title: Sox9iresGFP XY pups genomic landscape

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

institute: Francis Crick Institute

description:
Library name: YFPpos_ATAC_XY
10X Genomics

library_source: genomic single cell

data_processing:
All subsequent analyses were performed in R v.4.4.1 using the Seurat (v5) package.
Assembly: mm10
Supplementary files format and content: tab-delimited text containing output files from CellRanger ARC version 2.0.0

source_name: Pituitary

extract_protocol:
Ilumina 10X genomics nuclei extraction protocol
Ilumina 10X genomics expression and atac protocol

value: Pituitary

value: female

value: Stem cell

tag: library type

value: ATAC


title: Sox9iresGFP XX pups genomic landscape

status: Public on Mar 16 2026

type: SRA

country: United Kingdom

description:
Library name: YFPpos_ATAC_XX
10X Genomics

molecule: genomic DNA

organism: Mus musculus

tag: tissue

tag: Sex

value: male

tag: cell type

tag: genotype


title: Brain Organoid, MTK, Day 60, RNAseq, biol rep 2

city: Shanghai City

first: Yali

last: Li

address: No.320, Yueyang Avenue

country: China

institute: Center for Excellence in Molecular Cell Science

description:
D60_RNAseq_matrix.tsv
D60_MTK_RNAseq_2

library_source: transcriptomic

data_processing:
discarding low-quality reads
trimming adapter sequence
removing ribosomal RNA(rRNA)
non-rRNA sequencing reads were aligned to human genomic reference (hg38) using HISAT2
Assembly: GRCh38
Supplementary files format and content: matrix files

molecule: total RNA

organism: Homo sapiens

extract_protocol:
For RNA-seq, total mRNA was extracted from D60 organoids treated with DMSO, MTK or DEAB by using the RNeasy Mini kit. For Ribo-seq, cellular RNA were extracted by mild lysis buffer and Lysates oforganoids were treated with 750 U RNase I for 45 minutes at room temperature. Samples were then transferred to an ultracentrifuge tube on a sucrose cushion (~34%) and centrifuged at 70,000 rpm at 4C for 4 hr.
RNA libraries for bulk RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols. For riboseq, Ribosome-protected fragments were purified using miRNeasy RNA isolation kit (QIAGEN, cat. No. 217004). RNA was size selected by running a polyacrylamide gel, and then dephosphorylated, linker ligated, and then subjected to RT-PCR, circularization, rRNA depletion, and 10-12 cycles of PCR. The enzymes used were T4 PNK (NEB, cat. No. M0201S), T4 RNA ligase 2, truncated (NEB, cat. No. M0242S), Universal miRNA Cloning Linker (NEB, cat. No. S1315S), Superscript III (Invitrogen, cat. No 18080-044), Circ Ligase (Epicentre, cat. No. CL4111K), NEBNext® High-Fidelity 2X PCR Master Mix (cat. No. M0541L). Resulting fragments were size selected from an 8% acrylamide non-denaturing gel and purified by incubation overnight with DNA gel extraction buffer (300 mM NaCl, 10 mM Tris (pH 8) and 1 mM EDTA).

treatment_protocol: The medium with the addition of DMSO or 18.5 μM MTK or 10 μM DEAB was refreshed every day from day 20 to day 60.

tag: cell line

value: Human embryonic stem cells

value: WT

tag: treatment

value: cerebral differentiation with MTK treatment

tag: time

value: Day 60


title: Photoreceptor Nuclei, w1118 control, Zeitgeber Time 8, Replicate 2

city: West Lafayette

first: Seth

last: Lammert

state: IN

address: 175 South University Street

department: Biochemistry

country: USA

institute: Purdue University

data_processing:
Adaptors trimmed using Trimmomatic. Removed leading 5 bases from forward reads as per Ovation® SoLo® RNA-Seq library preparation kit specifications
Alignment using HISAT2
SAM file processing using SAMtools
BigWigs generated using deepTools, CPM-normalized
Assembly: BDGP6.46 (GCA_000001215.4)
Supplementary files format and content: CPM-normalized BigWigs

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: Outer photoreceptors

growth_protocol: Drosophila were maintained in population cages in a 25°C incubator with a 12:12 hour light:dark cycle.

extract_protocol:
100 male flies in triplicate were collected at 10 days post eclosion and at the indicated Zeitgeber times (ZT0, ZT4, ZT8, ZT12, ZT16, ZT20). GFP-positive photoreceptor nuclei were immunoprecipitated using the nuclei immunoenrichment protocol (dx.doi.org/10.17504/protocols.io.buiqnudw), followed by RNA isolation and purification.
10 ng of nuclear RNA was used to prepare libraries using the Ovation® SoLo® RNA-Seq library preparation kit from Tecan with Drosophila AnyDeplete probes.

