title: F111543

description:
30254-FF-1_Per-Site-Unphased-Methylation, 30254-FF-1_Per-Read-Unphased-Methylation, 30254-FF-1_Per-Read-Phased-Methylation-Haplotype1, 30254-FF-1_Per-Site-Phased-Methylation-Haplotype1, 30254-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 30254-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: ECMO_36_2 (methylation)

status: Public on Oct 15 2024

type: genomic

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation chip using standard Illumina protocol

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

data_processing: The raw signal data were normalized to control by GenomeStudio v2011.1 software.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: PBMC at 2hr

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and then applied on bisulfite treatment by EZ DNA Methylation Kit (ZYMO RESERCH) according to manufacturer's protocol.

tag: disease state

value: Acute myocardial infarction

tag: age

tag: gender

value: M

tag: outcome

value: Failure

tag: cell type

value: PBMC

tag: time


title: GX088-BO [RNA-seq]

type: SRA

city: HongKong

first: Suetyi

last: Leung

address: Queen Mary Hospital, Pokfulam Road

department: Department of Pathology

country: China

institute: The University of Hong Kong

library_source: transcriptomic

data_processing:
The RNAseq reads in FASTA format were aligned to the Genome Reference Consortium human build 37 (hg19) by STAR (version 2.5.2b).
Duplicate reads were removed from the BAM files and the transcript abundances were quantified by RSEM to calculate the transcripts per million (TPM) value for each gene.
Assembly: GRCh37
Supplementary files format and content: Log-normalized expression data for each sample in a tab-delimited text format.

molecule: total RNA

source_name: Human normal gastric organoid

growth_protocol: IM and normal gastric organoids were cultured in a standard gastric organoid medium containing Wnt-3A, R-spondin1, Noggin, B27, A83-01, EGF, N-acetylcysteine, Gastrin and FGF10. Normal colon and ileum organoids were cultured in a standard intestinal organoid medium containing Wnt-3A, R-spondin1, Noggin, B27, A83-01, EGF, N-acetylcysteine, Gastrin and SB202190.

extract_protocol:
RNA of organoids and frozen tissues were extracted using AllPrep® DNA/RNA/miRNA Universal Kit (Qiagen). following the manufacturers’ protocol.
Four micrograms of total RNA were used for cDNA library construction using the KAPA Stranded mRNA-Seq Kit (KR0960-v3.15), according to the manufacturer’s protocol. The library was amplified by 6 PCR cycles and sequenced using either the NovaSeq6000/HiSeqX Ten with paired end 151bp reads or the HiSeq1500 with paired end 101bp reads.

tag: tissue/cell type

value: Human normal gastric organoid

tag: culture condition

value: Culture condition:Standard gastric organoid medium


title: F111544

city: Vancouver

first: Marco

last: Marra

state: BC

address: 570 W 7th Ave

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

description:
30489-OCT-2_Per-Site-Unphased-Methylation, 30489-OCT-2_Per-Read-Unphased-Methylation, 30489-OCT-2_Per-Read-Phased-Methylation-Haplotype1, 30489-OCT-2_Per-Site-Phased-Methylation-Haplotype1, 30489-OCT-2_Per-Read-Phased-Methylation-Haplotype2 and 30489-OCT-2_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2

library_source: genomic

data_processing:
Per-site and per-read unphased methylation data detected from nanopore sequencing raw signals using nanopolish. Phased methylation data were obtained using NanoMethPhase.
Assembly: GRCh38
Supplementary files format and content: Phased and Unphased CpG methylation data in tsv.gz format.
Library strategy: NanoMethPhase

extract_protocol:
Frozen tissue sections were immersed in 420 μL of RLT Plus buffer (QIAGEN) containing tris(2-carboxyethyl)phosphine (a reducing agent; TCEP) and a unique sample tracking DNA plasmid, and gently agitated overnight at room temperature. Lysates were transferred from 2 mL tubes to wells of a 1.2 mL plate (Thermo Scientific, AB1127) to which was added 400 mL of 5x bind buffer (80 mL beads in 320 mL isopropyl alcohol). Following a 5 minute incubation at room temperature lysates were cleared on a Magnum FLX magnet place (Alpaqua Inc) for 6 minutes and the protein-containing supernatant removed. The beads, with bound nucleic acids, were washed by pipetting 10 times in wash buffer and returned to the magnet. Beads were washed three times in 70% ethanol then dried for 10 minutes. 40 mL nuclease-free water was added to the dried beads and returned to the magnet. The eluted total nucleic acids were transferred to a 96-well storage plate and aliquots taken for quantification using Invitrogen Qubit 4 Fluorometer (Thermo Fisher Q33226)  For samples with concentrations below 166 ng/µL or in volumes greater than 30 µL, 5000 ng of Total Nucleic Acid (TNA) was transferred to a 1.5 mL DNase/RNase free tube and concentrated without heat on the Savant SpeedVac Plus (SC210A) to a maximum volume of 30 µL. This 5000 ng sample in 30 µL was topped up with 10 µL of Qiagen Buffer EB (Cat.19086). The samples were then run on the SAGE Science Blue Pippin instrument using the High Pass Plus Cassette (BPPLUS 10) with a maximum of 4 samples per run. The start range was selected at 15,000 base pairs and the end range was selected at 150,000 base pairs yielding a targeted size of 82,500 base pairs. Following the run completion, each sample was eluted in 80 µL and each sample elution well was then washed with 80 µL of 10 mM Tris, 1mM EDTA containing 0.1% Tween to maximize sample recovery. The total volume of 160µL was then concentrated without heat to 50 µL using the SpeedVac Plus. Each sample was then quantified using the Invitrogen Qubit 4 Fluorometer (Q33226) and normalized to 2000 ng in 47.5 µL for PromethION genome sequencing.
Library construction and sequencing followed the Oxford Nanopore Technologies Genomic DNA by Ligation (SQK-LSK110) protocol. DNA libraries starting with 2 µg of sample per library. No shearing was performed. The NEBUltra-II kit, (New England Biolabs, Ipswich, MA, USA, cat. no. E7646A) was used for end-repair and A-tailing. NEBNext quick ligase (E6056S) was used to ligate the Oxford Nanopore sequencing adapter. A final size selection of 0.4:1 ratio beads:library (PCRClean – DX Aline Biosciences L/N 06180316) was done to select against smaller molecules. These library preparation steps were performed on Hamilton Nimbus96 liquid handlers. An example deck layout, in this case for the bead purification step, is shown in Extended Data Figure 1c. DNA libraries were loaded in R9.4.1 pore flow cells on PromethION 24 instrument running software version 19.06.9 (MinKNOW GUI v4.0.23). Sequencing was carried out for 72 hours. DNase I (Invitrogen cat no. AM2222) nuclease flush was performed after 24-48 hours by reloading the flow cell with the same library mix.

tag: tissue


title: F111537

description:
25484-OCT-1_Per-Site-Unphased-Methylation, 25484-OCT-1_Per-Read-Unphased-Methylation, 25484-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 25484-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 25484-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 25484-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F111538

description:
25583-OCT-1_Per-Site-Unphased-Methylation, 25583-OCT-1_Per-Read-Unphased-Methylation, 25583-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 25583-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 25583-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 25583-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: N18

city: Stanford

first: Yin

last: Liu

state: CA

address: 279 Campus Dr.

country: USA

institute: Stanford University

description: Low quality

data_processing:
Nextseq 500 was used for sequecing and de-multiplexed to generate a fastq file.
Raw reads were aligned to the NCBI RefSeq mouse transcriptome (modified to exclude model XR_/XM_ sequences and include the tdTomato sequence) using kallisto with default settings (Bray et al., 2016). Read count and transcripts per million (TPM) values from splice isoforms of the same genes were collapsed, and for quality control cells with less than 2,000,000 paired-end reads that mapped to endogenous genes or less than 10,000 endogenous genes with mapped paired-end reads were excluded from the following analysis.
The TPM table was log-transformed (log2(TPM+1)) and scaled, and PCA was performed using 305 glial cell-enriched genes (Li et al., 2016). Cells were plotted along the first two PCs and 7 cells clearly separated from the rest, which were considered glial contaminated.
Subtype identification was performed using an iterative cluster analysis described in the paper
Genome_build: Genome_build: NCBI RefSeq mouse transcriptome (mouse.rna.fna.gz downloaded from ftp://ftp.ncbi.nlm.nih.gov/refseq/M_musculus/mRNA_Prot on April 7, 2014)
Supplementary_files_format_and_content: tab-delimited table of TPM value for each gene and each sample
Supplementary_files_format_and_content: tab-delimited table of subtype identity of each high-quality sample

molecule: polyA RNA

organism: Mus musculus

source_name: vagal pulmonary sensory neurons

extract_protocol:
Mice were euthanized with CO2 and transcardially perfused with cold Hank's balanced salt solution (HBSS) (without Ca2+ and Mg2+). Vagal ganglia were quickly dissected after perfusion in cold buffered HBSS (10 mM HEPES, pH7.2-7.5) and each was cut into 2~3 pieces. Ganglion tissue was then digested with papain solution at 20 U/ml (Worthington LS003124, in buffered HBSS containing 0.5 mM EDTA, 1.5 mM CaCl2, 0.4 mg/ml L-cysteine, pre-warmed for 30 min for activation) for 10 min at 37°C, and then collagenase/dispase solution (collagenase IV, 300 U/ml, Worthington LS004186; dispase, 1mg/ml, Thermo Fisher Scientific 17105-041, in HBSS, pre-warmed) for 30 min at 37°C with tube inversion to agitate every 10 min. After centrifuging at 400 g for 4 min, tissue pellet was resuspended in 1 ml L15 medium (with 10mM HEPES pH 7.2-7.5 and 10% fetal bovine serum) and triturated using fire-polished Pasteur pipettes. A Percoll gradient spin was used to clear axonal debris and glial cells by layering the cell suspension onto a buffered L15 medium (10 mM HEPES)/Percoll (4:1) solution and then centrifuging for 9 min at 400 g. The cell pellet was resuspended in 2 ml buffered L15 medium, centrifuged again for 3 min at 750 g, and resuspended in 200 µl suspension medium (L15 medium, 10mM HEPES pH 7.2-7.5, 1mg/ml BSA, and 0.1% Pluronic F-68).
cDNA samples were prepared using SMART-Seq v3 Ultra Low Input RNA Kit (Clontech), and sequencing libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina FC-131-1096) and Index Adapters (Illumina, FC-131-1002), following the C1 system for mRNA Seq Protocol (Fluidigm).

