title: H9 TRE3G 2xFLAG-GSX2 WT 48hr -Dox Replicate 6

city: Cincinnati

first: Brian

last: Gebelein

state: OH

address: 3333 Burnet Avenue, MLC 7007

institute: Cincinnati Children's Hospital Medical Center

description: Library name: NoDox_48hr_Rep6

data_processing:
Quality-controlled FASTQ files were trimmed using TrimGalore to remove adapters and low-quality reads
Trimmed reads were aligned using Bowtie2 and duplicates were removed using Samtools
Reads overlapping blacklisted regions were removed and then peaks were called using HMMRATAC, selecting for peaks with score >10
Bigwig files were generated using Deeptools with 1x read per genome coverage (RPGC)
Assembly: hg38
Supplementary files format and content: gappedPeak filtered for score >10

growth_protocol: H9 hESC cultures were maintained in Essential 8 Flex Media in 5% CO2 environment at 37C

extract_protocol:
Monolayers were dissociated for 30 minutes with Accutase and then lysed for 3 minutes on ice. Nuclei were tagmented for 30 minutes at 37C in a 800rpm thermomixer.
Libraries were prepared using NEBNext Ultra II Q5 PCR Mastermix (NEB) for 6-11 total PCR cycles. Optimal number of cycles was determined by qPCR. Libraries were size-selected for 150-800 bp and then Agilent high-sensitivity D1000 screentape was used for QC.

treatment_protocol:
H9 hESC cultures were differentiated in Essential 6 Media supplemented with: (3 days) LDN193189, SB431542, XAV939; (3 days) LDN193189, SB431542; (4-6 days) IWP2, Activin A
Dox-induced cultures were treated with 100ng/mL doxycycline supplemented in differentiation media for 12-hours starting at Day 10

value: human embryonic stem cell

value: TRE3G 2xFLAGGSX2 WT

value: LGE-like differentiation


title: mmem_val_sl019

status: Public on Sep 30 2025

type: SRA

city: Santa Cruz

first: Upasna

last: Sharma

state: California

address: 1156 High St

department: MCD Biology

country: USA

institute: UCSC

library_source: transcriptomic

data_processing:
151 x 151 paired end reads. Sequencing libraries were not strand-specific.
Reads were trimmed by 31 bases from the 3' end to 120x120bp
Reads were mapped with Bowtie2 to the RepeatMasker library of mouse repeat elements.
After removing reads with both ends mapped to repeat elements, the remaining reads were mapped to the mm10 genome assembly using STAR.
Potential PCR duplicates were removed with samtools rmdup.
The coverage for each gene was extracted, then divided by 240 (based on 120x120bp mappings) for input as mapping counts to DESeq2
The DESeq2 sizeFactors were used to compute normalized read counts per gene for each sample
Assembly: mm10
Supplementary files format and content: DESeq2 normalized read counts per gene for each sample in tab-separated format
Supplementary files format and content: DESeq2 sizeFactors for each sample in text format

molecule: polyA RNA

organism: Mus musculus

source_name: preimplantation embryo

extract_protocol:
To prepare cell lysates, we first create a 1% solution of 2-mercaptoethanol in TCL buffer. We distribute 5 μl of this solution into each well of a skirted-side 96-well PCR plate, placing a single embryo in each well. The plate is then centrifuged for 1 minute at 800 × g at room temperature. Next, we add 10 μl of RNase-free H₂O to each lysate, followed by 2.2 volumes of RNA-SPRI beads. The lysates are incubated for 10 minutes on the bench to allow for RNA binding, and then the plate is placed on a 96-well plate magnet and incubated for 5 minutes to separate the beads. After carefully removing the supernatant, the beads are washed by adding 75 μl of 80% ethanol to each well. The plate is left to air dry at room temperature for 10 minutes. Finally, the RNA is eluted by adding 4 μl of RNase-free H₂O to each well.
To reverse transcribe mRNA, prepare the workspace, then elute RNA with a primer and dNTP mix. After initial incubation and centrifugation, add a mastermix with SuperScriptII buffer, DTT, betaine, MgCl₂, a template-switching oligo, RNase inhibitor, and reverse transcriptase. Reverse transcribe with a thermal cycler protocol (42°C for 90 mins, cycles at 50°C/42°C, then 70°C). For amplification, add KAPA HiFi mix and PCR primer, then amplify with 20 PCR cycles and store overnight at 4°C. Clean up with DNA SPRI beads, washing with ethanol, then elute in TE buffer. Measure size and concentration, then proceed with Nextera XT library prep: perform tagmentation, add NT Buffer, indexed primers, and amplify. Pool samples, perform SPRI bead cleanup, and measure for sequencing readiness.
single embryo mRNA-seq

treatment_protocol: Embryos were microinjected with either H3.3-GFP mRNA with LNA-containing scramble oligo (Ctrl_LNA) (control group) or H3.3-GFP mRNA plus tRFValCAC antisense LNA oligo (Val_LNA) (experimental group).

tag: tissue

value: preimplantation embryo

tag: cell type

value: 2-cell stage embryonic cells

tag: genotype

value: wild type

tag: treatment


title: AD 2

type: RNA

city: Changsha

first: Liang

last: Tang

address: No 1501, Leifeng road

country: China

institute: Changsha Medical University

description: Gene expression in AD group

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4*180k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software version10.7.1.1 (Agilent) using default parameters

molecule: total RNA

source_name: hippocampus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: hippocampus was obatained form Aβ25-35 induced AD model mice and control mice

value: hippocampus

tag: gender

value: male

tag: age

value: day 28


title: rh-16, E2, week 18

city: Lund

first: Joan

last: Escrivà-Font

state: Skåne

address: Sölvegatan 19

department: Department of Laboratory Medicine, Faculty of Medicine

country: Sweden

institute: Lund University

description: Library name: H26

data_processing:
Raw sequencing data was processed using the nf-core/rnaseq pipeline v3.9 (https://nf-co.re/rnaseq/3.9).
Reads were trimmed with Trim Galore
Reads were pseudo-aligned to the transcriptome using Salmon, with reference prepared from Macaca_mulatta.Mmul_10 genome and GTF (v110).
Salmon output files were imported with tximport into R.
More info on https://github.com/ConsiglioLab/Hahn_et_al_FHT.
Assembly: Mmul_10
Supplementary files format and content: quant_sf_all.tar.gz: contains all salmon quant.sf output files from the nf-core pipeline.
Supplementary files format and content: counts_lengthScaledTPM_allSamples.csv: tximport lengthScaledTPM
Supplementary files format and content: counts_TPM_allSamples.csv: tximport TPM

organism: Macaca mulatta

source_name: Whole blood

extract_protocol:
Whole blood from the study animals was collected in PAXgene Blood RNA tubes. RNA was extracted according to kit manufacturer instructions (PreAnalytiX, 762174).
cDNA libraries were prepared at Novogene Inc. from total RNA using the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB, E7770L).

treatment_protocol: Exogenous E2 or placebo were delivered via slow-release pellets on study weeks 0, 4, 7, 10, 13, 16, 19, 22, and 25. The 0.3 mg/kg E2 or placebo pellets were administered subcutaneously. For the mRNA vaccinations, four individual syringes per animal were prepared containing 15 μg of mRNA encoding 16055-ConM_SOSIPv8ds. Macaques in both groups A and B received first and second vaccinations at study weeks 18 and 22 respectively.

value: Whole blood

value: E2, LNP/mRNA

tag: weeks post_fht

tag: treatment group

tag: animal id

tag: Sex

tag: sequencing batch


title: rh-16, E2, week 27

description: Library name: H29


title: mmem_val_sl018


title: H9 TRE3G 2xFLAG-GSX2 WT 48hr -Dox Replicate 5

description: Library name: NoDox_48hr_Rep5

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: batch


title: rh-16, E2, week 19

description: Library name: H27


title: WT_02, Hippocampus_Cortex, WT , saline-treated

city: Munich

first: Peter

last: Androvic

state: Bavaria

address: Feodor-Lynen-Strasse 17

country: Germany

institute: LMU Hospital, Institute for Stroke and Dementia Research

data_processing:
Sequencing data were demultiplexed using bcl2fastq (Illumina). Quality control of reads was performed using FastQC and adaptor sequences were trimmed using TrimGalore. Reads were then aligned to GRCm38 (mm10) genome with added ERCC sequences using STAR(Dobin et al., 2013). Aligned reads were counted using the parameter “quantMode GeneCounts” in STAR and unstranded values were used for subsequent downstream analysis. Samples were further controlled for quality, leading to 71 QC-passing samples used in all downstream analyses.
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-delimited file with raw counts for each sample

extract_protocol:
RNA was isolated from PFA-fixed OCT-embedded frozen brain sections using an in house developed method that digest proteins to free crosslinked RNA(Farris et al., 2017; Nichterwitz et al., 2016; Thomsen et al., 2016). In brief, frozen brain sections (14 μm) were taken out of -80°C and incubated at RT for 5 min, avoiding drying out. 50 µL RNA isolation buffer per sample was prepared in advance and kept on ice, containing 38.75 µL of PKD buffer (157014133, Qiagen) with 10 µL proteinase K solution (19131, Qiagen) and 1.25 µL ERCC (1:60k) spike-in synthetic RNAs (Life Technologies). The target brain sections were covered with 50 µL isolation buffer and incubated at room temperature for 30 s. Target brain sections were scratched and the brain lysates were collected by pipetting with 200 µL tips, and snap-frozen in liquid nitrogen and stored at -80°C. Samples were thawed at room temperature for 3 min, then vortexed and spun down, followed by the incubation of samples at 56°C for 4 hours in a thermal cycler with the lid set at 66°C, checking hourly if the sample was dissolving. After the incubation, vortexing and spinning down the samples, they were transferred into pre-cooled 1.5 mL tubes on ice. Prepared oligo dT25 magnetic beads (61005, Invitrogen) with three washes of 1x hybridization buffer (HB), which contains 2x SSPE (Life Technologies, Cat#15591-043), 0.05% Tween-20 (1610781, Bio-Rad), 0.05% RNase Inhibitor (2313A, Takara). Resuspend the beads with half of the original volume in 2x HB for later usage. 10 µL washed dT25 beads (0.1 mg) was added into each sample to reverse crosslinked samples and heated the samples at 56°C for one minute. Placed the samples on ice after 10 min incubation at room temperature to allow mRNA hybridization. Then washed the beads two times in 100 µL of ice-cold 1x HB, followed by a subsequent wash using ice cold 1x PBS with 0.1% RNase Inhibitor inside. Removed PBS and resuspended with 15 µL RNase-free water. Incubated the sample-beads mixture at 80°C for two minutes to elute mRNA, then immediately pelleted on a room temperature magnet. Rapidly removed the supernatant containing mRNA and transfer to a new tube and store at -80°C. 0.1-0.5 µg mRNA from each sample was taken and continued with Smart-seq2 protocol
Libraries were prepared with SmartSeq2 protocol as described previously in (Safaiyan et al., 2021).
mRNA-Seq (SmartSeq2)

treatment_protocol: 5XFAD mice on B6/SJL background (34840-JAX, Tg6799), which are APP/PS1 double transgenic mice with five familial AD mutations(Oakley et al., 2006), and wild-type (WT) B6/SJL mice were purchased from the Jackson Laboratory. Mice were group-housed under specific pathogen-free conditions at the Center for Stroke and Dementia Research (CSD) at Ludwig-Maximilians-University (LMU) Munich. Mice had access to water and standard mouse chow (Ssniff Ms-H, Ssniff Spezialdiäten GmbH, Soest, Germany) ad libitum and were kept under a 12/12 h light-dark cycle in IVC System Typ II L-cages (528 cm2) equipped with solid floors and a layer of bedding. For cohort 1 of mice, 3-month-old female 5XFAD mice were divided into two experimental groups (2E treatment vs. saline group) using the block randomization method. The treatment group (5XFAD, n=8) was intraperitoneally (i.p.) injected with 2E with every other day from 3 months of age as following: 5 mg/kg for the first 6 weeks and followed by 2.5 mg/kg until 6 months of age. The vehicle group (5XFAD, n=9) and its WT littermates (n=10) were treated with the same volume of saline by i.p. injection. No clear conspicuous side effects (weight, anorexia, convulsion, or death) were not observed. All mice of cohort 1 used in this study were sacrificed at 6 months of age.

