title: DMSO 6 biol rep 3

city: Kalamazoo

first: Cindy

last: Linn

state: MI

address: 1903 W Michigan Ave

institute: Western Michigan University

description: Library name: Sample 12

data_processing:
Differential gene expression analysis between experimental and control groups was performed using DESeq2. The Wald test was used to calculate statistical significance and generate p-values and log2 fold changes. Genes with an adjusted p-value ≤ 0.05 and an absolute log2 fold change > 1 (log2 fold change > 1 or < -1) were considered significantly differentially expressed. A gene ontology (GO) analysis was performed by Genewiz on the statistically significant set of genes by implementing the software GeneSCF v.1.1-p2.
Assembly: Mus musculus (GRCm38) reference genome
Supplementary files format and content: Txt files provide gene id, chr, start, end, strand, length

source_name: Retina

growth_protocol: The neural retina was peeled from the eyecup after removing the cornea and lens and subsequently placed in a papain solution (Worthington Biochemical) at 37℃ for 15 minutes. After incubation, enzymatic activity was stopped using an ovomucoid inhibitor solution (Worthington Biochemical) and the solution was resuspended in DMEM/F12 with 10000 U/mL penicillin, 100 µg/mL streptomycin, and 0% FBS to starve off neuronal retinal cells. They were cultured in 100 mm dishes at 37℃ with 5% CO2 and the media was replaced every three days. After 5 days, the MG cells were incubated in DMEM/F12 containing 10% FBS. MG cells were passed at least three times to ensure a pure culture.For primary RPE cells, eyecups were removed from euthanized mice and was incubated in 1 mg/mL hyaluronidase for 45 minutes at 37℃. Hank’s buffered saline solution (Gibco) was added to stop the reaction, and the eyecup was transferred to a 0.5% trypsin solution (Gibco). The RPE cells were scraped from the posterior sclera and centrifuged in alpha-MEM culture media (Gibco). The remaining pellet was resuspended in alpha-MEM culture media supplemented with 5% fetal bovine serum (FBS) (Gibco), 10000 U/mL penicillin, 100 µg/mL streptomycin (Gibco), 20 μg/L hydrocortisone (Sigma-Aldrich), 250 mg/L Taurine (Sigma-Aldrich), 1:100 N1 supplement (Sigma-Aldrich), 1:100 non-essential amino acids (Gibco), and 0.013 μg/L triiodothyronine (Sigma-Aldrich) and cultured into 60 mm dishes. Cells were cultured at 37℃ with 5% CO2 and culture media was refreshed every three days. Once confluent, the RPE cells were switched to Dulbecco’s Modified Essential Medium (DMEM/F12) culture media (Gibco) with 10000 U/mL penicillin, 100 µg/mL streptomycin, and 10% FBS for 72 hours. RPE cells were passed at least three times to ensure a pure culture. Subsequently, the RPE cells were treated with culture media containing 100 nM PNU-282987 (Sigma-Aldrich) with 1% DMSO (Sigma-Aldrich) in experimental groups and 1% DMSO in control groups once they reached a ~80% confluency for 24 hours. A previous dose-response experiment from this laboratory determined RPE cells treated with 100 nM PNU-282987 elicit the most robust proliferative response. After 24 hours, the treated RPE cells were washed thoroughly with 1X phosphate-buffered saline (PBS) (Sigma-Aldrich) to remove any residual treatment media.

extract_protocol:
RNA was extracted from primary Müller glia (MG) cultures co-cultured with RPE cells in transwell plates under both experimental and control conditions using the Direct-zol RNA Miniprep kit (Zymo Research) according to the manufacturer’s instructions and eluted in DNase/RNase-free water. Concentration was ≥6 ng/uL and OD260/280≥ 2.0; OD260/230≥ 2.0; no degradation, no contamination
Following RNA QC, poly(A) selection was performed to enrich mRNA, followed by cDNA library preparation and sequencing on an Illumina® NovaSeq™ platform using a 2 × 150 bp paired-end sequencing configuration. Sequencing reads were trimmed and quality filtered using fastp v0.23.2 and aligned to the Mus musculus GRCm38 reference genome (ENSEMBL) using the STAR aligner v2.5.2b. Gene-level read counts were generated using featureCounts from the Subread package v1.5.2.

treatment_protocol: Primary MG cells were co-cultured in transwell plates for  2 hours and 6 hours with primary experimental (100 nM) or control-treated (0.1% DMSO) RPE cells

value: Retina

value: Primary Muller glia cells


title: HASMC normotensive hydrostatic pressure replicate 3

status: Public on Aug 12 2026

type: SRA

city: Shinjyuku

first: Takahiro

last: Kusume

address: 6-1-1, Shinjyuku

country: Japan

institute: Tokyo medical university

description: Library name: Pressure_N_3

library_source: transcriptomic

data_processing:
Raw reads were assessed using FastQC (v0.11.7).
Adapter sequences and low-quality bases were removed using Trimmomatic (v0.38).
Trimmed reads were aligned to the human reference genome (hg38) using HISAT2 (v2.1.0).
Gene-level read counts were generated using featureCounts (v1.6.3).
FPKM and TPM values were calculated from mapped reads.
Assembly: hg38
Supplementary files format and content: RawCount_Matrix_ann.txt contains gene-level read counts.
Supplementary files format and content: TPM_Matrix_ann.txt contains TPM-normalized expression values.

molecule: total RNA

organism: Homo sapiens

source_name: Aorta

growth_protocol: Human aortic smooth muscle cells were purchased from Kurabo (KS-4009, Kurabo, Osaka, Japan) and maintained in HuMedia-SG2 medium (KS2170, Kurabo) containing 5% fetal bovine serum (FBS), insulin (5 μg /ml), human epidermal growth factor (0.5 ng/ml), human basic fibroblast growth factor (2 ng/ml), gentamicin (50 μg /ml) and amphotericin B (50 ng/ml) with 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Venlo, the Netherlands).
RNA-seq libraries were prepared from total RNA using poly(A) selection with the NE Next Poly(A) mRNA Magnetic Isolation Module, followed by library construction using the NE Next Ultra II Directional RNA Library Prep Kit (New England Biolabs).

treatment_protocol: Cells were cultured under control (no mechanical loading), cyclic stretch (10%), normotensive cyclic hydrostatic pressure (120/60 mmHg), or hypertensive cyclic hydrostatic pressure (180/120 mmHg) conditions for 24 h before RNA extraction.

tag: tissue

value: Aorta

tag: cell line

value: Human aortic smooth muscle cells

tag: cell type

value: vascular smooth muscle cell

tag: genotype

value: WT

tag: treatment

value: Cyclic hydrostatic pressure (120/60 mmHg, 1Hz)


title: E. coli BL21 cells, pNP1528

city: Bunkyo-ku

first: Hiroshi

last: Nishimasu

state: Tokyo

address: 7-3-1 Hongo

institute: University of Tokyo

description: Library name: BL21_pNP1528

data_processing:
Paired-end RNA-Seq reads from each sample were aligned to the respective plasmid and genomic reference sequences using Burrows-Wheeler Aligner-MEM. Aligned reads were filtered using SAMTools for reads that originated from the strand that encodes the bRNAs. For each locus of interest on the reference sequences, we used the Pysam Python module to count the coverage depth at the single-base level from these filtered reads, with a quality threshold of 0. Coverage depths were normalized using the total number of reads (CPM).
Since the E. coli Mach1 genome has three separate IS621 loci that are highly homologous with one another, many of the RNA-Seq reads that mapped to these regions were expected to lack unique mapping to one of the three loci. Thus, among the reads that were mapped to any of the IS621 loci, pairs of reads where either pair had a mapping quality of zero (meaning the read can map equally well to other parts of the reference sequence) were classified as “nonspecific” reads, and the coverage from these reads was counted separately from the reads that mapped specifically to one of the three IS621 loci.
Assembly: Sequences for the Mach1 genome and plasmids pNP1528 and pNP3499 were used as references for the alignments.
Supplementary files format and content: bigWig files containing normalized coverage depths (CPM) of bridge recombinase loci.

organism: Escherichia coli

growth_protocol: E. coli cells were harvested from bacterial plates 24h after plating at 37°C.

extract_protocol:
RNA was extracted using a Direct-zol RNA miniprep kit (Zymo Research).
RNA libraries for RNA-seq were prepared using Novogene's RNA library preparation protocols.

value: WT + pNP1528


title: DMSO 6 biol rep 2

country: USA

description: Library name: Sample 11

organism: Mus musculus


title: E. coli BL21 cells, pNP3499

description: Library name: BL21_pNP3499

value: WT + pNP3499


title: Colon,Lactation,Goat-6

city: Cerdanyola del Vallès

first: Diego

middle: Alonso

last: Vargas Donayre

state: Barcelona

address: Carrer de la Vall Moronta

department: Plant and Animal Genomics

country: Spain

institute: Centre for Research in Agricultural Genomics (CRAG)

description: Library name: CO6

data_processing:
Raw reads with less than 100 bp and less than 85% of bases with Q>30 were discarded using Fastp. SILVA database rRNA database release 138.2 was used to eliminate rRNA contamination.
Filtered reads were mapped to the goat reference genome  with STAR and transcript structure recovery was conducted with StringTie. Novel lncRNAs were characterized with an internal protocol
Gene level estimated counts and offsets matrices were generated using tximport. Count data was normalized to CPM with edgeR. Genes with a CPM value greater than 0.5 in at least 3 samples in a tissue were considered as expressed. Null expressed genes were removed. Tissue-specificty of each gene was measured by the tau-index.
Assembly: ARS1.2
Supplementary files format and content: 33tissues_gene_counts.tsv.gz , tab-delimited text file includes raw gene count.
Supplementary files format and content: 33tissues_gene_length.tsv.gz , tab-delimited text file includes gene count offset.
Supplementary files format and content: 33tissues_CPM.tsv.gz , tab-delimited text file includes processed CPM
Supplementary files format and content: lncRNAs.gtf.gz , gtf file including novel lncRNA
Supplementary files format and content: 33tissues_tau.tsv.gz , tab-delimited text file includes tau-index for each expressed gene

organism: Capra hircus

source_name: Colon

extract_protocol:
RNA was extracted using the RiboPure™ Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol.
Strand-specific library construction was performed with VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina.

value: Colon


title: Colon,Lactation,Goat-3

description: Library name: CO3


title: E. coli Mach1 cells

description: Library name: Mach1_WT


title: HASMC normotensive hydrostatic pressure replicate 2

description: Library name: Pressure_N_2


title: DMSO 6 biol rep 1

description: Library name: Sample 10


title: Colon,Dry,Goat-54

description: Library name: CO54


title: HASMC normotensive hydrostatic pressure replicate 1

description: Library name: Pressure_N_1


title: EP cells, Lactate, 5

city: Philadelphia

first: Makarand

last: Risbud

state: PA

address: 1015 Walnut Street

institute: Thomas Jefferson University

description:
Library name: 5-Plus
Lactate=treated sample (5.plus) 5

data_processing:
The sequence reads were aligned by STAR 2.5.2b and hit counts were calculated by using feature Counts from the Subread package v.1.5.2.
Assembly: Rnor6
Supplementary files format and content: tab delimited text files for each sample of hits count table
Supplementary files format and content: tab delimited text file with TPM values for each sample

organism: Rattus norvegicus

source_name: Intervertebral disc

growth_protocol: Primary endplate cells isolated from rat intervertebral discs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidifed atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested from cultured cells using the RNeasy® Micro kit (Qiagen).
RNA samples were quantified with Qubit and assessed using the Agilent TapeStation. Libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit and NEBNext Poly(A) mRNA Magnetic Isolation Module, involving mRNA enrichment, fragmentation, cDNA synthesis, adapter ligation, indexing, and PCR enrichment. Validated libraries were sequenced on an Illumina NovaSeq in 2x150bp paired-end mode, and data were demultiplexed with bcl2fastq allowing one index mismatch.

treatment_protocol: Cells were treated with either 20mM sodium L-lactate (Sigma) or 20mM NaCl in DMEM supplemented with 10% FBS for 24 hours in 5% O2 (Baker Ruskinn).