tag: genotype

value: Wildtype

value: post natal 6-12 weeks


title: N17

description: Glial contaminated


title: GX087-BO [RNA-seq]


title: GX077-BO [RNA-seq]


title: F111540

description:
233152-OCT-1_Per-Site-Unphased-Methylation, 233152-OCT-1_Per-Read-Unphased-Methylation, 233152-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 233152-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 233152-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 233152-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX041-BO [RNA-seq]


title: N177


title: F111535

description:
21933-OCT-1_Per-Site-Unphased-Methylation, 21933-OCT-1_Per-Read-Unphased-Methylation, 21933-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 21933-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 21933-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 21933-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: ECMO_35_2 (methylation)

value: Dilated cardiomyopathy, DCMP

value: F


title: GX076-BO [RNA-seq]


title: GX056-BO [RNA-seq]


title: F111536

description:
23738-OCT-1_Per-Site-Unphased-Methylation, 23738-OCT-1_Per-Read-Unphased-Methylation, 23738-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 23738-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 23738-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 23738-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: N174


title: N172


title: N170


title: ECMO_39_2 (methylation)

value: Success


title: N169


title: ECMO_32_2 (methylation)


title: GX026-BO [RNA-seq]


title: GX017-BO [RNA-seq]


title: GX014-BO [RNA-seq]


title: F111532

description:
40489-OCT-1_Per-Site-Unphased-Methylation, 40489-OCT-1_Per-Read-Unphased-Methylation, 40489-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 40489-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 40489-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 40489-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX093-IM2O [RNA-seq]

tag: sample subtype reclassification

value: Reclassify as normal gastric organoid based on transcriptome data


title: ECMO_31_2 (methylation)

value: Arrhythmia


title: N168


title: ECMO_40_2 (methylation)


title: F111531

description:
40120-OCT-3_Per-Site-Unphased-Methylation, 40120-OCT-3_Per-Read-Unphased-Methylation, 40120-OCT-3_Per-Read-Phased-Methylation-Haplotype1, 40120-OCT-3_Per-Site-Phased-Methylation-Haplotype1, 40120-OCT-3_Per-Read-Phased-Methylation-Haplotype2 and 40120-OCT-3_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F111533

description:
40627-OCT-1_Per-Site-Unphased-Methylation, 40627-OCT-1_Per-Read-Unphased-Methylation, 40627-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 40627-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 40627-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 40627-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: N176


title: ECMO_34_2 (methylation)

value: Aortic dissection


title: GX092-AO [RNA-seq]


title: N167


title: ECMO_29_2 (methylation)

value: failure


title: F111530

description:
38063-OCT-1_Per-Site-Unphased-Methylation, 38063-OCT-1_Per-Read-Unphased-Methylation, 38063-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 38063-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 38063-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 38063-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX090-AO [RNA-seq]


title: N166


title: ECMO_30_2 (methylation)


title: F111529

description:
37840-OCT-1_Per-Site-Unphased-Methylation, 37840-OCT-1_Per-Read-Unphased-Methylation, 37840-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 37840-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 37840-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 37840-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX089-AlO [RNA-seq]


title: N165


title: GX089-AgO [RNA-seq]


title: F111528

description:
37155-OCT-1_Per-Site-Unphased-Methylation, 37155-OCT-1_Per-Read-Unphased-Methylation, 37155-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 37155-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 37155-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 37155-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: ECMO_27_2 (methylation)


title: F111527

description:
37619-OCT-1_Per-Site-Unphased-Methylation, 37619-OCT-1_Per-Read-Unphased-Methylation, 37619-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 37619-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 37619-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 37619-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: N163


title: F111534

description:
44208-OCT-2_Per-Site-Unphased-Methylation, 44208-OCT-2_Per-Read-Unphased-Methylation, 44208-OCT-2_Per-Read-Phased-Methylation-Haplotype1, 44208-OCT-2_Per-Site-Phased-Methylation-Haplotype1, 44208-OCT-2_Per-Read-Phased-Methylation-Haplotype2 and 44208-OCT-2_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: N164


title: ECMO_33_2 (methylation)

value: Congestive heart failure


title: F111526

description:
36750-OCT-1_Per-Site-Unphased-Methylation, 36750-OCT-1_Per-Read-Unphased-Methylation, 36750-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 36750-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 36750-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 36750-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX087-IM2O [RNA-seq]


title: N162


title: GX086-IM2O [RNA-seq]


title: F111525

description:
36509-OCT-1_Per-Site-Unphased-Methylation, 36509-OCT-1_Per-Read-Unphased-Methylation, 36509-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 36509-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 36509-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 36509-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: ECMO_25_2 (methylation)

value: Dilated cardiomyopathy


title: ECMO_28_2 (methylation)


title: GX080-IMO [RNA-seq]


title: ECMO_26_2 (methylation)

value: Acute myocardial infarction


title: ECMO_24_2 (methylation)

value: M


title: ECMO_22_2 (methylation)

value: Acute myocarditis


title: N151


title: N150


title: F111523

description:
32398-OCT-1_Per-Site-Unphased-Methylation, 32398-OCT-1_Per-Read-Unphased-Methylation, 32398-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 32398-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 32398-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 32398-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX058-AO [RNA-seq]


title: GX072-AO [RNA-seq]


title: N149


title: GX076-IMOL [RNA-seq]

source_name: Human IM organoid long-term

value: Human IM organoid long-term

tag: long-term culture

value: Continuously culture in vitro for over 6 months


title: F111520

description:
30078-OCT-1_Per-Site-Unphased-Methylation, 30078-OCT-1_Per-Read-Unphased-Methylation, 30078-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 30078-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 30078-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 30078-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: N146


title: F111521

description:
31030-OCT-1_Per-Site-Unphased-Methylation, 31030-OCT-1_Per-Read-Unphased-Methylation, 31030-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 31030-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 31030-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 31030-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: N152


title: F111524

description:
36621-OCT-1_Per-Site-Unphased-Methylation, 36621-OCT-1_Per-Read-Unphased-Methylation, 36621-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 36621-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 36621-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 36621-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX072-IMOL [RNA-seq]

value: Culture condition:Standard gastric organoid medium


title: N145

value: Wildtype


title: ECMO_20_2 (methylation)

value: Failure

value: PBMC


title: ECMO_23_2 (methylation)

value: F


title: F111518

description:
30425-OCT-1_Per-Site-Unphased-Methylation, 30425-OCT-1_Per-Read-Unphased-Methylation, 30425-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 30425-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 30425-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 30425-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: N148

value: post natal 6-12 weeks


title: ECMO_17_2 (methylation)


title: F111522

description:
31183-OCT-1_Per-Site-Unphased-Methylation, 31183-OCT-1_Per-Read-Unphased-Methylation, 31183-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 31183-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 31183-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 31183-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: N143


title: GX082-AO [RNA-seq]

value: Human normal gastric organoid


title: F111515

description:
27177-OCT-1_Per-Site-Unphased-Methylation, 27177-OCT-1_Per-Read-Unphased-Methylation, 27177-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 27177-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 27177-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 27177-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX099-IMO [RNA-seq]

source_name: Human IM organoid

value: Human IM organoid


title: ECMO_16_2 (methylation)

value: Dilated cardiomyopathy, DCMP


title: GX059-IMOL [RNA-seq]


title: GX001-IM3O_P30 [RNA-seq]


title: N144


title: N140


title: GX098-IMO [RNA-seq]


title: F111517

description:
29759-OCT-1_Per-Site-Unphased-Methylation, 29759-OCT-1_Per-Read-Unphased-Methylation, 29759-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 29759-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 29759-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 29759-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F111513

description:
25572-OCT-1_Per-Site-Unphased-Methylation, 25572-OCT-1_Per-Read-Unphased-Methylation, 25572-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 25572-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 25572-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 25572-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F111516

description:
26852-FF-1_Per-Site-Unphased-Methylation, 26852-FF-1_Per-Read-Unphased-Methylation, 26852-FF-1_Per-Read-Phased-Methylation-Haplotype1, 26852-FF-1_Per-Site-Phased-Methylation-Haplotype1, 26852-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 26852-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: N138


title: N142


title: ECMO_19_2 (methylation)

value: Success


title: GX094-IMO [RNA-seq]


title: ECMO_10_2 (methylation)


title: N141


title: ECMO_8_2 (methylation)


title: F111512

description:
40723-OCT-1_Per-Site-Unphased-Methylation, 40723-OCT-1_Per-Read-Unphased-Methylation, 40723-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 40723-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 40723-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 40723-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: ECMO_11_2 (methylation)


title: GX092-BO [RNA-seq]

value: Reclassify as IM organoid based on transcriptome data


title: N137

value: CGRPalphaCreER/+; Ai14

tag: trreatment

value: 3mg Tamoxifen oral gavage


title: GX072-IM3OL [RNA-seq]


title: GX091-BlO [RNA-seq]


title: F111514

description:
25752-FF-1_Per-Site-Unphased-Methylation, 25752-FF-1_Per-Read-Unphased-Methylation, 25752-FF-1_Per-Read-Phased-Methylation-Haplotype1, 25752-FF-1_Per-Site-Phased-Methylation-Haplotype1, 25752-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 25752-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F111519

description:
28638-OCT-1_Per-Site-Unphased-Methylation, 28638-OCT-1_Per-Read-Unphased-Methylation, 28638-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 28638-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 28638-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 28638-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: N135


title: GX091-AgO [RNA-seq]


title: ECMO_6_2 (methylation)


title: GX088-IMO [RNA-seq]


title: ECMO_13_2 (methylation)

value: Acute myocardial infarction

value: M


title: N136


title: ECMO_14_2 (methylation)


title: N119

value: Phox2b-Cre; Ai14


title: F111509

description:
28131-OCT-1_Per-Site-Unphased-Methylation, 28131-OCT-1_Per-Read-Unphased-Methylation, 28131-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 28131-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 28131-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 28131-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: N118