tag: age

value: Day 10

value: Outer photoreceptors

tag: zeitgeber time


title: Brain Organoid, DMSO, Day 60, RNAseq, biol rep 2

description:
D60_RNAseq_matrix.tsv
D60_DMSO_RNAseq_2

value: cerebral differentiation with DMSO treatment


title: Photoreceptor Nuclei, w1118 control, Zeitgeber Time 4, Replicate 3


title: Brain Organoid, DMSO, Day 60, RNAseq, biol rep 3

description:
D60_RNAseq_matrix.tsv
D60_DMSO_RNAseq_3


title: Photoreceptor Nuclei, w1118 control, Zeitgeber Time 12, Replicate 1


title: WT_rapamycin_10

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

description: Library name: 1854_S14

data_processing:
Illumina Nextseq 6000 run folder demultpliexed using bcl2fastq v2.20.0.422
Map to custom Rat genome + hB27 + hB2M  using Tophat v.2.1.2
Calculate RPKM using Partek GS 7
Perform ANOVA comparisons using Partek GS 7
Plot PCA and Volcano Plots using Partek GS 7
Assembly: custom rat rn6 + hB27 + hB2M
Supplementary files format and content: Excel file containing RPKM values

molecule: polyA RNA

organism: Rattus norvegicus

source_name: colon

extract_protocol:
Colon tissue was homogenized in TRIzol reagent (Invitrogen) and RNA was isolated using a standard phenol-chloroform extraction method
Illumina standard protocol was used to generate libraries and paired-end, 50 base sequencing was performed on a Nextseq 6000 sequencer

value: colon

value: rapamycin

tag: batch


title: RNA-seq in HeLa Nigericin Replicate 1

city: Salt Lake City

first: Emily

middle: Rose

last: Wilson

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

description:
Library name: HeLa_Nigericin_rep1
Nigericin positive control

data_processing:
reads alignment: Bowtie2
read counts calculation: RSEM
Assembly: hg38
Supplementary files format and content: RSEM output

source_name: Cervical cancer cell line

growth_protocol: HeLa cells were cultured in complete DMEM (10% FBS, 1% Penicillin-Streptomycin; Corning) at humidified 37 degrees Celsius and 5% CO2 before and after treatment.

extract_protocol:
RNA was extracted using Quick-RNA Miniprep Kit (Zymo) at 48 hours for GeCas12a2 conditions or 5 hours for Nigericin condition and kept at -80 degrees Celsius until poly-A library preparation.
NEB Ultra II Directional RNA Library Prep with poly-A mRNA isolation

treatment_protocol: 250 pmol of GeCa12a2 in complex with either gGFP or gNT were delivered by electroporation to 5x10^5 HeLa cells. Control conditions were either treated with PBS electroporation or 5 uM Nigericin (MedChemExpress).

value: Cervical cancer cell line

value: HeLa

value: Nigericin


title: Brain Organoid, DEAB, Day 60, RNAseq, biol rep 1

description:
D60_RNAseq_matrix.tsv
D60_DEAB_RNAseq_1

value: cerebral differentiation with DEAB treatment


title: Sox9iresGFP XY pups transcriptome

description:
Library name: YFPpos_RNA_XY
10X Genomics

library_source: transcriptomic single cell

value: Pituitary

value: female

value: RNA


title: Sox9iresGFP XX pups transcriptome

description:
Library name: YFPpos_RNA_XX
10X Genomics

value: male

value: Stem cell


title: Photoreceptor Nuclei, w1118 control, Zeitgeber Time 8, Replicate 1


title: RNA-seq in HeLa gGFP-GeCas12a2 Replicate 1

description:
Library name: HeLa_gGFP_GeCas12a2_rep1
GFP-targeting guide


title: RNA-seq in HeLa gGFP-GeCas12a2 Replicate 3

description:
Library name: HeLa_gGFP_GeCas12a2_rep3
GFP-targeting guide


title: B27_vehicle_8

description: Library name: 1852_S22

value: vehicle


title: WT_rapamycin_6

description: Library name: 1848_S6

value: WT


title: RNA-seq in HeLa gGFP-GeCas12a2 Replicate 2

description:
Library name: HeLa_gGFP_GeCas12a2_rep2
GFP-targeting guide


title: WT_vehicle_1

description: Library name: 1851_S4


title: Photoreceptor Nuclei, w1118 control, Zeitgeber Time 4, Replicate 1


title: RNA-seq in HeLa gNT-GeCas12a2 Replicate 3

description:
Library name: HeLa_gNT_GeCas12a2_rep3
Non-targeting guide


title: B27_rapamycin_10

description: Library name: 1846_S12


title: RNA-seq in HeLa gNT-GeCas12a2 Replicate 1

description:
Library name: HeLa_gNT_GeCas12a2_rep1
Non-targeting guide


title: RNA-seq in HeLa gNT-GeCas12a2 Replicate 2

description:
Library name: HeLa_gNT_GeCas12a2_rep2
Non-targeting guide


title: WT_vehicle_6

description: Library name: 1850_S13


title: Photoreceptor Nuclei, w1118 control, Zeitgeber Time 4, Replicate 2


title: RNA-seq in HeLa Vehicle Replicate2

description:
Library name: HeLa_V_rep2
PBS negative control

value: PBS


title: WT_vehicle_2

description: Library name: 1845_S2


title: WT_rapamycin_4

description: Library name: 1844_S1


title: Photoreceptor Nuclei, w1118 control, Zeitgeber Time 0, Replicate 3

value: Day 10


title: RNA-seq in HeLa Vehicle Replicate1

description:
Library name: HeLa_V_rep1
PBS negative control


title: B27_rapamycin_11

description: Library name: 1849_S21


title: Photoreceptor Nuclei, w1118 control, Zeitgeber Time 0, Replicate 2

value: Outer photoreceptors


title: Corpus luteum, day 6, rep 4

city: University Park

first: Camilla

middle: H. K.