value: Intervertebral disc

value: primary endplate cells

value: 20mM sodium L-lactate

tag: treatment duration

value: 24 hours


title: EP cells, Lactate, 4

description:
Library name: 4-Plus
Lactate=treated sample (4.plus) 4


title: Abomasum,Dry,Goat-64

description: Library name: AB64

source_name: Abomasum

value: Abomasum


title: DMSO 2 biol rep 3

description: Library name: Sample 9


title: Colon,Dry,Goat-64

description: Library name: CO64


title: EP cells, Lactate, 3

description:
Library name: 3-Plus
Lactate-treated sample (3.plus) 3


title: HASMC stretch replicate 3

description: Library name: Stretch_N_3

value: Cyclic stretch (10% ,1Hz)


title: HASMC stretch replicate 2

description: Library name: Stretch_N_2


title: DMSO 2 biol rep 2

description: Library name: Sample 8


title: DMSO 2 biol rep 1

description: Library name: Sample 7


title: Diaphragm,Lactation,Goat-2

description: Library name: DPH2

source_name: Diaphragm

value: Diaphragm


title: EP cells, Lactate, 2

description:
Library name: 2-Plus
Lactate-treated sample (2.plus) 2


title: HASMC stretch replicate 1

description: Library name: Stretch_N_1


title: PNU 6 biol rep 3

description: Library name: Sample 6

value: Retina


title: Diaphragm,Lactation,Goat-3

description: Library name: DPH3


title: PNU 6 biol rep 2

description: Library name: Sample 5

value: Primary Muller glia cells


title: HASMC control replicate 3

description: Library name: Static_3

value: Aorta

value: Static culture (no mechanical stress loading)


title: Diaphragm,Dry,Goat-54

description: Library name: DPH54


title: HASMC control replicate 2

description: Library name: Static_2

value: Human aortic smooth muscle cells

value: vascular smooth muscle cell


title: EP cells, No lactate 5

description:
Library name: 5-Minus
Control sample (5.minus) 5

value: 20mM NaCl


title: Diaphragm,Dry,Goat-64

description: Library name: DPH64


title: PNU 6 biol rep 1

description: Library name: Sample 4

value: WT


title: HASMC control replicate 1

description: Library name: Static_1


title: EP cells, Lactate, 1

description:
Library name: 1-Plus
Lactate-treated sample (1.plus) 1


title: EP cells, No lactate 4

description:
Library name: 4-Minus
Control sample (4.minus) 4


title: PNU 2 biol rep 3

description: Library name: Sample 3


title: Diaphragm,Dry,Goat-73

description: Library name: DPH73


title: EP cells, No lactate, 3

description:
Library name: 3-Minus
Control sample (3.minus) 3


title: Control 2; control (hemolytic uremic syndrome; normal marrow); bone marrow total RNA

city: Incheon

first: Jaeeun

last: Yoo

address: Bupyoung-gu

country: South Korea

institute: Incheon St. Mary Hospital

description: Library name: Control 2

data_processing:
Adapter/quality trimming with Trimmomatic (paired-end; ILLUMINACLIP TruSeq3-PE; LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).
Alignment to GRCh38 with HISAT2 v2.2.1 (prebuilt grch38_tran index).
BAM sorting and indexing with samtools v1.17.
Gene-level quantification with featureCounts (Subread v2.0.3), paired-end, reverse-stranded (-s 2), GENCODE v44 annotation.
Counts-per-million (CPM) normalization.
Assembly: GRCh38 (GENCODE v44)
Supplementary files format and content: Tab-delimited gene-level matrices; rows = Ensembl gene IDs (with GeneSymbol and GeneType); columns = 14 samples. processed_raw_counts_matrix.tsv = integer raw counts; processed_CPM_matrix.tsv = counts-per-million (CPM).

source_name: bone marrow

extract_protocol:
Total RNA extracted from bone-marrow aspirates using the High Pure RNA Isolation Kit (Roche).
TruSeq Stranded Total RNA Library Prep Globin Kit with Ribo-Zero rRNA removal (Illumina); 800 ng total RNA input.

value: bone marrow

value: not applicable

tag: disease group

value: control

tag: Sex

value: male

tag: age (years)


title: PNU 2 biol rep 2

description: Library name: Sample 2


title: Duodenum,Lactation,Goat-2

description: Library name: DU2

source_name: Duodenum

value: Duodenum


title: Control 1; control (suspected iron-deficiency anemia; normal marrow); bone marrow total RNA

description: Library name: Control 1


title: Duodenum,Lactation,Goat-3

description: Library name: DU3


title: PNU 2 biol rep 1

description: Library name: Sample 1


title: EP cells, No lactate, 2

description:
Library name: 2-Minus
Control sample (2.minus) 2

value: Intervertebral disc

value: primary endplate cells

value: 24 hours


title: EP cells, No lactate, 1

description:
Library name: 1-Minus
Control sample (1.minus) 1


title: U8; genetically-undefined BMF; bone marrow total RNA

description: Library name: U8

value: none identified

value: u-BMF


title: Single-nucleus RNA-seq of MASLD mouse model treated with Aza-TdC

city: Daejeon

first: Hanyong

last: Go

address: 125, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea

institute: KRIBB

description: Library name: 1xAZA-1

library_source: transcriptomic single cell

data_processing:
All data processing and analysis were performed using the Seurat package (v4.4.0). Seurat objects were independently generated for each sample group (Control, MASLD, and Aza-TdC). Quality control measures were applied to exclude cells with fewer than 5,000 genes, more than 20,000 read counts, and mitochondrial gene expression exceeding 15%. After filtering, the datasets were merged into a single Seurat object. The combined dataset was then normalized and scaled using the NormalizeData and ScaleData functions.
Differentially expressed features were selected using the FindVariableFeatures function, with the top 2,000 genes chosen for further analysis. Principal component analysis (PCA) was conducted with the RunPCA function to reduce dimensionality, and batch effects were corrected using the RunHarmony function from the Harmony package. Clustering analysis was performed using the FindNeighbors and FindClusters functions, with 20 principal components and resolution parameters tuned to yield 10–15 clusters. The resulting cell clusters were visualized using Uniform Manifold Approximation and Projection (UMAP).
Cell clusters were annotated using the computational tool singleR, which was supplemented by manual annotations based on established biological knowledge. For focused analysis of hepatocyte subsets, a separate Seurat object was created, and similar preprocessing steps (filtering, normalization, and scaling) were applied. Differential expression analysis between hepatocyte subsets from MASLD mice and Aza-TdC-treated groups was performed using the Wilcox test to identify genes that exhibited significant changes in expression across these conditions.
Assembly: mm10 (GRCm38)
Supplementary files format and content: barcodes.tsv: Contains the unique barcode identifiers for each nucleus. features.tsv: Lists the genes or features detected, with corresponding identifiers (e.g., Ensembl gene IDs or gene symbols). matrix.mtx: A sparse matrix file containing raw expression counts for each gene (row) in each nucleus (column).

molecule: nuclear RNA

source_name: Liver

growth_protocol: At 8 weeks of age, the mice were randomly divided into three groups.The control group was maintained on a standard diet (SD) (#2018S, Teklad Global 18% Protein Rodent Diet, ENVIGO). The MASLD group was fed a MASLD diet (#TD.190142, Teklad Custom Diet, ENVIGO, USA) supplemented with a sucrose solution (18.9 g/L D-glucose, 23.1 g/L fructose) for 18 weeks. The third group followed the same MASLD diet for 18 weeks, while also receiving Aza-TdC (2 mg/kg) daily by oral gavage from 14 week to 18 week.

extract_protocol:
To perform frozen tissue single-nucleus RNA-seq using the 10X Genomics protocol, homogenize 120 mg of cryopreserved tissue in chilled lysis buffer, filter through a 40 μm strainer, and pellet nuclei via centrifugation. Wash with RNase inhibitor buffer, and use FACS to isolate intact nuclei.
Resuspend nuclei in nuclease-free buffer at 700-1200 nuclei/μL for library preparation. Load the nuclei into the Chromium Controller for GEM generation and cDNA tagging, then purify, amplify cDNA, and contruct sequencing libraries using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics)

treatment_protocol: oral administration of 5-Aza-4′-thio-2′-deoxycytidine (Aza-TdC)

value: Liver

tag: diet

value: MASLD diet

tag: strain


title: Abomasum,Dry,Goat-73

description: Library name: AB73

value: Abomasum


title: U7; genetically-undefined BMF; bone marrow total RNA

description: Library name: U7


title: iHPC_snm3c

city: Austin

first: Anna

last: Warden

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

description:
Library name: BL_628
snm3C-seq

library_source: genomic

data_processing:
Raw sequencing FASTQ files were processed using map3C (Galasso, J., Wang, Y., Alber, F., Ernst, J. & Luo, C. map3C: a computational tool for processing multiomic single-cell Hi-C data. bioRxivorg 2025.10.10.681728 (2025) doi:10.1101/2025.10.10.681728.), following the workflow described previously. Briefly, sequencing reads were demultiplexed based on cell barcodes and aligned to the human reference genome (hg38) using the bisulfite-conversion-aware aligner BISCUIT (v1.5.0.20240506). DNA methylation calls were subsequently generated using the ALLCools (v1.0.23) package and stored in the ALLC file format for downstream analyses. Low quality cells were removed by requiring Biscuit mapping rate for both reads R1 and R2 > 0.5; total final reads > 500,000; mCCC level < 0.03; mCH level < 0.2; mCG level > 0.5. 728 cells were included in the downstream analysis.
For the cells passing quality control, we generated the methylome cell dataset (MCDS) from single-cell DNA methylome profiles of the snm3C-seq datasets using “allcools generate-dataset” command. This dataset comprises a cell-by-feature tensor that encompasses hypomethylation probability (hypo-score) in CGN contexts across non-overlapping 5kb bins (chrom5kb) on the hg38 genome, excluding chrX, chrY, and chrM. Bins overlapping ENCODE blacklist regions (https://github.com/Boyle-Lab/Blacklist) for hg38 were excluded. We performed clustering by (1) binarizing the matrix; (2) excluding 5kb bins that had a non-zero methylation level in below 10% of the cells; (3) normalized using term frequency–inverse document frequency (TF-IDF); and (4) reducing dimensionality using truncated singular value decomposition (SVD). Then, visualized using UMAP.
Assembly: hg38 GRCh38
Supplementary files format and content: map3C.srt.dedup.lcov.pairs.gz (3C contacts per cell); allc.tsv.gz (allC methylation per cell)
Supplementary files format and content: xeno_mg_CGN_chrom5k.mcad (h5ad file of 5kb bin mCG); map3c_meta.tsv (map3C single cell quality statistics)

molecule: genomic DNA

source_name: xenografted iHPC

extract_protocol:
Cells were crosslinked in 2% formaldehyde for 5 minutes at room temperature on a rotator. Glycine was added to achieve 0.2M glycine, and incubated for 5 min at room temperature on a rotator. Cells were centrifuged at 1,000 x g for 10 min at 4°C (in bucket rotor). Supernatant was removed and the pellet was resuspended in 1mL of cold DPBS. Cells were centrifuged at 2,500 x g for 5 min at 4°C (in bucket rotor). Supernatant was removed and the pellets were snap-frozen in liquid nitrogen and stored in -80°C. Cells were subjected to in situ 3C procedure following the steps in the Arima Single Cell 3C Beta Kit (Arima Genomics), with some modifications. Cells were lysed for 15 min on ice in 20uL of Lysis Buffer. 44uL of Conditioning Solution was added, and cells were transferred to a 0.2 mL PCR tube, and mixed gently by pipetting. Tubes were incubated at 62°C for 30 min in a thermal cycler, with the lid temperature set to 85°C. 20µL of Stop Solution 2 was added, and mixed gently by pipetting. Tubes were incubated at 37°C for 15 min in a thermal cycler with a lid temperature set to 85°C.  28µL of the restriction enzyme digestion mix (9.8uL water, 9.2uL Buffer H, 4.5uL Enzyme H1, 4.5uL Enzyme H2) was added and gently pipette mixed. Tubes were incubated in a thermal cycler for 37°C for 60 min, 65°C for 20 min, then 25°C for 10 min. 82uL of ligation mix was added (70uL Buffer C, 12uL Enzyme C) and gently mixed by pipetting, then incubated at 25°C for 15 min. Nuclei were transferred to a tube containing 850μL 1% BSA in DPBS on ice and filtered through a 30um Celltrics strainer to a new tube on ice. Nuclei were centrifuged at 1,000 x g for 10 min at 4°C (in bucket rotor). Supernatant was removed and pellets were resuspended each sample in 800uL of 1% BSA in DPBS. Nuclei were stained with DRAQ7 at 1:200 and mixed gently with a pipette and incubated on ice for 5 min. One tube of Proteinase K (Zymo cat. no. D3001-2-D) was dissolved in 1mL of Proteinase K Resuspension Buffer (Zymo cat. no. D3001-2-B) then added to a mix of 15mL M-Digestion Buffer 2x (Zymo cat. no. D5021-9) and 14mL water to make pK Digestion Buffer. 2uL of pK Digestion Buffer were added to each well of an Eppendorf twin.tec® PCR Plate 384 LoBind®, skirted, 45 µL, PCR clean (Eppendorf cat. No. 0030129547). Single DRAQ7 positive nuclei were sorted into individual wells of the 384-well plate using a Sony SH800 cell sorter. Plates were sealed then incubated in a thermal cycler at 50°C for 20 min with a heated lid at 85°C for nuclei digestion.
The snm3C-seq bisulfite conversion procedure and library preparation protocol was carried out as previously described (Zemke, N. R. et al. Epigenetic and 3D genome reprogramming during the aging of the human hippocampus. Science 393, (2026).). This procedure was automated using the Beckman Coulter Biomek i7 liquid handlers for all reactions in 384 and 96-well plates. The snm3C-seq libraries were shallow sequenced on the Element Aviti to ~1 million reads to check quality. Successful libraries were deeply sequenced on the NovaSeq X Plus instruments using 150 bp paired-end reads.

