylation


title: Tumor methylation  UHN34

description: Tumor methylation


title: Tumor methylation  UHN30

description: Tumor methylation


title: Tumor methylation  UHN29

description: Tumor methylation


title: Tumor methylation  UHN28

description: Tumor methylation


title: Tumor methylation  UHN26

description: Tumor methylation


title: Tumor methylation  UHN45

description: Tumor methylation


title: Tumor methylation  UHN23

description: Tumor methylation


title: Tumor methylation  UHN24

description: Tumor methylation


title: Tumor methylation  UHN22

description: Tumor methylation


title: Tumor methylation  UHN20

description: Tumor methylation


title: Tumor methylation  UHN25

description: Tumor methylation


title: Tumor methylation  UHN21

description: Tumor methylation


title: Tumor methylation  UHN19

description: Tumor methylation


title: Tumor methylation  UHN13

description: Tumor methylation


title: Tumor methylation  UHN14

description: Tumor methylation


title: Tumor methylation  UHN40

description: Tumor methylation


title: Tumor methylation  UHN11

description: Tumor methylation


title: Tumor methylation  UHN32

description: Tumor methylation


title: Tumor methylation  UHN17

description: Tumor methylation


title: Tumor methylation  UHN4

description: Tumor methylation


title: Tumor methylation  UHN6

description: Tumor methylation


title: Tumor methylation  UHN8

description: Tumor methylation


title: Tumor methylation  UHN5

description: Tumor methylation


title: Tumor methylation  UHN9

description: Tumor methylation


title: Tumor methylation  UHN7

description: Tumor methylation


title: Tumor methylation  UHN3

description: Tumor methylation


title: Tumor methylation  UHN2

description: Tumor methylation


title: Tumor methylation  UHN90

description: Tumor methylation


title: Tumor methylation  UHN154

description: Tumor methylation


title: Tumor methylation  UHN152

description: Tumor methylation


title: Tumor methylation  UHN12

description: Tumor methylation


title: Tumor methylation  UHN16

description: Tumor methylation


title: Tumor methylation  UHN149

description: Tumor methylation


title: Tumor methylation  UHN148

description: Tumor methylation


title: Tumor methylation  UHN142

description: Tumor methylation


title: Tumor methylation  UHN91

description: Tumor methylation


title: Tumor methylation  UHN147

description: Tumor methylation


title: Tumor methylation  UHN145

description: Tumor methylation


title: Tumor methylation  UHN140

description: Tumor methylation


title: Tumor methylation  UHN138

description: Tumor methylation


title: Tumor methylation  UHN122

description: Tumor methylation


title: Tumor methylation  UHN105

description: Tumor methylation


title: Tumor methylation  UHN139

description: Tumor methylation


title: Tumor methylation  UHN109

description: Tumor methylation


title: Tumor methylation  UHN102

description: Tumor methylation


title: Tumor methylation  UHN97

description: Tumor methylation


title: Tumor methylation  UHN104

description: Tumor methylation


title: Tumor methylation  UHN95

description: Tumor methylation


title: Tumor methylation  UHN80

description: Tumor methylation


title: Tumor methylation  UHN78

description: Tumor methylation


title: Tumor methylation  UHN64

description: Tumor methylation


title: Tumor methylation  UHN63

description: Tumor methylation


title: Tumor methylation  UHN57

description: Tumor methylation


title: Tumor methylation  UHN36

description: Tumor methylation


title: Tumor methylation  UHN27

description: Tumor methylation


title: Tumor methylation  UHN43

description: Tumor methylation


title: Tumor methylation  UHN48

description: Tumor methylation


title: Tumor methylation  UHN18

description: Tumor methylation


title: Tumor methylation  UHN10

description: Tumor methylation


title: Tumor methylation  UHN1

description: Tumor methylation


title: Tumor methylation  NW41

description: Tumor methylation


title: Tumor methylation  NW40

description: Tumor methylation


title: Tumor methylation  NW39

description: Tumor methylation


title: Tumor methylation  NW36

description: Tumor methylation


title: Tumor methylation  NW37

description: Tumor methylation


title: Tumor methylation  NW35

description: Tumor methylation


title: Tumor methylation  NW33

description: Tumor methylation


title: Tumor methylation  NW38

description: Tumor methylation


title: Tumor methylation  NW34

description: Tumor methylation


title: Tumor methylation  NW30

description: Tumor methylation


title: Tumor methylation  NW32