last: Hughes

state: PA

address: 439 Shortlidge Rd

department: Animal Science

institute: Penn State University

description: Library name: Day6_4_R1487

data_processing:
FASTQC was used to assess the quality of the raw sequencing reads
FASTP and SALMON were used for quantification and alignment
DEseq2 was used for statistical analysis
Quantification, alignment, and statistical analysis were performed according to the RaNAseq pipeline
Assembly: Cow, Bos taurus (ARS-UCD1.2)
Supplementary files format and content: Processed data file is a list of DEG from statistical analysis in DEseq2.

organism: Bos taurus

source_name: Corpus Luteum

growth_protocol: Cows were synchronized using CIDRs inserted for 7 days, with PGF2A (Lutalyse, Zoetis, 25 mg) injection on day 6 and ovulation induction via GnRH (Fertagyl, Merck, 86 mcg) on day 10 of the synch protocol. The day of standing estrus and ovulation induction was designated day 0 of the estrous cycle. On day 2, ovulation was confirmed via ultrasound. On day 4, CL samples were collected after slaughter because these CL are too immature to be collected via colpotomy. All CL collected after day 6 were collected via colpotomy.

extract_protocol:
Luteal tissue samples were homogenized in RNA lysis buffer and isolated using the miRCURY kit (Exiqon), according to the manufacturer’s protocol.
Library prep was performed using the Illumina Stranded mRNA Prep kit to create a uniquely indexed library for each sample. The pool was sequenced to obtain approximately 35 million reads per sample via a NextSeq 2000 P2 100 nt single-read sequencing run.

treatment_protocol: Cows were untreated

value: Corpus Luteum

value: Whole luteal tissue

value: Day 6


title: WT_rapamycin_9

description: Library name: 1847_S3

value: colon

value: rapamycin


title: B27_vehicle_11

description: Library name: 1841_B27_Vehicle_S20


title: RNA-seq in HeLa Vehicle Replicate3

description:
Library name: HeLa_V_rep3
PBS negative control

value: Cervical cancer cell line

value: HeLa


title: Corpus luteum, day 6, rep 1

description: Library name: Day6_1_R1483


title: Photoreceptor Nuclei, w1118 control, Zeitgeber Time 0, Replicate 1


title: B27_rapamycin_9

description: Library name: 1842_S23


title: B27_rapamycin_7

description: Library name: 1843_B27_Rapamycin_S10


title: Corpus luteum, day 4, rep 3

description: Library name: Day4_3_R1079

value: Day 4


title: Corpus luteum, day 4, rep 2

description: Library name: Day4_2_R1007


title: B27_vehicle_5

description: Library name: 1829_B27_Vehicle_S18


title: ISS-548

type: genomic

city: BETHESDA

first: Zhichao

last: Wu

address: BG 10 RM 4A31 MSC 1500, 10 CENTER DR

department: Center for Cancer Research

institute: NIH/NCI

description: Tumor

hyb_protocol: standard Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing: R package minfi v1.40.0

label: Cy5 and Cy3

source_name: ICMT

label_protocol: standard Illumina protocol

extract_protocol: genomic DNA was bisulfite-converted with the EZ DNA Methylation Kitm (Zymo Research D5001)

tag: gender

value: M

tag: progression-free survival

tag: progression status

tag: material

value: FFPE

tag: arraytype


title: plasmid pool, 580x

city: Houston

first: Fredrik

middle: Ivar

last: Thege

state: Texas

address: 6565 MD Anderson Blvd

department: Translational Molecular Pathology

institute: UT MD Anderson Cancer Center

description: Library name: 172_Onco1_pDNA_580x_S157_ME

library_source: genomic

data_processing:
Guide sequences from the Onco1 library were matched to FASTQ files to generate raw counts.
Supplementary files format and content: csv-file, table raw guide counts
Library strategy: CRISPR Screen

organism: Escherichia coli

extract_protocol:
Flash frozen tissues or cell pellets were homogenized in ATL buffer and genomic DNA was isolated using the Qiagen DNeasy blood and tissue kit. Plasmid DNA was isolated using Qiagen EndoFree MaxiPrep kit.
A region of genomic or plasmid DNA containing the guide sequences was amplified using direct PCR (NEBNext Ultra II Q5) with dual-indexed primers. Libraries were sequenced using 75 cycle single-end sequencing.

