title: U138MG cells, PTDSS1i, 100 nM 48h, rep3

first: Yixuan

last: Hu

address: No. 600 Dunyu Road,  Xihu District

institute: Westlake University

description:
Library name: Sample 12
Column name in raw_counts_All_Samples.txt: U138MG_PTDSS1i_3

data_processing:
Raw reads were filtered to remove adapters and low-quality bases using Trimmomatic.
Clean reads were aligned to the human reference genome (hg38) using STAR software.
Gene expression counts were generated using featureCounts.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file containing raw read counts for all genes.

source_name: brain

growth_protocol: KYSE30 cells were maintained at 37°C with 5% CO2 in RPMI-1640/Ham’s F-12 (1:1) medium supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) following the manufacturer's instructions. Genomic DNA was removed using gDNA wiper mix.
Libraries were constructed using the Illumina TruSeq RNA Sample Prep Kit v2. Poly-A mRNA was purified, fragmented, and reverse transcribed into cDNA. Adapters were ligated and the library was amplified by PCR.

treatment_protocol: Cells were treated with either DMSO (vehicle control) or 100 nM PTDSS1 inhibitor  for 48 hours.

value: brain

value: glioblastoma

value: WT

value: 100 nM PTDSS1 inhibitor

tag: batch


title: BC287

status: Public on Aug 05 2026

type: SRA

city: Chicago

first: Zhou

last: Zhang

state: IL

address: 680 North Lake Shore Drive, Suite 1400

department: Preventive Medicine

country: USA

institute: Northwestern University

description: Library name: BC287

library_source: other

data_processing:
Library strategy: 5hmC-Seal
Raw sequencing reads were trimmed for adaptor sequences using Trimmomatic
Low quality bases were also trimmed , followed by alignment to the current human genome reference (hg19) using Bowtie2 with the end-to-end alignment mode,Read pairs were concordantly aligned with fragment length ≤ 500 bp and with average ≤ 1 ambiguous base and up to four mismatched bases per 100 bp length.
Alignments with Mapping Quality Score ≥ 10 were counted for gene bodies, according to the gene start and gene end annotations by the GENCODE Project(release 19), using featureCounts without strand information.
Assembly: hg19
Supplementary files format and content: csv, genebody count of 5hmC

molecule: other

organism: Homo sapiens

source_name: Plasma

extract_protocol:
Briefly, circulating cfDNA was extracted from ~2-3 mL of plasma using the QIAamp Circulating Nucleic Acid Kit (Qiagen, Germany) according to manufacturer’s protocols. DNA concentration was quantified using a Qubit fluorometer (Thermo Fisher Scientific Inc.).
The cfDNA samples were randomized for constructing 5hmC-Seal libraries and subsequent sequencing. First, the Illumina-compatible adaptors were ligated onto the cfDNA samples per our published protocols. Next, T4 bacteriophage β-glucosyltransferase was used to transfer an engineered glucose moiety containing an azide group onto the hydroxyl group of 5hmC-modified fragments. The azide group was then reacted with a biotin-conjugated strained alkyne DBCO-PEG4-biotin (Sigma) via click chemistry to biotinylated the DNA fragments. Streptavidin beads (Thermo) were used for affinity enrichment of 5hmC-containing DNA fragments. The 5hmC-Seal libraries were subsequently constructed through PCR amplification using KAPA HyperPlus library construction kit (Roche) and paired-end sequenced (PE60) using the Illumina NextSeq500 platform (Illumina Inc., California, USA) at The University of Chicago Genomics Facility.

tag: tissue

value: Plasma


title: Tumor, innate agonist treated, channel 2, RNA

city: Cambridge

first: Tyler

middle: T

last: Dao

state: MA

address: 45 Carleton St

institute: Massachusetts Institute of Technology

description:
Library name: Masopust_053_6b_GEX_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

library_source: transcriptomic

data_processing:
Raw Illumina output files were processed to fastq files using the Cumulus V2.4.0 CellRanger pipeline on the Terra platform.
Assembly: mm10
Supplementary files format and content: Sample specific filtered_feature_bc_matrix.h5, adt.csv and hto.csv files were uploaded.
Library strategy: CITE-seq

molecule: polyA RNA

organism: Mus musculus

source_name: B16 tumors

extract_protocol:
Tumors were isolated, dissociated in gentleMACSTM C tubes and dissociator, and filtered. Single cells were processed via the 10x Genomics Next GEM single-cell 3' RNA-seq protocol.
Gene expression, ADT and HTO libraries were generated following the 10x Genomics 3' protocol.

value: B16 tumors

tag: cell line

value: B16.F10 melanoma

tag: cell type

value: Melanoma and infiltrated immune cells

tag: treatment

value: Innate agonist


title: U138MG cells, PTDSS1i, 100 nM 48h, rep2

city: Hangzhou

country: China

description:
Library name: Sample 11
Column name in raw_counts_All_Samples.txt: U138MG_PTDSS1i_2

molecule: total RNA

tag: genotype


title: BC285

description: Library name: BC285


title: BC283

description: Library name: BC283


title: Tumor, innate agonist treated, channel 1, RNA

description:
Library name: Masopust_053_6a_GEX_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing


title: BC239

description: Library name: BC239


title: U138MG cells, PTDSS1i, 100 nM 48h, rep1

description:
Library name: Sample 10
Column name in raw_counts_All_Samples.txt: U138MG_PTDSS1i_1


title: BC233

description: Library name: BC233


title: Tumor, irrelevant (48h) or relevant peptide treated (12h), channel 2, RNA

description:
Library name: Masopust_053_3b_GEX_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

value: Relevant and irrelevant peptide


title: BC232

description: Library name: BC232


title: U138MG cells, DMSO, 48h, rep3

description:
Library name: Sample 9
Column name in raw_counts_All_Samples.txt: U138MG_DMSO3

value: DMSO


title: BC186

description: Library name: BC186


title: BC167

description: Library name: BC167


title: U138MG cells, DMSO, 48h, rep2

description:
Library name: Sample 8
Column name in raw_counts_All_Samples.txt: U138MG_DMSO2


title: Tumor, relevant (48h) or irrelevant peptide treated (12h), channel 2, RNA

description:
Library name: Masopust_053_2b_GEX_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing


title: BC168

description: Library name: BC168


title: Tumor, irrelevant (48h) or relevant peptide treated (12h), channel 1, RNA

description:
Library name: Masopust_053_3a_GEX_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing


title: U138MG cells, DMSO, 48h, rep1

description:
Library name: Sample 7
Column name in raw_counts_All_Samples.txt: U138MG_DMSO1


title: BC164

description: Library name: BC164


title: BC163

description: Library name: BC163


title: BC153

description: Library name: BC153


title: BC148

description: Library name: BC148


title: KYSE30 cells, PTDSS1i, 100 nM 48h, rep3

description:
Library name: Sample 6
Column name in raw_counts_All_Samples.txt: KYSE30_PTDSS1i_3

source_name: esophagus

value: esophagus

value: esophagus squamous cell carcinoma


title: BC147

description: Library name: BC147


title: Tumor, baseline or relevant peptide treated (12h), channel 2, RNA

description:
Library name: Masopust_053_1b_GEX_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing

value: Baseline and relevant peptide


title: KYSE30 cells, PTDSS1i, 100 nM 48h, rep2

description:
Library name: Sample 5
Column name in raw_counts_All_Samples.txt: KYSE30_PTDSS1i_2


title: BC122

description: Library name: BC122


title: Tumor, baseline or relevant peptide treated (12h), channel 1, RNA

description:
Library name: Masopust_053_1a_GEX_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing


title: BC121

description: Library name: BC121


title: KYSE30 cells, PTDSS1i, 100 nM 48h, rep1

description:
Library name: Sample 4
Column name in raw_counts_All_Samples.txt: KYSE30_PTDSS1i_1


title: fk1

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

description: Library name: Sample 8

data_processing:
Reads were processed using an in-house pipeline and open-source R packages. Briefly, raw reads were first trimmed using cutadapt to remove low quality bases and reads. Trimmed reads were then aligned to the mouse genome mm10 with GENCODE annotation vM25 using STAR (v2.7.9a) with default parameters. Transcript quantification was performed using featureCounts from the subread package (v2.0.1). Further quality Control assessments were made using RSeQC and RSEM, and batch correction was performed using edgeR, EDASeq, and RUVSeq.
Principle component analysis and differential expression analysis for Control and FGFR1-CKO samples were determined using DESeq2 in negative binomial mode using batch-corrected transcripts from featureCounts (> 2-fold expression change, > 1 count per million (CPM), Benjamini corrected P < 0.05). Pairwise comparisons were made between Control vs FGFR1-CKO to determine differentially expressed genes (DEG).
Assembly: mm10
Supplementary files format and content: xlsx for filtered gene counts

source_name: femoral cortical bone

growth_protocol: All mice (Mus musculus) were housed in a pathogen-free barrier facility and handled in accordance with standard user protocols, animal welfare regulations, and the NIH Guide for the Care and Use of Laboratory Animals. All studies were performed under a protocol approved by the Institutional Animal Care and Use Committee at Washington University in Saint Louis.

extract_protocol:
Each femoral diaphysis was dissected, the marrow was flushed with PBS with an 26G needle, and the remaining cortical bone was snap frozen in liquid nitrogen and stored at −80°C until further processing. Frozen tissues were pulverized in a liquid nitrogen-cooled stainless-steel flask with a ball bearing in a Micro Dismembrator (Sartorius Inc.) at 2000 rpm for 20 40 sec. RNA was stabilized with Trizol Reagent (#10296– 010, Life Technologies Corporation, USA) and total RNA isolation was isolated with the RNeasy Mini Kit (#74106, Qiagen Inc., Germantown, MD) according to the manufacturer’s instructions.
Library preparation was performed with 200-500ng of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Roche). mRNA was then fragmented in reverse transcriptase buffer and then heating heated to 94°C for 8 min. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (#18080093, Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, followed by ligation of Illumina sequencing adapters. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq 6000 using paired end reads extending 150 bases.