value: brain cells

value: WT

value: saline-treated

value: 6 months


title: WT_01, Hippocampus_Cortex, WT , saline-treated


title: mmem_val_sl017


title: H9 TRE3G 2xFLAG-GSX2 WT 48hr -Dox Replicate 4

description: Library name: NoDox_48hr_Rep4


title: WT_05, Hippocampus_Cortex, WT , saline-treated


title: rh-16, E2, week 0

description: Library name: H23


title: AD 1

description: Gene expression in AD group


title: mmem_val_sl016


title: rh-16, E2, week 7

description: Library name: H24


title: H9 TRE3G 2xFLAG-GSX2 WT 48hr -Dox Replicate 1

description: Library name: NoDox_48hr_Rep1


title: rh-16, E2, week 13

description: Library name: H25


title: H9 TRE3G 2xFLAG-GSX2 WT 48hr -Dox Replicate 3

description: Library name: NoDox_48hr_Rep3


title: H9 TRE3G 2xFLAG-GSX2 WT 48hr -Dox Replicate 2

description: Library name: NoDox_48hr_Rep2


title: WT_04, Hippocampus_Cortex, WT , saline-treated


title: rh-15, E2, week 27

description: Library name: H22


title: rh-15, E2, week 23

description: Library name: H21


title: mmem_val_sl014


title: Control  3

description: Gene expression in control group


title: Control  1

description: Gene expression in control group


title: H9 TRE3G 2xFLAG-GSX2 WT 48hr +Dox Replicate 6

description: Library name: Dox_48hr_Rep6

value: 100ng/mL Dox


title: WT_03, Hippocampus_Cortex, WT , saline-treated


title: Control  2

description: Gene expression in control group


title: mmem_val_sl013


title: rh-15, E2, week 19

description: Library name: H20


title: H9 TRE3G 2xFLAG-GSX2 WT 48hr +Dox Replicate 5

description: Library name: Dox_48hr_Rep5


title: rh-15, E2, week 18

description: Library name: H19


title: WT_01, Hippocampus, WT , saline-treated

source_name: Hippocampus

value: Hippocampus


title: mmem_val_sl015


title: H9 TRE3G 2xFLAG-GSX2 WT 48hr +Dox Replicate 4

description: Library name: Dox_48hr_Rep4

value: human embryonic stem cell


title: rh-15, E2, week 13

description: Library name: H18


title: mmem_val_sl007


title: rh-15, E2, week 7

description: Library name: H17


title: H9 TRE3G 2xFLAG-GSX2 WT 48hr +Dox Replicate 3

description: Library name: Dox_48hr_Rep3

value: TRE3G 2xFLAGGSX2 WT


title: H9 TRE3G 2xFLAG-GSX2 WT 48hr +Dox Replicate 2

description: Library name: Dox_48hr_Rep2

value: LGE-like differentiation


title: mmem_val_sl005

value: preimplantation embryo


title: rh-15, E2, week 0

description: Library name: H16


title: WT_05, Hippocampus, WT , saline-treated


title: WT_02, Hippocampus, WT , saline-treated


title: WT_01, Cortex, WT , saline-treated

source_name: Cortex

value: Cortex


title: H9 TRE3G 2xFLAG-GSX2 WT 48hr +Dox Replicate 1

description: Library name: Dox_48hr_Rep1


title: mmem_val_sl006

value: 2-cell stage embryonic cells

value: wild type


title: WT_02, Cortex, WT , saline-treated


title: rh-14, E2, week 27

description: Library name: H15

value: male


title: mmem_val_sl004


title: H9 TRE3G 2xFLAG-GSX2 WT 24hr +Dox Replicate 3

description: Library name: Dox_24hr_Rep3


title: WT_05, Cortex, WT , saline-treated


title: rh-14, E2, week 23

description: Library name: H14


title: mmem_val_sl003


title: mmem_val_sl008


title: H9 TRE3G 2xFLAG-GSX2 WT 24hr +Dox Replicate 2

description: Library name: Dox_24hr_Rep2


title: WT_04, Cortex, WT , saline-treated


title: rh-14, E2, week 19

description: Library name: H13


title: mmem_val_sl002


title: rh-14, E2, week 18

description: Library name: H12


title: WT_03, Cortex, WT , saline-treated


title: mmem_val_sl001


title: H9 TRE3G 2xFLAG-GSX2 WT 24hr +Dox Replicate 1

description: Library name: Dox_24hr_Rep1


title: H9 TRE3G 2xFLAG-GSX2 WT 24hr -Dox Replicate 3

description: Library name: NoDox_24hr_Rep3


title: rh-14, E2, week 13

description: Library name: H11


title: WT_04, Brain_stem, WT , saline-treated


title: rh-14, E2, week 7

description: Library name: H10


title: Fiko, replicate 3,RNAseq

city: Guangzhou

first: Xiaoling

last: Wang

state: Guangdong

address: No. 195, West Dongfeng Road

institute: Guangzhou Medical University

data_processing:
the quality of the raw data was assessed using FastQC (v0.12.1). The adaptor sequences were trimmed, and low-quality bases were removed using Trim Galore (v0.6.10). Subsequently, the reads were aligned to the mouse reference genome (UCSC mm10) and only uniquely mapped reads (MAPQ > 10) were retained using HISAT2 (v2.2.1). SAMtools v1.7 was used to convert the SAM files to BAM files and to sort the BAM files. PicardMarkDuplicates 2.21.6 was used to remove duplicate reads in the bam files. MACS v.2.1.1 was used for ATAC-seq, CTCF and H3K27ac peak calling. BAM files were then converted to Bigwig files using deepTools (v3.5.4). Motif enrichment analysis was conducted using HOMER. Visualization of signal tracks was performed using IGV and WashU Epigenome Browser.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak,matrix files

source_name: the spleen and lymph nodes

extract_protocol:
FACS-sorted live Treg cells
A total of 200 ng of RNA was used as input for the SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech), following the manufacturer’s protocol. libraries for ATAC-seq CUT&Tag were following manufacturer's protocols

value: the spleen and lymph nodes

value: Treg cells from the spleen and lymph nodes

value: CtcfiKO


title: H9 TRE3G 2xFLAG-GSX2 WT 12hr +Dox Replicate 6

description: Library name: Dox_12hr_Rep6


title: H9 TRE3G 2xFLAG-GSX2 WT 24hr -Dox Replicate 2

description: Library name: NoDox_24hr_Rep2


title: AD_05, Hippocampus_Cortex, 5xFAD , saline-treated

value: brain cells


title: rh-14, E2, week 0

description: Library name: H9

value: Whole blood


title: Fiko, replicate 1,RNAseq


title: rh-10, Placebo, week 27

description: Library name: H8

value: Placebo, LNP/mRNA

value: Placebo


title: H9 TRE3G 2xFLAG-GSX2 WT 24hr -Dox Replicate 1

description: Library name: NoDox_24hr_Rep1


title: Fctr, replicate 3,RNAseq

value: Control


title: Fiko, replicate 2,RNAseq


title: AD_03, Hippocampus_Cortex, 5xFAD , saline-treated

value: saline-treated

value: 6 months


title: H9 TRE3G 2xFLAG-GSX2 WT 12hr +Dox Replicate 4

description: Library name: Dox_12hr_Rep4

value: human embryonic stem cell

value: TRE3G 2xFLAGGSX2 WT

value: 100ng/mL Dox


title: rh-10, Placebo, week 19

description: Library name: H6


title: WT_05, Brain_stem, WT , saline-treated

value: WT


title: rh-10, Placebo, week 23

description: Library name: H7


title: H9 TRE3G 2xFLAG-GSX2 WT 12hr +Dox Replicate 3

description: Library name: Dox_12hr_Rep3

value: LGE-like differentiation


title: H9 TRE3G 2xFLAG-GSX2 WT 12hr +Dox Replicate 5

description: Library name: Dox_12hr_Rep5


title: AD_06, Hippocampus_Cortex, 5xFAD , saline-treated


title: rh-10, Placebo, week 18

description: Library name: H5


title: AD_04, Hippocampus_Cortex, 5xFAD , saline-treated


title: H9 TRE3G 2xFLAG-GSX2 WT 12hr +Dox Replicate 2

description: Library name: Dox_12hr_Rep2


title: Ycko, replicate 3, RNAseq

value: CtcfcKo


title: WT_02, Brain_stem, WT , saline-treated


title: rh-10, Placebo, week 13

description: Library name: H4

value: male


title: Ycko, replicate 2, RNAseq

value: the spleen and lymph nodes


title: AD_02, Hippocampus_Cortex, 5xFAD , saline-treated


title: H9 TRE3G 2xFLAG-GSX2 WT 12hr +Dox Replicate 1

description: Library name: Dox_12hr_Rep1


title: rh-10, Placebo, week 7

description: Library name: H3


title: Ycko, replicate 1,RNAseq

value: Treg cells from the spleen and lymph nodes


title: H9 TRE3G 2xFLAG-GSX2 WT 12hr -Dox Replicate 6

description: Library name: NoDox_12hr_Rep6


title: AD_05, Hippocampus, 5xFAD , saline-treated

value: Hippocampus


title: rh-10, Placebo, week 0

description: Library name: H2


title: Yctr, replicate 3, RNAseq

value: CtrlCre


title: H9 TRE3G 2xFLAG-GSX2 WT 12hr -Dox Replicate 5

description: Library name: NoDox_12hr_Rep5


title: AD_03, Hippocampus, 5xFAD , saline-treated

value: brain cells


title: rh-09, Placebo, week 27

description: Library name: H1

value: Whole blood

value: Placebo, LNP/mRNA


title: Fctr, replicate 1,RNAseq

value: Control


title: rh-09, Placebo, week 23

description: Library name: G24

value: Placebo


title: H9 TRE3G 2xFLAG-GSX2 WT 12hr -Dox Replicate 4

description: Library name: NoDox_12hr_Rep4


title: AD_06, Hippocampus, 5xFAD , saline-treated

value: saline-treated

value: 6 months


title: H9 TRE3G 2xFLAG-GSX2 WT 12hr -Dox Replicate 3

description: Library name: NoDox_12hr_Rep3

value: human embryonic stem cell

value: TRE3G 2xFLAGGSX2 WT


title: WT_03, Brain_stem, WT , saline-treated

value: WT


title: AD_04, Hippocampus, 5xFAD , saline-treated


title: Yctr, replicate 1,RNAseq


title: rh-09, Placebo, week 19

description: Library name: G23


title: AD_02, Hippocampus, 5xFAD , saline-treated


title: rh-09, Placebo, week 18

description: Library name: G22


title: E14 mouse utricular sensory epithelium, scRNA-seq

city: SHANGHAI

first: yunzhong

last: zhang

state: SHANGHAI

address: 83 fenyang road, xuhui district

department: Department of ENT Institute and Otorhinolaryngology

institute: Eye & ENT Hospital of Fudan University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw fastq files were aligned to the mouse genome (assembly: GRCm39, Release 109) using the 10X Genomics Cell Ranger 3.1.0 pipeline. Gene expression levels and cell clustering were analyzed using the Seurat R package (v4.1.1). Variation in library size and technical noise were accounted for by normalizing the counts with SCTransform (v0.3.3). Cells of low quality, identified based on the number of reads mapped to each cell and the percentage of mitochondrial reads, were filtered out. Dimensionality reduction and cell clustering were performed using principal component analysis (RunPCA) on highly variable genes, followed by UMAP dimension reduction (RunUMAP). Clusters were pinpointed using the FindNeighbors and FindClusters functions. Garnett (v0.2.8) was used for cell type annotation based on our previously defined marker genes. Harmony was used for integrating utricle sensory epithelium sequencing data at different time points.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: utricular sensory epithelium

extract_protocol:
Utricles were harvested from E14 and P2 mice, followed by the careful mechanical removal of the otolithic membranes. Subsequently, the tissues were incubated with thermolysin to facilitate the detachment of the sensory epithelium. Utricular sensory epithelium were harvested into 1.5 ml tubes and incubated with Accutase (Thermo Fisher Scientific, 00-4666-56) for 15 min at 37°C in a water bath. Gentle trituration was performed every 5 min using a 200 µl low-retention pipette for a total of 50 times. The samples were then centrifuged at 300 × g for 5 min, and the dissociated cells were resuspended in 500 µl of DMEM/F12 and filtered through a 40-µm cell strainer (Millipore). After centrifuging at 300 × g for 5 min, the cell pellets were resuspended in PBS.
For single-cell sequencing, we used the 10X Genomics Chromium platform. Cell suspensions were loaded into the Chromium Controller Instrument, and the Chromium Next GEM Single Cell 3ʹ Library & Gel Bead Kit v3.1, Chromium Next GEM Chip G Single Cell Kit, and Chromium i7 Multiplex Kit were used for all downstream processes, including reverse transcription, cDNA amplification, and library construction. Twenty thousand cells from each sample were targeted for library preparation following the manufacturer's instructions.