value: E. coli


title: WT_rapamycin_2

description: Library name: 1831_WT_Rapamycin_S4


title: plasmid pool, 950x resequenced

description: Library name: A171_Onco1_pDNA_950x_N715_S516_S109


title: WT_vehicle_7

description: Library name: 1836_WT_Vehicle_S12


title: WT_rapamycin_5

description: Library name: 1822_S11


title: Corpus luteum, day 6, rep 2

description: Library name: Day6_2_R1484


title: B27_rapamycin_8

description: Library name: 1821_S10


title: WT_vehicle_8

description: Library name: 1840_WT_Vehicle_S14


title: WT_vehicle_9

description: Library name: 1838_WT_Vehicle_S13


title: IA17

description: Tumor


title: ISS-631

description: Tumor


title: B27_vehicle_10

description: Library name: 1835_B27_Vehicle_S19


title: Corpus luteum, day 6, rep 3

description: Library name: Day6_3_R1485


title: plasmid pool, 950x

description: Library name: 171_Onco1_pDNA_950x_S156_ME


title: rh2808, A004.01/A019.02/B012.03/B015.03/DR04.01/DR03.01, control

city: Madison

first: David

middle: H

last: O'Connor

state: WI

address: 585 Science Drive

department: Pathology and Laboratory Medicine

institute: University of Wisconsin-Madison

description:
Library name: M007236_rh2808_PBMC
10X Genomics

data_processing:
Reference genomes were created for each sample from the FASTA and GTF files for the given genotype (available as supplementary files on the sample records) using the Cell Ranger mkref command. The demultiplexing, barcode processing, gene counting and aggregation were done using Cell Ranger software v2.1.1 (https://support.10Xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mmul_10
Supplementary files format and content: Tab-separated values files and matrix files. GTF and FASTA files of the reference genome used to process samples with Cell Ranger

organism: Macaca mulatta

source_name: peripheral blood mononuclear

extract_protocol:
PBMC from Mauritian-origin cynomolgus and Indian-origin rhesus macaques were isolated from fresh whole blood by Ficoll-Plaque centrifugation and transported immediately to the University of Wisconsin Biotech Center for 5' RNAseq analysis
Chromium GEX libraries were generated according to the manufacter's instructions for 5' single cell RNAseq (v2 NextGEM User Guide Rev.E). Briefly, PBMC were resuspended in master mix and loaded together with partioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was reverse transcripted to full-length cDNA, which contains an Illumina R1 primer sequence, a 16 nt 10X Barcode, a 10 nt unique molecular identifier and a 13 nt template switch oligo. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR, enzymatically fragmented and appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During library construction An Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences plus i5 and i7 sample index sequences were added during library construction. The resulting templates from two animals were sequenced on a NovaSeq X+ instrument with a 1.5B flow cell. A modified sequencing protocol was used with 29 cycles for R1 to collect 10X barcode/UMI sequences, followed by 289 cycles for R2. This protocol maximized the amount of sequence data from the highly polymorphic 5' end of each cDNA molecule so that transcripts from closely related MHC alleles could be resolved.

value: peripheral blood mononuclear

value: control

value: 12.4 years

value: female


title: Corpus luteum, day 4, rep 1

description: Library name: Day4_1_R1006


title: WT_rapamycin_8

description: Library name: 1830_WT_Rapamycin_S3

value: WT


title: B27_vehicle_7

description: Library name: 1834_S20

value: vehicle


title: IA18

description: Tumor

value: F


title: HU69

description: Tumor


title: B27_rapamycin_12

description: Library name: 1827_B27_Rapamycin_S9


title: WT_rapamycin_7

description: Library name: 1828_WT_Rapamycin_S2


title: WT_vehicle_10

description: Library name: 1820_S5


title: B27_rapamycin_6

description: Library name: 1817_S8


title: B27_vehicle_9

description: Library name: 1814_S16


title: HP04

description: Tumor


title: IA14

description: Tumor


title: WT_vehicle_4

description: Library name: 1815_S17


title: B27_rapamycin_1

description: Library name: 1823_B27_Rapamycin_S7


title: TFAM at 30 nM concentration, UVC-irradiated DNA

type: protein

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to the desired concentration 190-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at room temperature. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa-488-conjugated antibody was diluted to 50 μg/ml in PBS / 2% milk, applied to the array, and incubated for 1 h at room temperature. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each hour-long incubation step, arrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars on an orbital shaker at 125 r.p.m.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa-488-conjugated antibody. Microarray TIF images were analyzed using GenePix Pro version 7.3 software (Molecular Devices)

data_processing: To correct for any possible non-uniformities in protein binding, we adjusted the Alexa 488 signals according to their positions on the microarray. Median adjusted signal intensities were calculated across the 10 replicates of each probe and expressed as z-scores (standard deviations from mean) relative to the distribution of the low-binding sequences identified from the universal 7-mer binding array experiment. The universal binding array sequences used for normalization have IDs containing universal_bottom.