treatment_protocol: Tamoxifen chow (400mg/kg, Envigo Teklad, Madison, WI, USA; TD.130860) from 12 to 16 weeks of age

value: femoral cortical bone

value: DMP1-CreER; Fgfr1f/f

value: Tamoxifen, 4 weeks


title: KYSE30 cells, DMSO, 48h, rep3

description:
Library name: Sample 3
Column name in raw_counts_All_Samples.txt: KYSE30_DMSO3


title: donor4;MGO;D15

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

country: Netherlands

institute: Utrecht University

description: Library name: d4MGO-D15

data_processing:
perform quality control on FastQ files (using FastQC)
align reads of each sample in a run against reference genome (using STAR) and add read groups (using Picard)
perform quality control on generated BAM files (using Picard)
count reads in features (using HTSeq-count)
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes raw count values for each Sample

source_name: hepatic organoid

extract_protocol:
RNeasy Mini Kit (Qiagen)
TruSeq Stranded mRNA Library Prep Kit (Illumina)

value: hepatic organoid


title: donor1;MGOSM;D8

description: Library name: d1MGOSM-D8


title: donor4;PCOSM;D8

description: Library name: d4PCOSM-D8


title: Tumor, relevant (48h) or irrelevant peptide treated (12h), channel 1, RNA

description:
Library name: Masopust_053_2a_GEX_FL
Libraries were sequenced first on a Nextseq2000 for quality control, and then a Novaseq6000 for deeper sequencing


title: fk5

description: Library name: Sample 7


title: KYSE30 cells, DMSO, 48h, rep2

description:
Library name: Sample 2
Column name in raw_counts_All_Samples.txt: KYSE30_DMSO2


title: donor3;MGOSM;D15

description: Library name: d3MGOSM-D15


title: eb3

description: Library name: Sample 5


title: KYSE30 cells, DMSO, 48h, rep1

description:
Library name: Sample 1
Column name in raw_counts_All_Samples.txt: KYSE30_DMSO1


title: donor1;MGO;D15;static

description: Library name: d1MGO-D15-SC


title: dz8

description: Library name: Sample 6


title: donor2;MGOSM;D15;static

description: Library name: d2MGOSM-D15-SC


title: donor3;PCOSM;D15

description: Library name: d3PCOSM-D15


title: donor1;MGOSM;D15

description: Library name: d1MGOSM-D15


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 71

first: Sudeshna

last: Das

state: Massachusetts

address: 65 Landsdowne St

institute: MGH

description: Library name: 112MG

library_source: transcriptomic single cell

data_processing:
Raw reads were processed using Cell Ranger 3.0.0 (10X Genomics) with default settings, pre-mRNA package and aligned to the human GRCh38 genome.
Assembly: GRCh38
Supplementary files format and content: matrix files and tab-separated files
Supplementary files format and content: .rds file

molecule: nuclear RNA

source_name: inferior temporal gyrus

extract_protocol:
Nuclei were isolated and sorted following published procedures. Briefly, 30-40 forty-μm-thick cryostat sections were lysed in a sucrose lysis buffer (10 mM Tris-HCl pH 8.0, 320 mM sucrose, 5 mM CaCl2, 3 μM Mg(Ac)2, 0.1 mM EDTA, 1 mM DTT, and 0.1% Triton X-100). The resulting lysates were filtered through a 70 μm-pore cell strainer and nuclei were purified from filtrates by ultracentrifugation (107,000xg for 1.5 h at 4oC) through a sucrose cushion (10 mM Tris-HCl pH 8.0, 1.8 M sucrose, 3 μM Mg(Ac)2, 0.1 mM EDTA, and 1 mM DTT). Supernatants were removed and pellets were resuspended in 2% BSA/PBS containing RNase inhibitor (0.2 U/μL, Roche). To enrich non-neuronal nuclei, we followed a strategy of depletion of neurons and oligodendrocytes. Nuclei were labeled with AlexaFluor647- conjugated mouse monoclonal anti-NeuN antibody (clone 1B7, Novus Biologicals, NBP1-92693AF647) and PE-conjugated mouse monoclonal anti-OLIG2 antibody (clone 211F1.1, EMD Millipore, MABN50A4). After washes, nuclei were stained with Sytox blue (Thermo Fisher) and sorted on a BD FACSAria Fusion. For each sample, we collected SytoxposNeuNposOLIG2neg and SytoxposNeuNnegOLIG2neg.
Single-nucleus cDNA libraries were prepared using the Chromium Single Cell 3' Reagents Kit V3 according to the manufacturer's protocol (10x Genomics). Pooled samples were sequenced on an Illumina NovaSeq 6000, targeting a minimum of 30,000 reads per cell. NeuN⁺OLIG2⁻ and NeuN⁻OLIG2⁻ nuclei were sorted into separate libraries, enabling increased sequencing depth and gene detection in non-neuronal cells relative to studies using non-enriched nuclei.

value: inferior temporal gyrus

value: brain vascular cells

tag: age

tag: Sex

value: F

value: Tauopathy


title: donor4;MGO;D8

description: Library name: d4MGO-D8


title: dq2

description: Library name: Sample 4


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 70

description: Library name: 51MG

value: M


title: donor1;MGOSM;D15;static

description: Library name: d1MGOSM-D15-SC


title: donor4;MGOSM;D15

description: Library name: d4MGOSM-D15


title: donor4;MGOSM;D8

description: Library name: d4MGOSM-D8


title: fn3

description: Library name: Sample 3


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 69

description: Library name: 53MG


title: donor3;MGO;D8

description: Library name: d3MGO-D8


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 68

description: Library name: 79MG


title: donor2;MGO;D8

description: Library name: d2MGO-D8


title: dn15

description: Library name: Sample 2


title: fn8

description: Library name: Sample 1


title: donor3;PCOSM;D8

description: Library name: d3PCOSM-D8


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 67

description: Library name: 77MG


title: donor2;PCOSM;D15

description: Library name: d2PCOSM-D15


title: donor1;MGO;D8

description: Library name: d1MGO-D8


title: Sox10 KO BG2 cells, clone 2, technical replicate 3

city: Ottawa

first: Luc

last: Sabourin

state: Ontario

address: 501 Smyth Rd

department: Cancer Research

country: Canada

institute: Ottawa Hospital Research Institute

description:
Library name: sgRNA2-2.3
sgKO2_3

data_processing:
Mouse RNA-seq reads were quality filtered using fastp. Filtered paired-end reads were aligned to the mm10 reference genome using subjunc. Gene-level counts were generated with summarizeOverlaps(), and differentially expressed genes were identified with DESeq2.
Assembly: GRCm38 - mm10
Supplementary files format and content: Processed data consists of gene-level RNA-seq read counts generated by summarizing reads overlapping annotated exons from the mm10 mouse genome (UCSC knownGene annotation) using the GenomicAlignments summarizeOverlaps approach. These raw counts were used as input for downstream differential expression analysis.

source_name: Mammary Tumor

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Invitrogen; 155960118) according to the manufacturers protocol. RNA was purified using the RNeasy Mini Kit (Qiagen; 74106) by following the RNA cleanup protocol with on-column DNase digestion.
polyA-enriched RNA (stranded)

value: Mammary Tumor

tag: strain

value: MMTV-NeuIresCre

value: Mammary Epithelial

value: Sox10 CRISPR Knockout


title: donor2;PCOSM;D8

description: Library name: d2PCOSM-D8


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 66

description: Library name: 11MG


title: donor2;MGO;D15

description: Library name: d2MGO-D15


title: Sox10 KO BG2 cells, clone 2, technical replicate 2

description:
Library name: sgRNA2-2.2
sgKO2_2


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 65

description: Library name: 61MG


title: donor4;PCOSM;D15

description: Library name: d4PCOSM-D15


title: Sox10 KO BG2 cells, clone 2, technical replicate 1

description:
Library name: sgRNA2-2.1
sgKO2_1


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 64

description: Library name: 89MG


title: donor3;MGO;D15

description: Library name: d3MGO-D15


title: donor2;MGOSM;D15

description: Library name: d2MGOSM-D15


title: donor1;MGO;D15

description: Library name: d1MGO-D15


title: Sox10 KO BG2 cells, clone 1, technical replicate 3

description:
Library name: sgRNA2-1.3
sgKO1_3


title: donor1;PCOSM;D15;static

description: Library name: d1PCOSM-D15-SC


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 63

description: Library name: 87MG


title: donor2;MGOSM;D8

description: Library name: d2MGOSM-D8


title: Sox10 KO BG2 cells, clone 1, technical replicate 2

description:
Library name: sgRNA2-1.2
sgKO1_2


title: donor2;MGO;D15;static

description: Library name: d2MGO-D15-SC


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 62

description: Library name: 71MG


title: donor1;PCOSM;D15

description: Library name: d1PCOSM-D15


title: Sox10 KO BG2 cells, clone 1, technical replicate 1

description:
Library name: sgRNA2-1.1
sgKO1_1


title: donor3;PCO;D15

description: Library name: d3PCO-D15


title: Wildtype BG2 cells, bulk sample, technical replicate 3

description:
Library name: NTC-3
NTC_3

value: Wildtype


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 61

description: Library name: 45MG


title: donor2;PCOSM;D15;static

description: Library name: d2PCOSM-D15-SC


title: donor3;MGOSM;D8

description: Library name: d3MGOSM-D8


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 60

description: Library name: 41MG


title: Wildtype BG2 cells, bulk sample, technical replicate 2

description:
Library name: NTC-2
NTC_2


title: donor1;PCOSM;D8

description: Library name: d1PCOSM-D8


title: HCD_1059_309_T1T2 ATAC

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

library_source: genomic

data_processing:
Raw sequencing reads were mapped to the hg38 version of the mouse genome using Bowtie
bigWig files were normalized to reads per million and generated using GenomicRanges and bedGraphToBigWig function from the UCSC genome browser
Assembly: hg38
Supplementary files format and content: reads per million normalized bigWig files

molecule: genomic DNA

source_name: blood

extract_protocol:
10,000 cells were sorted into 40% FBS in complete media.
10,000 cells were centrifuged for 10 minutes at 500xg, and tagmentation was performed by resuspending cells in 25 ul of Tagmentation mix (1X TD buffer (10 mM TAPS-NaOH pH 8.1, 5 mM MgCl2, 10% DMF), 2.5 μl Tn5 transposase, 0.1% Tween 20 and 0.02% Digitonin) and then incubated for 1 h at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

value: blood

tag: patient id

tag: disease

value: HC

tag: sledai

tag: race

value: Caucasian

tag: sorting markers


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 59

description: Library name: 39MG


title: HCD_981_1077_T1T2 ATAC


title: Wildtype BG2 cells, bulk sample, technical replicate 1

description:
Library name: NTC-1
NTC_1


title: HCD_1059_309_rN ATAC

value: rN


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 58

description: Library name: 105MG


title: HCD_530_109_T1T2 ATAC


title: Ocy454 cells, BGJ398, FGF2, Rep 3

city: Boston

first: Courtney

last: Mazur

address: 50 Blossom Street

department: Endocrine Unit

institute: Massachusetts General Hospital

description: Library name: BGJ398+FGF2_3

data_processing:
Transcript abundances were calculated using Salmon.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited files contain Salmon-calculated transcript abundances.

growth_protocol: Ocy454 cells were grown on standard tissue culture plastic in MEM alpha supplemented with 10% FBS and 1% antibiotic/antimycotic. Cells are cultured at 33C until confluent, then cultured at 37C to induce differentiation.

extract_protocol:
After 48 hours of treatment (on differentiation day 7), cells were lysed in guanidine-isothiocyanate lysis buffer containing 1% 2-mercaptoethanol. Lysates were passed through QIAshredder columns, then total RNA was isolated using the PureLink RNA Mini Kit with on-column DNase.
mRNA was purified by poly A enrichment, fragmented, and reverse transcribed using random hexamer primers. The library was then subject to end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Ocy454 cells were grown to confluence, then differentiated for five days at 37C. Cells were pretreated for one hour with the pan-FGFR inhibitor BGJ398 (200 nM) or with DMSO vehicle. Treatment media was then applied for 48 hr for each of four conditions in triplicate: DMSO, DMSO + FGF2 (2 ng/mL), BGJ398, BGJ398 + FGF2 (2 ng/mL).