value: utricular sensory epithelium


title: H9 TRE3G 2xFLAG-GSX2 WT 12hr -Dox Replicate 2

description: Library name: NoDox_12hr_Rep2

value: LGE-like differentiation


title: H9 TRE3G 2xFLAG-GSX2 WT 12hr -Dox Replicate 1

description: Library name: NoDox_12hr_Rep1


title: rh-09, Placebo, week 13

description: Library name: G21

value: male


title: DDX6deg_total_3

city: Boulder

first: Mika

last: Nevo

state: Colorado

address: 2315 Walnut St

institute: CU Boulder

description: Total

data_processing:
Mapping using hisat2
Annotating using featureCounts
Assembly: mm10
Supplementary files format and content: Matrix of Raw Counts
Supplementary files format and content: Deseq2 output tables

source_name: Naïve ES cells

extract_protocol: none provided

value: Naïve ES cells


title: H9 TRE3G 2xFLAG-GSX2 WT Day 10 Replicate 6

description: Library name: Day10_Rep6


title: DDX6deg_total_2

description: Total


title: AD_01, Hippocampus, 5xFAD , saline-treated


title: H9 TRE3G 2xFLAG-GSX2 WT Day 10 Replicate 5

description: Library name: Day10_Rep5


title: AD_03, Cortex, 5xFAD , saline-treated

value: Cortex


title: Yctr, replicate 2, RNAseq

value: the spleen and lymph nodes

value: Treg cells from the spleen and lymph nodes


title: rh-09, Placebo, week 0

description: Library name: G19


title: DDX6deg_total_1

description: Total


title: H9 TRE3G 2xFLAG-GSX2 WT Day 10 Replicate 4

description: Library name: Day10_Rep4


title: AD_06, Cortex, 5xFAD , saline-treated

value: brain cells


title: rh-08, Placebo, week 27

description: Library name: G18

value: Whole blood


title: H9 TRE3G 2xFLAG-GSX2 WT Day 10 Replicate 3

description: Library name: Day10_Rep3


title: rh-08, Placebo, week 23

description: Library name: G17

value: Placebo, LNP/mRNA


title: P2 mouse utricular sensory epithelium, scRNA-seq

description: 10x Genomics


title: AD_04, Cortex, 5xFAD , saline-treated


title: Fctr, replicate 2,RNAseq

value: Control


title: DDX6deg_poly_2

description: Polysome


title: H9 TRE3G 2xFLAG-GSX2 WT Day 10 Replicate 2

description: Library name: Day10_Rep2


title: AD_02, Cortex, 5xFAD , saline-treated


title: rh-08, Placebo, week 19

description: Library name: G16

value: Placebo


title: rh-08, Placebo, week 18

description: Library name: G15


title: control_total_3

description: Total


title: DDX6deg_poly_1

description: Polysome


title: TRE3G 2xFLAG-GSX2 WT Day 10.5, 2% Input, Replicate 3

description: Library name: Input_Rep3

data_processing:
Quality-controlled FASTQ files were trimmed using TrimGalore to remove adapters and low-quality reads
Trimmed reads were aligned using Bowtie2 and duplicates were removed using Samtools
Reads overlapping blacklisted regions were removed and then peaks were called against input controls using MACS3 (p-value threshold: 1E-3)
Bigwig files were generated using Deeptools with 1x read per genome coverage (RPGC)
Assembly: hg38
Supplementary files format and content: narrowPeak (except for Input control)

extract_protocol:
Monolayers were dissociated with Accutase for 30 minutes and fixed in 1% formaldehyde in DPBS for 10 minutes at room temperature. After quenching and cell lysis, chromatin was sonicated using a Covaris S220 sonicatior
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina and Multiplex Oligos for Illumina kits (NEB). 15µg of sonicated chromatin was used as starting material for input and IP. 60ng of each reaction  were amplified for 4-5 cycles and then size-selected for <500bp. Agilent high-sensitivity D1000 screentapes were used for library QC prior to sequencing.

treatment_protocol:
H9 hESC cultures were differentiated in Essential 6 Media supplemented with: (3 days) LDN193189, SB431542, XAV939; (3 days) LDN193189, SB431542; (4-6 days) IWP2, Activin A
Dox-induced cultures were treated with 100ng/mL doxycycline supplemented in standard differentiation media for 12-hours starting at Day 10

value: 100ng/mL Dox


title: AD_05, Cortex, 5xFAD , saline-treated

value: saline-treated

value: 6 months


title: rh-09, Placebo, week 7

description: Library name: G20


title: AD_01, Cortex, 5xFAD , saline-treated


title: H9 TRE3G 2xFLAG-GSX2 WT Day 10 Replicate 1

description: Library name: Day10_Rep1

value: human embryonic stem cell

value: TRE3G 2xFLAGGSX2 WT


title: rh-08, Placebo, week 13

description: Library name: G14


title: rh-08, Placebo, week 0

description: Library name: G12


title: AD_05, Brain_stem, 5xFAD , saline-treated


title: TRE3G 2xFLAG-GSX2 WT Day 10.5, 2% Input, Replicate 2

description: Library name: Input_Rep2


title: control_total_1

description: Total


title: TRE3G 2xFLAG-GSX2 WT Day 10.5, 2% Input, Replicate 1

description: Library name: Input_Rep1


title: control_poly_3

description: Polysome


title: DDX6deg_poly_3

description: Polysome


title: TRE3G 2xFLAG-GSX2 WT Day 10.5, M2 FLAG ChIP, Replicate 3

description: Library name: ChIP_2xFLAG_GSX2_WT_Rep3

tag: chip antibody

value: M2 FLAG (Sigma Aldrich, F1804)


title: AD_04, Brain_stem, 5xFAD , saline-treated


title: rh-13, E2, week 23

description: Library name: G10

value: E2, LNP/mRNA


title: TRE3G 2xFLAG-GSX2 WT Day 10.5, M2 FLAG ChIP, Replicate 2

description: Library name: ChIP_2xFLAG_GSX2_WT_Rep2

value: LGE-like differentiation


title: control_poly_2

description: Polysome

value: Naïve ES cells


title: TRE3G 2xFLAG-GSX2 WT Day 10.5, M2 FLAG ChIP, Replicate 1

description: Library name: ChIP_2xFLAG_GSX2_WT_Rep1


title: AD_02, Brain_stem, 5xFAD , saline-treated


title: control_poly_1

description: Polysome


title: rh-13, E2, week 19

description: Library name: G9

value: male


title: AD_01, Brain_stem, 5xFAD , saline-treated


title: mES_Ago2_KO_cyto_2

description: Cytoplasm


title: rh-13, E2, week 18

description: Library name: G8


title: MCF10AK666NRep5

city: Nashville

first: Yu

state: TN

address: 2525 West End Ave, Ste 1020

institute: VUMC

description:
Library name: 12100-RB-0044
MCF10A Heterozygous K666N mutant cells

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt (v4.8)
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC (v0.12.1)
Reads were aligned to the Gencode GRCh38.p13 genome using STAR (v2.7.11a)
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimitedtext file includes raw counts for each sample
Supplementary files format and content: csv files include FPKM values for each sample

source_name: breast

growth_protocol: MCF7 cells were grown in DMEM with 10% FBS and 1% Penicillin/Streptomycin. MCF-10A cells were grown in DMEM/F12 with 5% horse serum, 1% Penicillin/Streptomycin, 20 ng/mL epidermal growth factor (EGF), 10 μg/mL human recombinant insulin, 0.5 μg/mL hydrocortisone, and 0.1 μg/mL cholera toxin. T47D cells were grown in RPMI with 10% FBS, 1% Penicillin/Streptomycin, and 0.2 Units/mL human recombinant insulin. Gene-targeted derivatives were cultured as their respective parentals.

extract_protocol:
total RNA was harvested using the Qiagen RNeasy kit.
Library preparation was completed using the Illumina Ribo-Zero Plus rRNA Depletion Kit

value: breast

value: breast cancer cell line

value: MCF10A K666N Rep5


title: 2E_07, Hippocampus_Cortex, 5xFAD , 2E-treated

value: brain cells


title: rh-13, E2, week 13

description: Library name: G7

value: Whole blood


title: control_total_2

description: Total


title: AD_03, Brain_stem, 5xFAD , saline-treated


title: 2E_06, Hippocampus_Cortex, 5xFAD , 2E-treated


title: MCF10AK666NRep2

description:
Library name: 12100-RB-0032
MCF10A Heterozygous K666N mutant cells

value: MCF10A K666N Rep2


title: mES_Ago2_KO_pbody_2

description: Pbody


title: mES_Ago2_KO_cyto_1

description: Cytoplasm


title: 2E_05, Hippocampus_Cortex, 5xFAD , 2E-treated


title: rh-13, E2, week 0

description: Library name: G5


title: rh-13, E2, week 7

description: Library name: G6


title: rh-13, E2, week 27

description: Library name: G11


title: AD_06, Brain_stem, 5xFAD , saline-treated


title: rh-07, Placebo, week 27

description: Library name: G4

value: Placebo, LNP/mRNA

value: Placebo


title: mES_Ago2_KO_pbody_1

description: Pbody


title: 2E_04, Hippocampus_Cortex, 5xFAD , 2E-treated


title: MCF10AK666NC4PreCre

description:
Library name: 12100-RB-0030
Pre-Cre clone for MCF10A K666N derivatives. Contains the antibiotic selection cassette, limiting expression of the edited allele

value: MCF10A K666N C4 PreCre


title: MEF-reprog-d3-NudT21_cyto_2

description: Cytoplasm

source_name: Embryonic Fibroblasts

value: Embryonic Fibroblasts


title: 2E_02, Hippocampus_Cortex, 5xFAD , 2E-treated

value: 6 months


title: rh-07, Placebo, week 23

description: Library name: G3


title: MCF10AK700EK11B

description:
Library name: 12100-RB-0028
MCF10A Heterozygous K700E mutant cells

value: MCF10A K700E K11B


title: MCF10APrt

description:
Library name: 12100-RB-0027
MCF10As are a breast epithelial cell line. Parentals are unedited

value: MCF10A Parental


title: 2E_08, Hippocampus_Cortex, 5xFAD , 2E-treated


title: rh-07, Placebo, week 18

description: Library name: G1


title: MEF-reprog-d3-ctrl_cyto_1

description: Cytoplasm


title: MCF7A47DRevWTD10

description:
Library name: 12100-RB-0014
Re-single cell diluted clones derived from K700E mutant clone A47D that have lost the mutation and are wildtype

value: MCF7 A4 7D RevWT D10


title: 2E_07, Hippocampus, 5xFAD , 2E-treated

value: Hippocampus


title: MCF10AK666NRep1

description:
Library name: 12100-RB-0031
MCF10A Heterozygous K666N mutant cells

value: MCF10A K666N Rep1


title: rh-07, Placebo, week 13

description: Library name: F24

value: male


title: MEF-ctrl_cyto_2

description: Cytoplasm


title: rh-07, Placebo, week 7

description: Library name: F23


title: MEF-ctrl_cyto_1

description: Cytoplasm


title: MCF7R625H12DF8

description:
Library name: 12100-RB-0026
MCF7 R625H mutant clone derived from PreCre clone 12D. Variable VAFs due to mutation reversion.