title: GX085-IMO [RNA-seq]


title: ECMO_42_0 (methylation)

source_name: PBMC at 0hr

value: Congestive heart failure


title: GX099-IM2O [RNA-seq]

value: Culture condition:Standard gastric organoid medium


title: ECMO_40_0 (methylation)


title: ECMO_21_2 (methylation)


title: F111506

description:
39880-OCT-2_Per-Site-Unphased-Methylation, 39880-OCT-2_Per-Read-Unphased-Methylation, 39880-OCT-2_Per-Read-Phased-Methylation-Haplotype1, 39880-OCT-2_Per-Site-Phased-Methylation-Haplotype1, 39880-OCT-2_Per-Read-Phased-Methylation-Haplotype2 and 39880-OCT-2_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX078-IM2O [RNA-seq]


title: N117


title: F111507

description:
41529-OCT-1_Per-Site-Unphased-Methylation, 41529-OCT-1_Per-Read-Unphased-Methylation, 41529-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 41529-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 41529-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 41529-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: ECMO_41_0 (methylation)

value: Acute myocarditis


title: ECMO_7_2 (methylation)


title: N116


title: F111510

description:
34117-OCT-2_Per-Site-Unphased-Methylation, 34117-OCT-2_Per-Read-Unphased-Methylation, 34117-OCT-2_Per-Read-Phased-Methylation-Haplotype1, 34117-OCT-2_Per-Site-Phased-Methylation-Haplotype1, 34117-OCT-2_Per-Read-Phased-Methylation-Haplotype2 and 34117-OCT-2_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX076-IMO [RNA-seq]


title: GX076-IM2O [RNA-seq]


title: N115


title: GX072-IMO [RNA-seq]


title: F111504

description:
32655-OCT-1_Per-Site-Unphased-Methylation, 32655-OCT-1_Per-Read-Unphased-Methylation, 32655-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 32655-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 32655-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 32655-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: N113


title: GX062-IMO [RNA-seq]


title: N112


title: ECMO_38_0 (methylation)


title: F111501

description:
20600-OCT-3_Per-Site-Unphased-Methylation, 20600-OCT-3_Per-Read-Unphased-Methylation, 20600-OCT-3_Per-Read-Phased-Methylation-Haplotype1, 20600-OCT-3_Per-Site-Phased-Methylation-Haplotype1, 20600-OCT-3_Per-Read-Phased-Methylation-Haplotype2 and 20600-OCT-3_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F111505

description:
39078-OCT-1_Per-Site-Unphased-Methylation, 39078-OCT-1_Per-Read-Unphased-Methylation, 39078-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 39078-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 39078-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 39078-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX072-IM3O [RNA-seq]


title: F111508

description:
50479-OCT-1_Per-Site-Unphased-Methylation, 50479-OCT-1_Per-Read-Unphased-Methylation, 50479-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 50479-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 50479-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 50479-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F111503

description:
31191-OCT-1_Per-Site-Unphased-Methylation, 31191-OCT-1_Per-Read-Unphased-Methylation, 31191-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 31191-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 31191-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 31191-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: ECMO_37_0 (methylation)

value: Failure


title: N111


title: N110


title: F111499

description:
37095-OCT-1_Per-Site-Unphased-Methylation, 37095-OCT-1_Per-Read-Unphased-Methylation, 37095-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 37095-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 37095-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 37095-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: N109


title: ECMO_35_0 (methylation)

value: PBMC


title: GX059-IMO-P15 [RNA-seq]


title: ECMO_39_0 (methylation)

value: F


title: F111500

description:
23674-FF-4_Per-Site-Unphased-Methylation, 23674-FF-4_Per-Read-Unphased-Methylation, 23674-FF-4_Per-Read-Phased-Methylation-Haplotype1, 23674-FF-4_Per-Site-Phased-Methylation-Haplotype1, 23674-FF-4_Per-Read-Phased-Methylation-Haplotype2 and 23674-FF-4_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F111511

description:
36686-OCT-1_Per-Site-Unphased-Methylation, 36686-OCT-1_Per-Read-Unphased-Methylation, 36686-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 36686-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 36686-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 36686-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: ECMO_34_0 (methylation)

value: Aortic dissection


title: ECMO_5_2 (methylation)


title: GX062-IM2O [RNA-seq]


title: GX054-IM2O [RNA-seq]


title: N114

value: post natal 6-12 weeks


title: N107


title: F111497

description:
39432-OCT-1_Per-Site-Unphased-Methylation, 39432-OCT-1_Per-Read-Unphased-Methylation, 39432-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 39432-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 39432-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 39432-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: ECMO_36_0 (methylation)


title: ECMO_32_0 (methylation)


title: GX049-IMO [RNA-seq]

value: Human IM organoid


title: N106


title: D74665

description:
40168-PB_Per-Site-Unphased-Methylation, 40168-PB_Per-Read-Unphased-Methylation, 40168-PB_Per-Read-Phased-Methylation-Haplotype1, 40168-PB_Per-Site-Phased-Methylation-Haplotype1, 40168-PB_Per-Read-Phased-Methylation-Haplotype2 and 40168-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: N105


title: GX040-IMO [RNA-seq]


title: N104


title: ECMO_33_0 (methylation)


title: D74661_F48644

description:
42120-OCT-1_Per-Site-Unphased-Methylation, 42120-OCT-1_Per-Read-Unphased-Methylation, 42120-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 42120-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 42120-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 42120-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: N92


title: D74663

description:
48919-OCT-1_Per-Site-Unphased-Methylation, 48919-OCT-1_Per-Read-Unphased-Methylation, 48919-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 48919-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 48919-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 48919-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: ECMO_29_0 (methylation)

value: failure


title: GX031-IMO [RNA-seq]


title: F111502

description:
25751-OCT-1_Per-Site-Unphased-Methylation, 25751-OCT-1_Per-Read-Unphased-Methylation, 25751-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 25751-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 25751-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 25751-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX023-IM3dysO [RNA-seq]


title: ECMO_26_0 (methylation)


title: GX023-IM2O [RNA-seq]


title: D74658

description:
32654-FF-1_Per-Site-Unphased-Methylation, 32654-FF-1_Per-Read-Unphased-Methylation, 32654-FF-1_Per-Read-Phased-Methylation-Haplotype1, 32654-FF-1_Per-Site-Phased-Methylation-Haplotype1, 32654-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 32654-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: ECMO_30_0 (methylation)

value: Success


title: F111498

description:
42324-OCT-1_Per-Site-Unphased-Methylation, 42324-OCT-1_Per-Read-Unphased-Methylation, 42324-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 42324-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 42324-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 42324-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX014-IM2O [RNA-seq]


title: N91


title: N90


title: D36494

description:
30078-PB_Per-Site-Unphased-Methylation, 30078-PB_Per-Read-Unphased-Methylation, 30078-PB_Per-Read-Phased-Methylation-Haplotype1, 30078-PB_Per-Site-Phased-Methylation-Haplotype1, 30078-PB_Per-Read-Phased-Methylation-Haplotype2 and 30078-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX001-IM3O [RNA-seq]


title: D36497

description:
38013-PB_Per-Site-Unphased-Methylation, 38013-PB_Per-Read-Unphased-Methylation, 38013-PB_Per-Read-Phased-Methylation-Haplotype1, 38013-PB_Per-Site-Phased-Methylation-Haplotype1, 38013-PB_Per-Read-Phased-Methylation-Haplotype2 and 38013-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: N88


title: N86


title: H020-NileO

library_source: transcriptomic single cell

data_processing:
Sequence data was mapped to the human genome (GRCh38) using CellRanger (version 2.2.1). Unique molecular identifier (UMI) count matrices were pre-processed and filtered by scatter R package (version 1.10.0, BioConductor).
We excluded cells with very low and very high UMI counts, as well as cells with a high percentage of counts assigned to mitochondrial or ribosomal genes, low expression of the housekeeping genes (GAPDH & ACTB) or the gene counts and read counts were not correlated using robust linear model in MASS (R package, Version 7.3). Genes that had less than 10 total counts across a dataset, or were expressed in less than 5 individual cells, were also removed.
Log-normalized expression was obtained by NormalizeData function of the Seurat package (Version 3.2.3).
The doublets were removed by the DoubletFinder (R package, Version 2.0.2).
Assembly: GRCh38
Supplementary files format and content: UMI count data as well as Log-normalized expression data for each cell in a tab-delimited text format, with gene symbols in rows and cell ID in columns.

source_name: Human normal ileum organoid

growth_protocol: IM and normal gastric organoids were cultured in a standard gastric organoid medium containing Wnt-3A, R-spondin1, Noggin, B27, A83-01, EGF, N-acetylcysteine, Gastrin and FGF10. Normal intestianl organoids were cultured in a standard intestinal organoid medium containing Wnt-3A, R-spondin1, Noggin, B27, A83-01, EGF, N-acetylcysteine, Gastrin and SB202190.

extract_protocol:
Organoids with or without differentiation and spheroid samples were dissociated into single cells using TrypLE and single cells were FACS-sorted based on standard parameters for forward scatter area versus forward scatter peak liner. Dead cells were removed based on DAPI staining.
Single cells were encapsulated into Gel Beads. Libraries were constructed using a Chromium Single Cell 5' Library & Gel Bead Kit (10x genomics) according to the manufacturer's instructions.

treatment_protocol: IM and normal gastric organoids were cultured in a standard gastric organoid medium, while normal intestinal organoids were cultured in a standard intestinal organoid medium. Differentiated organoids have been cultured in a standard gastric/intestinal organoid medium without Wnt-3A for 4 days. IM spheroids have been cultured in a standard gastric organoid medium in ultra-low binding plate for over 3 months.