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 57

description: Library name: 47MG


title: HCD_530_109_rN ATAC


title: SLE_2906_3353_T1T2 ATAC

value: SLE

value: AA


title: Ocy454 cells, BGJ398, FGF2, Rep 2

description: Library name: BGJ398+FGF2_2


title: SLE_2906_3353_rN ATAC


title: SLE_2675_2445_rN ATAC


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 56

description: Library name: 13MG


title: Ocy454 cells, BGJ398, FGF2, Rep 1

description: Library name: BGJ398+FGF2_1


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 55

description: Library name: 57MG


title: SLE_3032_3551_T1T2 ATAC

value: Hispanic


title: Ocy454 cells, DMSO, FGF2, Rep 3

description: Library name: DMSO+FGF2_3


title: SLE_3032_3551_rN ATAC


title: HCD_838_1218_T1T2 ATAC


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 54

description: Library name: 21MG

value: inferior temporal gyrus


title: HCD_838_1218_rN ATAC


title: Ocy454 cells, DMSO, FGF2, Rep 2

description: Library name: DMSO+FGF2_2


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 53

description: Library name: 37MG

value: brain vascular cells


title: SLE_2957_3465_rN ATAC


title: SLE_2885_3053_T1T2 ATAC

value: F


title: Ocy454 cells, DMSO, FGF2, Rep 1

description: Library name: DMSO+FGF2_1


title: SLE_2885_3053_rN ATAC


title: SLE_2914_3379_T1T2 ATAC


title: SLE_2914_3379_rN ATAC


title: Ocy454 cells, BGJ398, Control, Rep 3

description: Library name: BGJ398_3


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 51

description: Library name: 3MG

value: Tauopathy


title: SLE_3034_2664_T1T2 ATAC


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 52

description: Library name: 27MG


title: Ocy454 cells, BGJ398, Control, Rep 2

description: Library name: BGJ398_2


title: SLE_3254_3651_rN ATAC


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 50

description: Library name: 9MG


title: Ocy454 cells, BGJ398, Control, Rep 1

description: Library name: BGJ398_1


title: SLE_3275_3763_T1T2 ATAC


title: SLE_3030_3550_rN ATAC


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 49

description: Library name: 69MG

value: M


title: Ocy454 cells, DMSO, Control, Rep 3

description: Library name: DMSO_3

value: DMSO


title: SLE_2930_3434_T1T2 ATAC


title: SLE_3117_3239_T1T2 ATAC


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 48

description: Library name: 65MG


title: Ocy454 cells, DMSO, Control, Rep 2

description: Library name: DMSO_2


title: HCD_862_456_rN ATAC


title: SLE_1638_1655_rN ATAC


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 47

description: Library name: 75MG


title: SLE_1724_1324_T1T2 ATAC


title: Ocy454 cells, DMSO, Control, Rep 1

description: Library name: DMSO_1


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 46

description: Library name: 93MG


title: SLE_2886_3054_T1T2 ATAC


title: Naive,NT, ATAC

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

description:
Library name: Naive_ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC fragment sequence

library_source: genomic single cell

data_processing:
Multiome samples were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using Cellranger count pipeline
Assembly: mm10
Supplementary files format and content: Cellranger output files:h5 files for ATAC+GEX multiome and atac_fragments.tsv.gz file for each sample
Supplementary files format and content: Cl13D8_WT_filtered_feature_bc_matrix.h5,Cl13D8_WT_atac_fragments.tsv.gz,Cl13D8_KO_filtered_feature_bc_matrix.h5,Cl13D8_KO_atac_fragments.tsv.gz,Cl13D15_WT_filtered_feature_bc_matrix.h5,Cl13D15_WT_atac_fragments.tsv.gz,Cl13D15_KO_filtered_feature_bc_matrix.h5,Cl13D15_KO_atac_fragments.tsv.gz,Cl13D22_WT_filtered_feature_bc_matrix.h5,Cl13D22_WT_atac_fragments.tsv.gz,Cl13D22_KO_filtered_feature_bc_matrix.h5, Cl13D22_KO_atac_fragments.tsv.gz,ArmD8_D30WT_filtered_feature_bc_matrix.h5,ArmD8_D30WT_atac_fragments.tsv.gz,Nave_NIP_filtered_feature_bc_matrix.h5,Nave_NIP_atac_fragments.tsv.gz

source_name: spleen

extract_protocol:
Nuclei were encapsulated in gel bead-in-emulsion (GEM) using a 10x chromium controller with Chromium Next GEM Single Cell Multiome Gel Bead Kit and GEM Kit
Libraries for scRNA-seq and scATAC-seq were generated according to the manufacturer’s instructions (10x Genomics Single Cell Multiome assay).

value: spleen

tag: transgenic mouse_strain

value: NIP

value: CD4 T cell

tag: genetic modification

tag: infection

tag: time post_infection


title: SLE_1724_1324_rN ATAC

tag: tissue

tag: batch


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 45

description: Library name: 67MG

tag: cell type


title: SLE_2886_3054_rN ATAC


title: HCD_722_761_T1T2 ATAC


title: Ctrl, Arm pool, ATAC

description:
Library name: Arm_ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC fragment sequence

value: Ctrl

value: LCMV Armstrong

value: Day 8 and 30 (pooled)


title: HCD_1176_1842_T1T2 ATAC

value: blood

value: HC


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 44

description: Library name: 97MG


title: HCD_1176_1842_rN ATAC

value: rN


title: D22 KO, Cl13, ATAC

description:
Library name: D22_KO_ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC fragment sequence

value: TOX KO

value: LCMV cl13

value: Day 22


title: HCD_691_1086_T1T2 ATAC

value: AA


title: HCD_623_1256_T1T2 ATAC

value: F


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 43

description: Library name: 101MG

value: inferior temporal gyrus

value: brain vascular cells

value: Tauopathy


title: D22 Ctrl, Cl13, ATAC

description:
Library name: D22_Ctrl_ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC fragment sequence

value: spleen


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 42

description: Library name: 103MG

value: M


title: HCD.875.1610.T1-2 ATAC


title: HCD.875.1610.rN ATAC


title: D15 KO, Cl13, ATAC

description:
Library name: D15_KO_ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC fragment sequence

value: NIP

value: CD4 T cell

value: Day 15


title: SLE.2898.3314.rN ATAC

value: SLE


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 41

description: Library name: 85MG


title: SLE.2900.3328.T1-2 ATAC

value: blood


title: SLE.2900.3328.rN ATAC


title: D15 Ctrl, Cl13, ATAC

description:
Library name: D15_Ctrl_ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC fragment sequence

value: Ctrl


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 40

description: Library name: 95MG


title: SLE.2880.3039.rN ATAC

value: rN


title: D8 KO, Cl13, ATAC

description:
Library name: D8_KO_ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC fragment sequence

value: TOX KO

value: Day 8


title: SLE.2891.420.T1-2 ATAC


title: Vascular cells, Progressive Supranuclear Palsy (PSP), Donor 39

description: Library name: 83MG


title: SLE.2891.420.rN ATAC


title: D8 Ctrl, Cl13, ATAC

description:
Library name: D8_Ctrl_ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC fragment sequence

value: LCMV cl13


title: SLE.3136.3378.rN ATAC

value: AA


title: Naive, NT,GEX

description:
Library name: Naive_RNA
RNA: read1 contains cell barcode and UMI; read2 contains the transcript sequence


title: Vascular cells, Pick's Disease (PiD), Donor 38

description: Library name: 55MG


title: SLE.2932.3240.rN ATAC

value: F


title: Vascular cells, Pick's Disease (PiD), Donor 37

description: Library name: 81MG

value: inferior temporal gyrus


title: SLE.2911.2209.T1-2 ATAC


title: SLE.2911.2209.rN ATAC


title: Ctrl, Arm pool, GEX

description:
Library name: Arm_RNA
RNA: read1 contains cell barcode and UMI; read2 contains the transcript sequence

value: LCMV Armstrong

value: Day 8 and 30 (pooled)


title: SLE.2913.559.T1-2 ATAC

value: Caucasian


title: Vascular cells, Pick's Disease (PiD), Donor 36

description: Library name: 91MG

value: brain vascular cells

value: M

value: Tauopathy


title: SLE.2913.559.rN ATAC


title: HCD.878.1606.rN ATAC

value: HC

value: Hispanic


title: D22 KO, Cl13, GEX

description:
Library name: D22_KO_RNA
RNA: read1 contains cell barcode and UMI; read2 contains the transcript sequence

value: spleen

value: NIP

value: CD4 T cell

value: Day 22


title: Vascular cells, Pick's Disease (PiD), Donor 35

description: Library name: 5MG


title: D22 Ctrl, Cl13, GEX

description:
Library name: D22_Ctrl_RNA
RNA: read1 contains cell barcode and UMI; read2 contains the transcript sequence

value: Ctrl


title: HCD.1171.1296.rN ATAC

value: blood

value: rN


title: HCD.1171.1296.T1-2 ATAC

value: F

value: AA


title: HCD.796.1235.rN ATAC


title: D15 KO, Cl13, GEX

description:
Library name: D15_KO_RNA
RNA: read1 contains cell barcode and UMI; read2 contains the transcript sequence

value: TOX KO

value: LCMV cl13

value: Day 15


title: Vascular cells, Pick's Disease (PiD), Donor 33

description: Library name: 116MG

value: inferior temporal gyrus

value: brain vascular cells


title: HCD.646.1234.rN ATAC


title: HCD.646.1234.T1-2 ATAC


title: HCD.918.1215.T1-2 ATAC


title: D8 KO, Cl13, GEX

description:
Library name: D8_KO_RNA
RNA: read1 contains cell barcode and UMI; read2 contains the transcript sequence

value: Day 8


title: HCD.918.1215.rN ATAC

value: HC


title: Vascular cells, Pick's Disease (PiD), Donor 34

description: Library name: 23MG

value: M

value: Tauopathy


title: D15 Ctrl, Cl13, GEX

description:
Library name: D15_Ctrl_RNA
RNA: read1 contains cell barcode and UMI; read2 contains the transcript sequence

value: spleen

value: NIP


title: 4798-013-60

first: Minyi

last: Lee

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University Chobanian & Avedisian School of Medicine

description: Library name: 4798-013-60

data_processing:
Demultiplexing and creation of FASTQ files were automatically performed using the Illumina BaseSpace platform with default parameters.
Reads were aligned to the Genome Reference Consortium human build 37 (GRCh37) using STAR v2.6.0c.
Both gene and transcript level counts were calculated using RSEM v1.3.1 with annotation from Ensembl build 107.
Assembly: hg37
Supplementary files format and content: counts.tsv: tab-separated values (TSV) file containing 57736 x 183 matrix of "expected_count" values computed by RSEM

source_name: Bronchial brushing

extract_protocol:
Total RNA was isolated from bronchial brushings using the miRNeasy Mini Kit (Qiagen, Valencia, CA).
Libraries were generated using the Illumina TruSeq RNA Access kit (Illumina, San Diego, CA)

value: Bronchial brushing

tag: subject id

tag: cancer status

value: Benign

tag: smoking status

value: Former

value: male

tag: nodule size_(cm)

tag: tfa (total_fat_area)

tag: fev1 percent_predicted

tag: fev1/fvc ratio

tag: copd status

value: TRUE


title: Vascular cells, Pick's Disease (PiD), Donor 32

description: Library name: 19MG

tag: age

tag: Sex

value: F


title: LN-18 sgATM mock rep3

city: Guangzhou

first: xiaohui

last: chen

address: No.106 Zhongshan 2nd Road,Yuexiu District

institute: Guangdong Provincial People's Hospital

description: Library name: LN18sgATM_3

data_processing:
we aligned reads of all samples to the Homo sapiens reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: GRCm38
Supplementary files format and content: genes_fpkm_expression.xlsx

source_name: Brain

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)

value: Brain

tag: cell line

value: Glioblastoma cells

tag: genotype

value: sgATM (ATM KO)

tag: treatment

value: Mock


title: 4714-017-60

description: Library name: 4714-017-60

value: Malignant


title: LN-18 wild-type mock rep3

description: Library name: LN18_3

value: sgNC (wild-type)


title: SLE.3202.2491.rN ATAC

value: blood

tag: patient id

value: rN

tag: disease

value: SLE

tag: sledai

tag: race

value: AA

tag: sorting markers


title: Vascular cells, Pick's Disease (PiD), Donor 31

description: Library name: 63MG

tag: tissue

value: inferior temporal gyrus

tag: cell type

value: brain vascular cells

value: M

tag: batch

value: Tauopathy


title: SLE.2711.871.rN ATAC


title: D8 Ctrl, Cl13, GEX

description:
Library name: D8_Ctrl_RNA
RNA: read1 contains cell barcode and UMI; read2 contains the transcript sequence

value: spleen

tag: transgenic mouse_strain

value: NIP

value: CD4 T cell

tag: genetic modification

value: Ctrl

tag: infection

value: LCMV cl13

tag: time post_infection

value: Day 8


title: SLE.1731.1738.rN ATAC

value: F


title: Vascular cells, Corticobasal Degeneration (CBD), Donor 30

description: Library name: 43MG

tag: age


title: SLE.1929.1537.T1-2 ATAC

tag: Sex

value: Multi


title: Vascular cells, Corticobasal Degeneration (CBD), Donor 29

description: Library name: 110MG


title: SLE.1551.1597.rN ATAC


title: S54192_KI_EPCAM_plus

city: Milan

first: Sara

last: Sigismund

address: via adamello 16

country: Italy

institute: European Institute of Oncology

description:
Library name: Sample_2
10X Genomics

data_processing:
Read alignment, UMI counting, cell-containing barcode (CB) calling were performed using the “cellranger count” from CellRanger (v6.0) on the mouse reference genome Mmu38
Assembly: Mmu38
Supplementary files format and content: barcodes.tsv: tab separated value files
Supplementary files format and content: genes.tsv: tab separated value files
Supplementary files format and content: matrix.mtx: matrix files

source_name: mammary glands

growth_protocol: Mammary glands were collected at 18-weeks of age, from 7 EPN3-KI mice and 5 CTRL mice and immediately digested for single cell isolation.