label: Alexa 488

molecule: protein

source_name: Human TFAM

label_protocol: TFAM was tagged with N-terminal His tag. Protein-bound arrays were incubated with Penta-His Alexa 488 antibody (Qiagen)

growth_protocol: For TFAM expression, cells were grown as described in Ngo et al. 2011 (PMID 22037171)

extract_protocol: His-tagged TFAM was purified as described in Ngo et al. 2011 (PMID 22037171)

tag: transcription factor

value: TFAM

tag: protein concentration

value: Protein concentration:30nM

value: 30 nM TFAM, with UVC exposure


title: B27_vehicle_6

description: Library name: 1819_S19

tag: tissue

value: colon


title: WT_vehicle_5

description: Library name: 1816_S18


title: WT_rapamycin_1

description: Library name: 1813_S7

value: rapamycin


title: TFAM at 30 nM concentration

value: 30 nM TFAM, no UVC exposure


title: WT_rapamycin_3

description: Library name: 1807_WT_Rapamycin_S1


title: B27_rapamycin_5

description: Library name: 1818_S9


title: r22016, A004.01/A004.01/B048.01/B048.01/DR06.01/DR01.01, control

description:
Library name: M007236_r22016_PBMC
10X Genomics

value: 2.4 years

tag: Sex


title: HP57

description: Tumor

value: M


title: methylation, PA_003_F

city: Los Angeles

first: Frederique

last: Ruf-Zamojski

state: CA

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

hyb_protocol: The bisulfite-converted amplified DNA products were denatured into single strands and hybridized to the Illumina Infinium Human Methylation EPIC Bead Chip array (Illumina Inc.).

scan_protocol: The hybridized BeadChips were stained, washed, and scanned for the intensities of the unmethylated and methylated bead types using Illumina's iScan System.

data_processing:
The DNA methylation beta values were obtained from the raw IDAT files by using the ChAMP package in R. Samples from the same individual were processed together across all experimental stages to negate any methodological batch effects.
PitTumorNF_methyl_processed.txt: Intensity and average beta

label: Cy3 and Cy5

source_name: non-functioning pituitary adenoma

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from cryopreserved isolated nuclei from pituitary adenomas using the genomic DNA isolation Monarch kit (New England BioLabs #T3010) following manufacturer’s instructions. All DNA samples were quantified using both absorbance (NanoDrop 2000; Thermo Fisher Scientific, Waltham, MA) and fluorescence-based methods (Qubit; Thermo Fisher Scientific) using standard dyes selective for double-stranded DNA, minimizing the effects of contaminants that affect the quantitation. DNA methylation was assessed using Illumina Infinium Human MethylationEPIC Bead Chip array (Illumina Inc., San Diego, CA) according to the manufacturer's instructions at the University of Minnesota Genomic Center. Briefly, 500 ng of DNA from each sample was treated with sodium bisulfite, using the EZ-96 DNA Methylation-Gold kit (Zymo Research, CA, USA).

value: non-functioning pituitary adenoma


title: TFAM at 300 nM concentration, UVC-irradiated DNA

value: Protein concentration:300nM

value: 300 nM TFAM, with UVC exposure


title: HO76

description: Tumor

value: FFPE


title: B27_vehicle_4

description: Library name: 1806_B27_Vehicle_S16


title: kdm4ab-2

city: shanghai

first: xiaohui

last: chen

address: No.999, Huchenghuan Rd, Nanhui New City, Shanghai, P.R. China

institute: Shanghai Ocean University

description:
Library name: sample8
Column name in all.count.txt ：ab2.bam

data_processing:
Data Quality Control
The original fluorescence image files obtained from Illumina platform are transformed to short reads (Raw data) by base calling and these short reads are recorded in FASTQ format (Cock P. et al, 2010), which contains sequence information and corresponding sequencing quality information.
Sequence artifacts, including reads containing adapter contamination, low-quality nucleotides and unrecognizable nucleotide (N), undoubtedly set the barrier for the subsequent reliable bioinformatics analysis. Hence quality control is an essential step and applied to guarantee the meaningful downstream analysis. we used Fastp (version 0.23.1)(Chen S. et al, 2018) to perform basic statistics on the quality of the raw reads.
Assembly: Zebrafish(GRCZ11/danRer11)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Danio rerio

source_name: Embryos

extract_protocol:
Extract total RNA using the Trizol method for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo_x0002_attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.After library quality control, quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Embryos

value: kdm4ab knockout


title: methylation, PA_002_M


title: X917

description: Tumor

value: IlluminaHumanMethylationEPIC


title: kdm4ab-3

description:
Library name: sample9
Column name in all.count.txt ：ab3.bam


title: GT76

description: Tumor


title: WT_vehicle_3

description: Library name: 1809_WT_Vehicle_S11

value: WT

value: vehicle


title: methylation, PA_001_M


title: B27_vehicle_2

description: Library name: 1811_S15


title: methylation, PA_004_M


title: HD09

description: Tumor

value: F


title: HI84

description: Tumor


title: B27_vehicle_3

description: Library name: 1808_B27_Vehicle_S17


title: Z443

description: Tumor


title: wt-3

description:
Library name: sample3
Column name in all.count.txt ：wt3.bam


title: FV96

description: Tumor


title: GY07

description: Tumor


title: TFAM at 300 nM concentration

value: TFAM

value: 300 nM TFAM, no UVC exposure


title: B27_rapamycin_2

description: Library name: 1802_B27_Rapamycin_S5

value: colon


title: B27_vehicle_1

description: Library name: 1804_B27_Vehicle_S15


title: ISS-651

description: Tumor


title: ISS-543

description: Tumor


title: wt-2

description:
Library name: sample2
Column name in all.count.txt ：wt2.bam


title: MM131047

city: New Orleans

first: Hong-Wen

last: Deng

state: LA

institute: Tulane University

description:
Library name: MM131047
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