value: Human normal ileum organoid

value: Culture condition:Standard intestinal organoid medium


title: ECMO_23_0 (methylation)


title: N87

value: CGRPalphaCreER/+; Ai14

value: 3mg Tamoxifen oral gavage


title: H020-NileO differentiated

value: Culture condition:Standard intestinal organoid medium without Wnt-3A for 4 days


title: ECMO_31_0 (methylation)

value: Arrhythmia


title: ECMO_25_0 (methylation)

value: Dilated cardiomyopathy

value: M


title: GX060-IMO [RNA-seq]

value: Culture condition:Standard gastric organoid medium


title: GX106-AL1c

source_name: Human IM tissue

value: Human IM tissue


title: ECMO_24_0 (methylation)

value: Acute myocardial infarction

value: Failure

value: PBMC


title: N85

value: post natal 6-12 weeks


title: D36500

description:
40627-PB_Per-Site-Unphased-Methylation, 40627-PB_Per-Read-Unphased-Methylation, 40627-PB_Per-Read-Phased-Methylation-Haplotype1, 40627-PB_Per-Site-Phased-Methylation-Haplotype1, 40627-PB_Per-Read-Phased-Methylation-Haplotype2 and 40627-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: ECMO_22_0 (methylation)

value: Acute myocarditis

value: F


title: GX098-IMO differentiated

value: Human IM organoid


title: GX006-IM3O [RNA-seq]


title: GX091-AgOIMO-spheroid

source_name: Human IM spheroid

value: Human IM spheroid

tag: copy number profile

value: with CNV

value: Culture condition:In ultra-low binding plate with standard gastric organoid medium


title: N84

value: CGRPalphaCreER/+; Ai14

value: 3mg Tamoxifen oral gavage


title: BAT3

type: RNA

city: Nanjing

first: Xiaohong

last: Jiang

address: 163 Xianlin Rd.

institute: Nanjing University

description: brown adipose tissue from C57BL/6 mouse housed at room temperature

hyb_protocol: Biotin-labelled miRNAs were used for hybridization on each miRNA microarray chip containing probes in triplicate.

scan_protocol: standard Affymetrix protocol

data_processing: Raw data were normalized to U6 and analysed using GenePix Pro 4.0 software

label: biotin

source_name: brown adipose tissue

label_protocol: Procedures were performed as described on the web site of CapitalBio.

growth_protocol: 8-week-old male C57BL/6J mices are raised under room temperature

extract_protocol: Total RNA from each pooled sample was isolated using the TRIzol method for Affymetrix miRNA microarray analysis.

treatment_protocol: No treatment


title: N83

value: Phox2b-Cre; Ai14


title: N81


title: ECMO_28_0 (methylation)

value: Dilated cardiomyopathy

value: Success


title: GX091-AgOIMO

value: Culture condition:Standard gastric organoid medium


title: N82


title: N80


title: ECMO_20_0 (methylation)

value: M


title: GX085-IMO-spheroid


title: BAT2


title: N79


title: ECMO_27_0 (methylation)

value: Arrhythmia


title: Drosophila_bipectinata_testes_NG_61_61b_S32

city: Davis

first: Ben

last: Hopkins

address: One Shields Avenue

department: Evolution & Ecology

institute: UC Davis

data_processing:
After quality filtering with trimmomatic, we obtained 10, 22, 38, and 54 million reads for each of the 4 or five libraries.
Mapped paired-end reads to the genome and annotation from each species using STAR v. 2.5.3 (Dobin et al. 2013).
Assemlbed reference-only transcripts using Stringtie v. 1.3.4 (Pertea et al. 2015) to estimate expression in Transcrpts per million (TPM).
Assembly: Flybase: Dmel_r6.12, Dsim_r2.02, Dyak_r1.05, Dana_r1.05  NCBI: Dbia_2.0, Dbip_2.0, Dele_2.0, Deug_2.0, Dfic_2.0, Dkik_2.0, Dtak_2.0
Supplementary files format and content: Tab delimmited TPM files. One column for each biological replicate

organism: Drosophila bipectinata

source_name: testes

extract_protocol:
We isolated mRNA from total RNA using NEBNext Poly(A) mRNA magnetic isolation.
Constructed RNA-seq directional paired-end libraries using NEBNext Ultra Directional RNA Library prep kit. We quantified library size using NEBNext Library Quant Kit (New England BioLabs, Ipswich, MA)

value: testes

tag: sample id

tag: library name

tag: strain information


title: BAT1


title: Drosophila_bipectinata_testes_G_59_59b_S13


title: GX085-IMO differentiated

value: Culture condition:Standard gastric organoid medium without Wnt-3A for 4 days


title: ECMO_16_0 (methylation)

tag: disease state

value: Dilated cardiomyopathy, DCMP

value: Failure

value: PBMC


title: Drosophila_ananassae_testes_NG_66_66b_S5

organism: Drosophila ananassae


title: GX085-IMO

value: Human IM organoid


title: ECMO_19_0 (methylation)

value: Acute myocardial infarction

tag: age


title: ECMO_17_0 (methylation)

tag: gender


title: ECMO_21_0 (methylation)

tag: outcome


title: Drosophila_ananassae_ag_NG_105_105b_S39

source_name: accessory glands

value: accessory glands


title: N89

value: post natal 6-12 weeks


title: iWAT2

description: inguinal white adipose tissue from C57BL/6 mouse housed at room temperature

source_name: inguinal white adipose tissue


title: N76


title: GX076-IMO differentiated


title: GX076-IMO


title: N77


title: Drosophila_ananassae_ag_NG_101_101_S17


title: iWAT1


title: GX072-IMO differentiated


title: Drosophila_kikkawai_testes_G_z12_130917_I1135

organism: Drosophila kikkawai


title: N75


title: ECMO_13_0 (methylation)

tag: cell type


title: GX072-IMO


title: iWAT3


title: ECMO_11_0 (methylation)

value: Acute myocarditis

value: F

tag: time


title: N72

value: Phox2b-Cre; Ai14


title: Drosophila_kikkawai_testes_G_z12_131017_I1125


title: N73


title: GX072-AO differentiated

tag: tissue/cell type

value: Human normal gastric organoid


title: N74


title: ECMO_10_0 (methylation)

value: Success


title: N71


title: High grade 52

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

country: Spain

institute: Hospital Clínic

description: Hybridized to Affymetrix OncoScan FFPE Assay

hyb_protocol: Affymetrix OncoScan™ FFPE Assay kit

scan_protocol: Affymetrix® GeneChip® Scanner 3000G to detect target bound to Oncoscan array after staining with Biotin.

data_processing:
Nexus biodiscovery software version 9.0
primary data description: Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb.

label: Biotin

source_name: cervical LN

label_protocol: Affymetrix OncoScan™ FFPE Assay kit

extract_protocol: DNA from formalin-fixed paraffin-embedded (FFPE) tissue was extracted after dewaxing and proteinase K digestion applying standard phenol/chloroform purification procedures

tag: type of sample

value: B-NHL with intermediate features between BL and DLBCL

value: female

tag: tissue type

value: FFPE

value: cervical LN


title: Drosophila_kikkawai_ag_G_z11_131017_I1125

tag: tissue


title: GX072-AO

tag: culture condition

value: Culture condition:Standard gastric organoid medium


title: eWAT1

description: epididymal white adipose tissue from C57BL/6 mouse housed at room temperature

source_name: epididymal white adipose tissue

tag: genotype


title: ECMO_5_0 (methylation)

value: M


title: High grade 53

source_name: cavum

value: cavum


title: Drosophila_kikkawai_testes_G_z12_131220_I433

value: testes


title: ECMO_7_0 (methylation)

value: PBMC


title: GX059-IMO differentiated

value: Human IM organoid

value: Culture condition:Standard gastric organoid medium without Wnt-3A for 4 days


title: N70

value: Wnt1-Cre; Ai14

value: post natal 6-12 weeks


title: ECMO_14_0 (methylation)

value: Acute myocardial infarction


title: GX059-IMO


title: Drosophila_kikkawai_ag_G_z11_131220_I433

value: accessory glands


title: High grade 50

source_name: LN

value: male

value: LN


title: N69


title: High grade 51

source_name: Liver

value: B-NHL with intermediate features between BL and DLBCL

value: Liver


title: ECMO_8_0 (methylation)

value: Acute myocarditis

value: F

value: Failure


title: High grade 46

label: Genomic DNA

source_name: breast

value: female

value: FFPE

value: breast


title: Drosophila_elegans_testes_NG_94_94b_S9

organism: Drosophila elegans

value: testes

value: IR-MTK


title: High grade 47

source_name: peritoneum

value: peritoneum


title: GX036-AO differentiated

source_name: Human normal gastric organoid

value: Human normal gastric organoid

value: with CNV

value: Culture condition:Standard gastric organoid medium without Wnt-3A for 4 days


title: Drosophila_elegans_ag_G_99_99b_S18

value: accessory glands


title: N67

source_name: vagal pulmonary sensory neurons

value: Wnt1-Cre; Ai14

value: post natal 6-12 weeks


title: Drosophila_elegans_ag_G_99_99c_S38


title: N66


title: High grade 41

source_name: intestine

value: B-NHL with intermediate features between BL and DLBCL

value: male

value: intestine


title: High grade 44

source_name: pleural effusion

value: pleural effusion


title: N65


title: Drosophila_yakuba_testes_NG_80_80_S10

organism: Drosophila yakuba


title: GX035-AOIMO differentiated

source_name: Human IM organoid

value: Human IM organoid


title: GX059-BO differentiated


title: Drosophila_yakuba_testes_NG_28_28b_S139


title: N64


title: N68


title: High grade 40

value: cervical LN


title: GX098-IMO

value: Culture condition:Standard gastric organoid medium


title: GX035-AOIMO


title: GX059-BO


title: GX023-BO


title: N62


title: GX023-BO differentiated


title: N63


title: High grade 39

source_name: larynx

value: FFPE

value: larynx


title: High grade 37


title: N61


title: Drosophila_yakuba_testes_G_69_69b_S32

value: testes


title: Drosophila_yakuba_ag_NG_33_33b_S136


title: Drosophila_yakuba_testes_G_69_69_S22


title: GX001-IM3O-spheroid

source_name: Human IM spheroid

value: Human IM spheroid

value: Culture condition:In ultra-low binding plate with standard gastric organoid medium


title: GX036-AO

value: Human normal gastric organoid

value: with CNV


title: ECMO_6_0 (methylation)