extract_protocol:
Single, live EpCAMpos cells (500-1000 cells/μL) were mixed with the reverse transcription mix using 10x Genomics Chromium Single-cell 3’ reagent kit (protocol V3.1) according to the manufacturer’s protocol and then loaded onto 10x Genomics Single-Cell 3’ Chips (www.10xgenomics.com).
Libraries were generated as by manufacturers’ instructions (protocol V3.1).

treatment_protocol: After overnight digestion, epithelial cells were purified using the EasySep™ Mouse Epithelial Cell Enrichment Kit, according to the manufacturer’s protocol. Following purification, epithelial cells were incubated with 10% BSA-PBS for blocking and stained for 45 min at 4°C with EpCAM-APC conjugated antibody in 1% BSA-PBS and live/dead viability stain (BV-510) diluted 1:1000. Single, live EpCAMpos cells were then purified by FACS-sorting using a BD InFlux V7 flow cytometer.

value: mammary glands

value: Mammary epithelial cells

value: Live, EpCAM pos cells from KI mice


title: Vascular cells, Corticobasal Degeneration (CBD), Donor 28

description: Library name: 17MG


title: S54191_CTRL_EPCAM_plus

description:
Library name: Sample_1
10X Genomics

value: Live, EpCAM pos cells from CTRL mice


title: SLE_3441_1609_rN

data_processing:
Raw sequencing reads were mapped to the hg38 version of the mouse genome using STAR and the GENCODE v27 reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: hg38
Supplementary files format and content: tab delimited text file of RPKM normalized read counts for each gene

extract_protocol:
5,000 cells were FACS sorted into RLT + 1%BME and snap frozen using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

value: blood

value: rN

value: SLE

value: AA


title: SLE_3441_1609_T1T2


title: SLE.1929.1537.rN ATAC


title: SLE_3275_3763_T11_T2


title: Mouse skin tissue, UV irradiated, day 5

city: Zurich

first: Adrian

last: Salas-Bastos

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

description:
Library name: SCC-CTL_D5
BD Rhapsody™ Whole Transcriptome Analysis (WTA)

data_processing:
datasets were mapped against a Mus musculus customized genome annotation file using the workflow manager cwlref-runner (version 1.0) and the BD rhapsody pipeline version 2.2.1
Assembly: Mus musculus genome annotation file (GRCm39 assembly, release M26 [2021-04-20]), plus the transgene tdTomato
Supplementary files format and content: The processed data file is a .tar.gz file containing the files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz for the respective sample

source_name: Irradiated skin

extract_protocol:
Upon sacrifice, 4 cm2 tissue of day-5  irradiated skin was excised post-mortem. First, skin was cut into strips using a sterile blade, then digested with 10 ml of DMEM/F12 without phenol-red containing 1.5 mg/ml collagenase I, 10% FBS, 100 U/ml Penicillin-Streptomycin and 1:1000 Protector RNase Inhibitor for 2 hours at 37°C with agitation. Samples were centrifuged, and the cell-containing supernatant was passed through a 40-μm cell strainer and set aside on ice. The remaining skin pieces were further digested with 2 ml DMEM/F12 containing 0.025% Trypsin-EDTA and 2 mM EDTA for 5 minutes at 37°C with agitation. Trypsin was inactivated and the remaining skin pieces were passed three times through an 18G needle and five times through a 21G needle. The digested skin suspension was then filtered through a 40-μm cell strainer and combined with the previously obtained cell suspension that was kept on ice. Samples were washed once with HBSS, centrifuged, and resuspended in DMEM/F12 medium containing 10% FBS, 1% Penicillin-Streptomycin, and 1:1000 Protector RNase Inhibitor. Debris and cell clumps were filtered out manually using 40-μm mesh filters. Dead cells were then removed with EasySep™ Dead Cell Removal (Annexin V) Kit), according to manufacturer’s instructions.
single-cell suspensions were processed using the BD Rhapsody™ Whole Transcriptome Analysis (WTA) Reagent Kit (BD Bioesciences), and approximately 100,000 cells per samples were loaded into a BD Rhapsody cartridge. Cell capture, barcoding, reverse transcription, and library construction were performed according to the manufacturer’s protocol.

treatment_protocol: WT  mouse of 9 weeks old was exposed to a single UV-irradiation dose (5.0 J/cm2 UVA + 1.5 J/cm2 UVB) during resting hair phase under general anesthesia with isoflurane. The UV-exposed area was 4cm2.

value: Irradiated skin

value: Skin cells

value: WT

value: UV irradiation

tag: time

value: Day 5

value: Female

value: 9 weeks


title: Vascular cells, Corticobasal Degeneration (CBD), Donor 27

description: Library name: 1MG

value: inferior temporal gyrus

value: brain vascular cells

value: M

value: Tauopathy


title: SLE_3275_3763_rN

value: F


title: Vascular cells, Corticobasal Degeneration (CBD), Donor 26

description: Library name: 25MG


title: SLE_3218_3711_T1T2


title: KO primary TECs 4

city: Ji Nan

first: Guo

last: jialin

address: 107 Wenhua Xilu, Jinan, Shandong, China

institute: Shandong University

description: Library name: Sample8

data_processing:
Read quality was assessed by FastQC, and reads were aligned to the  genome assembly using STAR (version 2.4.1d).
Raw counts were normalized, and DESeq2 (Bioconductor package, version 1.34.0) in R studio (version 4.1.1) was used to identify differentially expressed genes (DEGs).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv file include FPKM values for each Samples

source_name: kidnrey

growth_protocol: Primary TECs were cultured in DMEM/F12 medium supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin-streptomycin Solution with 5% CO2 at 37℃

extract_protocol:
RNA was harvested with TRIzol method. 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using RNA 6000 Nano Assay Kit following manufacturer's instruction

value: kidnrey

tag: cell line

value: primary cells

tag: genotype

value: ALDH5 knockout

value: no treatment


title: SLE_3218_3711_rN

value: blood

tag: patient id

value: rN

value: SLE

value: AA


title: SLE_3117_3239_T1T2

tag: disease


title: KO primary TECs 3

description: Library name: Sample7

value: ALDH4 knockout

tag: treatment


title: Vascular cells, Corticobasal Degeneration (CBD), Donor 25

description: Library name: 99MG


title: SLE_3117_3239_rN

tag: sledai

tag: race


title: KO primary TECs 2

description: Library name: Sample6

tag: tissue

value: ALDH3 knockout


title: SLE_3034_2664_T1T2

tag: cell type

tag: sorting markers


title: hepAGT-/-, epididymal white adipose tissue, thermoneutral housing, Western diet, biol rep 21

city: Lexington

first: Liyuan

last: Zhu

state: KY

address: 741 South Limestone Street

institute: University of Kentucky

description: Library name: TNKOE21

data_processing:
FASTQ reads were adapter-trimmed and quality-filtered using fastp.
Trimmed reads were aligned to the mouse GRCm38/mm10 reference genome using STAR v2.6.1d, and gene-level read counts were generated using featureCounts v1.5.0-p3.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file containing raw gene-level read counts for all submitted samples. Rows correspond to genes/features and columns correspond to library names listed in the SAMPLES section.

source_name: epididymal white adipose tissue

growth_protocol: Male hepAGT+/+ and hepAGT-/- littermate mice were maintained in a barrier facility on a 14:10-hour light:dark cycle. Mice were housed at room temperature (20-22 degrees C) or thermoneutrality (30 degrees C) and fed a Western diet (TD.88137; 21% milk fat and 0.2% cholesterol) for 12 weeks.

extract_protocol:
Tissue samples were snap-frozen in homogenization solution (#Z305H, Promega) containing 1-thioglycerol (#A208B, Promega). Total RNA was extracted using Maxwell RSC simplyRNA Tissue Kits (#AS1340, Promega) according to the manufacturer's protocol.
Bulk mRNA-seq libraries were prepared by Novogene from total RNA using NEBNext Ultra RNA Library Prep Kits for Illumina (New England Biolabs). Libraries were sequenced in paired-end mode on an Illumina NovaSeq 6000 platform.

treatment_protocol: Mice were assigned to room-temperature or thermoneutral housing and fed Western diet for 12 weeks. Liver, brown adipose tissue, and epididymal white adipose tissue were collected at study termination for bulk RNA-seq.

value: epididymal white adipose tissue

value: hepAGT-/-

value: Western diet for 12 weeks; thermoneutral housing (30 degrees C)

value: male


title: hepAGT-/-, liver, thermoneutral housing, Western diet, biol rep 22

description: Library name: TNKOL22

source_name: liver

value: liver


title: 786-O,LINC02068-kd1,rep1

city: Shanghai

first: Wenjie

last: Xu

address: Dongan road

institute: Fudan University

description:
Library name: sample1
shRNA1-1

data_processing:
QC reports were generated from FastQC (version: 0.11.9)
Following quality assessment, Low-quality reads were trimmed and adapters were removed with Trim Galore (version: 0.6.7)
Cleaned data were then aligned to the reference genome (hg38) using HISAT2 (version: 2.2.1)
Reads for genes were counted from the sorted BAM file using StringTie (version: 2.2.1)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: kidney

growth_protocol: Human clear cell renal cell carcinoma (ccRCC) tumor tissues and matched adjacent normal kidney tissues were collected from patients undergoing surgical resection at Fudan University Shanghai Cancer Center (FUSCC). Fresh tissues were immediately snap-frozen and stored at −80°C until RNA extraction. For cell line experiments, 786-O cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum under standard culture conditions.

extract_protocol:
Total RNA was extracted from snap-frozen ccRCC tumor tissues, matched adjacent normal kidney tissues, and cultured 786-O cells using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. RNA quality and concentration were assessed using a NanoDrop spectrophotometer and agarose gel electrophoresis. High-quality RNA samples were used for subsequent library preparation.
RNA sequencing libraries were prepared using the Abclonal RNA-seq Library Preparation Kit (RK20348) according to the manufacturer's instructions. Briefly, total RNA was processed for library construction, followed by RNA fragmentation, reverse transcription, adapter ligation, PCR amplification, and library quality assessment. Qualified libraries were sequenced on an Illumina sequencing platform in paired-end mode.

treatment_protocol: No specific treatment was applied before RNA extraction.