value: breast

value: MCF7 R625H 12D F8


title: 2E_05, Hippocampus, 5xFAD , 2E-treated


title: 2E_06, Hippocampus, 5xFAD , 2E-treated


title: rh-07, Placebo, week 0

description: Library name: F22


title: MCF10AK700EK32B

description:
Library name: 12100-RB-0029
MCF10A Heterozygous K700E mutant cells

value: breast cancer cell line

value: MCF10A K700E K32B


title: rh-06, Placebo, week 27

description: Library name: F21

value: Whole blood


title: rh-07, Placebo, week 19

description: Library name: G2


title: MEF-reprog-d3-NudT21_cyto_1

description: Cytoplasm


title: MEF-reprog-d3-ctrl_cyto_2

description: Cytoplasm


title: 2E_03, Hippocampus_Cortex, 5xFAD , 2E-treated

value: brain cells


title: MCF7R625H12DG5

description:
Library name: 12100-RB-0025
MCF7 R625H mutant clone derived from PreCre clone 12D. Variable VAFs due to mutation reversion.

value: MCF7 R625H 12D G5


title: 2E_02, Hippocampus, 5xFAD , 2E-treated


title: rh-06, Placebo, week 23

description: Library name: F20

value: Placebo, LNP/mRNA

value: Placebo


title: MEF-reprog-d3-NudT21_pbody_1

description: Pbody

value: Embryonic Fibroblasts


title: MEF-reprog-d3-NudT21_pbody_2

description: Pbody


title: MCF7R625C5H5H

description:
Library name: 12100-RB-0023
MCF7 R625C mutant clone derived from PreCre clone 5H. Variable VAFs due to mutation reversion.

value: MCF7 R625C 5H 5H


title: 2E_08, Hippocampus, 5xFAD , 2E-treated

value: 6 months


title: rh-06, Placebo, week 19

description: Library name: F19


title: MCF7A47DRevWTH7

description:
Library name: 12100-RB-0013
Re-single cell diluted clones derived from K700E mutant clone A47D that have lost the mutation and are wildtype

value: MCF7 A4 7D RevWT H7


title: MEF-reprog-d3-ctrl_pbody_1

description: Pbody


title: MCF7R625C6EB8

description:
Library name: 12100-RB-0024
MCF7 R625C mutant clone derived from PreCre clone 6E. Variable VAFs due to mutation reversion.

value: MCF7 R625C 6E B8


title: MCF7R625C5H4H

description:
Library name: 12100-RB-0022
MCF7 R625C mutant clone derived from PreCre clone 5H. Variable VAFs due to mutation reversion.

value: MCF7 R625C 5H 4H


title: 2E_03, Hippocampus, 5xFAD , 2E-treated

value: Hippocampus


title: rh-06, Placebo, week 18

description: Library name: F18

value: male


title: MEF-ctrl_pbody_2

description: Pbody


title: MCF7R625H12DPreCre

description:
Library name: 12100-RB-0021
MCF7 R625H PreCre Mutant clone 12D, again PreCre cells contain the antibiotic selection cassettee leading to variable mutant allele expression.

value: breast

value: MCF7 R625H 12D PreCre


title: 2E_01, Hippocampus, 5xFAD , 2E-treated


title: rh-06, Placebo, week 13

description: Library name: F17


title: MEF-ctrl_pbody_1

description: Pbody


title: rh-06, Placebo, week 7

description: Library name: F16


title: 2E_04, Hippocampus, 5xFAD , 2E-treated


title: mES_primed_cyto_2

description: Cytoplasm

source_name: Primed ES cells

value: Primed ES cells


title: MCF7R625C5HPreCre

description:
Library name: 12100-RB-0019
MCF7 R625C PreCre Mutant clone 5H, again PreCre cells contain the antibiotic selection cassettee leading to variable mutant allele expression.

value: breast cancer cell line

value: MCF7 R625C 5H PreCre


title: 2E_06, Cortex, 5xFAD , 2E-treated

value: brain cells

value: Cortex


title: MEF-reprog-d3-ctrl_pbody_2

description: Pbody


title: MCF7K700EC212G

description:
Library name: 12100-RB-0018
MCF7 K700E mutant clone derived from PreCre clone C2. Variable VAFs due to mutation reversion.

value: MCF7 K700E C2 12G


title: mES_primed_cyto_1

description: Cytoplasm


title: 2E_05, Cortex, 5xFAD , 2E-treated


title: rh-06, Placebo, week 0

description: Library name: F15

value: Whole blood

value: Placebo


title: mES_naive_cyto_2

description: Cytoplasm

value: Naïve ES cells


title: MCF7K700EA47D

description:
Library name: 12100-RB-0017
MCF7 K700E mutant clone derived from PreCre clone A4. Variable VAFs due to mutation reversion.

value: MCF7 K700E A4 7D


title: 2E_04, Cortex, 5xFAD , 2E-treated

value: 6 months


title: MCF7K700EC2PreCre

description:
Library name: 12100-RB-0016
MCF7 K700E PreCre Mutant clone C2, again PreCre cells contain the antibiotic selection cassettee leading to variable mutant allele expression.

value: MCF7 K700E C2 PreCre


title: MCF7K700EA4PreCre

description:
Library name: 12100-RB-0015
MCF7 K700E PreCre Mutant clone A4, again PreCre cells contain the antibiotic selection cassettee leading to variable mutant allele expression.

value: MCF7 K700E A4 PreCre


title: mES_primed_pbody_2

description: Pbody


title: 2E_02, Cortex, 5xFAD , 2E-treated


title: rh-05, Placebo, week 23

description: Library name: F13

value: Placebo, LNP/mRNA


title: rh-05, Placebo, week 19

description: Library name: F12

value: male


title: 2E_03, Cortex, 5xFAD , 2E-treated


title: rh-05, Placebo, week 18

description: Library name: F11


title: mES_primed_pbody_1

description: Pbody


title: 2E_07, Cortex, 5xFAD , 2E-treated


title: MCF7ReScd

description:
Library name: 12100-RB-0010
An unedited, single cell diluted, monoclonal control

value: breast

value: MCF7 Re Scd


title: mES_naive_pbody_2

description: Pbody


title: rh-05, Placebo, week 13

description: Library name: F10


title: 2E_01, Cortex, 5xFAD , 2E-treated


title: MCF7Prt

description:
Library name: 12100-RB-0009
MCF7 is a breast cancer cell line. Parental is unedited cells

value: MCF7 Parental


title: MCF7R625C6EPreCre

description:
Library name: 12100-RB-0020
MCF7 R625C PreCre Mutant clone 6E, again PreCre cells contain the antibiotic selection cassettee leading to variable mutant allele expression.

value: breast cancer cell line

value: MCF7 R625C 6E PreCre


title: 2E_08, Cortex, 5xFAD , 2E-treated

value: brain cells


title: mES_naive_pbody_1

description: Pbody


title: rh-05, Placebo, week 27

description: Library name: F14


title: rh-05, Placebo, week 7

description: Library name: F9


title: rh-05, Placebo, week 0

description: Library name: F8


title: PB_D29-CL

city: Pirassununga

first: Flavio

middle: Vieira

last: Meirelles

state: Sao Paulo

address: Duque de caxias

department: Veterinary Medicine

country: Brazil

institute: University of Sao Paulo

description:
Single-Oocyte-PB WGBS
wgbs_count_table.txt
wgbs_count_table.txt

data_processing:
Trimgalore / cutadapt
STAR/Bismark
featurecounts
DEESEQ2/methylKit
PCIT / CETF
Assembly: ARS-UCD 1.2
Supplementary files format and content: Raw counts for each sample in .txt file
Supplementary files format and content: NDA

organism: Bos taurus

source_name: First polar body

extract_protocol:
The SMART-Seq®HT kit (Takara Bio, USA) / EpiTect Fast Bisulfite
NextEra XT Stranded mRNA Sample Prep kit following manufacturer instructions/NEBNext Ultra II DNA library

value: First polar body

value: Diploid

value: First polar body_Diploid


title: 2E_07, Brain_stem, 5xFAD , 2E-treated


title: T47DK700E8F11G

description:
Library name: 12100-RB-0007
Heterozygous K700E mutant cells, clone 11G. Derived from PreCre clone 8F


title: rh-11, E2, week 27

description: Library name: F7

value: Whole blood

value: E2, LNP/mRNA


title: PB_D27-BL


title: 2E_06, Brain_stem, 5xFAD , 2E-treated


title: T47DK700E8F9F

description:
Library name: 12100-RB-0006
Heterozygous K700E mutant cells, clone 9F. Derived from PreCre clone 8F


title: T47DK700E4G2F

description:
Library name: 12100-RB-0005
Heterozygous K700E mutant cells, clone 2F. Derived from PreCre clone 4G


title: mES_naive_cyto_1

description: Cytoplasm

value: Naïve ES cells


title: PB_D10-CL


title: T47DK700E8FPreCre

description:
Library name: 12100-RB-0003
T47D K700E PreCre Clone 8F. "Pre-Cre" is an intermediate state in the editing process where there is an intronic selection cassettee that disrupts expression of the mutant allele, but the extent of mutant expression around the cassettee may vary.

value: T47D K700E 8F PreCre


title: T47DK700E4G1H

description:
Library name: 12100-RB-0004
Heterozygous K700E mutant cells, clone 1H. Derived from PreCre clone 4G


title: rh-11, E2, week 23

description: Library name: F6


title: PB_D24-BL


title: 2E_04, Brain_stem, 5xFAD , 2E-treated

value: 6 months


title: 2E_02, Brain_stem, 5xFAD , 2E-treated


title: PB_B23-CL


title: rh-11, E2, week 13

description: Library name: F3


title: T47DPrt

description:
Library name: 12100-RB-0001
T47D is a breast cancer cell line - The "Parentals" are unedited cells

value: T47D Parental


title: PB_B21-BL


title: T47DK700E4GPreCre

description:
Library name: 12100-RB-0002
T47D K700E PreCre Clone 4G. "Pre-Cre" is an intermediate state in the editing process where there is an intronic selection cassettee that disrupts expression of the mutant allele, but the extent of mutant expression around the cassettee may vary.