source_name: PBMC at 0hr

value: Acute myocarditis

value: F

value: Success

value: PBMC


title: N60

value: Wnt1-Cre; Ai14

value: post natal 6-12 weeks


title: High grade 38

source_name: cecal appendix

value: B-NHL with intermediate features between BL and DLBCL

value: male

value: cecal appendix


title: GX001-IM3O differentiated

value: Human IM organoid

value: Culture condition:Standard gastric organoid medium without Wnt-3A for 4 days


title: High grade 36

value: FFPE

value: LN


title: Drosophila_yakuba_testes_NG_28_28_S87

source_name: testes

value: testes


title: High grade 33

value: intestine


title: Drosophila_kikkawai_ag_G_z11_130917_I1135

source_name: accessory glands

value: accessory glands


title: Drosophila_yakuba_ag_NG_33_33_S84


title: N58


title: eWAT2

source_name: epididymal white adipose tissue


title: N59


title: eWAT3


title: Drosophila_yakuba_ag_NG_26_26_S80


title: Drosophila_yakuba_ag_G_92_92_S17


title: High grade 28

source_name: ileocolic LN

value: ileocolic LN


title: Drosophila_ananassae_testes_NG_66_66_S1


title: N78

value: Phox2b-Cre; Ai14


title: deGrad_GFPcbp_R5

city: Madison

first: Melissa

last: Harrison

state: Wisconsin

address: 6204B Biochemical Sciences Building, 440 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin- Madison

data_processing:
Alignment of reads to the Drosophila melanogaster dm6 reference genome was done with HISAT2 v2.1.0 with a mapping quality threshold of ≥ 3074. Reads below this threshold were rejected as were reads that mapped to the mitochondrial or scaffold DNA.
Aligned reads were annotated to genes using FeatureCounts 2.0 from Subread.
Assembly: dm6
Supplementary files format and content: bigwig files were formed from merged replicates and z-score normalized

organism: Drosophila melanogaster

source_name: Embryo (15min into NC14)

growth_protocol: Drosophila embryos were maintained at 25˚C on molasses plates for 90mins after egg laying in which they were then mounted for live imaging on a fluorescent scope and precisely staged by nuclear density at nuclear cycle 10 for catalytic inactivation experiments or 15min into nuclear cycle 14 for CBP knockdown experiments.

extract_protocol:
Live imaging was performed on a Nikon Eclipse Ti2 inverted fluorescent microscope. Embryos were processed for single embryo RNA-seq exactly 15 min into NC14. For optogenetic experiments, His2Av-RFP and CBPCRY2;His2Av-RFP embryos were treated with a repeating sequence of 60s exposure to 470nm filtered light followed immediately by a 10 ms exposure to 555nm. This sequence was initiated upon entry into NC10 and ended 15 min into nuclear-cycle 14. The single embryo was transferred from the imaging disc into 40µL Trizol and pierced with a sterile needle to free RNA into solution. Individual embryos were homogenized with a sterile pestle. After, 960µL of Trizol supplemented with 200µg/mL glycogen was added. RNA was extracted, cleaned, and concentrated through ethanol precipitation.
Libraries were prepared using the Illumina TrueSeq RNA prep kit V2.

treatment_protocol: CRY2-CBP and his2avRFP controls were left in the dark or treated with blue light from NC10 till 15min into nuclear cycle 14.

value: Embryo (15min into NC14)

tag: treatment


title: deGrad_GFPcbp_R4


title: High grade 22

source_name: abdominal mass

value: abdominal mass


title: deGrad_GFPcbp_R3


title: Drosophila_ananassae_testes_NG_50_50_S90


title: N57

value: CGRPalphaCreER/+; Ai14

tag: trreatment

value: 3mg Tamoxifen oral gavage


title: N55

value: post natal 6-12 weeks


title: Drosophila_ananassae_testes_G_49_49_S87

tag: sample id


title: High grade 21

source_name: tonsil

value: B-NHL with intermediate features between BL and DLBCL

value: tonsil


title: GFPcbp_R7

description: GFPNEJ.bw


title: High grade 20

source_name: stomach

value: male

value: stomach


title: N54


title: N56


title: High grade 18


title: Drosophila_ananassae_ag_NG_105_105_S31

tag: library name


title: High grade 29


title: GFPcbp_R6

description: GFPNEJ.bw


title: N53


title: Drosophila_ananassae_ag_G_35_35_S86

tag: strain information


title: GFPcbp_R5

description: GFPNEJ.bw


title: GX001-IM3O

value: Human IM organoid

tag: copy number profile

value: with CNV

value: Culture condition:Standard gastric organoid medium


title: High grade 16

value: female

value: FFPE


title: WT_Dark_R5

value: his2avRFP III

value: Dark


title: Drosophila_ananassae_ag_G_35_35b_S138

value: accessory glands


title: High grade 15


title: WT_Dark_R4

value: Embryo (15min into NC14)


title: N51

tag: age


title: N50


title: High grade 10

source_name: spleen

tag: gender

value: spleen


title: Drosophila_takahashii_testes_NG_67_67b_S8

organism: Drosophila takahashii

value: testes


title: N49

source_name: vagal pulmonary sensory neurons

value: CGRPalphaCreER/+; Ai14

value: 3mg Tamoxifen oral gavage


title: Drosophila_takahashii_ag_G_112_112_S31


title: WT_Dark_R3


title: High grade 9

source_name: intestine

value: B-NHL with intermediate features between BL and DLBCL

value: intestine


title: WT_Dark_R2


title: WT_Dark_R1


title: High grade 8

source_name: retroperitoneum

value: male

value: retroperitoneum


title: CRY2_Dark_R4

value: CRY2nej;his2avRFP III


title: N48

value: post natal 6-12 weeks


title: Drosophila_eugracilis_ag_G_z15_131220_I433

organism: Drosophila eugracilis


title: High grade 5

value: stomach


title: High grade 7


title: N45


title: N47


title: N46


title: Drosophila_ficusphila_testes_G_z8_130917_I1135

organism: Drosophila ficusphila


title: High grade 4

source_name: breast

value: female

value: breast


title: N52


title: High grade 13

value: FFPE


title: Drosophila_ficusphila_testes_G_z8_131017_I1125


title: deGrad_GFPcbp_R2


title: N40

value: Wildtype


title: Drosophila_biarmipes_testes_NG_78_78b_S6

organism: Drosophila biarmipes


title: deGrad_GFPcbp_R1


title: High grade 2

value: abdominal mass


title: N39


title: Drosophila_eugracilis_testes_G_z16_130917_I1135


title: Drosophila_biarmipes_ag_NG_113_113_S40

value: accessory glands


title: GFPcbp_R4

description: GFPNEJ.bw

value: Embryo (15min into NC14)


title: Drosophila_elegans_testes_NG_94_94_S8

value: testes

value: IR-MTK


title: Drosophila_elegans_testes_NG_68_68b_S9


title: Drosophila_ficusphila_testes_G_z8_131220_I433


title: N37


title: N36


title: GFPcbp_R3

description: GFPNEJ.bw


title: N35


title: N34


title: Drosophila_elegans_testes_NG_68_68_S85


title: GFPcbp_R2

description: GFPNEJ.bw


title: N43

value: CGRPalphaCreER/+; Ai14

value: 3mg Tamoxifen oral gavage


title: Drosophila_elegans_testes_G_40_40_S82


title: GFPcbp_R1

description: GFPNEJ.bw


title: WT_Bluelight_R4

value: his2avRFP III

value: Blue light


title: Drosophila_eugracilis_testes_G_z16_131017_I1125


title: Drosophila_elegans_ag_NG_53_53_S98


title: N33


title: WT_Bluelight_R3


title: N38


title: N29


title: N30


title: Drosophila_elegans_ag_NG_38_38b_S140


title: WT_Bluelight_R2


title: Drosophila_elegans_ag_G_99_99_S30


title: CRY2_Dark_R3

value: Dark


title: N28


title: Drosophila_elegans_ag_NG_38_38_S88


title: Drosophila_yakuba_testes_NG_80_80b_S10


title: CRY2_Dark_R2

value: CRY2nej;his2avRFP III


title: N27

value: post natal 6-12 weeks


title: N25


title: Drosophila_simulans_testes_NG_81_81_S18

organism: Drosophila simulans


title: Drosophila_yakuba_ag_G_92_92b_S16


title: CRY2_Bluelight_R3


title: N24


title: N23


title: CRY2_Dark_R1


title: N31


title: Drosophila_simulans_testes_NG_32_32_S95


title: Drosophila_simulans_testes_G_87_87b_S23


title: CRY2_Bluelight_R1


title: N22


title: Drosophila_elegans_testes_G_40_40b_S6


title: CRY2_Bluelight_R2


title: CRY2_Bluelight_R4


title: Drosophila_simulans_testes_NG_32_32b_S145


title: Drosophila_simulans_testes_G_87_87_S11


title: N21


title: Drosophila_simulans_ag_NG_91_91_S20


title: N20


title: WT_Bluelight_R1


title: N16


title: N14


title: Drosophila_melanogaster_testes_G_108_108_S29

value: y; cn bw sp


title: Drosophila_melanogaster_testes_NG_84_84b_S15


title: Drosophila_simulans_ag_NG_64_64b_S21


title: Drosophila_melanogaster_ag_G_111_111_S37


title: N12


title: Drosophila_melanogaster_ag_G_109_109_S30


title: N13


title: Drosophila_simulans_ag_NG_64_64_S6


title: Drosophila_simulans_ag_G_29_29_S81


title: N11


title: Brain, SIVE, rep2, GEX

city: Omaha

first: Howard

middle: S

last: Fox

state: Nebraska

address: 42nd and Emile

institute: University of Nebraska Medical Center

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using the Cell Ranger arc software v2.0.2
Assembly: Mmul10, NCBI RefSeq assembly plus SIVmac251 sequence (Gene bank assession number: PP236443)
Supplementary files format and content: FASTQ files contain the sequenced data
Supplementary files format and content: Fragment files contain reference genome chromosome of fragment, ajusted start and end position of fragment on chromosome, cell barcode, and total number of read pairs associated with this fragment