value: kidney

value: human renal cell carcinoma

value: LINC02068 knockdown


title: Vascular cells, Corticobasal Degeneration (CBD), Donor 24

description: Library name: 73MG

value: inferior temporal gyrus

value: brain vascular cells

value: F

tag: batch

value: Tauopathy


title: KO primary TECs 1

description: Library name: Sample5

value: kidnrey

value: primary cells

value: ALDH2 knockout

value: no treatment


title: 4438-082-60

description: Library name: 4438-082-60

value: Bronchial brushing

tag: subject id

tag: cancer status

value: Benign

tag: smoking status

value: Former

tag: nodule size_(cm)

tag: tfa (total_fat_area)

tag: fev1 percent_predicted

tag: fev1/fvc ratio

tag: copd status

value: FALSE


title: SLE_2930_3434_T1T2

value: blood

tag: patient id

value: SLE

tag: Sex

value: AA


title: SLE_3034_2664_rN

value: rN

tag: disease


title: Vascular cells, Control, Donor 5, rep 2

description: Library name: 33MG

tag: age

value: M


title: SLE_2930_3434_rN

tag: sledai

tag: race


title: WT primary TECs 4

description: Library name: Sample4

tag: tissue

tag: cell line

tag: cell type

tag: genotype

value: WT

tag: treatment


title: SLE_2918_846_T1T2

tag: batch

tag: sorting markers


title: WT primary TECs 3

description: Library name: Sample3


title: Vascular cells, Control, Donor 4, rep 2

description: Library name: 59MG

value: inferior temporal gyrus

value: brain vascular cells


title: SLE_2906_3353_T1T2

value: F


title: SLE_2918_846_rN


title: Vascular cells, Control, Donor 3, rep 2

description: Library name: 107MG

value: Tauopathy


title: SLE_2886_3054_T1T2


title: WT primary TECs 2

description: Library name: Sample2

value: kidnrey

value: primary cells


title: Vascular cells, Control, Donor 2, rep 2

description: Library name: 15MG


title: SLE_2886_3054_rN


title: SLE_2906_3353_rN


title: SLE_2885_3053_T1T2


title: WT primary TECs 1

description: Library name: Sample1

value: no treatment


title: Vascular cells, Control, Donor 1, rep 2

description: Library name: 7MG


title: SLE_2885_3053_rN


title: SLE_2675_2445_T1T2


title: Vascular cells, Alzheimer's disease, Donor 23

description: Library name: H351

value: AD Progression


title: organ of corti, STZ-induced diabetes 62

city: Taipei

first: Shing-Hwa

last: Liu

address: No.1 Jen Ai road section 1

department: College of Medicine

country: Taiwan

institute: National Taiwan University

description: Library name: D62-O

data_processing:
NovaSeq X Plus Sequencing System for 2 x 151bp paired-end sequencing
The paired reads in the trimmed sequences were analyzed by RNA-Seq Analysis using CLC Genomics Workbench v10
Assembly: Mus musculus GRCm38
Supplementary files format and content: csv files includes FPKM values for each Sample

source_name: cochlear tissues

extract_protocol:
RNA from tissues were homogenized in TRIzol reagent
mRNA libraries for RNA-seq were prepared using the Illumina® NEBNext® Ultra™ RNA-seq library kit following the manufacturer's protocol.

value: cochlear tissues

value: STZ


title: SLE_2675_2445_rN


title: SLE_2590_289_T1T2


title: modiolus of corti, STZ-induced diabetes 62

description: Library name: D62-M


title: Vascular cells, Alzheimer's disease, Donor 22

description: Library name: H333


title: SLE_2590_289_rN


title: SLE_1724_1324_rN


title: organ of corti, STZ-induced diabetes 37

description: Library name: D37-O


title: SLE_1724_1324_T1T2


title: Vascular cells, Alzheimer's disease, Donor 21

description: Library name: H319


title: lateral wall of corti, STZ-induced diabetes 62

description: Library name: D62-L


title: SLE_1638_1655_T1T2


title: SLE_1638_1655_rN


title: 4238-021-60

description: Library name: 4238-021-60

value: Bronchial brushing

tag: subject id

tag: cancer status

value: Benign

tag: smoking status

value: Current

value: male

tag: nodule size_(cm)

tag: tfa (total_fat_area)

value: TRUE


title: modiolus of corti, STZ-induced diabetes 37

description: Library name: D37-M


title: hepAGT+/+, liver, room temperature, Western diet, biol rep 12

description: Library name: RTWTL12

value: liver

value: hepAGT+/+

value: Western diet for 12 weeks; room temperature housing (20-22 degrees C)

tag: Sex


title: HCD_D6_1177_T1T2

value: blood

tag: patient id

tag: disease

value: HC

value: Caucasian


title: Vascular cells, Alzheimer's disease, Donor 20

description: Library name: H265

value: inferior temporal gyrus

value: brain vascular cells

tag: age

value: F


title: Healthy bone reference sample 4

city: México city

first: Rogelio Frank

last: Jiménez-Ortega

state: Alcaldía Tlalpan

address: Calzada México-Xochimilco No. 289

department: Subdirección de investigación Biomédica

country: Mexico

institute: Instituto Nacional de Rehabilitación

description:
Library name: ID-11
Condition: Healthy bone; source folder: 20171010_11; raw files are listed as FASTQ files from lanes L001-L004 exactly as uploaded to GEO.

data_processing:
FASTQ files were quality-controlled and processed through a standardized RNA-seq workflow.
Reads were aligned or quantified against the human GRCh38/hg38 reference genome/transcriptome.
Gene-level raw count and TPM-normalized expression matrices were generated for downstream differential expression and pathway analyses.
Assembly: GRCh38/hg38
Supplementary files format and content: counts_matrix.tsv.gz: tab-delimited gene-level raw count matrix; rows are genes/features and columns are GEO library identifiers ID-1 through ID-14.
Supplementary files format and content: TPM_normalized_matrix.tsv.gz: tab-delimited gene-level TPM-normalized matrix; rows are genes/features and columns are GEO library identifiers ID-1 through ID-14.

source_name: bone tissue

growth_protocol: Not applicable; human biospecimens were analyzed.

extract_protocol:
Total RNA was extracted from human tissue-derived biospecimens according to the laboratory protocol used for this RNA-seq experiment. RNA quality-control criteria and extraction reagent/kit details should be confirmed by the submitter if requested by GEO.
RNA-seq libraries were prepared for paired-end sequencing using an Illumina-compatible library preparation workflow. Library preparation kit, RNA selection/depletion strategy, read length, and sequencing chemistry should be confirmed by the submitter if requested by GEO.

treatment_protocol: Samples were classified by biological condition as osteosarcoma tumor or healthy bone reference samples.

value: bone tissue

tag: disease state

value: Healthy bone


title: Vascular cells, Alzheimer's disease, Donor 19

description: Library name: H247

tag: tissue

value: AD Progression


title: HCD_D6_1177_rN

value: rN

tag: sledai

tag: race


title: lateral wall of corti, STZ-induced diabetes 37

description: Library name: D37-L

value: cochlear tissues

value: STZ


title: organ of corti, STZ-induced diabetes 36

description: Library name: D36-O


title: Vascular cells, Alzheimer's disease, Donor 18

description: Library name: H237

tag: cell type


title: HCD_D0_2164_T1T2


title: HCD_981_1077_T1T2


title: HCD_D0_2164_rN


title: lateral wall of corti, STZ-induced diabetes 36

description: Library name: D36-L

tag: treatment


title: HCD_981_1077_rN

tag: batch


title: HCD_874_858_rN

tag: sorting markers


title: HCD_874_858_T1T2


title: Vascular cells, Alzheimer's disease, Donor 15

description: Library name: H183


title: Vascular cells, Alzheimer's disease, Donor 17

description: Library name: H211

value: M


title: modiolus of corti, STZ-induced diabetes 36

description: Library name: D36-M


title: HCD_862_456_rN


title: HCD_862_456_T1T2


title: Vascular cells, Alzheimer's disease, Donor 14

description: Library name: H163


title: organ of corti, control 45

description: Library name: C45-O

value: citrate buffer


title: HCD_838_1218_rN


title: Vascular cells, Alzheimer's disease, Donor 16

description: Library name: H199


title: Vascular cells, Alzheimer's disease, Donor 13

description: Library name: H131


title: lateral wall of corti, control 45

description: Library name: C45-L


title: HCD_722_761_rN


title: HCD_722_761_T1T2


title: modiolus of corti, control 45

description: Library name: C45-M


title: HCD_691_1086_T1T2

value: AA


title: HCD_691_1086_rN


title: HCD_623_1256_T1T2


title: Vascular cells, Alzheimer's disease, Donor 11

description: Library name: H99


title: organ of corti, control 44

description: Library name: C44-O


title: HCD_530_109_T1T2


title: HCD_623_1256_rN


title: modiolus of corti, control 44

description: Library name: C44-M


title: Vascular cells, Alzheimer's disease, Donor 10

description: Library name: H97


title: HCD_1176_1842_T1T2


title: Vascular cells, Alzheimer's disease, Donor 9

description: Library name: H65


title: lateral wall of corti, control 44

description: Library name: C44-L


title: HCD_1059_309_T1T2


title: HCD_1059_309_rN


title: modiolus of corti, control 28

description: Library name: C28-M


title: organ of corti, control 28

description: Library name: C28-O


title: Vascular cells, Alzheimer's disease, Donor 8

description: Library name: H53


title: HCD.875.1610.T1T2


title: HCD.875.1610.rN


title: SLE.2898.3314.T1T2

value: SLE


title: CC4268LL

first: Stephan

last: Wueest

address: Lenggstrasse 30

institute: University Children's Hospital Zurich

description: Library name: Sample 10_OE_5

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: Mus musculus
Supplementary files format and content: txt fike containing fpkm counts for all samples

source_name: Liver

extract_protocol:
Total RNA was extracted with the NucleoSpin® RNA isolation kit (Macherey-Nagel, Düren, Germany).
Library was prepared with specific protocols for directional and non-directional libraries, including end repair, A-tailing, adapter ligation, size selection, and amplification.

value: Liver

tag: genotype

value: ASK1+hep (OE)

value: 7w HFD


title: SLE.2893.428.rN

value: blood


title: Vascular cells, Control, Donor 7

description: Library name: H191

value: inferior temporal gyrus


title: Vascular cells, Control, Donor 6

description: Library name: H111

value: brain vascular cells


title: HCD_838_1218_T1T2

value: HC

value: F

value: Caucasian


title: lateral wall of corti, control 28

description: Library name: C28-L


title: SLE.2898.3314.rN


title: Vascular cells, Control, Donor 5, rep 1

description: Library name: H299

value: AD Progression


title: SLE.2900.3328.T1T2


title: CC4265L

description: Library name: Sample 9_OE_4


title: CC4191L

description: Library name: Sample 8_OE_3


title: SLE.2880.3039.T1T2


title: SLE.2880.3039.rN

value: rN


title: SLE.2891.420.rN


title: Vascular cells, Control, Donor 4, rep 1

description: Library name: H257


title: healthy control 1

status: Public on Aug 06 2026

city: Nanning City

first: Qicheng

last: Long

state: Guangxi Zhuang Autonomous Region

address: No.6 Shuangyong Road

department: Department of Intensive Care Unit

institute: The First Affiliated Hospital of Guangxi Medical University

description: Library name: HC1

data_processing:
Raw sequencing reads were filtered using SOAPnuke to remove adapter contamination, low-quality reads, and reads containing excessive ambiguous bases. Clean reads were aligned to the human reference genome (GRCh38) using Bowtie. Known miRNAs were identified based on miRBase, and novel miRNAs were predicted using miRDeep. Read counts for each miRNA were calculated, and expression levels were normalized as transcripts per million (TPM). Differential expression analysis was performed using DESeq2 based on the raw read counts.
The processed expression matrices include both known miRNAs annotated in miRBase and putative novel miRNAs predicted by miRDeep. Novel miRNAs are represented by their miRDeep-assigned identifiers.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes raw counts and RPM table for all Samples

source_name: Peripheral blood

extract_protocol:
Total RNA was extracted from peripheral whole blood samples using a commercially available RNA extraction kit according to the manufacturer’s instructions. The concentration and purity of the extracted RNA were assessed using a NanoDrop spectrophotometer, and RNA integrity was evaluated using an Agilent Bioanalyzer or equivalent platform. Only RNA samples that met the quality control requirements were used for subsequent library construction.
small RNA libraries were constructed separately. Briefly, small RNAs were ligated with 3′ and 5′ adapters, reverse-transcribed into cDNA, amplified by PCR, and purified to obtain the final small RNA libraries.