value: T47D K700E 4G PreCre


title: rh-11, E2, week 7

description: Library name: F2

value: male


title: rh-11, E2, week 18

description: Library name: F4


title: PB_B20-BL


title: 2E_08, Brain_stem, 5xFAD , 2E-treated


title: rh-11, E2, week 0

description: Library name: F1


title: 2E_03, Brain_stem, 5xFAD , 2E-treated


title: AP CTO mouse tumor organoids; vehicle control; replicate 3

status: Public on Sep 29 2025

city: Barcelona

first: Adria-Jaume

last: Roura

address: Carrer de Baldiri Reixac, 10

country: Spain

institute: IRB Barcelona

description:
Library name: Sample 21
Column name in raw_counts_CTO13_samples.txt: 3145_2025

data_processing:
Trim Galore (v0.0.6) was utilized for quality control and adapter trimming of FASTQ files
Single-end reads were aligned to the mm10 mouse genome using STAR (v2.7.10a)
The count matrix was generated with Rsubread’s featureCounts function, using the GENCODE (vM25/Ensembl100) primary assembly GTF annotation
Differential expression analysis was performed with DESeq2 (v1.42.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: CRISPR-generated Tumor Organoid (CTO)

extract_protocol:
RNA  was extracted using the PureLinkTM RNA Mini Kit (Life Technologies, 12183025) and PureLinkTM DNAse (Life Technologies, 12185010) following the manufacturer’s specifications. RNA was eluted using distilled water (Invitrogen, 10977-035) and the concentration was determined using the Nanodrop 1000 spectrophotometer (ThermoFisher)
Libraries were prepared using RNA-seq Stranded mRNA Library Illumina and sequenced with Illumina NextSeq 2000 P3. Trim Galore (v0.0.6) was utilized for quality control and adapter trimming of FASTQ files

value: CRISPR-generated Tumor Organoid (CTO)

value: Epithelial malignant cells

value: AP mutant


title: AP CTO mouse tumor organoids; RM-044; replicate 3

description:
Library name: Sample 24
Column name in raw_counts_CTO13_samples.txt: 3154_2025

value: RM-044 KRASi


title: APK CTO mouse tumor organoids; MRTX; replicate 3

description:
Library name: Sample 18
Column name in raw_counts_CTO20_samples.txt: 3172_2025

value: APK mutant

value: MRTX


title: AP CTO mouse tumor organoids; vehicle control; replicate 1

description:
Library name: Sample 19
Column name in raw_counts_CTO13_samples.txt: 3143_2025


title: Human Lungs

city: New Haven

first: Andrés

last: Hidalgo

address: 10 Amistad Street

institute: Yale University

description: Library name: TMA9

data_processing:
Manual detection of spots under the tissue: 10X Genomics Loupe Browser v.8.1.2
Reads alignment: 10X Genomics Spaceranger Count v.3.1.1 passing following parameters: —cytaimage —loupe-alignment and —image
Assembly: GRCh38-2020-A
Supplementary files format and content: filtered_feature_bc_matrix.h5: filtered feature barcode matrix in h5 format
Supplementary files format and content: raw_feature_bc_matrix.h5: raw feature barcode matrix in h5 format
Supplementary files format and content: raw_probe_bc_matrix.h5
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: aligned_tissue_image.jpg: aligned tissue image to the expression spots
Supplementary files format and content: cytassist_image.tiff: cytassist image used by SpaceRanger
Supplementary files format and content: detected_tissue_image.jpg: Image containing the detected spots under tissue
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.parquet: list of spatial barcodes and the coordinates specifying spots in parquet format
Supplementary files format and content: b2c_TMA9_mpp0.38_prob0.1_nms0.1.h5ad: h5ad object containing the output of bin2cell. Used for downstream analyses.
Supplementary files format and content: H1-RTF6MBB-A1-fiducials-image-registration: contains the manual detection of spots under the tissue. Passed to SpaceRanger with —loupe-alignment argument.
Supplementary files format and content: CytAssist_TMA9.tif: contains the CytAssist image passed with the —cytaimage argument to SpaceRanger
Supplementary files format and content: HnE_TMA9.tif: contains the high resolution HnE image passed with the —image argument to SpaceRanger
Library strategy: Spatial Transcriptomics

source_name: Lung

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) pulmonary invasive adenocarcinoma and adjacent lung tissue sections (5 μm) were mounted on Visium CytAssist HD slides (10x Genomics). Sections underwent deparaffinization, decrosslinking, probe hybridization, ligation, and extension according to the manufacturer’s protocol.
Spatial barcoding and sample indexing were performed on Visium CytAssist HD slides (10x Genomics) following the manufacturer’s instructions. Final libraries were assessed for quality and fragment size using an Agilent Bioanalyzer High Sensitivity chip, and sequenced on an Illumina NovaSeq X Plus platform (PE100, 1.5B reads/lane).

value: Lung

value: Lungs cell types


title: 2E_05, Brain_stem, 5xFAD , 2E-treated

value: brain cells


title: AP CTO mouse tumor organoids; vehicle control; replicate 2

description:
Library name: Sample 20
Column name in raw_counts_CTO13_samples.txt: 3144_2025


title: 2E_01, Brain_stem, 5xFAD , 2E-treated


title: AP CTO mouse tumor organoids; RM-044; replicate 2

description:
Library name: Sample 23
Column name in raw_counts_CTO13_samples.txt: 3153_2025


title: rh-11, E2, week 19

description: Library name: F5

value: Whole blood


title: APK CTO mouse tumor organoids; MRTX; replicate 1

description:
Library name: Sample 16
Column name in raw_counts_CTO20_samples.txt: 3170_2025


title: APK CTO mouse tumor organoids; MRTX; replicate 2

description:
Library name: Sample 17
Column name in raw_counts_CTO20_samples.txt: 3171_2025


title: APK CTO mouse tumor organoids; RM-044; replicate 2

description:
Library name: Sample 14
Column name in raw_counts_CTO20_samples.txt: 3168_2025


title: APK CTO mouse tumor organoids; vehicle control; replicate 3

description:
Library name: Sample 12
Column name in raw_counts_CTO20_samples.txt: 3163_2025


title: APK CTO mouse tumor organoids; vehicle control; replicate 2

description:
Library name: Sample 11
Column name in raw_counts_CTO20_samples.txt: 3162_2025


title: APK CTO mouse tumor organoids; RM-044; replicate 3

description:
Library name: Sample 15
Column name in raw_counts_CTO20_samples.txt: 3169_2025


title: APK CTO mouse tumor organoids; RM-044; replicate 1

description:
Library name: Sample 13
Column name in raw_counts_CTO20_samples.txt: 3167_2025


title: AKTP MTO mouse tumor organoids; MRTX; replicate 1

description:
Library name: Sample 7
Column name in raw_counts_MTO93_samples.txt: 3182_2025

source_name: Mouse Tumor Organoids (MTO)

value: Mouse Tumor Organoids (MTO)

value: AKTP mutant


title: AKTP MTO mouse tumor organoids; MRTX; replicate 3

description:
Library name: Sample 9
Column name in raw_counts_MTO93_samples.txt: 3184_2025


title: AKTP MTO mouse tumor organoids; RM-044; replicate 3

description:
Library name: Sample 6
Column name in raw_counts_MTO93_samples.txt: 3181_2025


title: AKTP MTO mouse tumor organoids; MRTX; replicate 2

description:
Library name: Sample 8
Column name in raw_counts_MTO93_samples.txt: 3183_2025


title: AP CTO mouse tumor organoids; RM-044; replicate 1

description:
Library name: Sample 22
Column name in raw_counts_CTO13_samples.txt: 3152_2025


title: AKTP MTO mouse tumor organoids; RM-044; replicate 1

description:
Library name: Sample 4
Column name in raw_counts_MTO93_samples.txt: 3179_2025


title: AKTP MTO mouse tumor organoids; RM-044; replicate 2

description:
Library name: Sample 5
Column name in raw_counts_MTO93_samples.txt: 3180_2025


title: AKTP MTO mouse tumor organoids; vehicle control; replicate 2

description:
Library name: Sample 2
Column name in raw_counts_MTO93_samples.txt: 3174_2025


title: AKTP MTO mouse tumor organoids; vehicle control; replicate 3

description:
Library name: Sample 3
Column name in raw_counts_MTO93_samples.txt: 3175_2025


title: AKTP MTO mouse tumor organoids; vehicle control; replicate 1

description:
Library name: Sample 1
Column name in raw_counts_MTO93_samples.txt: 3173_2025


title: APK CTO mouse tumor organoids, RM-044, replicate 3

description:
Library name: Sample 12
Column name in raw_counts_All_samples.txt: 2903_2024_S49


title: APK CTO mouse tumor organoids, RM-044, replicate 2

description:
Library name: Sample 11
Column name in raw_counts_All_samples.txt: 2901_2024_S48


title: APK CTO mouse tumor organoids, vehicle control, replicate 3

description:
Library name: Sample 9
Column name in raw_counts_All_samples.txt: 2898_2024_S46


title: APK CTO mouse tumor organoids, vehicle control, replicate 1

description:
Library name: Sample 7
Column name in raw_counts_All_samples.txt: 2896_2024_S44


title: APK CTO mouse tumor organoids, vehicle control, replicate 2

description:
Library name: Sample 8
Column name in raw_counts_All_samples.txt: 2897_2024_S45


title: AKTP MTO mouse tumor organoids, RM-044, replicate 2

description:
Library name: Sample 5
Column name in raw_counts_All_samples.txt: 2856_2024_S42


title: APK CTO mouse tumor organoids, RM-044, replicate 1

description:
Library name: Sample 10
Column name in raw_counts_All_samples.txt: 2900_2024_S47


title: AKTP MTO mouse tumor organoids, RM-044, replicate 3

description:
Library name: Sample 6
Column name in raw_counts_All_samples.txt: 2857_2024_S43


title: AKTP MTO mouse tumor organoids, RM-044, replicate 1

description:
Library name: Sample 4
Column name in raw_counts_All_samples.txt: 2855_2024_S41


title: AKTP MTO mouse tumor organoids, vehicle control, replicate 3

description:
Library name: Sample 3
Column name in raw_counts_All_samples.txt: 2854_2024_S40


title: AKTP MTO mouse tumor organoids, vehicle control, replicate 2

description:
Library name: Sample 2
Column name in raw_counts_All_samples.txt: 2853_2024_S39


title: AKTP MTO mouse tumor organoids, vehicle control, replicate 1

description:
Library name: Sample 1
Column name in raw_counts_All_samples.txt: 2852_2024_S38


title: Adult SVZ/NSCs rep3

city: Valencia

first: Jordi

last: Planells

state: Valencia

address: Doctor Moliner, 50 street

department: Biologia celular, biologia funcional y antropologia fisica

institute: Universitat de València

description: Library name: NSCs_rep3

data_processing:
Raw data quality was assessed with FastQC (0.12.1)
Pre-processing has been performed with MEDUSA pipeline (1.0.0, Wilson et al. 2012). Briefly, reads were aligned to mm10 reference genome. Samtools was used to discard reads un-aligned, discordant or optical duplicated.
Signal tracks were produced with deeptools bamCoverage (3.5.4) function using high quality reads (--minMappingQuality 1) at nucleotide resolution (--binSize 1), discarding reads overlapping blacklisted regions (--blacklist https://github.com/Boyle-Lab/Blacklist)
Differential methylation was modeled with MEDIPS R package (1.5.4) with the following arguments: MSet1 = iPSC_meth, MSet2 = NSC_meth, CSet = CS,diffnorm = "tmm", p.adj = "bonferroni", diff.method = "edgeR", MeDIP = TRUE, minRowSum = 10.
Adjacent windows were merged with mergeByHMP function in extraChIPs package (1.6.4) and mean harmonic values were calculated.
Assembly: mm10
Supplementary files format and content: Windows with differential methylation information obtained with MEDIPS in compressed tabular format (one for all samples)
Supplementary files format and content: Scaled methylation signal in bigWig format (one per sample)

source_name: Brain

growth_protocol: NSCs were grown as detailed in Belenguer et al. 2016 (https://doi.org/10.1016/j.diff.2016.01.005). For iPSCs growth 2i media supplemented with N2B27, LIF (1x, 1000x stock, homemade), iMEK inhibitor (1 µM, 10 mM stock, Millipore, Cat. No. 444968), and iGSK3β inhibitor (3 µM, 10 mM stock, Millipore, Cat. No. 361571) was used.

extract_protocol:
DNA easy (Qiagen)
NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina

treatment_protocol: To generate iPSCs from adult NSCs exogenous Oct4 together with Klf4 (2F) were virally transfected for reprogramming as previously described (Kim et al., 2008; Kim et al., 2009). Parallely, in NSCs, a pMXs mCherry vector was used as a control transfection.

value: Brain

value: Adult NSCs

value: mCherry control transfection


title: dxo1_path_3

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

description: Library name: dxo1_path_3

data_processing:
In our sequencing strategy, the R1 reads of pooled libraries contain two parts of UMI split by the barcode. We rearrange UMI sequences to position them next to each other: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Fastq files for read R2 of pooled libraries were demultiplexed into separate fastq files for each replicate using BRBseqTools (v 1.6) Demultiplex and R1 with parameters -p UB -UMI 14 -n 1. The resulting reads were trimmed to eliminate potential contamination with the poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then, they were mapped using STAR (v 2.7.8a) with parameters --sjdbOverhang 99 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the deduplicated counts for each gene were obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes.
Assembly: TAIR10
Supplementary files format and content: count text files

organism: Arabidopsis thaliana

source_name: 6-week-old plants

growth_protocol: Plants were grown at growth chambers under a 16 h light/8 h dark (long-day).