organism: Macaca mulatta

source_name: Brain

extract_protocol:
A necropsy was performed on deeply anesthetized (ketamine plus xylazine) animals, following intracardial perfusion with sterile PBS containing 1 U/ml heparin. Brains were harvested, and approximately half of the brain was taken for microglia/macrophage isolation. Briefly, the brain was minced and homogenized in cold Hank’s Balanced Salt Solution (HBSS). After being centrifuged, the brain tissue was digested at 37° C in HBSS containing 28 U/ml DNase I and 8 U/ml papain for 30 minutes. After digestion, the enzymes were inactivated by adding 2.5% FBS, and the cells were centrifuged and resuspended in cold HBSS. The cell suspension was mixed with 90% Percoll to yield a final concentration of 20% Percoll and centrifuged at 4° C for 15 minutes at 550 x g. The microglia/macrophage pallet at the bottom was resuspended in HBSS and passed through a 40 μm strainer to remove cell clumps and aggregates. Cells were again pelleted by centrifugation and resuspended in RBC lysis buffer for 3 minutes to eliminate contaminating red blood cells. A final wash was performed before the resulting cells were quantified on a hemocytometer and Coulter Counter Z1. The cells were resuspended in 10% DMSO and 90% fetal bovine serum and subjected to slow controlled freezing followed by storage in liquid N2. On the day of the experiment, cryopreserved cell isolates were rapidly thawed in a 37° C water bath. After the recovery, cells were washed and counted by Coulter Counter Z1. Once cell concentration was known, cells were transferred to ice-cold PBS and stained with CD11b and UV-blue live/dead. Cells were washed, resuspended in a flow cytometry staining buffer, and sorted on an Aria2 flow cytometer and then processed for the Multiome technique
Nuclei were isolated from the cells and permeabilized as the 10XGenomics protocol. Nuclei were then quantified on a hemocytometer and concentrated to approximately 2200-2400 nuclei per µL. Based on 10× Genomics parameters targeting 8000 nuclei, the ideal volume of cells was loaded onto the 10× Genomics (Pleasanton, CA, USA) Chromium Next GEM Chip J and placed into the Chromium Controller for nuclei capturing and library preparation. The prepared libraries were sequenced using Illumina (San Diego, CA, USA) Novaseq6000 sequencers.

treatment_protocol: Two rhesus macaques (21T and 34T) were intravenously inoculated with SIVmac251 and infection proceeded for 92 and 49 days, respectively. The other two rhesus macatues (104T and 106T) were uninfected controls

value: Brain

value: CD11b positive cells


title: Drosophila_ficusphila_ag_NG_103_103b_S34


title: Drosophila_ficusphila_testes_NG_89_89b_S14


title: Brain, Uninfected, rep2, GEX


title: N10


title: N9


title: Brain, Uninfected, rep1, GEX


title: Drosophila_ficusphila_ag_G_107_107_S27


title: Brain, SIVE, rep2, ATAC

library_source: genomic single cell


title: Drosophila_melanogaster_testes_G_110_110_S35


title: N7


title: Drosophila_melanogaster_testes_NG_84_84_S16


title: Brain, SIVE, rep1, GEX


title: Brain, SIVE, rep1, ATAC


title: N6


title: Drosophila_simulans_ag_G_29_29b_S5


title: Drosophila_melanogaster_ag_NG_30_30b_S137


title: Drosophila_melanogaster_ag_NG_30_30_S85


title: N8


title: Brain, Uninfected,  rep2, ATAC


title: Brain, Uninfected, rep1, ATAC


title: FlcnKO_sgTfeb_sgTfe3 JLR824

status: Public on Oct 14 2024

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

hyb_protocol: Labeled cDNA was included in a hybridization mix that was incubated on the Clariom S mouse array for 16 hours at 45◦c while rotating at 60 rpm.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

source_name: sgTfeb+Tfe3 transduced FlcnKO OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection

label_protocol: High-quality RNA was processed using Thermo Fisher (Affymetrix) Whole Transcript (WT) Plus assay kit

growth_protocol: OT-1 cells from WT-Cas9-KI-Flcnfl/fl or Cd4Cre-Cas9-KI-Flcnfl/fl mice were transduced with sgNTC, sgTfeb, or sgTfe3 in various combinations as indicated and transferred into WT mice, followed by LM-OVA infection. At day 7.5 p.i., siIEL OT-1 cells were sort purified

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen.

tag: strain


title: N5


title: FlcnKO_sgTfeb_sgTfe3 JLR822

value: sgTfeb+Tfe3 transduced FlcnKO OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: FlcnKO_sgTfeb JLR817

source_name: sgTfeb transduced FlcnKO OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: FlcnKO_sgTfe3 JLR819

source_name: sgTfe3 transduced FlcnKO OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: FlcnKO_sgTfe3 JLR820

value: sgTfe3 transduced FlcnKO OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: FlcnKO_sgTfe3 JLR821


title: sgTfeb_sgTfe3 JLR814

source_name: sgTfeb+Tfe3 transduced OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: sgTfeb_sgTfe3 JLR813

value: sgTfeb+Tfe3 transduced OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: sgTfeb_sgTfe3 JLR815


title: FlcnKO_sgTfeb JLR816

value: sgTfeb transduced FlcnKO OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: sgTfe3 JLR812

source_name: sgTfe3 transduced OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: sgTfe3 JLR810

value: sgTfe3 transduced OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: sgTfeb JLR809

description: sgTfeb

source_name: sgTfeb transduced OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: FlcnKO_sgTfeb JLR818


title: FlcnKO JLR804

description: FlcnKO

source_name: FlcnKO OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: sgTfeb JLR807

description: sgTfeb

value: sgTfeb transduced OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: sgNTC JLR802

description: sgNTC

source_name: sgNTC transduced OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: sgTfeb JLR808

description: sgTfeb


title: sgNTC JLR803

description: sgNTC

value: sgNTC transduced OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: FlcnKO JLR806

description: FlcnKO

value: FlcnKO OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: sgNTC siIEL (spike for sgRragc) JLR916

growth_protocol: sgNTC (GFP+) and sgLamtor4, sgRraga, or sgRragc (all Ametrine+)-transduced OT-1 cells were sort purified from the siIEL of the same LM-OVA-infected mice (with their respective sgNTC controls) at day 7.5 p.i

tag: cell type


title: sgNTC JLR801

description: sgNTC


title: sgNTC siIEL (spike for sgRragc) JLR918


title: sgTfe3 JLR811


title: sgNTC siIEL (spike for sgLamtor4) JLR902


title: FlcnKO JLR805

description: FlcnKO


title: sgRragc siIEL JLR921

description: sgRragc siIEL

source_name: sgRragc transduced OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: sgRragc siIEL JLR922

description: sgRragc siIEL

value: sgRragc transduced OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: sgNTC siIEL (spike for sgRragc) JLR915

description: sgNTC siIEL (spike for sgRragc)


title: sgNTC siIEL (spike for sgRragc) JLR917

description: sgNTC siIEL (spike for sgRragc)


title: sgRragc siIEL JLR919

description: sgRragc siIEL


title: sgNTC siIEL (spike for sgRraga) JLR911

description: sgNTC siIEL (spike for sgRraga)


title: sgRraga siIEL JLR912

description: sgRraga siIEL

source_name: sgRraga transduced OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: sgRragc siIEL JLR920

description: sgRragc siIEL


title: sgNTC siIEL (spike for sgRraga) JLR910

description: sgNTC siIEL (spike for sgRraga)


title: sgNTC siIEL (spike for sgRraga) JLR909

description: sgNTC siIEL (spike for sgRraga)


title: sgLamtor4 siIEL JLR908

description: sgLamtor4 siIEL

source_name: sgLamtor4 transduced OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: sgFlcn_siIEL JLR719

source_name: sgFlcn transduced OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection

growth_protocol: sgNTC (Ametrine+) and sgFlcn (GFP+)-transduced OT-1 cells were sort-purified from spleen and siIEL of the same LM-OVA-infected mice at day 7.5 p.i.


title: FlcnKO_sgTfeb_sgTfe3 JLR823


title: sgFlcn_siIEL JLR716

value: sgFlcn transduced OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: sgNTC_siIEL JLR715


title: sgFlcn_siIEL JLR717


title: sgFlcn_siIEL JLR718


title: sgLamtor4 siIEL JLR905

description: sgLamtor4 siIEL

value: sgLamtor4 transduced OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: sgNTC_siIEL JLR714


title: sgNTC siIEL (spike for sgLamtor4) JLR904

description: sgNTC siIEL (spike for sgLamtor4)


title: sgLamtor4 siIEL JLR906

description: sgLamtor4 siIEL


title: sgNTC siIEL (spike for sgLamtor4) JLR903

description: sgNTC siIEL (spike for sgLamtor4)


title: sgRraga siIEL JLR913

description: sgRraga siIEL

value: sgRraga transduced OT-1 cells sorted from 7.5 days siIEL after LM-OVA infection


title: sgNTC_siIEL JLR713


title: sgLamtor4 siIEL JLR907

description: sgLamtor4 siIEL


title: sgNTC siIEL (spike for sgLamtor4) JLR901

description: sgNTC siIEL (spike for sgLamtor4)


title: sgRraga siIEL JLR914

description: sgRraga siIEL


title: sgFlcn_siIEL JLR720


title: sgFlcn_spleen JLR710

source_name: sgFlcn transduced OT-1 cells sorted from 7.5 days spleen after LM-OVA infection


title: sgNTC_siIEL JLR711


title: sgNTC_spleen JLR705

source_name: sgNTC transduced OT-1 cells sorted from 7.5 days spleen after LM-OVA infection


title: sgFlcn_spleen JLR709

value: sgFlcn transduced OT-1 cells sorted from 7.5 days spleen after LM-OVA infection


title: sgNTC_siIEL JLR712


title: sgNTC_spleen JLR703

value: sgNTC transduced OT-1 cells sorted from 7.5 days spleen after LM-OVA infection


title: sgNTC_spleen JLR702


title: sgFlcn_spleen JLR707


title: sgNTC_spleen JLR704


title: sgFlcn_spleen JLR708


title: sgFlcn_spleen JLR706


title: sgNTC_spleen JLR701


title: Arg_free4

source_name: OT-1 cells activated in arginine-deficient culture medium without 5 ng/ml TGF-b stimulation for 2.5 days