value: Peripheral blood

value: healthy control


title: Vascular cells, Control, Donor 3, rep 1

city: Cambridge

description: Library name: H117

data_processing:
Raw reads were processed using Cell Ranger 3.0.0 (10X Genomics) with default settings, pre-mRNA package and aligned to the human GRCh38 genome.
Assembly: GRCh38
Supplementary files format and content: matrix files and tab-separated files
Supplementary files format and content: .rds file

extract_protocol:
Nuclei were isolated and sorted following published procedures. Briefly, 30-40 forty-μm-thick cryostat sections were lysed in a sucrose lysis buffer (10 mM Tris-HCl pH 8.0, 320 mM sucrose, 5 mM CaCl2, 3 μM Mg(Ac)2, 0.1 mM EDTA, 1 mM DTT, and 0.1% Triton X-100). The resulting lysates were filtered through a 70 μm-pore cell strainer and nuclei were purified from filtrates by ultracentrifugation (107,000xg for 1.5 h at 4oC) through a sucrose cushion (10 mM Tris-HCl pH 8.0, 1.8 M sucrose, 3 μM Mg(Ac)2, 0.1 mM EDTA, and 1 mM DTT). Supernatants were removed and pellets were resuspended in 2% BSA/PBS containing RNase inhibitor (0.2 U/μL, Roche). To enrich non-neuronal nuclei, we followed a strategy of depletion of neurons and oligodendrocytes. Nuclei were labeled with AlexaFluor647- conjugated mouse monoclonal anti-NeuN antibody (clone 1B7, Novus Biologicals, NBP1-92693AF647) and PE-conjugated mouse monoclonal anti-OLIG2 antibody (clone 211F1.1, EMD Millipore, MABN50A4). After washes, nuclei were stained with Sytox blue (Thermo Fisher) and sorted on a BD FACSAria Fusion. For each sample, we collected SytoxposNeuNposOLIG2neg and SytoxposNeuNnegOLIG2neg.
Single-nucleus cDNA libraries were prepared using the Chromium Single Cell 3' Reagents Kit V3 according to the manufacturer's protocol (10x Genomics). Pooled samples were sequenced on an Illumina NovaSeq 6000, targeting a minimum of 30,000 reads per cell. NeuN⁺OLIG2⁻ and NeuN⁻OLIG2⁻ nuclei were sorted into separate libraries, enabling increased sequencing depth and gene detection in non-neuronal cells relative to studies using non-enriched nuclei.


title: SN4491LR

description: Library name: Sample 6_OE_1


title: Vascular cells, Control, Donor 1, rep 1

description: Library name: H77


title: SLE.2911.2209.T1T2


title: SLE.2932.3240.T1T2


title: CC4297L

description: Library name: Sample 5_WT_5

value: ASK1f/f (Control)


title: MPMC1

first: Maeva

middle: general

last: Chauvin

address: 55 fruit st

institute: general hosp corp d/b/a mass general hosp

description: Library name: MPMC1

data_processing:
high-quality total RNA was used for mRNA enrichment using poly(A) selection (or rRNA depletion if applicable, if you know it). The enriched RNA was then fragmented and reverse-transcribed to generate first-strand and second-strand cDNA.
Libraries were sequenced on an Illumina platform to generate paired-end reads.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Omentum

extract_protocol:
Primary mesothelial cells were isolated from fresh omentum of C57BL/6J mice. Tissue samples were mechanically minced and enzymatically digested in DMEM supplemented with 5% serum, 2 mg/mL collagenase type I, and 40 U/mL DNase I at 37°C for 30 minutes. The resulting suspension was transferred into a dissociation tube and further processed using the gentleMACS dissociator system to facilitate tissue dissociation. The cell suspension was then filtered through a 70 µm cell strainer, washed, and plated in culture conditions.  Cells were cultured for one week prior to experimental treatment. Cancer-associated mesothelial cells (CAMCC and CAMCB) were generated by exposing primary mesothelial cells (MCs) to standardized cancer cell-conditioned media from two cell lines KPCA.C and KPCA.B respectively  for 72 hours.  Total RNA was extracted using the Qiagen RNA extraction kit following the manufacturer’s instructions.
RNA-seq libraries were prepared by Novogene using a standard Illumina-compatible library preparation protocol.

value: Omentum

tag: cell line

value: Primary MC

value: Primary Mesothelial cells


title: cfDNA, HNC patient 3, Pharynx-EP-M-2-M

first: Tianci

last: Wang

address: NO. 800 Dongchuan Road

department: School of Biomedical Engineering

institute: Shanghai Jiao Tong University

description: Library name: Sample 5

data_processing:
The quality of all three sequencing datasets was assessed using FastQC (v0.11.5) to obtain base quality scores and detect adapter sequences.
Next, Trim-Galore (v0.6.10) was used to remove adapters and low-quality reads.
After trimming, FastQC was used again to reassess sequence quality. Following adapter removal and quality filtering, Bismark (v0.24.2) was used to align the sequencing reads to the hg38 human reference genome, resulting in BAM files.
To determine whether the sequencing data contained the target regions, we used the sort function in samtools (v1.19) to sort the aligned BAM files.
After sorting, the bam2pat function in wgbstools (v0.2.2) was used to convert BAM files into PAT files.
Assembly: hg38
Supplementary files format and content: PAT files: DNA region and methylation statu of each CpG site of each read

source_name: plasma

extract_protocol:
cfDNA was extracted from patients' plasma using the QIAamp Circulating Nucleic Acid Kit
After bisulfite conversion using EZ DNA Methylation-Gold Kit and amplification of target region, libraries were constructed using NEBNext Ultra II Kit

value: plasma

value: cell-free DNA


title: SLE.2913.559.T1T2

value: SLE


title: SLE.2913.559.rN

value: blood


title: CC4192R

description: Library name: Sample 3_WT_3

value: Liver

value: 7w HFD


title: HCD.1171.1296.T1T2

value: HC

value: AA


title: HCD.1171.1296.rN

value: F


title: cfDNA, HNC patient 2, Pharynx-EP-M-2-M

description: Library name: Sample 3


title: HCD.796.1235.rN


title: HCD.646.1234.T1T2


title: cfDNA, HNC patient 1, Pharynx-EP-M-2-M

description: Library name: Sample 2


title: HCD.646.1234.rN


title: healthy control 3

description: Library name: HC3

data_processing:
For mRNA and lncRNA analysis, raw sequencing reads were filtered using SOAPnuke to remove adapter contamination, low-quality reads, and reads containing excessive ambiguous bases. Clean reads were aligned to the human reference genome using HISAT2. Novel transcripts were assembled using StringTie and compared with the reference annotation using Cuffcompare to identify putative novel lncRNA transcripts. Gene-level read counts were generated using featureCounts based on the final gene annotation. Gene expression levels were normalized and reported as fragments per kilobase of transcript per million mapped reads (FPKM). Differential expression analysis was performed using DESeq2 based on the raw read counts.Novel transcripts were assembled using StringTie and compared with the reference annotation using Cuffcompare. The processed expression matrices include both annotated genes and putative novel transcripts. Novel transcripts are represented by StringTie-generated XLOC identifiers.
For circRNA analysis, raw sequencing reads were filtered using SOAPnuke. Clean reads were aligned to the reference genome using both Bowtie2 and BWA. Candidate circular RNAs were identified independently using find_circ and CIRI, and the integrated results were used for downstream analysis. CircRNA expression levels were normalized as reads per million mapped reads (RPM). Differentially expressed circRNAs were identified using NOISeq.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM or RPM table for all Samples

extract_protocol:
Total RNA was extracted from peripheral whole blood samples using a commercially available RNA extraction kit according to the manufacturer’s instructions. The concentration and purity of the extracted RNA were assessed using a NanoDrop spectrophotometer, and RNA integrity was evaluated using an Agilent Bioanalyzer or equivalent platform. Only RNA samples that met the quality control requirements were used for subsequent library construction.
ribosomal RNA was removed from total RNA, and strand-specific transcriptome libraries were constructed following the standard protocol. The purified RNA was fragmented and reverse-transcribed into cDNA, followed by end repair, adaptor ligation, PCR amplification, and library purification


title: cfDNA, HNC patient 1, Pharynx-EP-M-2-U

description: Library name: Sample 1


title: HCD.918.1215.T1T2


title: EED-Mutant EGFR OFF tumor 1615

first: Yixiang

last: Li

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description:
Library name: EDN_1615
EDN_1615

data_processing:
Original data file from Illumina is transformed into sequenced reads (raw data, FASTQ formate files) by CASAVA base recognition.
Sequencing reads were mapped to the mm10 genome by STAR.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Lung tumor

growth_protocol: SCLC tumors were harvested at necropsy and were flash-frozen. 1014 RPR2 cells were cultured with RPMI-1640 with 10% FBS, P/S, and HITES (10 nM hydrocortisone (Sigma Aldrich # H0135), Insulin-Transferrin-Selenium (Gemini #400-145), and 10 nM beta-estradiol (Sigma Aldrich# E2257), 100 U/mL of penicillin (P), and 100 μg/mL of streptomycin (S)] and culture with 5% CO2 at 37C. EED-Mutant 1339 and 1344 cell lines were cultured with RPMI-1640 with 10% FBS, 100 U/mL of penicillin, and 100 μg/mL of streptomycin and 5% CO2 at 37C.

extract_protocol:
RNA was extracted using Quick-RNA™ Miniprep kit (Cat # R1055, Zymo Research, CA, USA) including a DNase digestion step according to the manufacturer’s instructions and RNA sequencing was performed.
The libraries for RNA-seq are prepared using NEBNext Ultra II non-stranded kit.  Paired end 150bp sequencing was performed on Novaseq6000 sequencer using S4 flow cell.

value: Lung tumor


title: HCD.918.1215.rN

first: Chris

last: Scharer

address: 1510 Clifton Rd, Suite 3086A

institute: Emory University

source_name: blood

value: rN


title: IGROV1 DARPP-32 knockdown (replicate 3)

city: Nottingham

first: Sarah

middle: Joanne

last: Storr

state: Nottinghamshire

address: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

description: Library name: IGROV1 DARPP-32 knockdown (replicate 3)

data_processing:
Quality control using Trim Galore
Pseudoalignment using Kallisto
Assembly: human
Supplementary files format and content: Kallisto h.5 abundance files

source_name: Ovarian

extract_protocol:
mRNA was purified from total RNA via poly-T oligo attached magnetic beads prior to fragmentation which was followed by first strand cDNA synthesis using random hexamer primers then second strand cDNA synthesis.
The library was complete following end-repair, A-tailing, adapter ligation, size selection, amplification and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyser for size detection before being sequenced on Illumina NovaSeq

value: Ovarian

value: DARPP-32 KD


title: SLE.3039.3553.rN


title: EED-Mutant EGFR OFF tumor 1602_1

description:
Library name: EDN_1602_1
EDN_1602_1


title: SLE.3202.2491.T1T2


title: Subject P110 (P110-T1F)

type: protein

city: Stanford

first: Paul

middle: Joseph

last: Utz

state: California

address: 269 Campus Dr

institute: Stanford University School of Medicine

description:
reason for sample removal: NA
Antibodies in samples bind to barcoded beads conjugated to antigens. Antibody reactivity was quantified by the fluorescence measured as MFI from the secondary antibody.
Luminex™ FLEXMAP 3D™

hyb_protocol: A fluorescent secondary antibody was added to a PBS solution containing conjugated beads bound to antibodies.