extract_protocol:
Total RNA was isolated using TRI Reagent (Sigma-Aldrich) according to the manufacturer’s instructions.
500 ng of RNA was used in reverse transcription with 50 mM of various barcoded oligo(dT) primers and SuperScript III. 0.25 of each reaction was pooled. cDNA pools were purified with Ampure beads (1.5x beads to sample volumes) and then eluted in 17 µl of water. 15 µl of the recovered cDNA pools were mixed by pipetting with 15 µl of the second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 µM dNTPs) and incubated overnight at 16°C. The reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 µl of water. 3 µl of the recovered dsDNA samples were used for tagmentation with 3 µl of 5x diluted B-loaded Tn5 enzyme (homemade) and 6 µl of freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). The reactions were mixed by pipetting and incubated for 7 minutes at 55°C, followed by 5 minutes at 80°C. Water was added to a total volume of 36 µl; samples were purified with Ampure beads (1.2x beads to sample volumes) and eluted with 21 µl of water. Illumina indexing PCRs were performed using 20 µl of the tagmented DNA in a 50 µl reaction with Q5 2× PCR Master Mix (NEB) and a final concentration of 0.5 µM of primers. Libraries were sequenced on the Illumina Next-seq to obtain two reads: R1 (containing barcode and UMI) and R2 (containing mRNA sequence).

treatment_protocol: 6-week-old plants were inoculated by spraying with the Pst suspension in 10 mM MgCl2.

value: 6-week-old plants

value: Pseudomonas syringae pv. tomato strain DC3000


title: Adult SVZ/NSCs rep2

description: Library name: NSCs_rep2


title: Adult SVZ/NSCs rep1

description: Library name: NSCs_rep1


title: Reprogrammed adult SVZ/NSCs rep1

description: Library name: iPSCs_rep1

value: Reprogrammed adult NSCs

value: Oct4 + Klf4 transfection


title: dxo1_path_2

description: Library name: dxo1_path_2


title: Reprogrammed adult SVZ/NSCs rep2

description: Library name: iPSCs_rep2


title: dxo1_path_1

description: Library name: dxo1_path_1


title: APK CTO mouse tumor organoids; vehicle control; replicate 1

description:
Library name: Sample 10
Column name in raw_counts_CTO20_samples.txt: 3161_2025

value: CRISPR-generated Tumor Organoid (CTO)

value: Epithelial malignant cells


title: dxo1_mock_4

description: Library name: dxo1_mock_4

value: mock


title: dxo1_mock_2

description: Library name: dxo1_mock_2


title: dxo1_mock_1

description: Library name: dxo1_mock_1


title: Col0_path_4

description: Library name: Col0_path_4


title: dxo1_mock_3

description: Library name: dxo1_mock_3


title: Col0_path_3

description: Library name: Col0_path_3


title: Col0_path_2

description: Library name: Col0_path_2


title: Col0_path_1

description: Library name: Col0_path_1


title: Col0_mock_3

description: Library name: Col0_mock_3


title: Col0_mock_2

description: Library name: Col0_mock_2


title: Col0_mock_1

description: Library name: Col0_mock_1


title: dxo1_path_4

description: Library name: dxo1_path_4


title: PCa_148

type: genomic

city: Camperdown

first: Jenna

last: Craddock

state: NSW

address: Johns Hopkins Dr

department: School of Medical Sciences

country: Australia

institute: University of Sydney

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: TSH030

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol.

scan_protocol: Standard Illumina protocol.

data_processing:
All samples were processed and normalised using the RnBeads pipeline using the rnb.execute.normalization() function with methods "scaling.internal" and "sesame.noobsb" for normalisation and background correction, respectively.
RnBeads computed normalised beta values.

label: Cy3 and Cy5

source_name: prostate tissue

label_protocol: Standard Illumina protocol.

extract_protocol: Snap-frozen tissue cores were retrieved and DNA extracted using the Qiagen AllPrep kit (Qiagen).

value: prostate tissue

value: male

tag: disease state

value: Prostate tumour

value: treatment-naïve


title: PCa_150

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: UP2048


title: PCa_152

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: TAF003


title: PCa_151

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: UP2077


title: PCa_149

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: TSH031


title: PCa_147

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: TSH027


title: PCa_146

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: TSH026


title: PCa_145

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: TSH024


title: PCa_140

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: TAf008


title: PCa_139

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: TAf007


title: PCa_141

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: TAf010


title: PCa_137

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: SMU0202


title: PCa_143

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: TSH020


title: PCa_138

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: SMU203


title: PCa_142

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: TSH019


title: PCa_135

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: SMU0210


title: PCa_136

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: SMU214


title: PCa_134

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: SMU201


title: PCa_132

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: SMU0147


title: Col0_mock_4

description: Library name: Col0_mock_4


title: PCa_130

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: PUH0052


title: PCa_133

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: SMU0170


title: PCa_131

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: PUH0058


title: PCa_129

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: PUH0033


title: PCa_126

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: KAL0026


title: PCa_127

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: KAL0061


title: PCa_128

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: PUH0019


title: PCa_125

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: KAL0114


title: PCa_123

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: KAL0009


title: PCa_122

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: KAL0008


title: PCa_124

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: KAL0113


title: PCa_121

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: KAL0007


title: PCa_144

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: TSH021


title: NoPCa_6

description: matrix_sample_id: TAF002

data_processing:
All samples were processed and normalised using the RnBeads pipeline using the rnb.execute.normalization() function with methods "scaling.internal" and "sesame.noobsb" for normalisation and background correction, respectively.
Matrix files includes RnBeads computed normalised beta values.

value: Non-tumour prostate tissue


title: NoPCa_5

description: matrix_sample_id: TAF001


title: NoPCa_7

description: matrix_sample_id: TAF004


title: PCa_68

description: matrix_sample_id: UP2119


title: PCa_69

description: matrix_sample_id: UP2133


title: PCa_65

description: matrix_sample_id: UP2099


title: PCa_70

description: matrix_sample_id: UP2204


title: PCa_66

description: matrix_sample_id: UP2113


title: PCa_67

description: matrix_sample_id: UP2116


title: PCa_64

description: matrix_sample_id: UP2052


title: PCa_63

description: matrix_sample_id: UP2039


title: PCa_62

description: matrix_sample_id: TSH029


title: NoPCa_4

description: matrix_sample_id: UP2037


title: NoPCa_3

description: matrix_sample_id: TSH033


title: NoPCa_2

description: matrix_sample_id: TSH022


title: PCa_61

description: matrix_sample_id: SMU0156


title: PCa_58

description: matrix_sample_id: SMU0204


title: PCa_59

description: matrix_sample_id: SMU205


title: PCa_60

description: matrix_sample_id: SMU0217


title: PCa_54

description: matrix_sample_id: PUH0087


title: PCa_55

description: matrix_sample_id: PUH0081


title: PCa_57

description: matrix_sample_id: SMU0118


title: PCa_53

description: matrix_sample_id: PUH0071


title: PCa_51

description: matrix_sample_id: PUH0050


title: PCa_50

description: matrix_sample_id: PUH0041


title: PCa_48

description: matrix_sample_id: PUH0031


title: PCa_46

description: matrix_sample_id: PUH0026


title: PCa_47

description: matrix_sample_id: PUH0028


title: PCa_49

description: matrix_sample_id: PUH0036


title: PCa_43

description: matrix_sample_id: PUH0022


title: PCa_41

description: matrix_sample_id: PUH0018


title: PCa_42

description: matrix_sample_id: PUH0020


title: PCa_44

description: matrix_sample_id: PUH0024


title: PCa_45

description: matrix_sample_id: PUH0025


title: PCa_40

description: matrix_sample_id: PUH0016


title: PCa_38

description: matrix_sample_id: PUH0012


title: PCa_33

description: matrix_sample_id: PUH0003


title: PCa_32

description: matrix_sample_id: PUH0002


title: PCa_30

description: matrix_sample_id: KAL0060


title: PCa_71

description: matrix_sample_id: UP2243


title: PCa_39

description: matrix_sample_id: PUH0014


title: PCa_52

description: matrix_sample_id: PUH0070


title: NoPCa_1

description: matrix_sample_id: KAL0040


title: PCa_31

description: matrix_sample_id: PUH0001


title: PCa_29

description: matrix_sample_id: KAL0039


title: PCa_34

description: matrix_sample_id: PUH0007


title: PCa_37

description: matrix_sample_id: PUH0010


title: PCa_28

description: matrix_sample_id: KAL0028


title: PCa_35

description: matrix_sample_id: PUH0008


title: PCa_25

description: matrix_sample_id: KAL0062


title: PCa_27

description: matrix_sample_id: KAL0018


title: PCa_24

description: matrix_sample_id: KAL0006


title: PCa_23

description: matrix_sample_id: KAL0048


title: PCa_22

description: matrix_sample_id: 20975


title: PCa_21

description: matrix_sample_id: 20841


title: PCa_18

description: matrix_sample_id: 20687


title: PCa_15

description: matrix_sample_id: 20247


title: PCa_17

description: matrix_sample_id: 20432


title: PCa_19

description: matrix_sample_id: 20769


title: PCa_36

description: matrix_sample_id: PUH0009


title: PCa_14

description: matrix_sample_id: 20005


title: PCa_13

description: matrix_sample_id: 19986


title: PCa_12

description: matrix_sample_id: 19967


title: PCa_10

description: matrix_sample_id: 19695


title: PCa_7

description: matrix_sample_id: 19121


title: PCa_6

description: matrix_sample_id: 19119


title: PCa_56

description: matrix_sample_id: SMU0114


title: PCa_8

description: matrix_sample_id: 19396


title: PCa_9

description: matrix_sample_id: 19601


title: PCa_26

description: matrix_sample_id: KAL0064


title: PCa_4

description: matrix_sample_id: 18109


title: PCa_5

description: matrix_sample_id: 18251


title: hepatic NEN [PHNET16]

city: Heidelberg

first: Stephanie

last: Roessler

address: Im Neuenheimer Feld 224

institute: Heidelberg University Hospital

description:
Infinium MethylationEPIC
PHNET16

hyb_protocol: supplier protocol (Illumina)

scan_protocol: supplier protocol (Illumina)

data_processing: Methylation data were processed using the R platform for statistical computing.

source_name: tumor

label_protocol: supplier protocol (Illumina)

extract_protocol: Genomic DNA of the formalin-fixed paraffin-embedded (FFPE) samples was extracted using the AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany).