description: Tumor methylation


title: Tumor methylation  NW31

description: Tumor methylation


title: Tumor methylation  NW29

description: Tumor methylation


title: Tumor methylation  NW26

description: Tumor methylation


title: Tumor methylation  NW28

description: Tumor methylation


title: Tumor methylation  NW21

description: Tumor methylation


title: Tumor methylation  NW27

description: Tumor methylation


title: Tumor methylation  UHN15

description: Tumor methylation


title: Tumor methylation  NW22

description: Tumor methylation


title: Tumor methylation  NW25

description: Tumor methylation


title: Tumor methylation  NW20

description: Tumor methylation


title: Tumor methylation  NW18

description: Tumor methylation


title: Tumor methylation  NW19

description: Tumor methylation


title: Tumor methylation  NW17

description: Tumor methylation


title: Tumor methylation  NW12

description: Tumor methylation


title: Tumor methylation  NW16

description: Tumor methylation


title: Tumor methylation  NW14

description: Tumor methylation


title: Tumor methylation  NW10

description: Tumor methylation


title: Tumor methylation  NW15

description: Tumor methylation


title: Tumor methylation  NW13

description: Tumor methylation


title: Tumor methylation  NW9

description: Tumor methylation


title: Tumor methylation  NW11

description: Tumor methylation


title: Tumor methylation  NW7

description: Tumor methylation


title: Tumor methylation  NW6

description: Tumor methylation


title: Tumor methylation  NW8

description: Tumor methylation


title: Tumor methylation  NW5

description: Tumor methylation


title: Tumor methylation  NW4

description: Tumor methylation


title: Tumor methylation  NW23

description: Tumor methylation


title: Tumor methylation  NW24

description: Tumor methylation


title: Tumor methylation  CW59

description: Tumor methylation


title: Tumor methylation  CW57

description: Tumor methylation


title: Tumor methylation  NW1

description: Tumor methylation


title: Tumor methylation  NW2

description: Tumor methylation


title: Tumor methylation  CW50

description: Tumor methylation


title: Tumor methylation  CW51

description: Tumor methylation


title: Tumor methylation  CW53

description: Tumor methylation


title: Tumor methylation  CW48

description: Tumor methylation


title: Tumor methylation  CW49

description: Tumor methylation


title: Tumor methylation  CW46

description: Tumor methylation


title: Tumor methylation  CW47

description: Tumor methylation


title: Tumor methylation  CW44

description: Tumor methylation


title: Tumor methylation  CW43

description: Tumor methylation


title: Tumor methylation  CW42

description: Tumor methylation


title: Tumor methylation  CW41

description: Tumor methylation


title: Tumor methylation  CW39

description: Tumor methylation


title: Tumor methylation  CW40

description: Tumor methylation


title: Tumor methylation  CW36

description: Tumor methylation


title: Tumor methylation  CW37

description: Tumor methylation


title: Tumor methylation  NW3

description: Tumor methylation


title: Tumor methylation  CW35

description: Tumor methylation


title: Tumor methylation  CW54

description: Tumor methylation


title: Tumor methylation  CW33

description: Tumor methylation


title: Tumor methylation  CW32

description: Tumor methylation


title: Tumor methylation  CW27

description: Tumor methylation


title: Tumor methylation  CW28

description: Tumor methylation


title: Tumor methylation  CW31

description: Tumor methylation


title: Tumor methylation  CW30

description: Tumor methylation


title: Tumor methylation  CW26

description: Tumor methylation


title: Tumor methylation  CW25

description: Tumor methylation


title: Tumor methylation  CW23

description: Tumor methylation


title: Tumor methylation  CW22

description: Tumor methylation


title: Tumor methylation  CW19

description: Tumor methylation


title: Tumor methylation  CW45

description: Tumor methylation


title: Tumor methylation  CW21

description: Tumor methylation


title: Tumor methylation  CW24

description: Tumor methylation


title: Tumor methylation  CW17

description: Tumor methylation


title: Tumor methylation  CW38

description: Tumor methylation


title: Tumor methylation  CW16

description: Tumor methylation


title: Tumor methylation  CW14

description: Tumor methylation


title: Tumor methylation  CW15

description: Tumor methylation


title: Tumor methylation  CW34

description: Tumor methylation


title: Tumor methylation  CW11

description: Tumor methylation