scan_protocol: A Luminex FlexMAP 3D instrument was used to quantify autoantibody levels in each sample by measuring fluorescence (in MFI) from each barcoded bead.

data_processing: See methods section for detailed description. MFI values for unconjugated beads were subtracted from MFI values for antigen conjugated bead IDs, with MFI averages calculated after background subtraction.

label: R-PE conjugated goat anti-human IgG secondary antibody

molecule: protein

source_name: Serum/Plasma

label_protocol: Secondary antibody with a conjugated fluorophore was added to a PBS solution containing conjugated beads bound to antibodies from samples.

extract_protocol: Blood was collected from patients and healthy controls. Blood was then processed into serum or plasma.

value: Serum/Plasma

tag: condition

value: Patient


title: IGROV1 DARPP-32 knockdown (replicate 2)

description: Library name: IGROV1 DARPP-32 knockdown (replicate 2)


title: SLE.3202.2491.rN


title: EED-Mutant EGFR OFF tumor 1562_2

description:
Library name: EDN_1562_2
EDN_1562_2


title: SLE.2711.871.T1T2


title: SLE.2711.871.rN


title: EED-Mutant EGFR ON tumor 1601_3

description:
Library name: EDP_1601_3
EDP_1601_3


title: SLE.0.1738.T1T2


description: Library name: IGROV1 DARPP-32 knockdown control (replicate 3)

value: Control


title: SLE.0.1738.rN


title: EED-Mutant EGFR ON tumor 1601_1

description:
Library name: EDP_1601_1
EDP_1601_1


title: SLE.0.1597.T1T2


title: SLE.0.1597.rN


title: EED-WT EGFR OFF tumor 1547_3

description:
Library name: CDN_1547_3
CDN_1547_3


title: SLE.0.3651.T1T2


description: Library name: IGROV1 DARPP-32 knockdown control (replicate 1)


title: EED-WT EGFR OFF tumor 1547_2

description:
Library name: CDN_1547_2
CDN_1547_2


title: SLE.0.3621.rN


title: BC400 5hmC_Seal

city: Chicago

first: Zhou

last: Zhang

address: 680 North Lake Shore Drive, Suite 1400

institute: Northwestern University

data_processing:
Library strategy: 5hmC-Seal
Raw sequencing reads were trimmed for adaptor sequences using Trimmomatic
Low quality bases were also trimmed , followed by alignment to the current human genome reference (hg19) using Bowtie2 with the end-to-end alignment mode,Read pairs were concordantly aligned with fragment length ≤ 500 bp and with average ≤ 1 ambiguous base and up to four mismatched bases per 100 bp length.
Alignments with Mapping Quality Score ≥ 10 were counted for gene bodies, according to the gene start and gene end annotations by the GENCODE Project(release 19), using featureCounts without strand information.
Genome_build: hg19

source_name: Plasma

extract_protocol:
Briefly, circulating cfDNA was extracted from ~2-3 mL of plasma using the QIAamp Circulating Nucleic Acid Kit (Qiagen, Germany) according to manufacturer’s protocols. DNA concentration was quantified using a Qubit fluorometer (Thermo Fisher Scientific Inc.).
The cfDNA samples were randomized for constructing 5hmC-Seal libraries and subsequent sequencing. First, the Illumina-compatible adaptors were ligated onto the cfDNA samples per our published protocols. Next, T4 bacteriophage β-glucosyltransferase was used to transfer an engineered glucose moiety containing an azide group onto the hydroxyl group of 5hmC-modified fragments. The azide group was then reacted with a biotin-conjugated strained alkyne DBCO-PEG4-biotin (Sigma) via click chemistry to biotinylated the DNA fragments. Streptavidin beads (Thermo) were used for affinity enrichment of 5hmC-containing DNA fragments. The 5hmC-Seal libraries were subsequently constructed through PCR amplification using KAPA HyperPlus library construction kit (Roche) and paired-end sequenced (PE60) using the Illumina NextSeq500 platform (Illumina Inc., California, USA) at The University of Chicago Genomics Facility.

value: Plasma

tag: population

value: EA

tag: diagnosis

value: MM

tag: molecule

value: circulating cell-free DNA (cfDNA)


title: BC397 5hmC_Seal


title: EED-WT EGFR OFF tumor 1547_1

description:
Library name: CDN_1547_1
CDN_1547_1


title: BC396 5hmC_Seal


title: BC393 5hmC_Seal


title: EED-WT EGFR OFF tumor 1543_2

description:
Library name: CDN_1543_2
CDN_1543_2


title: IGROV1 DDR1 knockdown (replicate 1)

description: Library name: IGROV1 DDR1 knockdown (replicate 1)

value: DDR1 KD


title: BC392 5hmC_Seal


title: 25 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 2, H3K27ac CUT&Tag

city: Houston

first: Yi-Lan

last: Weng

state: Texas

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

description: Library name: SS0630YC054

data_processing:
Raw paired-end reads were assessed for sequencing quality and adapter contamination, and low-quality bases and adapter sequences were trimmed using Trimmomatic.
RNA-seq reads were aligned to the human GRCh38/hg38 reference genome using the STAR aligner. Gene-level read counts were generated using STAR, followed by normalization and differential-expression analysis using DESeq2.
CUT&Tag reads were aligned to the human GRCh38/hg38 reference genome using STAR. Duplicate reads were handled and low-quality alignments were filtered before normalization. H3K27ac-enriched regions were identified by peak calling with MACS2.
Assembly: GRCh38/hg38
Supplementary files format and content: RNA-seq processed data include a gene-expression matrix and differential-expression analysis results in tab-delimited text format.
Supplementary files format and content: CUT&Tag processed data include genome-browser signal tracks in bigWig format.
Library strategy: CUT&Tag

growth_protocol: HMC3 human microglial cells were obtained from ATCC. Cells were maintained in high-glucose DMEM supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
For RNA-seq, total RNA was extracted using TRIzol reagent. For CUT&Tag, nuclei or permeabilized cells were prepared according to the CUT&Tag workflow, and tagmented DNA was purified using ampure beads.
RNA-seq libraries were prepared using the Smart-seq2 protocol with poly(A) RNA selection from 100 ng RNA, followed by amplification, indexing, and library purification. H3K27ac CUT&Tag libraries were generated using an anti-H3K27ac antibody and a protein A/G–Tn5 transposase-based CUT&Tag workflow, followed by PCR amplification, indexing, and library purification. All libraries were sequenced using paired-end sequencing.

treatment_protocol: HMC3 cells were treated with vehicle control or PFOS at 25 or 50 µM for 24 hours. For recovery samples, PFOS-containing medium was removed after 24 hours, cells were washed as appropriate, and fresh PFOS-free medium was added for an additional 24-hour recovery period.

value: microglial cell

value: 25 µM PFOS; 24 h treatment followed by 24 h recovery


title: BC390 5hmC_Seal


title: EED-WT EGFR OFF tumor 1543_1

description:
Library name: CDN_1543_1
CDN_1543_1


title: BC389 5hmC_Seal


description: Library name: IGROV1 DDR1 knockdown control (replicate 3)


description: Library name: IGROV1 DDR1 knockdown control (replicate 2)


description: Library name: IGROV1 DDR1 knockdown control (replicate 1)


title: BC385 5hmC_Seal


title: BC384 5hmC_Seal


title: EED-WT EGFR OFF tumor 1596_2

description:
Library name: CDN_1596_2
CDN_1596_2


title: BC383 5hmC_Seal


title: T47D DDR1 knockdown (replicate 3)

description: Library name: T47D DDR1 knockdown (replicate 3)

source_name: Breast

value: Breast


title: BC382 5hmC_Seal

value: AA


title: EED-WT EGFR OFF tumor 1595

description:
Library name: CDN_1595
CDN_1595


title: BC381 5hmC_Seal


title: T47D DDR1 knockdown (replicate 2)

description: Library name: T47D DDR1 knockdown (replicate 2)


title: SK-MEL-28, 10 uM ASO2 (NTC), biol rep 3

city: Seattle

first: Benjamin

last: Logsdon

state: WA

address: 1150 Eastlake Ave E Ste 600/700

institute: Cajal Therapeutics

description:
Library name: MB107-10uM-ASO2-rep3-33
column MB107-10uM-ASO2-rep3-33 in MB107_deseq2_tmm_norm_counts.tsv

data_processing:
Bcl -> FASTQ demultiplexing performed by Azenta (bcl2fastq).
Transcript-level quantification with Salmon v1.10.0 against the GENCODE human transcriptome (confirm release).
Transcript counts aggregated to gene level with tximport.
Gene-level counts normalized in DESeq2 v1.38.3 (TMM); differential expression testing by DESeq2 Wald test.
Assembly: GRCh38 (GENCODE release to be confirmed)
Supplementary files format and content: MB107_deseq2_tmm_norm_counts.tsv: tab-delimited gene x sample matrix of DESeq2 TMM-normalized counts. 14,892 Ensembl gene IDs x 36 samples; column names match *library name values (with ASO2-REP2-29 and ASO2-REP2-30 corresponding to library indices 29 and 30 -- see naming note in accompanying documentation).

growth_protocol: SK-MEL-28 cells (ATCC HTB-72; working stock SKMEL28_P4) cultured in EMEM (ATCC 30-2003) + 10% FBS (Atlas Biologicals F-0500-A) + 1% Penicillin/Streptomycin (Thermo Scientific 15140122). Cells were thawed at passage 4 in a 10 cm plate at 1.478e6 cells (~2.6e4 cells/cm^2), grown 3 days, then plated on 2025-09-29 into 24-well plates at 80,000 cells/well in 550 uL medium and grown ~24 h before transfection.

extract_protocol:
Cell pellets were lysed in 1 mL cold Trizol (Invitrogen 15596026) on ice, vortexed 2 x 30 s, incubated 5 min at RT; 200 uL chloroform added, shaken 15 s, incubated 3 min at RT, centrifuged 15 min at 12,000 x g / 4 C. The aqueous phase was mixed 1:1 with 70% ethanol and purified on Qiagen RNeasy MinElute Micro columns per the UPenn Trizol/Qiagen hybrid protocol (Buffer RW1 wash, two RPE washes, 80% EtOH wash, 5 min dry spin, elution in 15 uL nuclease-free water). RNA was quantified by NanoDrop (A260/A280 1.98-2.05, A260/A230 1.83-2.22 across 36 samples).
Total RNA (12 uL per sample, 160-427 ng/uL) was submitted to Azenta Life Sciences (project 30-1251841615) for standard bulk poly(A) RNA-Seq library preparation. Illumina 2x150 bp paired-end, ~25-35 M reads/sample. (Exact kit and stranded chemistry to be confirmed with Azenta; likely NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.)

treatment_protocol: On 2025-09-30, cells were transfected with one of four ASOs (ASO2 non-targeting control, ASO43 SNCA-dIRE-selective, ASO550 SNCA-dIRE-selective from Biospring; ASO387 SNCA-IRE-selective from IDT) at 0.2 uM, 2 uM, or 10 uM final concentration in the well. ASO stocks were pre-diluted to 2 mM in PBS, then serially diluted in water. For each transfection, 5.5 uL of 100x ASO in Opti-MEM (Gibco 31985062) and 1.5 uL Lipofectamine RNAiMAX (Thermo Fisher 13778150) in Opti-MEM were mixed 1:1, incubated 5 min at RT, and 50 uL of the ASO/lipid complex added dropwise to 500 uL of medium per well. n=3 biological replicates per (ASO x dose) condition. Cell pellets were collected 3 days post-transfection (2025-10-03) using Accutase, centrifuged at 500 x g / 5 min / 4 C, and stored at -80 C.