value: xenografted iHPC


title: Single-nucleus RNA-seq of MASLD mouse model

description: Library name: MASLD-4


title: monocytes_snm3c

description:
Library name: BL_627
snm3C-seq

source_name: xenografted monocytes

value: xenografted monocytes


title: Duodenum,Lactation,Goat-6

description: Library name: DU6


title: U6; genetically-undefined BMF; bone marrow total RNA

description: Library name: U6


title: guide barcode EB

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

description:
Library name: ucsf_perturbseq_1_guide_EB
Embryoid_Body_Day_8

data_processing:
STAR Suite v1.6.1
https://github.com/morphic-bio/STAR-suite
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: h5ad files containing filtered and unfiltered counts

extract_protocol:
Dual Index Chromium Next GEM Single Cell 3' HT Kit v3.1
Illumina NovaSeq X Plus

value: iPSC

tag: editing strategy

value: CRISPRi targeting gene promoter region, two guides per construct

tag: altered gene_symbol

tag: time

value: day 8

tag: model system

value: Embryoid body

tag: parental cell_line


title: U5; genetically-undefined BMF; bone marrow total RNA

description: Library name: U5

value: bone marrow


title: SD-5_Input

description: Library name: SD-5_Input

data_processing:
Reads were aligned to the mm10 reference genome using BWA-MEM2 (v2.2.1)
Peak calling using MACS3 (v3 .0.1)
Assembly: mm10
Supplementary files format and content: bw (bigwig)

extract_protocol:
150 mg of liver tissue were dissected from C57BL/6J mice, snap frozen in liquid nitrogen and stored at -80°C. Nuclei were isolated from mouse frozen tissue using the Singulator 100
10 ng of each sample was prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s guidelines

value: Standard diet

tag: chip antibody


title: Single-nucleus RNA-seq of control mouse

description: Library name: SD-4

tag: tissue


title: Duodenum,Dry,Goat-64

description: Library name: DU64

value: Duodenum


title: guide barcode iPSC

description:
Library name: ucsf_perturbseq_1_guide_iPSC
Embryoid_Body_Day_8

tag: cell line


title: Duodenum,Dry,Goat-54

description: Library name: DU54


title: U4; genetically-undefined BMF; bone marrow total RNA

description: Library name: U4

value: female


title: 1xAZA-8_H3K27Ac, ChIP

description: Library name: 1xAZA-8_H3K27Ac, ChIP

value: H3K27ac (Abcam, #ab4729)


title: Duodenum,Dry,Goat-73

description: Library name: DU73


title: transcriptome library EB

description:
Library name: ucsf_perturbseq_1_gene_expression_EB
Embryoid_Body_Day_8

tag: cell type


title: U3; genetically-undefined BMF; bone marrow total RNA

description: Library name: U3

tag: genotype

value: male


title: 1xAZA-4_H3K27Ac, ChIP

description: Library name: 1xAZA-4_H3K27Ac, ChIP

tag: treatment


title: Esophagus,Lactation,Goat-6

description: Library name: ES6

source_name: Esophagus

value: Esophagus


title: transcriptome library iPSC

description:
Library name: ucsf_perturbseq_1_gene_expression_iPSC
Embryoid_Body_Day_8


title: 1xAZA-2_H3K27Ac, ChIP

description: Library name: 1xAZA-2_H3K27Ac, ChIP


title: Esophagus,Dry,Goat-73

description: Library name: ES73


title: CBO-MOK20008P-Day9, MOK20008-WT-Day9 - 10x Genomics Flex scRNA-seq; Pool 2

description:
Library name: SC2300772
KOLF2.2J derived knockout cell line,PAX6 PTC, differentiated to cortical brain organoid - day9 (CBO-MOK20008P-Day9) KOLF2.2J WT differentiated to cortical brain organoid - day9 (MOK20008-WT-Day9) 10x Genomics Flex scRNA-seq; Pool 2

data_processing:
STAR Suite v1.6.1
https://github.com/morphic-bio/STAR-suite
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: h5ad counts files and summary txt files

extract_protocol:
Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples Rev E
Illumina NovaSeq X Plus

value: Termination codon

value: day 9

value: Cortical brain (dorsal forebrain patterning)


title: U1; genetically-undefined BMF; bone marrow total RNA

description: Library name: U1

value: none identified

value: u-BMF


title: MASLD-5_H3K27Ac, ChIP

description: Library name: MASLD-5_H3K27Ac, ChIP

value: Liver

value: MASLD diet


title: Frontal neocortex,Lactation,Goat-2

description: Library name: FN2

source_name: Frontal neocortex

value: Frontal neocortex


title: U2; genetically-undefined BMF; bone marrow total RNA

description: Library name: U2


title: CBO-MOK20008P-Day7, CBO-MOK20008P-Day8, MOK20008-WT-Day7, MOK20008-WT-Day8 - 10x Genomics Flex scRNA-seq; Pool 1

description:
Library name: SC2300771
KOLF2.2J derived knockout cell line,PAX6 PTC, differentiated to cortical brain organoid - day7 and day8 (CBO-MOK20008P-Day7, CBO-MOK20008P-Day8) KOLF2.2J WT differentiated to cortical brain organoid - day7 and day8  (MOK20008-WT-Day7, MOK20008-WT-Day8) 10x Genomics Flex scRNA-seq; Pool 1

value: iPSC

value: day 7, day 8


title: G4; genetically-defined BMF, dyskeratosis congenita; bone marrow total RNA

description: Library name: G4

value: bone marrow

value: TERT c.1892G>A

value: g-BMF


title: MASLD-4_H3K27Ac, ChIP

description: Library name: MASLD-4_H3K27Ac, ChIP


title: Frontal neocortex,Lactation,Goat-3

description: Library name: FN3


title: H295R cells, untreated

city: Augsburg

first: Victoria

middle: Elisabeth

last: Fincke

address: Stenglinstraße 2

country: Germany

institute: Childens Cancer Center - University hospital Augsburg

description: Library name: H295R_untreated

data_processing:
Raw data was processed using the Cell Ranger software suite (v8.0.1, 10x Genomics)
Assembly: GRCh38
Supplementary files format and content: Cell Ranger outputs were futher processed using Seurat (v5.3.0)

source_name: adrenocortical carcinoma cell line

growth_protocol: Cell lines we cultivated according to published protocols and kept at 37°C with 5% CO2.

extract_protocol:
For scRNA-seq analysis, cells were detachted usin 0.5% trypsin-ETDA and incubated for 5min at 37°C.
Library was constructed according to 10x Genomics protocol (Chromium Next GEM Single Cell 3' Kit v3.1)

treatment_protocol: Entinostat was added to the cell culture medium in according concentrations and incubaed for 72h.

value: adrenocortical carcinoma cell line

value: no treatment


title: G3; genetically-defined BMF, Fanconi anemia; bone marrow total RNA

description: Library name: G3

value: male


title: Frontal neocortex,Dry,Goat-54

description: Library name: FN54


title: ACC1 cells, treated with 0.5µM entinostat for 72h

description: Library name: ACC1_05uM_Enti

value: 0.5µM entinostat, 72 h


title: MASLD-3_H3K27Ac, ChIP

description: Library name: MASLD-3_H3K27Ac, ChIP

value: H3K27ac (Abcam, #ab4729)


title: G2; genetically-defined BMF, Fanconi anemia; bone marrow total RNA

description: Library name: G2

value: female


title: ACC1 cells, treated with 1µM entinostat for 72h

description: Library name: ACC1_1uM_Enti

value: 1µM entinostat, 72h


title: SD-5_H3K27Ac, ChIP

description: Library name: SD-5_H3K27Ac, ChIP

value: Standard diet


title: SD-4_H3K27Ac, ChIP

description: Library name: SD-4_H3K27Ac, ChIP


title: Frontal neocortex,Dry,Goat-73

description: Library name: FN73


title: H295R cells, treated with 0.5 µM entinostat for 72h

description: Library name: H295R_05uM_Enti


title: G1; genetically-defined BMF, Fanconi anemia; bone marrow total RNA

description: Library name: G1

value: FANCG c.307+1G>C (homozygous)


title: Frontal neocortex,Dry,Goat-64

description: Library name: FN64


title: Patient 10 Hematoma

city: New Haven

first: Yuki

last: Kawamura

address: 333 Cedar Street

institute: Yale School of Medicine

description:
Library name: CJ2113_ICH010_HF_HHT
10x Genomics

data_processing:
After sequencing, raw BCL files were converted to demultiplexed FASTQs using CellRanger software (3.1.0 for patients 1-8, 6.0.1 for patients 9-10).
Assembly: GRCh38 transcriptome (3.0.0)

molecule: polyA RNA

source_name: hematoma

extract_protocol:
Haematoma and peripheral blood (PB) samples were processed using a detailed protocol to minimize potential processing artifacts and batch effects in the resultant dataset. All steps were performed in a sterile tissue culture hood. Haematoma fluid (HF) was strained through 40 uM filters to remove pieces of clot and brain. The haematoma clot itself was repeatedly washed with ice-cold HBSS and passed through a filter until liquid was light pink to clear. PB and HF samples were spun 500g x 10m and resuspended at 50% hematocrit in HBSS. Exosome supernatant was spun 2000g x 10m, aliquoted, and frozen at -80ºC. Granulocyte cells were then depleted from samples using a Rosette-Sep kit (Stem Cell #15664); protocol performed on ice and according to manufacturer’s instructions. Granulocytes comprise the dominant cell population in similar samples, so depletion was performed to increase the relative proportion of the immune cells of interest. Red blood cell (RBC) lysis was then performed by adding 1:10 1X RBC lysis buffer (BD #555899) and incubating at room temperature for 10m, repeated 1-2 times until sample was clear. Supernatant was then aspirated, and samples were resuspended in 5 mL of a 23% Percoll solution in PBS, spun 500g x 15m, aspirated and washed once with 5 mL complete RPMI. Cells were then counted using a hemocytometer and resuspended in PBS + 0.04% BSA at 1x106 cells/mL.
A target of 10,000 cells from each blood and haematoma sample were processed using 10X Genomics 3’ Single Cell v3.1 kits. Cell suspensions were loaded onto Chromium Next GEN Chip G for GEM generation and barcoding. Other reagents were prepared and loaded according to the manufacturer's protocol. Library generation and amplification were performed by the Yale Center for Genome Analysis (YCGA) according to the manufacturer’s protocol.

value: hematoma


title: SD-3_H3K27Ac_ChIP

description: Library name: SD-3_H3K27Ac, ChIP

value: Liver


title: Hippocampus,Lactation,Goat-2

description: Library name: HIC2

source_name: Hippocampus

value: Hippocampus


title: H295R cells, treated with 1µM entinostat for 72h

description: Library name: H295R_1uM_Enti


title: Patient 10 Blood

description:
Library name: CJ2113_ICH010_Blood_HHT
10x Genomics

source_name: blood

value: blood


title: 1xAZA-8_HNF4a_ChIP

description: Library name: 1xAZA-8_HNF4a, ChIP

value: MASLD diet

value: Hnf4a (Abcam, #ab41898)


title: Hippocampus,Lactation,Goat-3

description: Library name: HIC3


title: ACC1 cells, untreated

description: Library name: ACC1_untreated


title: Patient 9 Hematoma

description:
Library name: CJ2110_ICH009_HF_HHT
10x Genomics


title: Hippocampus,Lactation,Goat-6

description: Library name: HIC6


title: Patient 9 Blood

description:
Library name: CJ2110_ICH009_Blood_HHT
10x Genomics


title: 1xAZA-4_HNF4a_ChIP

description: Library name: 1xAZA-4_HNF4a, ChIP


title: Hypothalamus,Lactation,Goat-2

description: Library name: HYT2

source_name: Hypothalamus

value: Hypothalamus


title: 1xAZA-2_HNF4a_ChIP

description: Library name: 1xAZA-2_HNF4a, ChIP


title: HCE exposed to Pseudomonas aeruginosa, biological rep 3

city: Oviedo

first: Noelia

last: Blanco-Agudín

state: Asturias

address: Facultad de Medicina

institute: University of Oviedo

description:
Library name: HCEpse3
HCE-2 exposed to P. aeruginosa for 15 h. Rep3

data_processing:
Raw reads were filtered to remove adapter sequences, low-quality reads and reads containing excessive ambiguous bases.
Clean reads were aligned to the human reference genome using HISAT2 v2.0.5.
Gene expression levels were quantified and normalized as FPKM values.
Differential gene expression analysis was performed between experimental groups and untreated controls.
Assembly: hg38
Supplementary files format and content: gene_count.xls contains raw read count values for all detected genes across all samples.
Supplementary files format and content: gene_fpkm.xls contains normalized gene expression values (FPKM) for all detected genes across all samples.

source_name: Corneal epithelium

growth_protocol: HCE-2 cells were cultured in Dulbecco’s modified Eagle’s medium/Ham’s F-12 (DMEM/F-12) supplemented with fetal bovine serum, insulin, and epidermal growth factor, and maintained at 37 °C in a humidified atmosphere containing 5% CO₂, as previously described (García et al., 2016).