data_processing:
Sequencing reads were quality-filtered and aligned to the human reference genome using BSMAP. Methylation levels at CpG sites were calculated as the ratio of methylated reads to total reads covering each site. CpG sites overlapping known SNPs were removed. Rank-based inverse normal transformation was applied for normalization. Reads with >10% unknown bases or >10% of bases with quality scores <20 were further excluded to obtain high-quality data. The cleaned reads were aligned to the GRCh37/hg19 human reference genome using BSMAP, then converted to GRCh38/hg38 using the UCSC LiftOver tool (https://genome.ucsc.edu/cgi-bin/hgLiftOver).
Assembly: GRCh38/hg38
Supplementary files format and content: Processed data files contain tab-delimited matrices of CpG-level DNA methylation beta values. Rows represent CpG loci with genomic coordinates, and columns represent individual samples. Chromosome-specific methylation matrices are provided in compressed format.

source_name: peripheral blood

extract_protocol:
Genomic DNA was extracted from purified peripheral blood monocytes using the QIAamp DNA Mini Kit (Qiagen) following the manufacturer’s protocol. DNA concentration and purity were evaluated using NanoDrop spectrophotometry and agarose gel electrophoresis.
Monocytes were isolated from peripheral blood mononuclear cells using negative selection. Genomic DNA was extracted and fragmented. Libraries were prepared following bisulfite conversion using the EZ DNA Methylation-Gold kit and sequenced on the Illumina HiSeq 4000 platform.

value: peripheral blood

tag: cell type

value: monocytes

tag: population

value: European American

value: male

tag: bmi

tag: smoke

tag: alcohol drinking


title: B27_rapamycin_3

description: Library name: 1803_B27_Rapamycin_S6

tag: genotype

tag: treatment

value: rapamycin


title: HN81

description: Tumor

value: M

tag: age


title: ISS-494

description: Tumor

tag: gender


title: GO47

description: Tumor

tag: progression-free survival


title: kdm4aa-1

description:
Library name: sample4
Column name in all.count.txt ：aa1.bam

value: kdm4aa knockout


title: MM131045

description:
Library name: MM131045
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM131040

description:
Library name: MM131040
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM131032

description:
Library name: MM131032
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: ISS-249

description: Tumor

tag: progression status

value: FFPE


title: ISS-143

description: Tumor

tag: material


title: GI29

description: Tumor

tag: arraytype


title: MM131026

description:
Library name: MM131026
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: GM05

description: Tumor


title: MM131012

description:
Library name: MM131012
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: kdm4aa-2

description:
Library name: sample5
Column name in all.count.txt ：aa2.bam

value: Embryos


title: kdm4ab-1

description:
Library name: sample7
Column name in all.count.txt ：ab1.bam

value: kdm4ab knockout


title: kdm4aa-3

description:
Library name: sample6
Column name in all.count.txt ：aa3.bam


title: L885.1

description: Tumor

value: IlluminaHumanMethylationEPIC


title: sheCherry_MTZ_1h

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

description: Library name: sheCherry_MTZ_1h

data_processing:
Cell Ranger is used in the analysis of 10x scRNA-Seq data. Raw reads were demultiplexed into Fastq format using cellranger mkfastq. Alignment, filtering, barcode counting, and UMI counting was done using cellranger’s count pipeline.
Assembly: danRer11
Supplementary files format and content: Expression matrix in h5 format

source_name: lateral line cells

extract_protocol:
600 mpeg1:EGFP;myo6b:mCherry-NTR2.0;she:H2A-mCherry triple-positive zebrafish larvae were dissociated on ice using 0.25% Trypsin-EDTA through gentle pipetting for 8min. The dissociated tissue was then filtered through a 70 µm filter. Following several washing steps with ice-cold 1XDPBS/0.04% BSA, the cells were filtered again through a 70 µm strainer. To stain nucleated cells, the suspension was incubated with DRAQ5 for 5 min on ice. Cells were sorted by the Stowers Institute Cytometry Core Facility using BD Influx Cell Sorter (BD Biosciences) and BD FACSymphony S6 (BD Biosciences) instruments. Sorted cells were spun down at 350 rcf at 4 °C for 2 min in a swinging bucket centrifuge with slow deceleration. The cell pellet was gently resuspended in 100 µL of 1X DPBS/0.04% BSA.
Cells with a viability of 80% or higher were loaded onto a Chromium X Series instrument (10x Genomics) and libraries prepared using the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10x Genomics) according to manufacturer’s instructions.