value: melanoma (metastatic melanoma-derived)

value: wild type

value: Non-targeting control ASO (ASO0002, Biospring); transfected with Lipofectamine RNAiMAX in Opti-MEM; 3-day incubation

tag: dose

value: 10 uM

tag: replicate


title: BC375 5hmC_Seal


title: EED-WT EGFR ON tumor 1533_1

city: Boston

description:
Library name: CDP_1533_1
CDP_1533_1

value: Lung tumor


title: T47D DDR1 knockdown (replicate 1)

description: Library name: T47D DDR1 knockdown (replicate 1)


title: BC386 5hmC_Seal


title: BC374 5hmC_Seal


title: EED-WT EGFR OFF tumor 1597_2

description:
Library name: CDN_1597_2
CDN_1597_2


title: EED-WT EGFR ON tumor 1525_1

description:
Library name: CDP_1525_1
CDP_1525_1


title: BC373 5hmC_Seal


title: Vascular cells, Alzheimer's disease, Donor 12

first: Sudeshna

last: Das

address: 65 Landsdowne St

institute: MGH

description: Library name: H129

source_name: inferior temporal gyrus

value: inferior temporal gyrus

value: brain vascular cells

tag: age

tag: Sex

value: F

value: AD Progression


title: HCD_530_109_rN

city: Atlanta

data_processing:
Raw sequencing reads were mapped to the hg38 version of the mouse genome using STAR and the GENCODE v27 reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: hg38
Supplementary files format and content: tab delimited text file of RPKM normalized read counts for each gene

extract_protocol:
5,000 cells were FACS sorted into RLT + 1%BME and snap frozen using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

tag: tissue

value: blood

tag: patient id

value: rN

tag: disease

value: HC

value: Caucasian


description: Library name: T47D DDR1 knockdown control (replicate 3)

tag: cell type

value: Control


title: EED-WT EGFR ON tumor 1520_1

description:
Library name: CDP_1520_1
CDP_1520_1


title: BC372 5hmC_Seal

value: Plasma

value: EA

value: MM

value: circulating cell-free DNA (cfDNA)


title: BC371 5hmC_Seal

value: AA


title: HCD_1176_1842_rN

tag: sledai

tag: race


title: BC367 5hmC_Seal


description: Library name: T47D DDR1 knockdown control (replicate 2)

value: Breast

tag: treatment


title: 1344 overexpressing WT EED rep2

description:
Library name: EED_WT_1344_r2
WT_1344_r2

source_name: 1344 EED-Mutant LUAD RPR2 cell line

value: 1344 EED-Mutant LUAD RPR2 cell line

value: LUAD cell line

tag: genotype


title: BC358 5hmC_Seal


description: Library name: T47D DDR1 knockdown control (replicate 1)

tag: cell line


title: BC357 5hmC_Seal


title: 1344 overexpressing WT EED rep1

description:
Library name: EED_WT_1344_r1
WT_1344_r1


title: SLE.2900.3328.rN

value: SLE

tag: batch

tag: sorting markers


title: BC356 5hmC_Seal

tag: population

tag: diagnosis


title: Human keratinocytes from female donor #3, 24h Ca2+ treatment

first: Anna

last: Mandinova

address: Charlestown Navy Yard Building 149, 149 13th Street

institute: Massachusetts General Hospital

description: Library name: S12

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
BAM files were generated as a result of this step. Below are the statistics of mapping the reads to the reference genome.
Assembly: GRCh38
Supplementary files format and content: counts

source_name: Skin

growth_protocol: Human primary keratinocytes were cultured in K-SFM supplemented with 30ug/ml BPE and 0.3ng/ml EGF with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from cells using RNeasy Mini Kit (Qiagen).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using the manufacturer's instructions (NEB). The sequencing library was validated on the Agilent TapeStation (Agilent Technologies), and quantified by using Qubit 2.0 Fluorometer (Invitrogen) as well as by quantitative PCR (KAPA Biosystems).

treatment_protocol: For differentiation, keratinocytes at a confluency of 50–60% were treated with 1.5 mM CaCl2 (C1016, Sigma-Aldrich) for 2, 6 or 24 hours.

value: Skin

value: Primary human keratinocytes

value: Epithelial cells

value: Differentiation with Ca2+


title: CC4123R

description: Library name: Sample 7_OE_2

value: Liver

value: ASK1+hep (OE)

value: 7w HFD


title: BC355 5hmC_Seal

tag: molecule


title: BC354 5hmC_Seal


title: BC353 5hmC_Seal


title: Human keratinocytes from female donor #3, 6h Ca2+ treatment

description: Library name: S11


description: Library name: IGROV1 DARPP-32 knockdown control (replicate 2)

value: Ovarian

value: Control


title: BC352 5hmC_Seal

value: Plasma

value: EA


title: BC351 5hmC_Seal

value: MM

value: circulating cell-free DNA (cfDNA)


title: 1344 overexpressing inactive form of EED rep2

description:
Library name: EED_MT_1344_r2
MT_1344_r2


title: BC350 5hmC_Seal

value: AA


title: Human keranitocytes from female donor #3, untreated

description: Library name: S9

value: Untreated


title: BC349 5hmC_Seal


title: 1344 overexpressing inactive form of EED rep1

description:
Library name: EED_MT_1344_r1
MT_1344_r1

value: 1344 EED-Mutant LUAD RPR2 cell line

value: LUAD cell line


title: Human keratinocytes from female donor #2, 24h Ca2+ treatment

description: Library name: S8

value: Skin


title: BC347 5hmC_Seal


title: BC346 5hmC_Seal


title: Human keratinocytes from female donor #2, 6h Ca2+ treatment

description: Library name: S7

value: Primary human keratinocytes


title: BC345 5hmC_Seal


title: 1339 overexpressing inactive form of EED rep1

description:
Library name: EED_MT_1339_r1
MT_1339_r1

source_name: 1339 EED-Mutant LUAD RPR2 cell line

value: 1339 EED-Mutant LUAD RPR2 cell line


title: BC344 5hmC_Seal


title: Human keratinocytes from female donor #2, 2h Ca2+ treatment

description: Library name: S6

value: Epithelial cells

value: Differentiation with Ca2+


title: BC343 5hmC_Seal


title: 1014 Eed sg2 rep2

description:
Library name: Eedsg2_1014_rep2
B_e2_un_2

value: SCLC cell line


title: Human keratinocytes from female donor #2, untreated

description: Library name: S5


title: BC341 5hmC_Seal


title: BC340 5hmC_Seal


title: 1014 Eed sg2 rep1

description:
Library name: Eedsg2_1014_rep1
B_e2_un_1


title: Human keratinocytes from female donor #1, 24h Ca2+ treatment

description: Library name: S4


title: 1014 Eed sg1 rep2

description:
Library name: Eedsg1_1014_rep2
B_e1_un_2


title: BC338 5hmC_Seal


title: BC337 5hmC_Seal


title: Human keratinocytes from female donor #1, 6h Ca2+ treatment

description: Library name: S3


title: BC336 5hmC_Seal


title: BC335 5hmC_Seal


title: 1014 sgControl rep2

description:
Library name: sgControl_1014_rep2
B_C0111_un_2


title: BC334 5hmC_Seal


title: Human keratinocytes from female donor #1, untreated

description: Library name: S1


title: BC333 5hmC_Seal


title: 1014 sgControl rep1

description:
Library name: sgControl_1014_rep1
B_C0111_un_1


title: BC332 5hmC_Seal


title: Human keratinocytes from male donor #3, 24h Ca2+ treatment

description: Library name: D3-24


title: BC380 5hmC_Seal


title: BC331 5hmC_Seal


title: 1014 Eed sg1 rep1

description:
Library name: Eedsg1_1014_rep1
B_e1_un_1


title: EED Mutant tumor #1261

description:
Library name: EED_Mutant_1261
E_1261_P

value: Lung tumor


title: BC330 5hmC_Seal


title: Human keratinocytes from male donor #3, 6h Ca2+ treatment

description: Library name: D3-6


title: BC329 5hmC_Seal


title: EED Mutant tumor #1260_4

description:
Library name: EED_Mutant_1260_4
E_1260_P_4


title: BC328 5hmC_Seal


title: BC327 5hmC_Seal


title: Human keratinocytes from male donor #3, 2h Ca2+ treatment

description: Library name: D3-2


title: EED Mutant tumor #1260_2

description:
Library name: EED_Mutant_1260_2
E_1260_P_2


title: Human keratinocytes from female donor #1, 2h Ca2+ treatment

description: Library name: S2


title: BC326 5hmC_Seal


title: Human keranitocytes from male donor #3, untreated

description: Library name: D3-CTR


title: EED Mutant tumor #1260_1

description:
Library name: EED_Mutant_1260_1
E_1260_P_1


title: BC321 5hmC_Seal


title: Human keratinocytes from male donor #2, 24h Ca2+ treatment

description: Library name: D2-24


title: BC320 5hmC_Seal


title: 1339 overexpressing WT EED rep2

description:
Library name: EED_WT_1339_r2
WT_1339_r2


title: EED Mutant tumor #1257

description:
Library name: EED_Mutant_1257
E_1257_P_1


title: BC318 5hmC_Seal


title: Human keratinocytes from male donor #2, 6h Ca2+ treatment

description: Library name: D2-6


title: 1339 overexpressing WT EED rep1

description:
Library name: EED_WT_1339_r1
WT_1339_r1


title: BC317 5hmC_Seal


title: Human keratinocytes from female donor #3, 2h Ca2+ treatment

description: Library name: S10


title: EED Mutant tumor #1256

description:
Library name: EED_Mutant_1256
E_1256_P


title: BC316 5hmC_Seal


title: Human keratinocytes from male donor #2, 2h Ca2+ treatment

description: Library name: D2-2


title: BC348 5hmC_Seal


title: EED Mutant tumor #1254

description:
Library name: EED_Mutant_1254
E_1254_P


title: 1339 overexpressing inactive form of EED rep2

description:
Library name: EED_MT_1339_r2
MT_1339_r2


title: BC314 5hmC_Seal


title: BC315 5hmC_Seal


title: Human keratinocytes from male donor #2, untreated

description: Library name: D2-CTR


title: BC313 5hmC_Seal


title: EED WT tumor #1267_2

description:
Library name: EED_WT_1267_2
C_1267_P_2


title: BC312 5hmC_Seal


title: Human keratinocytes from male donor #1, 24h Ca2+ treatment

description: Library name: D1-24


title: EED WT tumor #1267_1

description:
Library name: EED_WT_1267_1
C_1267_P_1


title: BC310 5hmC_Seal


title: BC309 5hmC_Seal


title: BC308 5hmC_Seal


title: Human keratinocytes from male donor #1, 6h Ca2+ treatment

description: Library name: D1-6


title: EED WT tumor #1262

description:
Library name: EED_WT_1262
C_1262_P


title: BC307 5hmC_Seal


title: BC342 5hmC_Seal


title: BC306 5hmC_Seal


title: EED WT tumor #1198

description:
Library name: EED_WT_1198
C_1198_P


title: BC305 5hmC_Seal


title: Human keratinocytes from male donor #1, 2h Ca2+ treatment

description: Library name: D1-2


title: Human keratinocytes from male donor #1, untreated

description: Library name: D1-CTR