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit with RNase-free DNase treatment (Qiagen, Venlo, The Netherlands).
mRNA was purified from total RNA, fragmented, and used for first-strand cDNA synthesis with random hexamer primers. Second-strand cDNA synthesis was performed using dUTP instead of dTTP. Subsequently, end repair, 3' adenylation, adapter ligation and PCR amplification were performed. Library quality was assessed using Qubit fluorometry, real-time PCR and Bioanalyzer analysis. Libraries were sequenced on an Illumina NovaSeq X Plus platform (25B flow cell) generating paired-end 150 bp reads.

treatment_protocol: HCE-2 cells were co-cultured for 15 h with either Pseudomonas aeruginosa or Staphylococcus epidermidis. To prevent bacterial overgrowth while maintaining host-microbe interactions, antibiotics were added at the minimum inhibitory concentration (MIC) specific for each bacterial species (gentamicin 6.25 µg/mL for P. aeruginosa and 0.5 µg/mL for S. epidermidis). Untreated cells cultured under identical conditions served as controls. Three biological replicates were analyzed per condition.

value: Corneal epithelium

value: HCE-2 ATCC CRL-11143

value: Corneal epithelial cell

value: Direct contact with P. aeruginosa


title: HCE exposed to Pseudomonas aeruginosa, biological rep 2

description:
Library name: HCEpse2
HCE-2 exposed to P. aeruginosa for 15 h. Rep2

value: HCE-2 ATCC CRL-11142


title: Patient 8 Hematoma

description:
Library name: MA_ICH_008_hem_HHT
10x Genomics


title: MASLD-5_HNF4a_ChIP

description: Library name: MASLD-5_HNF4a, ChIP


title: Hypothalamus,Lactation,Goat-3

description: Library name: HYT3


title: HCE exposed to Pseudomonas aeruginosa, biological rep 1

description:
Library name: HCEpse1
HCE-2 exposed to P. aeruginosa for 15 h. Rep1

value: HCE-2 ATCC CRL-11141


title: MASLD-4_HNF4a_ChIP

description: Library name: MASLD-4_HNF4a, ChIP


title: Patient 8 Blood

description:
Library name: MA_ICH_008_BLD_HHT
10x Genomics


title: Adrenal gland (cortex),Lactation,Goat-6

description: Library name: AGC6

source_name: Adrenal gland (cortex)

value: Adrenal gland (cortex)


title: Patient 7 Hematoma

description:
Library name: MA_ICH_007_hem_HHT
10x Genomics


title: Hypothalamus,Lactation,Goat-6

description: Library name: HYT6


title: MASLD-3_HNF4a_ChIP

description: Library name: MASLD-3_HNF4a, ChIP


title: HCE exposed to Staphylococcus epidermidis, biological rep 3

description:
Library name: HCEepi3
HCE-2 exposed to S. epidermidis for 15 h. Rep3

value: HCE-2 ATCC CRL-11140

value: Direct contact with S. epidermidis


title: HCE exposed to Staphylococcus epidermidis, biological rep 2

description:
Library name: HCEepi2
HCE-2 exposed to S. epidermidis for 15 h. Rep2

value: HCE-2 ATCC CRL-11139


title: Hypothalamus,Dry,Goat-54

description: Library name: HYT54


title: SD-5_HNF4a_ChIP

description: Library name: SD-5_HNF4a, ChIP

value: Standard diet


title: Patient 7 Blood

description:
Library name: MA_ICH_007_BLD_HHT
10x Genomics


title: Patient 6 Hematoma

description:
Library name: MA_ICH_006_hem_HHT
10x Genomics

value: hematoma


title: SD-4_HNF4a_ChIP

description: Library name: SD-4_HNF4a, ChIP

value: Liver


title: Hypothalamus,Dry,Goat-64

description: Library name: HYT64


title: Untreated HCE cells, biological rep 3

description:
Library name: HCE3
HCE-2 cultured under standard conditions. Untreated control. Rep3

value: HCE-2 ATCC CRL-11137

value: Untreated


title: SD-3_HNF4a_ChIP

description: Library name: SD-3_HNF4a, ChIP

value: Hnf4a (Abcam, #ab41898)


title: Patient 6 Blood

description:
Library name: MA_ICH_006_BLD_HHT
10x Genomics

value: blood


title: Kidney (medulla),Lactation,Goat-2

description: Library name: KM2

source_name: Kidney (medulla)

value: Kidney (medulla)


title: Kidney (medulla),Lactation,Goat-3

description: Library name: KM3


title: Porcine granulosa cells, hypoxia, m6A-IP, biol rep 3

city: Nanjing

first: Chengyu

last: Li

state: Jiangsu

address: No. 1 Weigang

department: College of Animal Science and Technology

country: China

institute: nanjing agriculture university

description:
Library name: H_3_IP
m6A-immunoprecipitated library, biological replicate 3; matched input library: H_3_input.
H_IPVSH_input_peak.txt

data_processing:
The submitted FASTQ files are the fastp v0.19.4-filtered CleanData delivered by LC-Bio. Adapter-contaminated, low-quality, and undetermined-base reads were removed with default parameters. Original instrument-generated unfiltered FASTQ files were not present in the available data delivery.
Sequence quality of the input and m6A-IP libraries was assessed using FastQC and RSeQC.
Clean reads were aligned to the Sus scrofa Sscrofa11.1 reference genome using HISAT2 v2.0.4 with Ensembl release 107 gene annotation.
For the input libraries, gene and transcript abundance was quantified as FPKM using StringTie v2.1.2. Differentially expressed genes and transcripts were identified using edgeR v4.1 with |log2(fold change)| ≥ 1 and P < 0.05.
m6A peaks and differentially methylated regions were identified using exomePeak v1.5.0. Peaks were assigned to gene features using ANNOVAR, and enriched motifs were analyzed using HOMER v4.10. Per-library coverage tracks are provided in bigWig format.
Assembly: Sscrofa11.1 (GCA_000003025.6; Ensembl release 107)
Supplementary files format and content: Tab-delimited text files contain gene-level FPKM values across the six input RNA-seq libraries and differential-expression statistics (fold change, P value, q value, and regulation).
Supplementary files format and content: Tab-delimited text files contain condition-level m6A peak calls and differential-peak statistics with genomic coordinates and gene annotations. bigWig files contain per-library genome coverage tracks.
Library strategy: MeRIP-Seq

organism: Sus scrofa

source_name: ovary

growth_protocol: Primary porcine follicular granulosa cells were recovered from antral follicles of sexually mature Duroc × Yorkshire × Landrace crossbred sows. Cells were cultured in DMEM/F-12 containing 15% fetal bovine serum and 100 U/mL penicillin-streptomycin at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was isolated and purified with TRIzol reagent. RNA quantity and purity were assessed with a NanoDrop ND-1000, and RNA integrity was assessed with an Agilent Bioanalyzer 2100. Poly(A)+ RNA was purified from 50 µg total RNA by two rounds of selection with Dynabeads Oligo(dT) (Thermo Fisher, 25-61005) and fragmented at 86°C for 7 min with the NEBNext Magnesium RNA Fragmentation Module. An aliquot was retained as input. For m6A-IP libraries, fragmented RNA was incubated for 2 h at 4°C with an m6A-specific antibody (Synaptic Systems, No. 202003) in IP buffer containing 50 mM Tris-HCl, 750 mM NaCl, and 0.5% Igepal CA-630.
Input and m6A-immunoprecipitated RNA were reverse-transcribed with SuperScript II. U-labeled second-strand cDNA was synthesized using E. coli DNA polymerase I, RNase H, and dUTP. After end repair, A-tailing, dual-index adapter ligation, and AMPure XP size selection (insert size 180-220 bp), UDG treatment and eight PCR cycles were performed. Libraries were sequenced as 150-bp paired-end reads on an Illumina NovaSeq 6000 by LC-Bio Technology (Hangzhou, China).

treatment_protocol: Cells were cultured for 12 h under normoxia (21% O2, 5% CO2, 74% N2) or hypoxia (1% O2, 5% CO2, 94% N2).

value: ovary

value: primary follicular granulosa cells

tag: batch


title: Untreated HCE cells, biological rep 1

description:
Library name: HCE1
HCE-2 cultured under standard conditions. Untreated control. Rep1

value: Corneal epithelium

value: HCE-2 ATCC CRL-11135

value: Corneal epithelial cell


title: Patient 5 Hematoma

description:
Library name: ICH005HF_HHT
10x Genomics


title: Porcine granulosa cells, hypoxia, input, biol rep 3

description:
Library name: H_3_input
Non-immunoprecipitated input library, biological replicate 3; used as the matched MeRIP-seq background control and for RNA-seq expression quantification.
4_genes_fpkm_expression.txt


title: Untreated HCE cells, biological rep 2

description:
Library name: HCE2
HCE-2 cultured under standard conditions. Untreated control. Rep2

value: HCE-2 ATCC CRL-11136


title: Patient 5 Blood

description:
Library name: ICH005PB_HHT
10x Genomics


title: Kidney (medulla),Lactation,Goat-6

description: Library name: KM6


title: HCE exposed to Pseudomonas aeruginosa extracellular vesicles, biological replicate 3

description:
Library name: VPHCE3
HCE-2 exposed to extracellular vesicles derived from P. aeruginosa for 15 h. Rep3

treatment_protocol: HCE-2 cells were exposed for 15 h to 1000 extracellular vesicles derived from Pseudomonas aeruginosa or Staphylococcus epidermidis per cell. Untreated cells were used as controls. Three biological replicates were analyzed per condition.

value: HCE-2 ATCC CRL-11143

value: Bacterial extracellular vesicles derived from P. aeruginosa


title: Patient 4 Hematoma

description:
Library name: ICH04_HF_MMT
10x Genomics


title: Porcine granulosa cells, hypoxia, m6A-IP, biol rep 2

description:
Library name: H_2_IP
m6A-immunoprecipitated library, biological replicate 2; matched input library: H_2_input.
H_IPVSH_input_peak.txt


title: Kidney (medulla),Dry,Goat-54

description: Library name: KM54


title: Patient 4 Blood

description:
Library name: ICH04_PB_HHT
10x Genomics


title: HCE exposed to Pseudomonas aeruginosa extracellular vesicles, biological replicate 2

description:
Library name: VPHCE2
HCE-2 exposed to extracellular vesicles derived from P. aeruginosa for 15 h. Rep2

value: HCE-2 ATCC CRL-11142


title: HCE exposed to Pseudomonas aeruginosa extracellular vesicles, biological replicate 1

description:
Library name: VPHCE1
HCE-2 exposed to extracellular vesicles derived from P. aeruginosa for 15 h. Rep1

value: HCE-2 ATCC CRL-11141


title: Patient 3 Hematoma

description:
Library name: ICH003_HF_HHT
10x Genomics

value: hematoma


title: Kidney (medulla),Dry,Goat-64

description: Library name: KM64


title: Porcine granulosa cells, hypoxia, input, biol rep 2

description:
Library name: H_2_input
Non-immunoprecipitated input library, biological replicate 2; used as the matched MeRIP-seq background control and for RNA-seq expression quantification.
4_genes_fpkm_expression.txt


title: Porcine granulosa cells, hypoxia, m6A-IP, biol rep 1

description:
Library name: H_1_IP
m6A-immunoprecipitated library, biological replicate 1; matched input library: H_1_input.
H_IPVSH_input_peak.txt


title: HCE exposed to Staphylococcus epidermidis extracellular vesicles, biological replicate 3

description:
Library name: VEHCE3
HCE-2 exposed to extracellular vesicles derived from S. epidermidis for 15 h. Rep3

value: HCE-2 ATCC CRL-11140

value: Bacterial extracellular vesicles derived from S. epidermidis


title: Adrenal gland (cortex),Dry,Goat-54

description: Library name: AGC54

value: Adrenal gland (cortex)


title: Patient 3 Blood

description:
Library name: ICH003_PB_HHT
10x Genomics


title: Porcine granulosa cells, hypoxia, input, biol rep 1

description:
Library name: H_1_input
Non-immunoprecipitated input library, biological replicate 1; used as the matched MeRIP-seq background control and for RNA-seq expression quantification.
4_genes_fpkm_expression.txt