value: lateral line cells

value: wildtype


title: GE29

description: Tumor


title: sheCherry_MTZ_0h

description: Library name: sheCherry_MTZ_0h


title: GD32

description: Tumor

value: F


title: MM131059

description:
Library name: MM131059
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: sheCherry_homeo

description: Library name: sheCherry_homeo

value: untreated


title: MM131058

description:
Library name: MM131058
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130991

description:
Library name: MM130991
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: mpegGFP_neo_1h

description: Library name: mpegGFP_neo_1h

source_name: macrophages

value: macrophages


title: mpegGFP_neo_0h

description: Library name: mpegGFP_neo_0h


title: wt-1

description:
Library name: sample1
Column name in all.count.txt ：wt1.bam

value: WT


title: MM131020

description:
Library name: MM131020
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: peripheral blood


title: ET90

description: Tumor


title: MM131041

description:
Library name: MM131041
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: monocytes


title: MM131046

description:
Library name: MM131046
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: European American


title: FI43

description: Tumor


title: MM131001

description:
Library name: MM131001
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: male


title: MM131025

description:
Library name: MM131025
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM131002

description:
Library name: MM131002
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: sheCherry_MTZ_neg_1h

description: Library name: sheCherry_MTZ_neg_1h


title: MM130967

description:
Library name: MM130967
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: FI19

description: Tumor


title: EO68

description: Tumor


title: EM79

description: Tumor


title: MM130992

description:
Library name: MM130992
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: sheCherry_neo_1h

description: Library name: sheCherry_neo_1h


title: FN41

description: Tumor


title: MM130975

description:
Library name: MM130975
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: sheCherry_neo_0h

description: Library name: sheCherry_neo_0h


title: MM130990

description:
Library name: MM130990
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: EI04

description: Tumor


title: mpegGFP_MTZ_0h

description: Library name: mpegGFP_MTZ_0h


title: EW89

description: Tumor


title: MM130956

description:
Library name: MM130956
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: EF56

description: Tumor


title: MM130948

description:
Library name: MM130948
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: GI22

description: Tumor


title: MM130986

description:
Library name: MM130986
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130993

description:
Library name: MM130993
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130973

description:
Library name: MM130973
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130964

description:
Library name: MM130964
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130971

description:
Library name: MM130971
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130965

description:
Library name: MM130965
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130947

description:
Library name: MM130947
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130944

description:
Library name: MM130944
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: mpegGFP_MTZ_neg_1h

description: Library name: mpegGFP_MTZ_neg_1h


title: GA54

description: Tumor


title: DW45

description: Tumor


title: Patient #5, primary breast cancer cells, Denosumab-non-responsive

city: Guangzhou

first: Chang

last: Gong

address: No. 107, Yanjiang West Road, Yuexiu Dist

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description:
Library name: Sample 5
Column name in gene_counts.txt: R_2

data_processing:
CLC Genomics Workbench v 11.0.1 software used for basecalling.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05).
Trimmed sequence reads were mapped to GRCh38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8).
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: csv include TPM values for each Sample

source_name: Human primary breast cancer cells

extract_protocol:
For Sample 1-6, RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
For Sample 1-6, RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

tag: subject status

value: Denosumab-non-responsive patient

value: Human primary breast cancer cells


title: Patient #4, primary breast cancer cells, Denosumab-non-responsive

description:
Library name: Sample 4
Column name in gene_counts.txt: R_1


title: MM130941

description:
Library name: MM130941
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130968

description:
Library name: MM130968
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: mpegGFP_homeo

description: Library name: mpegGFP_homeo


title: MM130940

description:
Library name: MM130940
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130949

description:
Library name: MM130949
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: mpegGFP_MTZ_1h

description: Library name: mpegGFP_MTZ_1h


title: MM130970

description:
Library name: MM130970
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: Patient #1, primary breast cancer cells, Denosumab-responsive

description:
Library name: Sample 1
Column name in gene_counts.txt: S_1

value: Denosumab-responsive patient


title: DG88

description: Tumor

value: FFPE


title: DQ02

description: Tumor


title: MM130931

description:
Library name: MM130931
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130930

description:
Library name: MM130930
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130936

description:
Library name: MM130936
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130938

description:
Library name: MM130938
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: DR93

description: Tumor


title: Patient #6, primary breast cancer cells, Denosumab-non-responsive

description:
Library name: Sample 6
Column name in gene_counts.txt: R_3


title: MM130958

description:
Library name: MM130958
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: DL39

description: Tumor

value: M


title: PPKS mouse lung, non-targeted sgRNA, survival endpoint, mouse FT0163

description:
Library name: FT0163_NT
150 PE

data_processing:
FASTQ files were aligned to the mm39 mouse transcriptome using the STAR aligner to generate raw counts.
Assembly: GRCm39 (mm39)
Supplementary files format and content: cvs-file, table with raw counts

source_name: Lung

extract_protocol:
total RNA was extracted from flash frozen lung tissues using Qiagen Allprep Mini kit (including optional on-column DNase treatment)
directional mRNA-seq libraries were generated and sequenced on an Illumina NovaSeq X Plus sequencer (150 cycles, paired end)

treatment_protocol: PPKS mice were treated with Sox2-targeting or non-targeting CMV-Cre/U6-sgRNA(MS2) lentivirus through nasal instillation. Tissues were harvested at survival endpoint.