value: tumor


title: PCa_3

description: matrix_sample_id: 17374


title: PCa_1

description: matrix_sample_id: 14227


title: PCa_2

description: matrix_sample_id: 17210


title: hepatic NEN [PHNET15]

description:
Infinium MethylationEPIC
PHNET15


title: hepatic NEN [PHNET14]

description:
Infinium MethylationEPIC
PHNET14


title: PB_B14-CL

description:
Single-Oocyte-PB WGBS
wgbs_count_table.txt
wgbs_count_table.txt

value: First polar body

value: Diploid

value: First polar body_Diploid


title: hepatic NEN [PHNET13]

description:
Infinium MethylationEPIC
PHNET13


title: PCa_20

description: matrix_sample_id: 20794


title: hepatic NEN [PHNET12]

description:
Infinium MethylationEPIC
PHNET12


title: hepatic NEN [PHNET10]

description:
Infinium MethylationEPIC
PHNET10


title: PCa_16

description: matrix_sample_id: 20426


title: hepatic NEN [PHNET08]

description:
Infinium MethylationEPIC
PHNET08


title: hepatic NEN [PHNET04]

description:
Infinium MethylationEPIC
PHNET04


title: hepatic NEN [PHNET05]

description:
Infinium MethylationEPIC
PHNET05


title: hepatic NEN [PHNET02]

description:
Infinium MethylationEPIC
PHNET02


title: PCa_11

description: matrix_sample_id: 19717


title: Pulmonary carcinoid_patient_179

description:
Infinium MethylationEPIC
242546

data_processing:
Methylation data were processed using the R platform for statistical computing.
Average Beta values in processed data file

label: Cy5 and Cy3

source_name: Pulmonary carcinoid

value: female

value: FFPE


title: Pulmonary carcinoid_patient_184

description:
Infinium MethylationEPIC
242560


title: Pulmonary carcinoid_patient_180

description:
Infinium MethylationEPIC
242548


title: Pulmonary carcinoid_patient_177

description:
Infinium MethylationEPIC
242542


title: hepatic NEN [PHNET03]

description:
Infinium MethylationEPIC
PHNET03


title: Pulmonary carcinoid_patient_183

description:
Infinium MethylationEPIC
242558


title: Pulmonary carcinoid_patient_181

description:
Infinium MethylationEPIC
242550


title: Pulmonary carcinoid_patient_176

description:
Infinium MethylationEPIC
242540


title: Pulmonary carcinoid_patient_171

description:
Infinium MethylationEPIC
242530


title: Pulmonary carcinoid_patient_185

description:
Infinium MethylationEPIC
242568


title: Pulmonary carcinoid_patient_172

description:
Infinium MethylationEPIC
242532


title: Pulmonary carcinoid_patient_174

description:
Infinium MethylationEPIC
242536


title: Pulmonary carcinoid_patient_178

description:
Infinium MethylationEPIC
242544


title: hepatic NEN [PHNET09]

description:
Infinium MethylationEPIC
PHNET09


title: hepatic NEN [PHNET06]

description:
Infinium MethylationEPIC
PHNET06


title: Pulmonary carcinoid_patient_170

description:
Infinium MethylationEPIC
242528


title: Pulmonary carcinoid_patient_165

description:
Infinium MethylationEPIC
242518


title: Pulmonary carcinoid_patient_173

description:
Infinium MethylationEPIC
242534


title: Pulmonary carcinoid_patient_186

description:
Infinium MethylationEPIC
242614


title: Pulmonary carcinoid_patient_164

description:
Infinium MethylationEPIC
242516


title: Pulmonary carcinoid_patient_166

description:
Infinium MethylationEPIC
242520


title: Pulmonary carcinoid_patient_182

description:
Infinium MethylationEPIC
242556


title: hepatic NEN [PHNET01]

description:
Infinium MethylationEPIC
PHNET01


title: Pulmonary carcinoid_patient_168

description:
Infinium MethylationEPIC
242524


title: Pulmonary carcinoid_patient_167

description:
Infinium MethylationEPIC
242522


title: hepatic NEN [PHNET07]