title: Liver,Lactation,Goat-2

description: Library name: LI2

value: Liver


title: Patient 2 Hematoma

description:
Library name: ICH002_HF_HHT
10x Genomics


title: HCE exposed to Staphylococcus epidermidis extracellular vesicles, biological replicate 2

description:
Library name: VEHCE2
HCE-2 exposed to extracellular vesicles derived from S. epidermidis for 15 h. Rep2

value: HCE-2 ATCC CRL-11139


title: Porcine granulosa cells, normoxia, m6A-IP, biol rep 3

description:
Library name: Control_3_IP
m6A-immunoprecipitated library, biological replicate 3; matched input library: Control_3_input.
Control_IPVSControl_input_peak.txt


title: Patient 2 Blood

description:
Library name: ICH002_PB_HHT
10x Genomics

value: blood


title: Lung,Lactation,Goat-2

description: Library name: LU2

source_name: Lung

value: Lung


title: Porcine granulosa cells, normoxia, input, biol rep 3

description:
Library name: Control_3_input
Non-immunoprecipitated input library, biological replicate 3; used as the matched MeRIP-seq background control and for RNA-seq expression quantification.
4_genes_fpkm_expression.txt

value: ovary

value: primary follicular granulosa cells


title: HCE exposed to Staphylococcus epidermidis extracellular vesicles, biological replicate 1

description:
Library name: VEHCE1
HCE-2 exposed to extracellular vesicles derived from S. epidermidis for 15 h. Rep1

value: Corneal epithelium

value: HCE-2 ATCC CRL-11138


title: Liver,Dry,Goat-73

description: Library name: LI73


title: Porcine granulosa cells, normoxia, m6A-IP, biol rep 2

description:
Library name: Control_2_IP
m6A-immunoprecipitated library, biological replicate 2; matched input library: Control_2_input.
Control_IPVSControl_input_peak.txt


title: Untreated HCE cells, biological replicate 3

description:
Library name: HCE3
HCE-2 cultured under standard conditions. Untreated control. Rep3

value: HCE-2 ATCC CRL-11137

value: Corneal epithelial cell

value: Untreated


title: Lung,Lactation,Goat-3

description: Library name: LU3


title: Patient 1 Hematoma

description:
Library name: ICH2232HF_HHT
10x Genomics


title: Patient 1 Blood

description:
Library name: ICH2232PB_HHT
10x Genomics


title: Untreated HCE cells, biological replicate 2

description:
Library name: HCE2
HCE-2 cultured under standard conditions. Untreated control. Rep2

value: HCE-2 ATCC CRL-11136


title: Porcine granulosa cells, normoxia, input, biol rep 2

description:
Library name: Control_2_input
Non-immunoprecipitated input library, biological replicate 2; used as the matched MeRIP-seq background control and for RNA-seq expression quantification.
4_genes_fpkm_expression.txt


title: Adrenal gland (cortex),Dry,Goat-64

description: Library name: AGC64


title: RH4 cells, 100 nM JQAD 6 h, RNA-seq

city: Cleveland

first: Matthew

last: Chang

state: Ohio

address: 2109 Adelbert Rd

institute: Case Western Reserve University School of Medicine

description: Library name: RH4_JQAD_100nM_6h_RNA_022924_CWRU

data_processing:
RNA-seq: RNA-seq FASTQ files were aligned to the human genome hg38 using STAR (v2.5.3a). Transcript-per-million (TPM) values were quantified using RSEM (v1.3.3). Gene set enrichment between two samples was determined using the NCI’s Gene Set Enrichment Analysis (GSEA) tool (v4.3.3). Custom gene set references were created by selecting up- and down-regulated gene sets from the log2 fold change (log2FC) metric, followed by rank-ordering. Genome-browser visualization was performed using IGV. Visualization and summary of GSEA results were performed using custom R scripts (https://github.com/GryderArt/VisualizeRNAseq).  ChIP-seq: ChIP-seq FASTQ files were aligned to the human genome hg38 and spike-in mouse genome mm10 using BWA (v0.7.17). Reads-per-million (RPM) values were quantified after fragment extension and shifting corrections. Peaks were called using MACS3 (v3.0.0a6) and HOMER (v4.9.1). Regions that were called as peaks but are overlapping black-listed regions defined by the ENCODE consortium were removed before further analysis. Heatmaps and metagene plots were generated with a custom plotBEDHeat.sh pipeline that implements the bedtools and deeptools packages. For multi-sample analysis, we used a custom runBedCovCompSpiked.sh pipeline that reads from multiple BAM files to generate normalized densities at BED peak regions. Previously determined RPM values were normalized using the mouse spike-in, where relative RPM (RRPM) values are defined by the following equation: RRPM = (human RPM in peak x 106) / total mouse reads. Super enhancers were identified using the ROSE2 package with a stitching parameter of 12,500 bp. Genome-browser visualization was performed by using IGV. Visualization of multi-sample analysis and super enhancers were performed by using custom R scripts (https://github.com/GryderArt/ChIPseqPipe).  ChRO-seq: Sequencing reads from were processed using the proseq2.0 pipeline (https://github.com/Danko-Lab/proseq2.0) to automate routine pre-processing, alignment, and coverage file generation. Paired-end FASTQ files were adapter-trimmed, quality filtered, and deduplicated based on UMI barcodes, then aligned to the reference genome using BWA. Aligned reads were converted to strand-specific coverage formats, reporting the 5′ end of nascent RNA reads.
Assembly: hg38
Supplementary files format and content: RNA-seq: TPM matrix of all protein-coding genes, ChIP-seq: BW files, ChRO-seq: BW files

growth_protocol: RH4 cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1x penicillin-streptomycin-glutamine. Cells were cultured in 5% CO2 at 37°C. Cell lines were authenticated upon receipt by short tandem repeat profiling and used for experimentation from frozen stocks. All cells were regularly tested for mycoplasma contamination.

extract_protocol:
RNA-seq: RH4 cells were collected via trypsinization. Samples were lysed and homogenized using Qiashredder homogenizer, and total RNA was extracted from the cells using RNeasy Plus Mini Kit. Quantity was measured by a Qubit 4 fluorometer.  ChIP-seq: RH4 cells were fixed with 1% paraformaldehyde, quenched with 2.5 M glycine, and snap-frozen at -80ºC overnight. DNA was digested using a MNase reaction mix. After incubation, the digestion reaction was stopped with EGTA. Cells were lysed using a RIPA buffer. After incubation on ice, lysates were centrifuged. For histone acetylation markers, lysates were spiked with chromatin extracted from mouse myoblast C2C12 cells at a defined and conserved ratio of 1:20 C2C12 chromatin to human chromatin and incubated with a conserved ratio of 1:1 antibody to human chromatin overnight. Lysates were then immunoprecipitated with Protein A/G beads, de-crosslinked with Proteinase K, followed by DNA purification. For RNA Pol2, lysates were incubated overnight with Dynabeads, de-crosslinked, and purified as described before.  ChRO-seq: ChRO-seq libraries were generated from RH4 rhabdomyosarcoma cells using a streamlined adaptation of the Danko laboratory protocol47. Isolated chromatin was subjected to nuclear run-on in the presence of biotin-11–labeled ribonucleotides to label nascent RNA, followed by extraction with TRI Reagent LS and phase separation using 1-bromo-3-chloropropane to reduce DNA contamination. Nascent RNA was ethanol-precipitated with GlycoBlue coprecipitant, fragmented by controlled base hydrolysis, and buffer-exchanged prior to adaptor ligation. A 3′ RNA adaptor was ligated off-bead using T4 RNA ligase I in the presence of ATP, PEG 8000, and SUPERase•In RNase inhibitor, with adaptor concentration scaled to chromatin input to minimize adaptor dimers. Biotinylated RNA was enriched using hydrophilic streptavidin magnetic beads, decapped on-bead with RNA 5′ pyrophosphohydrolase RppH in Thermopol buffer, and phosphorylated with T4 polynucleotide kinase. Following a second streptavidin enrichment, a 5′ RNA adaptor was ligated off-bead, and RNA was reverse transcribed using SuperScript IV reverse transcriptase.
RNA-seq: Samples were prepped with the NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads kit (New England Biolabs, cat. #E7765S) according to manufacturer's protocol.  ChIP-seq and ChRO-seq: Samples were prepped with the NEBNext® Multiplex Oligos for Illumina® kit (New England Biolabs, cat. #E6440S and #E7645S) according to manufacturer's protocol.  ChRO-seq: Libraries were amplified by PCR using indexed primers and SsoAdvanced Universal SYBR Green Supermix, with cycle number determined empirically by qPCR, purified by column cleanup and size selection, and assessed by Qubit fluorometry and TapeStation prior to sequencing.

treatment_protocol: RH4 cells were plated the day before treatment in 6-well or 15 cm dishes.

value: human alveolar rhabdomyosarcoma

value: 100 nM JQAD 6 h


title: TLE1ΔWD40 endogenous iPSCs 3rd replica

city: Berkeley

first: Michael

last: Rape

state: CA

address: 330F Li Ka Shing Center

department: MCB

institute: University of California Berkeley

description: Library name: dWD40T1_3rd

data_processing:
Novogene processing
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: files contain FPKM values

source_name: WTC11 iPSCs

extract_protocol:
Total RNA was purified using a nucleospin RNA kit (Macherey-Nagel, 740955). cDNA was generated using a RevertAid First Strand cDNA Synthesis kit (Thermo Fisher Scientific, K1622)
Wild-type, TLE1ΔWD40 iPSCs were subjected for neural conversion for 5 days and collected for transcriptomic analysis. Total RNA was extracted from cells using the NucleoSpinRNA kit (Macherey-Nagel, no. 740955) according to the manufacturer’s instructions. Library preparation, sequencing and bioinformatic statistical analysis was performed by Novogene Bioinformatics Technology Co., Ltd. (Beijing, China).

value: WTC11 iPSCs

value: iPSCs

value: Deletion of the WD40 gene region in the TLE1 loci

value: neural differentiation

value: day 5


title: Lung,Dry,Goat-64

description: Library name: LU64


title: RH4 cells, 100 nM JQAD 2 h, RNA-seq

description: Library name: RH4_JQAD_100nM_2h_RNA_022924_CWRU

value: 100 nM JQAD 2 h


title: TLE1ΔWD40 endogenous iPSCs 2nd replica

description: Library name: dWD40T1_2nd


title: Porcine granulosa cells, normoxia, m6A-IP, biol rep 1

description:
Library name: Control_1_IP
m6A-immunoprecipitated library, biological replicate 1; matched input library: Control_1_input.
Control_IPVSControl_input_peak.txt


title: Untreated HCE cells, biological replicate 1

description:
Library name: HCE1
HCE-2 cultured under standard conditions. Untreated control. Rep1

value: HCE-2 ATCC CRL-11135


title: RH4 cells, 1 uM JQAD 6 h, RNA-seq

description: Library name: RH4_JQAD_1uM_6h_RNA_022924_CWRU

value: 1 uM JQAD 6 h


title: Porcine granulosa cells, normoxia, input, biol rep 1

description:
Library name: Control_1_input
Non-immunoprecipitated input library, biological replicate 1; used as the matched MeRIP-seq background control and for RNA-seq expression quantification.
4_genes_fpkm_expression.txt

value: ovary

value: primary follicular granulosa cells


title: rBMSC Cur-CD treatment 3

city: Zibo

first: Yu

last: Zhang

address: No. 2018 Jiangmeng Road, Zhoucun District

institute: Qilu Medical University

description: Library name: Sample_350-3

data_processing:
Raw sequencing data (base calling) was generated using Bcl2fastq v2.20.0.422, resulting in paired-end FASTQ files.
Assembly: Rattus norvegicus Rnor_6.0 (rn6), Ensembl annotation
Supplementary files format and content: Tab-delimited .xls file named all.fpkm_anno.xls, containing gene ID, gene symbol, gene description, and FPKM expression values for all 6 samples.

source_name: bone marrow mesenchymal stem cell

growth_protocol: Rat bone marrow mesenchymal stem cells (rBMSCs) were isolated from femurs and tibias of SD rats. Bone marrow was flushed using α-MEM with 10% FBS. After centrifugation, cells were cultured in complete α-MEM medium at 37°C and 5% CO₂. Phenotype was confirmed by flow cytometry, and cells were passaged at >90% confluency. For osteogenic differentiation, rBMSCs were seeded in 6-well plates at 5×10⁴ cells/mL. At 80% confluency, the medium was replaced with osteogenic induction medium, refreshed every 2-3 days for 21 days.