growth_protocol: OT-1 cells were activated in control or arginine-deficient culture medium with or without stimulation of  5 ng/ml TGF-b for 2.5 days

tag: cell line


title: Arg_cntl_plus_TGFb2

source_name: OT-1 cells activated in control culture medium with 5 ng/ml TGF-b stimulation for 2.5 days


title: a194es

city: Philadelphia

first: Sydney

middle: M

last: Shaffer

state: PA

address: BRB II/III, Room 445, 421 Curie Blvd

institute: University of Pennsylvania

description: 10X Genomics

data_processing:
Raw sequencing data was demultiplexed and converted to FASTQ files using CellRanger, then aligned to the human reference genome GRCh38 using STARsolo to generate count matrices.
Assembly: GRCh38
Supplementary files format and content: *matrix.mtx: Sparse count matrix
Supplementary files format and content: *features.tsv: Tab-separated list of features (genes or clone) and identifiers for type of feature.
Supplementary files format and content: *barcodes.tsv: 10X cell barcodes

extract_protocol:
The biopsies were immediately transferred and processed in ice-cold phosphate buffered saline. To dissociate the tissue into single cells, the biopsies were chopped with a scalpel and enzymatically digested in multiple rounds using Liberase TH and DNase I at 37°C, with gentle agitation. The resulting cell suspensions were filtered, washed, and prepared for 10x Genomics single-cell RNA sequencing library preparation targeting 5,000-10,000 cells per sample.
Library construction was performed following the 10X Genomics 3' v3.1 protocol. In brief, single cells were encapsulated into gel bead-in-emulsions (GEMs) using a chromium controller. PolyA RNA from each cell was reverse transcribed into cDNA. cDNA from all cells were pooled and cleaned up using Dynabeads before being PCR amplified and size selected using AMPure XP beads. Full-length cDNA was then fragmented before adding sequencing primers and indices and doing a final amplication. The final product was again cleaned using AMPure XP beads and sequenced.

value: human esophagus

value: squamous


title: a193es

description: 10X Genomics


title: Arg_free3

value: activated in arginine-deficient culture medium without 5 ng/ml TGF-b stimulation for 2.5 days


title: Arg_cntl_plus_TGFb3

value: activated in control culture medium with 5 ng/ml TGF-b stimulation for 2.5 days


title: APC (min/+) mouse HFD Control 3

city: NEW ORLEANS

first: Suzana

middle: D

last: Savkovic

state: LA

address: 1430 Tulane Ave JBJ 315

institute: Tulane University

description:
HFD_DGAT1&2Treated_vs_HFD_Untreated.xlsx
RD_Untreated_vs_HFD_Untreated.xlsx

data_processing:
Paired-end reads were aligned to hg38 genome using STAR(v.2.6.1d).
Abundance levels were calculated using Kallisto(v.0.46.0) a
Differential expression testing performed using DESeq2.
Assembly: mouse, mm10 and human, hg38
Supplementary files format and content: Excel files with TPMs and results of differential expression testing from DESeq2

source_name: Colon

extract_protocol:
Zymogen, Dnase Treated
High Output Paired End Read

value: Colon

tag: genome build

value: Colon from APC (min/+) mice on High Fat Diet that were treated with placebo using an oral gavage.


title: APC (min/+) mouse HFD DGAT1/2 Inhs. 2

description: HFD_DGAT1&2Treated_vs_HFD_Untreated.xlsx

value: Colon from APC (min/+) mice on High Fat Diet that were treated with DGAT1/2 inhinitors using an oral gavage.


title: APC (min/+) mouse RD Control 3

description:
RD_DGAT1&2Treated_vsRD_Untreated.xlsx
RD_Untreated_vs_HFD_Untreated.xlsx

value: Colon from APC (min/+) mice on Regular Diet that were treated with placebo using an oral gavage.


title: APC (min/+) mouse HFD DGAT1/2 Inhs. 3


title: APC (min/+) mouse HFD Control 2


title: APC (min/+) mouse RD DGAT1/2 Inhs. 2

value: Colon from APC (min/+) mice on Regular Diet that were treated with DGAT1/2 inhibitors using an oral gavage.


title: APC (min/+) mouse RD Control 1


title: APC (min/+) mouse HFD DGAT1/2 Inhs. 1


title: Arg_free_plus_TGFb2

source_name: OT-1 cells activated in arginine-deficient culture medium with 5 ng/ml TGF-b stimulation for 2.5 days


title: Arg_free_plus_TGFb1

value: activated in arginine-deficient culture medium with 5 ng/ml TGF-b stimulation for 2.5 days


title: Arg_free2


title: APC (min/+) mouse RD DGAT1/2 Inhs. 1


title: APC (min/+) mouse HFD Control 1


title: Arg_free_plus_TGFb3


title: Arg_cntl_plus_TGFb1


title: Arg_cntl1

source_name: OT-1 cells activated in control culture medium without 5 ng/ml TGF-b stimulation for 2.5 days


title: Arg_cntl3

value: activated in control culture medium without 5 ng/ml TGF-b stimulation for 2.5 days


title: Arg_free_plus_TGFb4


title: Arg_free1


title: APC (min/+) mouse RD Control 2


title: Arg_cntl2


title: APC (min/+) mouse RD DGAT1/2 Inhs. 3


title: a189es2

description: 10X Genomics


title: a189es1

description: 10X Genomics


title: a185es

description: 10X Genomics


title: CD4+ Treg,D5,Stim,ZNF217 KO,IgG (EpiCypher, 13-0042) [TF KO]

city: San Francisco

first: Alexander

last: Marson

address: 1650 Owens St

institute: UCSF Gladstone Institutes

data_processing:
Bcl2fastq (v2.19) with the settings --minimum-trimmed-read-length 8 was used to generate fastqs.
the fastqs were trimmed with cutadapt (v1.18)
Bowtie2 (v2.2.5) was used to align the trimmed fastqs to GRCh38 using settings --local --very-sensitive --no-mixed --no-discordant --phred33 --dovetail -I 10 -X 700 -p 8 -q and E. coli (EMBL accession U00096.2) with settings --local --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant --phred33 -I 10 -X 700 -p 8 -q.
Bam files were generated with samtools(version 1.9) view -bS -F 0x04 and bam to bed conversion performed with bedtools (v2.30.0) bamtobed -bedpe.
Bedfiles were filtered to include only paired reads of less than 1000 bp with the command awk '$1==$4 && $6-$2 < 1000 {print $0}' samplename.bed before generating bedgraph files using bedtools (version 2.30.0) genomecov -bg.
Peak calling was performed using the bedgraph files as input with SEACR49 (v1.3). Each H3K27ac bed file was compared to the respective donor and KO condition IgG file to identify peaks about the background using the norm and stringent options.
ChIP-seq blacklist regions were removed from filtered SEACR files prior to generating the sample by peak matrix
The sample matrix was reduced across all peaks within the dataset and segmented into regions of 5000 bps.
Assembly: GRCh38
Supplementary files format and content: Scaled bedgraphs are provided for H3K27ac samples and unscaled bedgraphs for IgG control samples
Supplementary files format and content: SEACR peaks are provided for H3K27ac samples
Library strategy: CUT&RUN

source_name: Lymphocyte

growth_protocol: CD4+ regulatory and effector T cells were isolated from fresh Peripheral Blood Leukopaks (STEMCELL Technologies, #70500) from healthy human donors, after institutional review board–approved informed written consent (STEMCELL Technologies). The contents of the Leukopaks were washed twice with a 1X volume of EasySep buffer (DPBS, 2% fetal Bovine Serum (FBS), 1mM pH 8.0 EDTA) using centrifugation. The washed cells were resuspended at 200E6 cells/mL in EasySep buffer and isolated with the EasySep™ Human CD4+CD127lowCD25+ Regulatory T Cell Isolation Kit (STEMCELL Technologies, #18063), according to the manufacturer’s protocol. Following isolation with the kit, Tregs were stained Alexa Fluor® 647 anti-human CD25 Antibody (Biolegend, #302618), PE anti-Human CD127 (Beckon Dickinson, #557938), and Pacific Blue™ anti-human CD4 Antibody (Biolegend, #344620) and isolated using FACS to ensure a pure population without contaminating effector cells. After sorting pure CD4+CD127lowCD25+ Regulatory T Cells, the cells were seeded at 1x106 cells/mL in XVIVO-15 (Lonza, #02-053Q) supplemented with 55 uM 2-mercaptoethanol, 4 mM N-acetyl L-cysteine, and 200 U/mL IL-2 (Amerisource Bergen, #10101641). Teffs were seeded at 1x106 cells/mL in RPMI-1640 supplemented with 10% FCS, 2 mM L-Glutamine (Fisher Scientific #25030081), 10 mM HEPES (Sigma, #H0887-100ML), 1X MEM Non-essential Amino Acids (Fisher, #11140050), 1 mM Sodium Pyruvate (Fisher Scientific #11360070), 100 U/mL Penicillin-Streptomycin (Sigma, #P4333-100ML), and 50 U/mL IL-2 (Amerisource Bergen, #10101641). Both cell subsets were then stimulated with ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator (STEMCELL Technologies, #10990) at 25 uL/mL for Tregs and 6.25 uL/mL for Teff. Following activation and electroporation, cells were split 1:2 every 48 hours to maintain an approximate density of 1x106 cells/mL and supplemented with respective doses of IL-2.