value: Lung

value: Whole lung tumor

value: PPKS


title: MM130943

description:
Library name: MM130943
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130926

description:
Library name: MM130926
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: Patient #2, primary breast cancer cells, Denosumab-responsive

description:
Library name: Sample 2
Column name in gene_counts.txt: S_2


title: MM130934

description:
Library name: MM130934
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130920

description:
Library name: MM130920
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: PPKS mouse lung, non-targeted sgRNA, survival endpoint, mouse FT0029

description:
Library name: FT0029_NT
150 PE


title: CT21

description: Tumor

value: IlluminaHumanMethylationEPIC


title: MM130925

description:
Library name: MM130925
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130917

description:
Library name: MM130917
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: PPKS mouse lung, non-targeted sgRNA, survival endpoint, mouse FT0486

description:
Library name: FT0486_NT
150 PE


title: MM130919

description:
Library name: MM130919
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: PPKS mouse lung, non-targeted sgRNA, survival endpoint, mouse FT0008

description:
Library name: FT0008_NT
150 PE


title: Patient #3, primary breast cancer cells, Denosumab-responsive

description:
Library name: Sample 3
Column name in gene_counts.txt: S_3


title: MM130918

description:
Library name: MM130918
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130959

description:
Library name: MM130959
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: CR62

description: Tumor

value: F


title: CI54

description: Tumor


title: MM130928

description:
Library name: MM130928
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130916

description:
Library name: MM130916
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: DB87

description: Tumor


title: PPKS mouse lung, Sox2-targeted sgRNA, survival endpoint, mouse FT0057

description:
Library name: FT0057_Sox2
150 PE


title: MM130923

description:
Library name: MM130923
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130915

description:
Library name: MM130915
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: DR21

description: Tumor


title: CD84

description: Tumor


title: MM130932

description:
Library name: MM130932
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130927

description:
Library name: MM130927
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130914

description:
Library name: MM130914
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130908

description:
Library name: MM130908
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: CB62

description: Tumor


title: MM130907

description:
Library name: MM130907
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: PPKS mouse lung, Sox2-targeted sgRNA, survival endpoint, mouse FT0035

description:
Library name: FT0035_Sox2
150 PE


title: MM130906

description:
Library name: MM130906
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: DB47

description: Tumor


title: BF39

description: Tumor


title: BJ35

description: Tumor


title: MM130913

description:
Library name: MM130913
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130904

description:
Library name: MM130904
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: Control-3

city: Worcester

first: Marcus

last: Ruscetti

state: MA

address: 364 Plantation Street

department: MCCB

institute: UMass Chan Medical School

description:
Library name: Control-3
Column name in raw counts_All_Samples.txt: Control-3

data_processing:
Raw FASTQ files were processed using the OneStopRNAseq platform, which performed read alignment, quality control, feature counting, differential gene expression analysis, and other downstream analyses.
Reads were aligned to mm39 with STAR.
Feature counting was performed using featureCounts with the annotation file Mus_musculus.GRCm39.111.gtf.
Assembly: mm39
Supplementary files format and content: Tab-delimited Excel files including raw counts, TPM, and FPKM values for each sample.

source_name: iWAT

extract_protocol:
Total RNA was extracted from iWAT tissues using TRIzol reagent.
One microgram of total RNA per sample was used to generate RNA-seq libraries in biological triplicates, using KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche, Cat#KK8561). The amplified libraries were sequenced on an Illumina NovaSeq X platform.

value: iWAT

value: WT mice fed with high-fat diet

value: Control

tag: batch


title: Control-2

description:
Library name: Control-2
Column name in raw counts_All_Samples.txt: Control-2

tag: tissue


title: MM130898

description:
Library name: MM130898
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: peripheral blood

tag: Sex


title: MM130905

description:
Library name: MM130905
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

tag: cell type

value: monocytes


title: PPKS mouse lung, Sox2-targeted sgRNA, survival endpoint, mouse FT0007

description:
Library name: FT0007_Sox2
150 PE


title: MM130901

description:
Library name: MM130901
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

tag: population

value: European American


title: BL48

description: Tumor


title: B2022.38636

description: Tumor


title: PPKS mouse lung, Sox2-targeted sgRNA, survival endpoint, mouse FT0011

description:
Library name: FT0011_Sox2
150 PE


title: Control-1

description:
Library name: Control-1
Column name in raw counts_All_Samples.txt: Control-1


title: MM130902

description:
Library name: MM130902
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: male

tag: bmi


title: MM130891

description:
Library name: MM130891
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

tag: smoke


title: MM130886

description:
Library name: MM130886
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

tag: alcohol drinking


title: MM130899

description:
Library name: MM130899
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130889

description:
Library name: MM130889
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: ADISSP-3

description:
Library name: ADISSP-3
Column name in raw counts_All_Samples.txt: Adissp-3

tag: genotype

value: ADISSP