extract_protocol:
Total RNA was extracted from rBMSC cell pellets using TRIzol reagent following the manufacturer's instructions. RNA quality and quantity were assessed using NanoDrop spectrophotometer and Agilent Bioanalyzer. RNA integrity number (RIN) values were confirmed to be ≥7.0 for all samples prior to library construction.
PolyA-tailed mRNA was enriched from total RNA via oligo(dT) magnetic beads. Purified mRNA was fragmented into short fragments using fragmentation buffer. First-strand cDNA was synthesized using random hexamer primers and reverse transcriptase, followed by second-strand cDNA synthesis. After end repair, A-tailing, and adapter ligation, the cDNA fragments were PCR-amplified to create the final sequencing libraries. Library quality was verified using Agilent Bioanalyzer, and libraries were quantified by qPCR before sequencing.

value: bone marrow mesenchymal stem cell

value: Cur-CD treatment + osteogenic induction


title: TLE1ΔWD40 endogenous iPSCs 1st replica

description: Library name: dWD40T1_1st


title: HCE exposed to Staphylococcus epidermidis, biological rep 1

description:
Library name: HCEepi1
HCE-2 exposed to S. epidermidis for 15 h. Rep1

value: Corneal epithelium

value: HCE-2 ATCC CRL-11138

value: Corneal epithelial cell

value: Direct contact with S. epidermidis


title: Mandibular lymph node,Dry,Goat-73

description: Library name: MLN73

source_name: Mandibular lymph node

value: Mandibular lymph node


title: rBMSC Cur-CD treatment 2

description: Library name: Sample_350-2


title: rBMSC Cur-CD treatment 1

description: Library name: Sample_350-1


title: Control cells 2nd replica

description: Library name: WT_2ND

value: WTC11 iPSCs

value: WT


title: Masseter muscle,Dry,Goat-64

description: Library name: MM64

source_name: Masseter muscle

value: Masseter muscle


title: Masseter muscle,Lactation,Goat-3

description: Library name: MM3


title: RH4 cells, 100 nM IHK-44 6 h, RNA-seq

description: Library name: RH4_IHK-44_100nM_6h_RNA_022924_CWRU

value: human alveolar rhabdomyosarcoma


title: rBMSC control 3

description: Library name: Sample_0-3

value: osteogenic induction (control)


title: Masseter muscle,Dry,Goat-73

description: Library name: MM73


title: Adrenal gland(medulla),Lactation,Goat-2

description: Library name: AGM2

source_name: Adrenal gland(medulla)

value: Adrenal gland(medulla)


title: rBMSC control 1

description: Library name: Sample_0-1


title: 6C_multiomeRNA, male, Cocaine-sired

city: Pittsburgh

first: BaDoi

middle: Nguyen

last: Phan

address: 5000 Forbes Ave

department: Anesthesiology

institute: Stanford University

description:
Library name: 6C_multiomeRNA
Rat_transgen_multiomeRNA_refined_all_SeuratObj_N5.h5Seurat

data_processing:
We aligned single nuclei RNA-seq (snRNA-seq) reads to the rat genome (rn7) for each output using the CellRanger pipeline. We used an alternate rn7 gene annotation which borrows higher quality reference annotations from the mouse mm10 Refseq annotations. Compared to the base rn7 gene annotations, the mm10 liftoff increased the number of sequenced reads attributable to a gene by over 150%. These annotations are deposited in Carnegie Mellon University's Kilthub repository resource (https://kilthub.cmu.edu/articles/dataset/Alternate_gene_annotations_for_rat_macaque_and_marmoset_for_single_cell_RNA_and_ATAC_analyses/21176401) and https://github.com/pfenninglab/custom_ArchR_genomes_and_annotations. We utilized miQC to identify damaged nuclei based on the relationship between mitochondrial UMI counts and the number of captured genes. Damaged cells were called using a posterior probability cutoff of 0.75. Additionally, we employed scds to detect doublets using its hybrid algorithm, and cells with scds.hybrid_score > 1.0 were classified as doublets. To combine cells across samples, we applied normalization using variance-stabilizing SCTransform and glmGamPoi methods on each sample. Furthermore, we jointly embedded cells across samples through reciprocal PCA integration. In the joint embedding, we initially over-clustered the dataset using FindClusters (algorithm = 2, resolution = 1) and removed clusters with more than 10% of cells flagged by miQC and scds. During clustering analysis, doublet cells tended to project into the UMAP space as long streaks between two well-defined cell types, while low-quality cell types appeared as amorphous cell types without clear boundaries. Using these characteristics of the cluster and individual cells flagged by miQC and scds as damaged or doublets aided curation of a final high quality single cell multiomic dataset.
Assembly: rn7
Supplementary files format and content: seurat objects of single cell gene expression and cell annotations
Supplementary files format and content: archr files of single cell ATAC and annotations

source_name: Nucleus accumbens

extract_protocol:
Nuclei dissociation from fresh frozen nucleus accumbens of experimentally naïve methamphetamine-sired, cocaine-sired, and saline-sired male offspring (n=4/group) was performed using the 10X Genomics Demonstrated Protocol “Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + Gene Expression Sequencing”. Intact nuclei were sorted from debris by 7-AAD staining using the MoFlo Astrios EQ Cell Sorter (Rutgers Flow Cytometry/Cell Sorting Core Facility). Nuclei (up to 20,000 per pooled sample loaded across two wells on the chip) were first transposed in bulk, and then encapsulated with a gel bead using the 10X Genomics Chromium Controller (10X Genomics, Pleasanton, CA).
Within each nanoliter-scale partition, RNA and transposed DNA fragments were labeled with 10X barcodes, where each barcode sequence represents the same unique cell. Nuclei suspensions are incubated in a Transposition Mix, and the transposase simultaneously cleaves DNA in open chromatin regions and adds adapter sequences to the ends of the DNA fragments. Single Cell Multiome ATAC + GEX Gel Beads include a poly(dT) sequence that enables production of barcoded, full-length cDNA from poly-adenylated mRNA for gene expression library and a spacer sequence that enables barcode attachment to transposed DNA fragments for ATAC library. Libraries were generated, quality checked, and sequenced on the Illumina Novaseq 6000 (Psomagen, Rockville, MD) with a target of 25 thousand reads/cell for ATAC-seq and 25-50 thousand reads/cell for RNA-seq.

treatment_protocol: Male Sprague-Dawley rat offspring that are experimentally naïve from  methamphetamine-sired, cocaine-sired, and saline-sired litters

value: Nucleus accumbens

value: male

value: Sprague-Dawley

value: Cocaine-sired


title: TLE1R610S endogenous iPSCs 3rd replica

description: Library name: R610S_3

extract_protocol:
Total RNA was purified using a nucleospin RNA kit (Macherey-Nagel, 740955). cDNA was generated using a RevertAid First Strand cDNA Synthesis kit (Thermo Fisher Scientific, K1622)
Wild-type, TLE1R610S iPSCs were subjected for neural conversion for 5 days and collected for transcriptomic analysis. Total RNA was extracted from cells using the NucleoSpinRNA kit (Macherey-Nagel, no. 740955) according to the manufacturer’s instructions. Library preparation, sequencing and bioinformatic statistical analysis was performed by Novogene Bioinformatics Technology Co., Ltd. (Beijing, China).

value: iPSCs

value: endogenous point mutation in the loci of the TLE1 gene

value: neural differentiation

value: day 5


title: Medulla oblongata,Lactation,Goat-2

description: Library name: MO2

source_name: Medulla oblongata

extract_protocol:
RNA was extracted using the RiboPure™ Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol.
Strand-specific library construction was performed with VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina.

value: Medulla oblongata


title: RH4 cells, 1 uM IHK-44 2 h, RNA-seq

description: Library name: RH4_IHK-44_1uM_2h_RNA_022924_CWRU

value: 1 uM IHK-44 2 h


title: TLE1R610S endogenous iPSCs 2nd replica

description: Library name: R610S_2


title: RH4 cells, 100 nM dCBP 6 h, RNA-seq

description: Library name: RH4_dCBP_100nM_6h_RNA_022924_CWRU

value: 100 nM dCBP 6 h


title: 5M_multiomeRNA, male, Methamphetamine-sired

description:
Library name: 5M_multiomeRNA
Rat_transgen_multiomeRNA_refined_all_SeuratObj_N5.h5Seurat

value: Methamphetamine-sired


title: Medulla oblongata,Lactation,Goat-3

description: Library name: MO3


title: TLE1R610S endogenous iPSCs 1st replica

description: Library name: R610S_1

value: WTC11 iPSCs


title: RH4 cells, 100 nM dCBP 2 h, RNA-seq

description: Library name: RH4_dCBP_100nM_2h_RNA_022924_CWRU

value: 100 nM dCBP 2 h


title: Control cells 3rd replica

description: Library name: WT_3

value: WT


title: RH4 cells, 1 uM dCBP 6 h, RNA-seq

description: Library name: RH4_dCBP_1uM_6h_RNA_022924_CWRU

value: human alveolar rhabdomyosarcoma

value: 1 uM dCBP 6 h


title: 3C_multiomeRNA, male, Cocaine-sired

description:
Library name: 3C_multiomeRNA
Rat_transgen_multiomeRNA_refined_all_SeuratObj_N5.h5Seurat

value: Nucleus accumbens


title: Adrenal gland(medulla),Lactation,Goat-3

description: Library name: AGM3

value: Adrenal gland(medulla)


title: Control cells 2nd replica

description: Library name: WT_2


title: RH4 cells, 1 uM dCBP 2 h, RNA-seq

description: Library name: RH4_dCBP_1uM_2h_RNA_022924_CWRU

value: 1 uM dCBP 2 h


title: 2M_multiomeRNA, male, Methamphetamine-sired

description:
Library name: 2M_multiomeRNA
Rat_transgen_multiomeRNA_refined_all_SeuratObj_N5.h5Seurat

value: male

value: Sprague-Dawley


title: Neck skin,Dry,Goat-64

description: Library name: NSK64

source_name: Neck skin

value: Neck skin


title: 1S_multiomeRNA, male, Saline-sired

description:
Library name: 1S_multiomeRNA
Rat_transgen_multiomeRNA_refined_all_SeuratObj_N5.h5Seurat

value: Saline-sired


title: RH4 cells, 100 nM A485 6 h, RNA-seq

description: Library name: RH4_A485_100nM_6h_RNA_022924_CWRU


title: FBXL14ΔCTE endogenous iPSCs 3rd replica

description: Library name: dCTE_6th

extract_protocol:
Total RNA was purified using a nucleospin RNA kit (Macherey-Nagel, 740955). cDNA was generated using a RevertAid First Strand cDNA Synthesis kit (Thermo Fisher Scientific, K1622)
Wild-type, FBXL14ΔCTE, TLE1ΔWD40 or TLE1R610S iPSCs were subjected for neural conversion for 5 days and collected for transcriptomic analysis. Total RNA was extracted from cells using the NucleoSpinRNA kit (Macherey-Nagel, no. 740955) according to the manufacturer’s instructions. Library preparation, sequencing and bioinformatic statistical analysis was performed by Novogene Bioinformatics Technology Co., Ltd. (Beijing, China).