description:
Infinium MethylationEPIC
PHNET07


title: Pulmonary carcinoid_patient_162

description:
Infinium MethylationEPIC
242510


title: Pulmonary carcinoid_patient_169

description:
Infinium MethylationEPIC
242526


title: Pulmonal NEC_patient_160

description:
Infinium MethylationEPIC
242620

source_name: Pulmonal NEC


title: Pulmonal NEC_patient_159

description:
Infinium MethylationEPIC
242616


title: Pulmonal NEC_patient_158

description:
Infinium MethylationEPIC
242612


title: Pulmonal NEC_patient_157

description:
Infinium MethylationEPIC
242608


title: Pulmonal NEC_patient_156

description:
Infinium MethylationEPIC
242606


title: Pulmonal NEC_patient_154

description:
Infinium MethylationEPIC
242602


title: Pulmonal NEC_patient_153

description:
Infinium MethylationEPIC
242600


title: Pulmonal NEC_patient_155

description:
Infinium MethylationEPIC
242604


title: Pulmonal NEC_patient_151

description:
Infinium MethylationEPIC
242596


title: Pulmonal NEC_patient_150

description:
Infinium MethylationEPIC
242594


title: Pulmonary carcinoid_patient_163

description:
Infinium MethylationEPIC
242514


title: Pulmonal NEC_patient_144

description:
Infinium MethylationEPIC
242582


title: Pulmonal NEC_patient_147

description:
Infinium MethylationEPIC
242588


title: Pulmonal NEC_patient_146

description:
Infinium MethylationEPIC
242586


title: Pulmonal NEC_patient_145

description:
Infinium MethylationEPIC
242584


title: Pulmonal NEC_patient_138

description:
Infinium MethylationEPIC
242570


title: Pulmonal NEC_patient_141

description:
Infinium MethylationEPIC
242576


title: Pulmonal NEC_patient_143

description:
Infinium MethylationEPIC
242580


title: Pulmonal NEC_patient_140

description:
Infinium MethylationEPIC
242574


title: Pulmonal NEC_patient_142

description:
Infinium MethylationEPIC
242578


title: Pulmonal NEC_patient_148

description:
Infinium MethylationEPIC
242590


title: NEN stomach_patient_137

description:
Infinium MethylationEPIC
240124

source_name: NEN stomach


title: NEN stomach_patient_136

description:
Infinium MethylationEPIC
240116


title: Pulmonal NEC_patient_139

description:
Infinium MethylationEPIC
242572


title: Pulmonal NEC_patient_161

description:
Infinium MethylationEPIC
242624


title: NEN stomach_patient_134

description:
Infinium MethylationEPIC
240110


title: NEN stomach_patient_135

description:
Infinium MethylationEPIC
240114


title: NEN stomach_patient_133

description:
Infinium MethylationEPIC
240106


title: NEN stomach_patient_132

description:
Infinium MethylationEPIC
240104


title: Pulmonal NEC_patient_152

description:
Infinium MethylationEPIC
242598


title: NEN stomach_patient_131

description:
Infinium MethylationEPIC
240102


title: NEN rectum_patient_130

description:
Infinium MethylationEPIC
240046

source_name: NEN rectum


title: NEN rectum_patient_129

description:
Infinium MethylationEPIC
240032


title: NEN rectum_patient_128

description:
Infinium MethylationEPIC
240030


title: NEN rectum_patient_126

description:
Infinium MethylationEPIC
240012


title: NEN pancreas_patient_124

description:
Infinium MethylationEPIC
240096

source_name: NEN pancreas


title: Pulmonal NEC_patient_149

description:
Infinium MethylationEPIC
242592


title: Pulmonary carcinoid_patient_175

description:
Infinium MethylationEPIC
242538


title: NEN pancreas_patient_125

description:
Infinium MethylationEPIC
240098


title: NEN pancreas_patient_122

description:
Infinium MethylationEPIC
240092


title: NEN pancreas_patient_120

description:
Infinium MethylationEPIC
240088


title: NEN pancreas_patient_121

description:
Infinium MethylationEPIC
240090


title: NEN pancreas_patient_123

description:
Infinium MethylationEPIC
240094


title: NEN pancreas_patient_119

description:
Infinium MethylationEPIC
240086


title: NEN pancreas_patient_118

description:
Infinium MethylationEPIC
240084


title: NEN pancreas_patient_116

description:
Infinium MethylationEPIC
240080


title: NEN pancreas_patient_117

description:
Infinium MethylationEPIC
240082


title: NEN pancreas_patient_114

description:
Infinium MethylationEPIC
240076


title: PCa_195

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DSM088


title: PCa_194

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DOD042


title: PCa_196

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DOD032


title: NEN pancreas_patient_112

description:
Infinium MethylationEPIC
240072


title: NoPCa_70

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DSM020


title: PCa_193

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DOD038


title: NoPCa_69

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DSM035


title: NEN pancreas_patient_110

description:
Infinium MethylationEPIC
240068


title: NEN pancreas_patient_113

description:
Infinium MethylationEPIC
240074


title: NEN pancreas_patient_111

description:
Infinium MethylationEPIC
240070


title: NEN pancreas_patient_108

description:
Infinium MethylationEPIC
240062


title: NEN rectum_patient_127

description:
Infinium MethylationEPIC
240026


title: PCa_190

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DOD082


title: NEN pancreas_patient_105

description:
Infinium MethylationEPIC
240052


title: NEN pancreas_patient_106

description:
Infinium MethylationEPIC
240054


title: PCa_187

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DOD075


title: NEN pancreas_patient_107

description:
Infinium MethylationEPIC
240058


title: NEN pancreas_patient_103

description:
Infinium MethylationEPIC
240048


title: NEN pancreas_patient_104

description:
Infinium MethylationEPIC
240050


title: PCa_188

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DOD080


title: PCa_185

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DOD069


title: PCa_186

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DOD072


title: NEN pancreas_patient_115

description:
Infinium MethylationEPIC
240078


title: PCa_184

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DOD058


title: NEN liver metastasis_patient_102

description:
Infinium MethylationEPIC
242626

source_name: NEN liver metastasis


title: NEN liver metastasis_patient_101

description:
Infinium MethylationEPIC
242622


title: NEN liver metastasis_patient_100

description:
Infinium MethylationEPIC
242618


title: PCa_182

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DOD030


title: NEN liver metastasis_patient_099

description:
Infinium MethylationEPIC
242610


title: PCa_183

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DOD057


title: NEN pancreas_patient_109

description:
Infinium MethylationEPIC
240064


title: NEN liver metastasis_patient_098

description:
Infinium MethylationEPIC
240240


title: PCa_181

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DOD028


title: NoPCa_68

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DOD029


title: PCa_191

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DOD083


title: PCa_192

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DSM030


title: NEN liver metastasis_patient_096

description:
Infinium MethylationEPIC
240194


title: NEN liver metastasis_patient_097

description:
Infinium MethylationEPIC
240220


title: NoPCa_67

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DOD005


title: NEN liver metastasis_patient_095

description:
Infinium MethylationEPIC
240192


title: PCa_189

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DOD081


title: PCa_180

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DOD012


title: U_13

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: NAM5056

value: Unknown


title: NEN liver metastasis_patient_093

description:
Infinium MethylationEPIC
240186


title: NEN ileum_patient_092

description:
Infinium MethylationEPIC
240008

source_name: NEN ileum


title: NoPCa_66

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: NAM5052


title: NEN ileum_patient_091

description:
Infinium MethylationEPIC
240006


title: PCa_179

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: NAM5050


title: NEN ileum_patient_090

description:
Infinium MethylationEPIC
240004


title: NEN ileum_patient_089

description:
Infinium MethylationEPIC
240000


title: U_10

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: NAM0011


title: U_11

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: NAM0012


title: NEN ileum_patient_088

description:
Infinium MethylationEPIC
239996


title: NEN ileum_patient_087

description:
Infinium MethylationEPIC
239994


title: U_8

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: NAM0009


title: U_9

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: NAM0010


title: NEN ileum_patient_086

description:
Infinium MethylationEPIC
239992


title: NEN ileum_patient_082

description:
Infinium MethylationEPIC
239974


title: U_4

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: NAM0005


title: NEN ileum_patient_084

description:
Infinium MethylationEPIC
239980


title: U_5

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: NAM0006


title: NEN ileum_patient_085

description:
Infinium MethylationEPIC
239988


title: NEN ileum_patient_081

description:
Infinium MethylationEPIC
239972


title: U_6

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: NAM0007


title: U_2

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: NAM0003


title: U_3

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: NAM0004


title: NEN liver metastasis_patient_094

description:
Infinium MethylationEPIC
240190


title: NEN ileum_patient_083

description:
Infinium MethylationEPIC
239978


title: U_12

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: NAM0013


title: NEN duodenum_patient_080

description:
Infinium MethylationEPIC
240128

source_name: NEN duodenum


title: NEN duodenum_patient_078

description:
Infinium MethylationEPIC
240120


title: PCa_177

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: 19585


title: PCa_176

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DSM068


title: PCa_175

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DSM049


title: NEN duodenum_patient_079

description:
Infinium MethylationEPIC
240122


title: NEN duodenum_patient_076

description:
Infinium MethylationEPIC
240112


title: NEN duodenum_patient_077

description:
Infinium MethylationEPIC
240118


title: NEN colon transverse_patient_074

description:
Infinium MethylationEPIC
240014

source_name: NEN colon transverse


title: PCa_173

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DSM042


title: PCa_174

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DSM045


title: U_7

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: NAM0008


title: NEN colon sigmoid_patient_073

description:
Infinium MethylationEPIC
240038

source_name: NEN colon sigmoid


title: PCa_172

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DSM039


title: PCa_171

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DSM026


title: NEN colon sigmoid_patient_072

description:
Infinium MethylationEPIC
240036


title: PCa_170

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DSM024


title: NEN colon sigmoid_patient_071

description:
Infinium MethylationEPIC
240022


title: PCa_169

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DSM021


title: NEN colon ascending_patient_070

description:
Infinium MethylationEPIC
240044

source_name: NEN colon ascending


title: NEN colon ascending_patient_069

description:
Infinium MethylationEPIC
240042


title: PCa_168

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DSM015


title: PCa_167

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DSM014


title: NEN colon ascending_patient_068

description:
Infinium MethylationEPIC
240040


title: NEN colon ascending_patient_067

description:
Infinium MethylationEPIC
240034


title: PCa_165

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DSM007


title: PCa_166

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DSM013


title: NEN colon ascending_patient_066

description:
Infinium MethylationEPIC
240024


title: PCa_164

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DOD040


title: PCa_163

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DOD039


title: NEN colon ascending_patient_064

description:
Infinium MethylationEPIC
240018


title: PCa_162

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DOD037


title: NEN colon ascending_patient_065

description:
Infinium MethylationEPIC
240020


title: NEN colon ascending_patient_063

description:
Infinium MethylationEPIC
240016


title: NEN appendix_patient_062

description:
Infinium MethylationEPIC
239970

source_name: NEN appendix


title: PCa_161

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: DOD008


title: PCa_160

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: SMU250


title: PCa_159

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: SMU241


title: NEN appendix_patient_060

description:
Infinium MethylationEPIC
239966


title: NEN appendix_patient_061

description:
Infinium MethylationEPIC
239968


title: NEN duodenum_patient_075

description:
Infinium MethylationEPIC
240100


title: PCa_157

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: SMU243


title: NEN appendix_patient_058

description:
Infinium MethylationEPIC
239962


title: PCa_158

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: SMU275


title: PCa_156

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: SMU271


title: NEN appendix_patient_056

description:
Infinium MethylationEPIC
239958


title: NEN appendix_patient_057

description:
Infinium MethylationEPIC
239960


title: NEN appendix_patient_059

description:
Infinium MethylationEPIC
239964


title: PCa_154

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: KAL0047


title: PCa_153

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: KAL0012


title: NEN appendix_patient_055

description:
Infinium MethylationEPIC
239956


title: PCa_120

description: matrix_sample_id: DOD031


title: NEN appendix_patient_054

description:
Infinium MethylationEPIC
239954


title: NEN appendix_patient_053

description:
Infinium MethylationEPIC
239952


title: PCa_119

description: matrix_sample_id: DSM091


title: NEN appendix_patient_052

description:
Infinium MethylationEPIC
239950


title: NoPCa_64

description: matrix_sample_id: DOD048


title: NEN appendix_patient_051

description:
Infinium MethylationEPIC
239948


title: NoPCa_65

description: matrix_sample_id: DOD049


title: NEN appendix_patient_050

description:
Infinium MethylationEPIC
239946


title: NoPCa_62

description: matrix_sample_id: DOD046


title: NoPCa_63

description: matrix_sample_id: DOD047


title: NEN appendix_patient_049

description:
Infinium MethylationEPIC
239944


title: NEN appendix_patient_048

description:
Infinium MethylationEPIC
239942


title: NoPCa_61

description: matrix_sample_id: DOD044


title: Merkel cell carcinoma_patient_046

description:
Infinium MethylationEPIC
240162

source_name: Merkel cell carcinoma


title: PCa_155

description:
MatrixProcessed_GEO_addition.txt
matrix_sample_id: KAL0052


title: NoPCa_60

description: matrix_sample_id: DOD036


title: NoPCa_59

description: matrix_sample_id: DSM012


title: Merkel cell carcinoma_patient_047

description:
Infinium MethylationEPIC
240164


title: Merkel cell carcinoma_patient_045

description:
Infinium MethylationEPIC
240160


title: Merkel cell carcinoma_patient_044

description:
Infinium MethylationEPIC
240158


title: NoPCa_58

description: matrix_sample_id: DSM081


title: NoPCa_57

description: matrix_sample_id: DSM078


title: Merkel cell carcinoma_patient_042

description:
Infinium MethylationEPIC
240150


title: NoPCa_56

description: matrix_sample_id: DSM050


title: NoPCa_55

description: matrix_sample_id: DSM048


title: Merkel cell carcinoma_patient_043

description:
Infinium MethylationEPIC
240152


title: hepatic NEN_patient_039

description:
Infinium MethylationEPIC
240292

source_name: hepatic NEN


title: Merkel cell carcinoma_patient_040

description:
Infinium MethylationEPIC
240136


title: Merkel cell carcinoma_patient_041

description:
Infinium MethylationEPIC
240146


title: NoPCa_52

description: matrix_sample_id: DSM041


title: NoPCa_54

description: matrix_sample_id: DSM046


title: hepatic NEN_patient_038

description:
Infinium MethylationEPIC
240288


title: NoPCa_53

description: matrix_sample_id: DSM043


title: hepatic NEN_patient_036

description:
Infinium MethylationEPIC
240272


title: hepatic NEN_patient_037

description:
Infinium MethylationEPIC
240274


title: NoPCa_50

description: matrix_sample_id: DSM019


title: hepatic NEN_patient_035

description:
Infinium MethylationEPIC
240268


title: NoPCa_51

description: matrix_sample_id: DSM040


title: hepatic NEN_patient_034

description:
Infinium MethylationEPIC
240262


title: PCa_117

description: matrix_sample_id: DSM025


title: PCa_118

description: matrix_sample_id: DOD045


title: hepatic NEN_patient_032

description:
Infinium MethylationEPIC
240258


title: NoPCa_45

description: matrix_sample_id: DSM028


title: NoPCa_44

description: matrix_sample_id: DSM027


title: NoPCa_48

description: matrix_sample_id: DSM017


title: hepatic NEN_patient_031

description:
Infinium MethylationEPIC
240252


title: hepatic NEN_patient_033

description:
Infinium MethylationEPIC
240260


title: NoPCa_46

description: matrix_sample_id: DSM029


title: hepatic NEN_patient_028

description:
Infinium MethylationEPIC
240244


title: hepatic NEN_patient_029

description:
Infinium MethylationEPIC
240246


title: hepatic NEN_patient_030

description:
Infinium MethylationEPIC
240248


title: NoPCa_43

description: matrix_sample_id: DSM037


title: NoPCa_42

description: matrix_sample_id: DSM036


title: hepatic NEN_patient_026

description:
Infinium MethylationEPIC
240238


title: hepatic NEN_patient_025

description:
Infinium MethylationEPIC
240236


title: NoPCa_49

description: matrix_sample_id: DSM018


title: NoPCa_41

description: matrix_sample_id: DSM034


title: PCa_116

description: matrix_sample_id: DSM033


title: NEN liver metastasis_patient_024

description:
Infinium MethylationEPIC
240232


title: NEN liver metastasis_patient_023

description:
Infinium MethylationEPIC
240228


title: P_PCa_7

description: matrix_sample_id: DSM010

value: Presumably prostate tumour


title: NEN liver metastasis_patient_027

description:
Infinium MethylationEPIC
240242


title: NoPCa_39

description: matrix_sample_id: TAF014


title: NoPCa_38

description: matrix_sample_id: TAF013


title: PCa_115

description: matrix_sample_id: TAF012


title: NoPCa_37

description: matrix_sample_id: DOD088


title: EXCLUDED_patient_019

description:
Infinium MethylationEPIC
240214

source_name: EXCLUDE______hepatic NEN


title: hepatic NEN_patient_020

description:
Infinium MethylationEPIC
240216


title: PCa_114

description: matrix_sample_id: DOD087

source_name: prostate tissue


title: hepatic NEN_patient_018

description:
Infinium MethylationEPIC
240212


title: NEN liver metastasis_patient_022

description:
Infinium MethylationEPIC
240222


title: PCa_113

description: matrix_sample_id: DOD086


title: hepatic NEN_patient_015

description:
Infinium MethylationEPIC
240206


title: hepatic NEN_patient_016

description:
Infinium MethylationEPIC
240208


title: NoPCa_36

description: matrix_sample_id: DOD085


title: hepatic NEN_patient_017

description:
Infinium MethylationEPIC
240210


title: NoPCa_47

description: matrix_sample_id: DSM023


title: hepatic NEN_patient_021

description:
Infinium MethylationEPIC
240218


title: hepatic NEN_patient_014

description:
Infinium MethylationEPIC
240204


title: hepatic NEN_patient_013

description:
Infinium MethylationEPIC
240198


title: NoPCa_35

description: matrix_sample_id: DOD079


title: NoPCa_40

description: matrix_sample_id: DSM032


title: P_PCa_6

description: matrix_sample_id: DSM022


title: NoPCa_34

description: matrix_sample_id: DOD078


title: Merkel cell carcinoma_patient_012B

description:
Infinium MethylationEPIC
240156


title: NoPCa_33

description: matrix_sample_id: DOD076


title: Merkel cell carcinoma_patient_012A

description:
Infinium MethylationEPIC
240154


title: Merkel cell carcinoma_patient_011B

description:
Infinium MethylationEPIC
240140


title: PCa_111

description: matrix_sample_id: DOD074


title: Merkel cell carcinoma_patient_011A

description:
Infinium MethylationEPIC
240138


title: Merkel cell carcinoma_patient_010B

description:
Infinium MethylationEPIC
240134


title: NoPCa_32

description: matrix_sample_id: DOD071


title: PCa_109

description: matrix_sample_id: DOD068


title: Merkel cell carcinoma_patient_010A

description:
Infinium MethylationEPIC
240132


title: PCa_108

description: matrix_sample_id: DOD067


title: NEN pancreas_patient_009

description:
Infinium MethylationEPIC
240056


title: PCa_112

description: matrix_sample_id: DOD084


title: NEN pancreas_patient_008

description:
Infinium MethylationEPIC
240060


title: NEN liver metastasis_patient_008

description:
Infinium MethylationEPIC
240170


title: PCa_106

description: matrix_sample_id: DOD065


title: PCa_105

description: matrix_sample_id: DOD062


title: NEN liver metastasis_patient_006

description:
Infinium MethylationEPIC
240196


title: NoPCa_31

description: matrix_sample_id: DOD064


title: NEN duodenum_patient_007

description:
Infinium MethylationEPIC
239976


title: NEN liver metastasis_patient_007

description:
Infinium MethylationEPIC
240166


title: NoPCa_29

description: matrix_sample_id: DOD061


title: NoPCa_28

description: matrix_sample_id: DOD060


title: NEN ileum_patient_006

description:
Infinium MethylationEPIC
240010


title: NoPCa_27

description: matrix_sample_id: DOD059


title: NEN ileum_patient_005

description:
Infinium MethylationEPIC
239990


title: NEN liver metastasis_patient_004

description:
Infinium MethylationEPIC
240176


title: PCa_104

description: matrix_sample_id: DOD055


title: PCa_110

description: matrix_sample_id: DOD073


title: NEN ileum_patient_004

description:
Infinium MethylationEPIC
239984


title: PCa_107

description: matrix_sample_id: DOD066


title: PCa_103

description: matrix_sample_id: DOD053


title: NoPCa_24

description: matrix_sample_id: DOD052


title: NoPCa_30

description: matrix_sample_id: DOD063


title: NEN liver metastasis_patient_009

description:
Infinium MethylationEPIC
240184


title: NoPCa_23

description: matrix_sample_id: DOD050


title: NoPCa_22

description: matrix_sample_id: DSM004


title: NEN liver metastasis_patient_002

description:
Infinium MethylationEPIC
240182


title: NEN ileum_patient_003

description:
Infinium MethylationEPIC
239982


title: NoPCa_21

description: matrix_sample_id: DSM008


title: P_PCa_5

description: matrix_sample_id: DSM002


title: NEN liver metastasis_patient_001

description:
Infinium MethylationEPIC
240178


title: NoPCa_26

description: matrix_sample_id: DOD056


title: NoPCa_20

description: matrix_sample_id: DSM003


title: NEN ileum_patient_001

description:
Infinium MethylationEPIC
239986