extract_protocol:
CUT&RUN from isolated nuclei was performed according to the manufacturer’s protocol with the EpiCypher CUTANA™ ChIC/CUT&RUN Kit and provided reagents. In brief, 5E5 T cells per reaction  were washed with PBS before nuclear isolation using the EpiCypher recommended lysis buffer consisting of 20 mM HEPES pH 7.9 (Sigma-Aldrich), 10 mM KCl (Sigma-Aldrich), 0.1% Triton X-100 (Sigma-Aldrich), 20% Glycerol (Sigma-Aldrich), 1 mM MnCl2 (Sigma-Aldrich), 1X cOmplete Mini-Tablet (Roche), and 0.5 mM Spermidine (Sigma-Aldrich). The cells were resuspended in 100 ul per reaction cold nuclear extraction buffer and incubated on ice for 10 minutes. Following lysis, nuclei were pelleted and resuspended in 100 ul per reaction of nuclear extraction buffer. The isolated nuclei were then frozen at -80 in extraction buffer until DNA isolation. After thawing the samples at 37C, the nuclei were bound to activated conA beads. After adsorption of nuclei to beads, permeabilization was performed with 0.01% digitonin containing buffer. Antibodies for H3K27ac (EpiCypher) and IgG (EpiCypher) were added at 500 ng per reaction. Following overnight antibody binding, pAG-MNase addition, and chromatin cleavage, 0.5 ng of the provided E. coli DNA was added to each sample following chromatin cleavage by MNase. The provided spin columns and buffers were used for DNA isolation and purification.
The resulting DNA was prepared for sequencing using the CUTANA™ CUT&RUN Library Prep Kit (Cat 141002) according to the manufacturer’s protocol.

treatment_protocol: Stimulated cells were activated with ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator (STEMCELL Technologies, #10990) 48 hours prior to collection

value: Lymphocyte

tag: antibody

value: IgG (EpiCypher, 13-0042)

tag: donor

value: Treg

value: Stim

tag: guide

tag: group

value: TF KO


title: CD4+ Treg,D5,Resting,BATF KO,IgG (EpiCypher, 13-0042) [TF KO]

tag: tissue

value: Resting

tag: genotype

value: BATF


title: CD4+ Treg,D5,Resting,TAF5L KO,IgG (EpiCypher, 13-0042) [TF KO]

tag: treatment


title: CD4+ Treg,D5,Stim,BATF KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D5,Stim,AAVS1 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D5,Stim,USP22 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D5,Resting,ZNF217 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D4,Stim,BATF KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D4,Resting,USP22 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D5,Stim,TAF5L KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D4,Resting,BATF KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D4,Stim,AAVS1 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D4,Resting,ATXN7L3 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D4,Stim,USP22 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D4,Resting,ZNF217 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D4,Stim,ZNF217 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D5,Resting,AAVS1 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D5,Resting,ATXN7L3 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D5,Resting,USP22 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D4,Resting,TAF5L KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Teff,D3,Stim,USP22 KO,IgG (EpiCypher, 13-0042) [TF KO]

value: Teff


title: CD4+ Treg,D4,Stim,TAF5L KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Teff,D3,Stim,ZNF217 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Teff,D3,Stim,BATF KO,IgG (EpiCypher, 13-0042) [TF KO]


title: a188es

description: 10X Genomics

value: human esophagus

value: squamous


title: CD4+ Treg,D4,Resting,AAVS1 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Teff,D3,Stim,TAF5L KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D5,Stim,ATXN7L3 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Teff,D3,Stim,ATXN7L3 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D4,Stim,ATXN7L3 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Teff,D3,Stim,AAVS1 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Teff,D3,Resting,USP22 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Teff,D3,Resting,BATF KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Teff,D3,Resting,AAVS1 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Teff,D3,Resting,ZNF217 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Teff,D1,Stim,ZNF217 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Teff,D1,Resting,ZNF217 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Teff,D1,Stim,BATF KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Teff,D1,Resting,TAF5L KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Teff,D1,Resting,USP22 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Teff,D1,Stim,AAVS1 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Teff,D1,Stim,USP22 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Teff,D1,Resting,ATXN7L3 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D5,Stim,TAF5L KO,H3K27ac (EpiCypher, 13-0045) [TF KO]

value: H3K27ac (EpiCypher, 13-0045)


title: CD4+ Teff,D1,Resting,BATF KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D5,Stim,BATF KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D5,Stim,ATXN7L3 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D1,Resting,AAVS1 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D5,Stim,USP22 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D5,Stim,AAVS1 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D5,Stim,ZNF217 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D5,Resting,ZNF217 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D5,Resting,USP22 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D3,Resting,ATXN7L3 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Teff,D3,Resting,TAF5L KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Teff,D1,Stim,TAF5L KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D5,Resting,TAF5L KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D5,Resting,BATF KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D5,Resting,ATXN7L3 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D5,Resting,AAVS1 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D4,Stim,USP22 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D4,Stim,BATF KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D1,Stim,ATXN7L3 KO,IgG (EpiCypher, 13-0042) [TF KO]


title: CD4+ Treg,D4,Stim,TAF5L KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D4,Stim,ATXN7L3 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D4,Resting,USP22 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D4,Resting,ZNF217 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D3,Stim,TAF5L KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D3,Stim,BATF KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D4,Resting,TAF5L KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D3,Stim,ZNF217 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D4,Resting,ATXN7L3 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D4,Resting,BATF KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D4,Resting,AAVS1 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D3,Stim,AAVS1 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D3,Resting,USP22 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D3,Resting,TAF5L KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D3,Stim,ATXN7L3 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D3,Resting,BATF KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D1,Stim,TAF5L KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D3,Resting,ZNF217 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D1,Stim,BATF KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D3,Resting,ATXN7L3 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D3,Resting,AAVS1 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D4,Stim,ZNF217 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D1,Stim,ATXN7L3 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D3,Stim,USP22 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D1,Stim,USP22 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D1,Resting,ZNF217 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D4,Stim,AAVS1 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D1,Resting,TAF5L KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D1,Stim,AAVS1 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D1,Resting,BATF KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D1,Stim,ZNF217 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Teff,D1,Resting,USP22 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D3,Stim,MED12 KO,IgG (EpiCypher, 13-0042) [Mediator KO]

value: Mediator KO


title: CD4+ Treg,D3,Stim,AAVS1 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Treg,D3,Stim,MED11 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Teff,D1,Resting,ATXN7L3 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D3,Resting,AAVS1 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Treg,D3,Resting,MED11 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Treg,D3,Resting,MED24 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Teff,D1,Resting,AAVS1 KO,H3K27ac (EpiCypher, 13-0045) [TF KO]


title: CD4+ Treg,D3,Resting,MED12 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Teff,D3,Stim,AAVS1 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Teff,D3,Resting,MED12 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Treg,D1,Stim,MED24 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Teff,D3,Resting,AAVS1 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Treg,D1,Stim,MED12 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Teff,D3,Stim,MED24 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Treg,D1,Stim,AAVS1 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Teff,D3,Stim,MED11 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Teff,D3,Resting,MED11 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Treg,D1,Resting,MED11 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Treg,D1,Resting,MED12 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Treg,D3,Stim,MED24 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Treg,D1,Resting,MED24 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Teff,D1,Stim,MED12 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Teff,D1,Stim,MED11 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Treg,D1,Resting,AAVS1 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Teff,D1,Stim,AAVS1 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Teff,D1,Resting,AAVS1 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Teff,D3,Stim,MED12 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Teff,D1,Resting,MED11 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Teff,D3,Resting,MED24 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Teff,D1,Resting,MED24 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Treg,D3,Stim,MED12 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Teff,D1,Resting,MED12 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Treg,D3,Stim,MED24 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Treg,D3,Stim,AAVS1 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Treg,D1,Stim,MED11 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Treg,D3,Resting,AAVS1 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Treg,D3,Resting,MED11 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Teff,D3,Stim,MED12 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Teff,D3,Stim,MED11 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Teff,D1,Stim,MED24 KO,IgG (EpiCypher, 13-0042) [Mediator KO]


title: CD4+ Teff,D3,Resting,MED11 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Teff,D3,Resting,MED12 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Treg,D1,Stim,MED24 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Treg,D1,Stim,MED12 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Teff,D3,Resting,AAVS1 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Treg,D3,Stim,MED11 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Treg,D3,Resting,MED12 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Treg,D1,Stim,AAVS1 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Treg,D3,Resting,MED24 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Teff,D3,Stim,MED24 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Treg,D1,Resting,MED24 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Teff,D1,Stim,MED24 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Treg,D1,Resting,MED11 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Teff,D1,Stim,MED11 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Treg,D1,Stim,MED11 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Teff,D1,Resting,MED24 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Teff,D1,Resting,MED12 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Teff,D3,Stim,AAVS1 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Treg,D1,Resting,AAVS1 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Teff,D1,Resting,MED11 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Teff,D1,Stim,MED12 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Teff,D1,Resting,AAVS1 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: CD4+ Teff,D3,Resting,MED24 KO,H3K27ac (EpiCypher, 13-0045) [Mediator KO]


title: 205030230139_R01C01

city: Detroit

last: Pilsner

state: MI

address: 275 E Hancock St

department: Department of Obstetrics and Gynecology

institute: Wayne State University

description:
sperm DNA methylation
Processed_methylation_data_matrix_EARTH.RData

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to  Illumina Infinium HumanMethylationEPIC BeadChip using standard Illumina protocol

data_processing:
Sperm DNA methylation was assessed using Illumina's EPIC Infinium Methylation Beadchip. Raw idat files were imported into R and within-array normalization and dye-bias equalization of Type I and Type II probes was performed using normal-exponential convolution method (Noob) via  minfi package. Batch effects were corrected with the ComBat function in the sva package while cross-hybridizing probes were removed using the DMRcate package. probes with detection pvalue >0.01 were also exluced prior to downstream analysis.
Processed matrix contains the NOOB-normalized beta values representing the percent CpG methylation for all the CpGs that passed the preprocessing method.

source_name: normal sperm sample

extract_protocol: Standard Illumina Protocol

treatment_protocol: Sperm from semen was extracted using gradient method and purified DNA was isolated our previously developed method of beads, RLT and TCEPS

value: sperm

tag: cohort

value: EARTH

tag: bmi

tag: race

tag: creatinine

tag: specific gravity

tag: batch

tag: mehp

tag: mecpp

tag: mcmhp

tag: mehhp

tag: meohp

tag: mcpp

tag: mop

tag: mchp

tag: mbzp

tag: minp

tag: mmp

tag: mep

tag: mbp

tag: mibp

tag: mcnp

tag: mcop

tag: mhbp

tag: mhibp

tag: mhinch

tag: mcoch


title: 205030230139_R03C01

tag: tissue

tag: cohort

tag: bmi

tag: race

tag: creatinine

tag: specific gravity

tag: batch

tag: mehp

tag: mecpp

tag: mcmhp

tag: mehhp