value: iPSCs

value: deletion of the C terminal extension region in the FBXL14 gene loci

value: neural differentiation

value: day 5


title: Neck skin,Dry,Goat-73

description: Library name: NSK73


title: Mandibular lymph node,Lactation,Goat-6

description: Library name: MLN6

value: Mandibular lymph node


title: RH4 cells, 100 nM A485 2 h, RNA-seq

description: Library name: RH4_A485_100nM_2h_RNA_022924_CWRU


title: 6C_multiomeATAC, male, Cocaine-sired

description:
Library name: 6C_multiomeATAC
Rat_Transgen_NAc_scATAC_clusterRat_ArchRProject.tar.gz

library_source: genomic single cell

value: Cocaine-sired


title: RH4 cells, 1 uM JQAD 2 h, RNA-seq

description: Library name: RH4_JQAD_1uM_2h_RNA_022924_CWRU

value: 1 uM JQAD 2 h


title: Neurohypophysis,Dry,Goat-73

description: Library name: NYP73

source_name: Neurohypophysis

value: Neurohypophysis


title: 5M_multiomeATAC, male, Methamphetamine-sired

description:
Library name: 5M_multiomeATAC
Rat_Transgen_NAc_scATAC_clusterRat_ArchRProject.tar.gz

value: Methamphetamine-sired


title: RH4 cells, 1 uM A485 6 h, RNA-seq

description: Library name: RH4_A485_1uM_6h_RNA_022924_CWRU

value: human alveolar rhabdomyosarcoma


title: FBXL14ΔCTE endogenous iPSCs 2nd replica

description: Library name: dCTE_5th

value: WTC11 iPSCs


title: Adrenal gland(medulla),Lactation,Goat-6

description: Library name: AGM6

value: Adrenal gland(medulla)


title: Control cells 3rd replica

description: Library name: WT_3RD

value: WT


title: RH4 cells, 100 nM IHK-44 2 h, RNA-seq

description: Library name: RH4_IHK-44_100nM_2h_RNA_022924_CWRU


title: FBXL14ΔCTE endogenous iPSCs 1st replica

description: Library name: dCTE_3rd


title: Control cells 1st replica

description: Library name: WT_1ST


title: RH4 cells, 1 uM A485 2 h, RNA-seq

description: Library name: RH4_A485_1uM_2h_RNA_022924_CWRU


title: RH4 cells, 1 uM IHK-44 6 h, RNA-seq

description: Library name: RH4_IHK-44_1uM_6h_RNA_022924_CWRU

value: 1 uM IHK-44 6 h


title: Ovary,Lactation,Goat-6

description: Library name: OV6

source_name: Ovary

value: Ovary


title: Control cells 3rd replica

description: Library name: WT_6th


title: RH4 cells, NT 6 h, RNA-seq

description: Library name: RH4_NT_6h_RNA_022924_CWRU

value: NT 6 h


title: 4S_multiomeATAC, male, Saline-sired

description:
Library name: 4S_multiomeATAC
Rat_Transgen_NAc_scATAC_clusterRat_ArchRProject.tar.gz

value: Nucleus accumbens

value: male

value: Sprague-Dawley

value: Saline-sired


title: 3C_multiomeATAC, male, Cocaine-sired

description:
Library name: 3C_multiomeATAC
Rat_Transgen_NAc_scATAC_clusterRat_ArchRProject.tar.gz


title: Ovary,Dry,Goat-64

description: Library name: OV64


title: Control cells 2nd replica

description: Library name: WT_5th

value: iPSCs

value: neural differentiation

value: day 5


title: RH4 cells, NT 2 h, RNA-seq

description: Library name: RH4_NT_2h_RNA_022924_CWRU

value: NT 2 h


title: 2M_multiomeATAC, male, Methamphetamine-sired

description:
Library name: 2M_multiomeATAC
Rat_Transgen_NAc_scATAC_clusterRat_ArchRProject.tar.gz


title: Rostral colliculus,Dry,Goat-54

description: Library name: RC54

source_name: Rostral colliculus

value: Rostral colliculus


title: Control cells 1st replica

description: Library name: WT_3rd


title: 1S_multiomeATAC, male, Saline-sired

description:
Library name: 1S_multiomeATAC
Rat_Transgen_NAc_scATAC_clusterRat_ArchRProject.tar.gz


title: RH4 cells, DMSO 6 h, ChRO-seq

description: Library name: RH4_DMSO_6h_ChRO_rep2_082725_NovaSeq-X_A_lane8

library_source: other

data_processing:
RNA-seq: RNA-seq FASTQ files were aligned to the human genome hg38 using STAR (v2.5.3a). Transcript-per-million (TPM) values were quantified using RSEM (v1.3.3). Gene set enrichment between two samples was determined using the NCI’s Gene Set Enrichment Analysis (GSEA) tool (v4.3.3). Custom gene set references were created by selecting up- and down-regulated gene sets from the log2 fold change (log2FC) metric, followed by rank-ordering. Genome-browser visualization was performed using IGV. Visualization and summary of GSEA results were performed using custom R scripts (https://github.com/GryderArt/VisualizeRNAseq).  ChIP-seq: ChIP-seq FASTQ files were aligned to the human genome hg38 and spike-in mouse genome mm10 using BWA (v0.7.17). Reads-per-million (RPM) values were quantified after fragment extension and shifting corrections. Peaks were called using MACS3 (v3.0.0a6) and HOMER (v4.9.1). Regions that were called as peaks but are overlapping black-listed regions defined by the ENCODE consortium were removed before further analysis. Heatmaps and metagene plots were generated with a custom plotBEDHeat.sh pipeline that implements the bedtools and deeptools packages. For multi-sample analysis, we used a custom runBedCovCompSpiked.sh pipeline that reads from multiple BAM files to generate normalized densities at BED peak regions. Previously determined RPM values were normalized using the mouse spike-in, where relative RPM (RRPM) values are defined by the following equation: RRPM = (human RPM in peak x 106) / total mouse reads. Super enhancers were identified using the ROSE2 package with a stitching parameter of 12,500 bp. Genome-browser visualization was performed by using IGV. Visualization of multi-sample analysis and super enhancers were performed by using custom R scripts (https://github.com/GryderArt/ChIPseqPipe).  ChRO-seq: Sequencing reads from were processed using the proseq2.0 pipeline (https://github.com/Danko-Lab/proseq2.0) to automate routine pre-processing, alignment, and coverage file generation. Paired-end FASTQ files were adapter-trimmed, quality filtered, and deduplicated based on UMI barcodes, then aligned to the reference genome using BWA. Aligned reads were converted to strand-specific coverage formats, reporting the 5′ end of nascent RNA reads.
Assembly: hg38
Supplementary files format and content: RNA-seq: TPM matrix of all protein-coding genes, ChIP-seq: BW files, ChRO-seq: BW files
Library strategy: GRO-Seq

molecule: other

value: DMSO 6 h


title: RH4 cells, DMSO 6 h, RNA-seq

description: Library name: RH4_DMSO_6h_RNA_022924_CWRU

value: human alveolar rhabdomyosarcoma


title: R8226_DMSO_3

city: 徐州市

first: Tengyuan

last: Liu

state: 江苏省

address: 云龙区骆驼山

institute: xuzhou medical university

description:
Library name: Sample 12
fpkm_KM_R8226_DMSO_3

data_processing:
SOAPnuke (v2.2.1);HISAT2(v2.2.1);Bowtie2 (v2.4.5);RSEM (v1.3.1);Pheatmap (v1.0.12);DESeq2(v1.34.0);DEGseq(v1.48.0);qvalue
Raw sequencing reads were filtered using SOAPnuke to remove reads containing adapters, reads with more than 20% low-quality bases (Q ≤ 15), and reads with more than 5% ambiguous bases ('N'). Clean reads were obtained in FASTQ format.
Clean reads were aligned to a transcriptome reference (including known and novel, coding and non-coding transcripts) using Bowtie2.
Gene expression levels were quantified with RSEM (v1.3.1). Differential gene expression was analyzed using DESeq2 (v1.34.0), DEGseq (v1.48.0), or PoissonDis, with Q value ≤ 0.05 or FDR ≤ 0.001 as significance thresholds.
Hierarchical clustering and heatmap visualization were performed using pheatmap (v1.0.12). GO and KEGG enrichment analyses were conducted based on the hypergeometric test, and adjusted using Q value ≤ 0.05.
Assembly: GRCh38.p13
Supplementary files format and content: excel files include raw counts data of each sample
Supplementary files format and content: excel files include FPKM data of each sample

growth_protocol: RPMI8226 and KMS11 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37℃ and 5% CO2.

extract_protocol:
Cells were harvested and total RNA was extracted using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). Only 1μg RNA with high quality was used to construct sequencing library.
Total RNA was used for library preparation using the Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). mRNA was enriched using oligo(dT) magnetic beads, fragmented, and reverse transcribed to synthesize double-stranded cDNA. End repair, A-tailing, and adaptor ligation were performed, followed by PCR amplification. The resulting libraries were circularized and amplified by rolling circle amplification (RCA) to produce DNA nanoballs (DNBs). Libraries were sequenced on the MGISEQ platform (G400/T7/T10) with paired-end 100/150 bp reads following the manufacturer's protocol.

treatment_protocol: RPMI8226 and KMS11 cells cells were treated with 1uM BBI608 or DMSO for 24 hours.

value: multiple myeloma cells

value: DMSO treatment for 24 hours


title: Rhinencephalon,Lactation,Goat-3

description: Library name: RHI3

data_processing:
Raw reads with less than 100 bp and less than 85% of bases with Q>30 were discarded using Fastp. SILVA database rRNA database release 138.2 was used to eliminate rRNA contamination.
Filtered reads were mapped to the goat reference genome  with STAR and transcript structure recovery was conducted with StringTie. Novel lncRNAs were characterized with an internal protocol
Gene level estimated counts and offsets matrices were generated using tximport. Count data was normalized to CPM with edgeR. Genes with a CPM value greater than 0.5 in at least 3 samples in a tissue were considered as expressed. Null expressed genes were removed. Tissue-specificty of each gene was measured by the tau-index.
Assembly: ARS1.2
Supplementary files format and content: 33tissues_gene_counts.tsv.gz , tab-delimited text file includes raw gene count.
Supplementary files format and content: 33tissues_gene_length.tsv.gz , tab-delimited text file includes gene count offset.
Supplementary files format and content: 33tissues_CPM.tsv.gz , tab-delimited text file includes processed CPM
Supplementary files format and content: lncRNAs.gtf.gz , gtf file including novel lncRNA
Supplementary files format and content: 33tissues_tau.tsv.gz , tab-delimited text file includes tau-index for each expressed gene

source_name: Rhinencephalon

value: Rhinencephalon


title: RH4 cells, 100 nM IHK-44 6 h, Pol2, ChIP-seq

description: Library name: RH4_IHK44_6h_Pol2_ChIP_031025_CWRU


title: Rhinencephalon,Lactation,Goat-2

description: Library name: RHI2


title: RH4 cells, DMSO 2 h, RNA-seq

description: Library name: RH4_DMSO_2h_RNA_022924_CWRU

value: DMSO 2 h


title: 4S_multiomeRNA, male, Saline-sired

description:
Library name: 4S_multiomeRNA
Rat_transgen_multiomeRNA_refined_all_SeuratObj_N5.h5Seurat


title: Neck skin,Dry,Goat-54

description: Library name: NSK54

value: Neck skin


title: P157_27Sep

city: Stanford

first: Zhuoqing

last: Fang

state: California

address: 300 Pasteur Drive

institute: Stanford

description: Library name: P157_27Sep

data_processing:
CITE-seq files were demultipexed with cellranger mkfastq, and then processed by cellranger count pipeline
Assembly: GRCh38
Supplementary files format and content: cell ranger output files: barcodes.tsv.gz, matrix.mtx.gz, features.tsv.gz
Library strategy: CITE-seq

source_name: Blood

extract_protocol:
Live frozen PBMCs were thawed and washed twice with RPMI supplemented with 10% fetal bovine serum (FBS) and 20 µg/mL DNase I (Sigma-Aldrich), and resuspended in 1× PBS. Cells were washed with PBS and stained with Zombie Aqua Fixable Viability Dye according to the manufacturer’s recommendations. Live cells were fluorescence-activated cell sorted (FACS) into PBS supplemented with 5% FBS. Sorted cells were stained with a cocktail of TotalSeq™-A oligonucleotide-conjugated antibodies (BioLegend) in PBS containing 5% FBS, 2 mM EDTA, and 5 mg/mL human IgG, following the manufacturer’s recommendations, to enable cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq). Cells were washed twice with PBS supplemented with 5% FBS and resuspended in PBS supplemented with 1% BSA (Miltenyi) and 0.5 U/µL RNase inhibitor (Sigma-Aldrich). Approximately 9,000 cells were targeted for each experiment.
The PBMC suspension was used as input for automated microfluidic single-cell capture and barcoding using the 10x Genomics Chromium iX platform. Cells were mixed with the reverse transcription master mix and subjected to partitioning along with Chromium gel beads to generate single-cell gel beads in emulsion (GEMs) using the Chromium Single Cell 3′ Gene Expression v3 chemistry (10x Genomics). Feature Barcoding technology (10x Genomics) was used for generation of antibody-derived tag (ADT) libraries from TotalSeq™-A antibodies, according to the manufacturer’s protocol. Individual cells were uniquely barcoded during GEM generation and reverse transcription. Following reverse transcription, cDNA was recovered and purified using Dynabeads™ MyOne™ Silane beads (Thermo Fisher Scientific) and SPRIselect beads (Beckman Coulter). Gene expression and ADT libraries were constructed according to the manufacturer’s instructions. Constructed libraries underwent quality control assessment using a High Sensitivity D1000 DNA ScreenTape (Agilent) and were quantified using a Qubit Fluorometer (Thermo Fisher Scientific) and a KAPA Library Quantification Kit (KAPA Biosystems) on the AriaMx instrument (Agilent).

value: Blood

value: PBMCs

tag: cohort

value: AZ

tag: arm

tag: ethnicity

value: Black

tag: participant id

value: Secondary_Day 1

tag: particiant visit


title: R8226_DMSO_2

description:
Library name: Sample 11
fpkm_KM_R8226_DMSO_2

value: WT


title: Reticulum,Lactation,Goat-2

description: Library name: RT2

source_name: Reticulum

value: Reticulum


title: R8226_DMSO_1

description:
Library name: Sample 10
fpkm_KM_R8226_DMSO_1


title: RH4 cells, 100 nM IHK-44 2 h, Pol2, ChIP-seq

description: Library name: RH4_IHK44_2h_Pol2_ChIP_031025_CWRU


title: RH4 cells, DMSO 6 h, Pol2, ChIP-seq

description: Library name: RH4_DMSO_6h_Pol2_ChIP_031025_CWRU


title: Reticulum,Dry,Goat-54

description: Library name: RT54


title: P154_27Sep

description: Library name: P154_27Sep


title: KMS11_DMSO_3

description:
Library name: Sample 9
fpkm_KMS11_DMSO_3


title: RH4 cells, 100 nM IHK-44 30 m, H2BK20ac, ChIP-seq

description: Library name: RH4_IHK44_30m_H2BK20ac_ChIP_082925_NovaSeq


title: P155_27Sep

description: Library name: P155_27Sep


title: Rumen,Lactation,Goat-2

description: Library name: RU2

source_name: Rumen

value: Rumen


title: P153_27Sep

description: Library name: P153_27Sep

value: Primary_Day 1


title: KMS11_DMSO_2

description:
Library name: Sample 8
fpkm_KMS11_DMSO_2


title: Subcutaneous fat,Lactation,Goat-6

description: Library name: SF6

source_name: Subcutaneous fat

value: Subcutaneous fat


title: RH4 cells, 100 nM IHK-44 30 m, H2BK16ac, ChIP-seq

description: Library name: RH4_IHK44_30m_H2BK16ac_ChIP_031025_CWRU


title: Control cells 1st replica

description: Library name: WT_1

value: WTC11 iPSCs

value: iPSCs

value: neural differentiation

value: day 5


title: P152_27Sep

description: Library name: P152_27Sep

value: Pre-vaccination


title: KMS11_DMSO_1

description:
Library name: Sample 7
fpkm_KMS11_DMSO_1

value: multiple myeloma cells

value: DMSO treatment for 24 hours


title: RH4 cells, 100 nM IHK-44 6 h, H2BK20ac, ChIP-seq

description: Library name: RH4_IHK44_6h_H2BK20ac_ChIP_082925_NovaSeq

value: human alveolar rhabdomyosarcoma


title: P151_27Sep

description: Library name: P151_27Sep

value: Blood

value: PBMCs


title: Subcutaneous fat,Dry,Goat-73

description: Library name: SF73


title: Adenohypophysis,Lactation,Goat-3

description: Library name: AYP3

source_name: Adenohypophysis

value: Adenohypophysis


title: KMS11_B608_3

description:
Library name: Sample 6
fpkm_KMS11_B608_3

value: 1000nM BBI608 treatment for 24 hours


title: P150_27Sep

description: Library name: P150_27Sep

value: AZ

value: Black


title: RH4 cells, 100 nM IHK-44 6 h, H2BK16ac, ChIP-seq

description: Library name: RH4_IHK44_6h_H2BK16ac_ChIP_031025_CWRU


title: KMS11_B608_2

description:
Library name: Sample 5
fpkm_KMS11_B608_2

value: WT


title: RH4 cells, 100 nM IHK-44 2 h, H2BK20ac, ChIP-seq

description: Library name: RH4_IHK44_2h_H2BK20ac_ChIP_082925_NovaSeq


title: Thyroid,Lactation,Goat-3

description: Library name: THY3

source_name: Thyroid

value: Thyroid


title: KMS11_B608_1

description:
Library name: Sample 4
fpkm_KMS11_B608_1


title: P149_27Sep

description: Library name: P149_27Sep

value: Primary_Day 1


title: Thyroid,Lactation,Goat-6

description: Library name: THY6


title: P148_27Sep

description: Library name: P148_27Sep


title: RH4 cells, 100 nM IHK-44 2 h, H2BK16ac, ChIP-seq

description: Library name: RH4_IHK44_2h_H2BK16ac_ChIP_031025_CWRU


title: R8226_B608_3

description:
Library name: Sample 3
fpkm_KM_R8226_B608_3


title: Adenohypophysis,Lactation,Goat-6

description: Library name: AYP6


title: R8226_B608_2

description:
Library name: Sample 2
fpkm_KM_R8226_B608_2


title: P147_27Sep

description: Library name: P147_27Sep

value: NX

value: 3rd dose

value: Tertiary_Day 1


title: Adenohypophysis,Dry,Goat-54

description: Library name: AYP54


title: RH4 cells, DMSO 6 h, H2BK20ac, ChIP-seq

description: Library name: RH4_DMSO_6h_H2BK20ac_ChIP_082925_NovaSeq

value: DMSO 6 h


title: P146_27Sep

description: Library name: P146_27Sep


title: RH4 cells, DMSO 6 h, H2BK16ac, ChIP-seq

description: Library name: RH4_DMSO_6h_H2BK16ac_ChIP_031025_CWRU


title: R8226_B608_1

description:
Library name: Sample 1
fpkm_KM_R8226_B608_1


title: Bridge (brainstem),Lactation,Goat-3

description: Library name: BRG3

source_name: Bridge (brainstem)

value: Bridge (brainstem)


title: P145_27Sep

description: Library name: P145_27Sep

value: Secondary_Day 7


title: OE21 cells, RNA-Seq, STM9005, 3 days, rep3

city: Cambridge

first: Harry

last: Fischl

address: Babraham Research Campus

institute: Storm Therapeutics

description: Library name: OE21_STM9005_3d_rep3

data_processing:
Paired-end reads were adapter trimmed using Trim Galore and counts per transcript and gene were determined using Salmon (Patro et al., 2027). Differential RNA, translation and translational efficency levels were determined using DESeq2 (Love et al., 2014, Chothani et al., 2019).
Assembly: GRCh38
Supplementary files format and content: csv file containing the RNA-seq count per gene for each replicate for both the 1 day and 3 day time point
Supplementary files format and content: csv file containing gene baseMean, log2FC and adjusted p-value for treated v control samples for differential Ribo-seq levels, RNA-seq levels and translational efficiency and associated integrated Ribo-seq and RNA-seq analysis translational efficiency class (Chothani et al., 2019)

extract_protocol:
Cell culture media was removed and cells were incubated (2 min, 37°C) with new media supplemented with 100 µg/mL cycloheximide (Merck, C4859), washed with PBS supplemented with 20 µg/mL cycloheximide, and lysed with 400 µL lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2 (Invitrogen, 89880), 1 mM DL-Dithiothreitol (DTT, Merck, 43815), 1% Triton X-100 (Thermo Scientific, 10671652), 0.1 % IGEPAL CA-630 (Merck, I8896), 100 µg/mL cycloheximide, 25 U/mL TURBO DNase (Invitrogen, AM2239) using a cell scraper. Lysate was triturated 10x through a 26-gauge needle and cell debris pelleted by centrifugation at 20,000 x g, 5 min, 4°C. Total RNA was purified from 100 µL cleared lysate using Trizol reagent according to the manufacturer’s instructions.
mRNA-seq libraries were generated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490S) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760S).

treatment_protocol: OE21 cells were treated with DMSO or 1 µM STM9005 for 1 or 3 days

value: Oesophageal carcinoma

value: STM9005 3 days


title: H23_MRTX849_3

city: Shanghai

first: Shaofei

last: Wang

state: Shanghai

address: 131 Dongan Road, Xuhui District, Shanghai 200032, P.R. China

institute: Fudan University

description:
Library name: Sample9
H23_MRTX849_3 FPKM

data_processing:
The raw sequencing reads were filtered and trimmed using SOAPnuke (v1.5.6) prior to alignment and the resultant clean reads were then mapped to the human genome GRCh38/hg38 with STAR (v2.5.3a). The quantification of expression levels of genes and transcripts was conducted by RSEM (v1.3.1)] and the differential expression analysis was performed using DESeq2 package (v1.4.5).
Assembly: GRCh38
Supplementary files format and content: NCI-H23_KRASi_24h_FPKMs.txt

source_name: lung

growth_protocol: The NCI-H23 human NSCLC cells, were cultured with RPMI 1640 medium containing 10% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37℃ in a humidified 5% CO2 incubator.

extract_protocol:
Total RNA was isolated from the cells using PureLink RNA Mini Kit (Cat. No. #12183025, Invitrogen) according to the manufacturer's instructions.
After the assessment of RNA quality by the Fragment Analyzer System (Alignment), cDNA libraries were prepared using MGIEasy Fast RNA Library Prep Kit (Cat. No. 940-000890-00, MGI) from RNA for sequencing on MGISEQ-2000RS platform (MGI Tech Co. Ltd.) to generate 50 bp single-end reads.

treatment_protocol: The NCI-H23 cells were treated with vehicle (DMSO) or KRAS inhibitor, either AMG-510 (1 μM) or MRTX849 (100 nM), for 24h. Three biological replicates were prepared for each condition.

value: lung

value: NSCLC

value: KRAS-mutant


title: Bridge (brainstem),Lactation,Goat-6

city: Cerdanyola del Vallès

first: Diego

last: Vargas Donayre

address: Carrer de la Vall Moronta

institute: Centre for Research in Agricultural Genomics (CRAG)

description: Library name: BRG6


title: OE21 cells, RNA-Seq, STM9005, 3 days, rep2

description: Library name: OE21_STM9005_3d_rep2


title: P144_27Sep

description: Library name: P144_27Sep

value: Blood

value: PBMCs


title: Colon,Dry,Goat-73

description: Library name: CO73

source_name: Colon

value: Colon


title: H23_MRTX849_2

description:
Library name: Sample8
H23_MRTX849_2 FPKM


title: OE21 cells, RNA-Seq, STM9005, 3 days, rep1

description: Library name: OE21_STM9005_3d_rep1


title: P143_27Sep

description: Library name: P143_27Sep

value: Black


title: H23_MRTX849_1

description:
Library name: Sample7
H23_MRTX849_1 FPKM


title: Diaphragm,Lactation,Goat-6

description: Library name: DPH6

source_name: Diaphragm

value: Diaphragm


title: P142_27Sep

description: Library name: P142_27Sep

value: Pre-vaccination


title: OE21 cells, RNA-Seq, DMSO, 3 days, rep3

description: Library name: OE21_DMSO_3d_rep3

value: DMSO 3 days


title: H23_AMG510_3

description:
Library name: Sample6
H23_AMG-510_3 FPKM


title: Esophagus,Lactation,Goat-2

description: Library name: ES2

source_name: Esophagus

value: Esophagus


title: P141_27Sep

description: Library name: P141_27Sep

value: NX


title: H23_AMG510_2

description:
Library name: Sample5
H23_AMG-510_2 FPKM


title: Esophagus,Lactation,Goat-3

description: Library name: ES3


title: P136_26Sep

description: Library name: P136_26Sep

value: AZ


title: H23_AMG510_1

description:
Library name: Sample4
H23_AMG-510_1 FPKM


title: Esophagus,Dry,Goat-54

description: Library name: ES54


title: OE21 cells, RNA-Seq, STM9005, 1 day, rep3

description: Library name: OE21_STM9005_1d_rep3

value: STM9005 1 day


title: Esophagus,Dry,Goat-64

description: Library name: ES64


title: OE21 cells, RNA-Seq, STM9005, 1 day, rep2

description: Library name: OE21_STM9005_1d_rep2


title: H23_DMSO_3

description:
Library name: Sample3
H23_DMSO_3 FPKM

value: DMSO (24h)


title: SPBC patient 3

type: genomic

city: Santa Monica

first: Melanie

last: Goldfarb

address: 2200 Santa Monica blvd

department: Surgical Oncology

institute: Saint Johns Cancer Institute

description:
DNA from breast cancer FFPE tissue
JW-SBC-04

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC 850K Beadchip using standard Illumina protocol

scan_protocol: The array was scanned with the iScan system from Illumina according to the manufacturer's guidelines.

data_processing:
Data normalization and quality control were performed using the R package ChAMP (v.2.36.0). Batch effects were tested and corrected using the ComBat function in ChAMP, and probes with a detection p-value above 0.01 were excluded. Probes targeting non-CG dinucleotides, single nucleotide polymorphisms, and chromosome Y were removed from downstream analyses
processed value definition: Beta-values, corrected for batch effect from the different sample origin and other potential batches in the arrays

label: Cy3 and Cy5

source_name: Breast Cancer

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from 10-15 um thick tissue sections by microdissection with a needle. Genomic DNA was isolated using the Quick-DNA FFPE Miniprep kit (#D3067; Zymo Research, CA.). Genomic DNA was quantified by Qubit® 3.0 Fluorometer (Q33216; Thermo Fisher Scientific, CA). Genomic DNA was converted with Sodium bisulfite using EZ DNA Methylation-Direct (#D5021, Zymo Research, CA), following the manufacturer's recommendations

tag: batcharray

value: Array 1

value: Breast Cancer

tag: age at diagnosis

tag: breast cancer subtype

tag: Sex

value: Female

tag: tumor histology

value: Invasive ductal carcinoma

tag: grade

value: Grade I (well differentiated)