title: EED-Mutant RPR2 LUAD tumor 1420

description: Library name: EED_mutant_RPR2_LUAD_1420

data_processing:
Cell ranger version 6.0.2 pipeline (10× Genomics) was used to align sequencing data to the custom mouse reference genome and generate the gene-level counts matrix.
Assembly: Custom reference genome was established by adding EGFP and Cas9 sequence to the mouse genome (mm10-2020-A).
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: Tumors were harvested at necropsy and were flash-frozen

extract_protocol:
Briefly, 3-4 month old male and female homozygous BL6J LSL-Cas9 mice (Jackson No. 026175) were intratracheally injected with EED-Mutant or EED-WT adenovirus. Once mice became symptomatic from their tumors, mice were euthanized and lung tumors dissected and finely minced mechanically using a razor blade and then enzymatically digested with Mouse Tumor Dissociation Kit (Miltenyi Biotec, #130-096-730) following the manufacturer’s instruction. Briefly, minced tumor tissue was transferred to a gentleMACS C Tube containing enzyme mix prepared with 20% of Enzyme R option to preserve cell surface epitopes. Dissociation using the gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec, #130-096-427) was performed using the 37C_m_TDK_2 gentleMACS Program. The single cell suspensions were resuspended in RPMI containing 10% FBS and subsequently passed through a 70 μm Cell Strainer (Greiner, #542070) and centrifuged at 300 x g for 3 min followed by 2 washes with 0.04% UltraPure Bovine Serum Albumin (Invitrogen, AM2616) in DPBS. Finally, dissociated cells were resuspended in DPBS with 0.04% UltraPure BSA and cell counts were measured with a Vi-CELL XR Cell Viability Analyzer (Beckman Coulter). Cells were then diluted in 0.04% BSA/DPBS at a cell concentration of 1000 cells/µL. About 16,000 cells were loaded onto a 10× Genomics ChromiumTM instrument (10× Genomics) according to the manufacturer’s instructions.
The scRNA-seq libraries were processed using Chromium Next GEM Single Cell 5' Kit v2 kit (10× Genomics). Quality controls for amplified cDNA libraries and final sequencing libraries were performed using Bioanalyzer High Sensitivity DNA Kit (Agilent). The sequencing libraries for scRNAseq were normalized to 4 nM concentration and pooled. The pooled sequencing libraries were sequenced on Illumina NovaSeq S4 300 cycle platform. The sequencing parameters used were: Read 1 of 26bp, Read 2 of 90bp, Index 1 of 10bp and Index 2 of 10bp.


title: BC303 5hmC_Seal

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

library_source: genomic

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

molecule: genomic DNA

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

tag: population

value: EA

tag: diagnosis

value: MM

tag: molecule

value: circulating cell-free DNA (cfDNA)


title: BC304 5hmC_Seal


title: BC339 5hmC_Seal


title: MDA-MB-231 shMAFF 3

city: Headington

first: Eui Jung

last: Moon

address: Old Road Campus Research Building, Roosevelt Drive

department: Department of Oncology

country: United Kingdom

institute: University of Oxford

description: Library name: MAFF_CTL3

library_source: transcriptomic

data_processing:
Data processing and sequence alignment were performedbyNovogene UK. The sequencing reads/raw reads were filtered 1) to remove reads with adapter contamination, 2) to remove reads when uncertain nucleotides constitute more than 10 per cent of either read (N > 10%) and 3) to remove reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50 per cent of the read. Alignments were performed with HISAT2 to the reference.
Assembly: Paired-end reads were mapped to GRCh38 genome by Novogene UK.
Supplementary files format and content: CSV file with FPKM values

molecule: total RNA

growth_protocol: MDA-MB-231 cells were purchased from ATCC and maintained at 37C in a humidified incubator with 5% CO2 in DMEM supplemented with 10% fetal bovine serum (F7524, Sigma Aldrich) and 1% antibiotic/antimycotic (15240-062, Gibco). Cells were routinely tested for mycoplasma.

extract_protocol:
RNA was collected from MDA-MB-231 with MAFF knockdown by using Rneasy kit (Qiagen). RNA samples were sent to Novogene (Cambridge, UK) for library preparation and sequencing. Sequencing was performed by Novoseq 6000.
Library construction was performedbyNovogene UK using polyA enrichment library preparation procedure.

tag: cell line

tag: cell type

value: a human breast cancer

tag: genotype

value: MAFF knockdown

tag: treatment


title: BC302 5hmC_Seal


title: SLE.2891.420.T1T2

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

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

molecule: polyA RNA

source_name: blood

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

tag: patient id

tag: disease

value: SLE

tag: sledai

tag: Sex

value: F

tag: race

value: AA

tag: batch

tag: sorting markers


title: EED-Mutant RPR2 LUAD tumor 1408

city: Boston

first: Yixiang

last: Li

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: Library name: EED_mutant_RPR2_LUAD_1408

library_source: transcriptomic single cell

organism: Mus musculus

source_name: Lung tumor

value: Lung tumor


title: BC301 5hmC_Seal


title: BC300 5hmC_Seal


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

city: Cambridge

first: Sudeshna

last: Das

state: Massachusetts

address: 65 Landsdowne St

institute: MGH

description: Library name: H85

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

value: M

value: AD Progression


title: MDA-MB-231 shMAFF 2

description: Library name: MAFF_CTL2


title: BC299 5hmC_Seal


title: EED-Mutant RPR2 LUAD tumor 1349

description: Library name: EED_mutant_RPR2_LUAD_1349


title: MDA-MB-231 shMAFF 1

description: Library name: MAFF_CTL1


title: BC297 5hmC_Seal


title: BC296 5hmC_Seal


title: EED-Mutant RPR2 LUAD tumor 1261

description: Library name: EED_mutant_RPR2_LUAD_1261


title: HAM2Minus

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

description: Library name: HAM2Minus

data_processing:
Honeycomb BeeNet
Assembly: GRCh38.104
Supplementary files format and content: Transcript count matrices and cell QC in TSV format from BeeNet outputs

source_name: PBMC

extract_protocol:
Honeycomb scRNA isolation
scRNA

value: PBMC


title: CC4266R

city: Zurich

first: Stephan

last: Wueest

address: Lenggstrasse 30

country: Switzerland

institute: University Children's Hospital Zurich

description: Library name: Sample 4_WT_4

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

value: ASK1f/f (Control)

value: 7w HFD


title: BC293 5hmC_Seal

value: Plasma

value: EA

value: MM


title: EED-Mutant RPR2 LUAD tumor 1257

description: Library name: EED_mutant_RPR2_LUAD_1257


title: HAM2Exo

description: Library name: HAM2Exo

value: HTLV-I exosome treated


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

city: Shanghai

first: Tianci

last: Wang

address: NO. 800 Dongchuan Road

department: School of Biomedical Engineering

country: China

institute: Shanghai Jiao Tong University

description: Library name: Sample 4

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: BC291 5hmC_Seal

value: circulating cell-free DNA (cfDNA)


title: EED-Mutant RPR2 LUAD tumor 61_4

description: Library name: EED_mutant_RPR2_LUAD_61_4


title: BC290 5hmC_Seal


title: BC292 5hmC_Seal


title: HAM1Minus

description: Library name: HAM1Minus


title: BC289 5hmC_Seal


title: CC4124L

description: Library name: Sample 2_WT_2


title: SN4490R

description: Library name: Sample 1_WT_1


title: hypothalamic tissue from control #4 [Flox_04]

city: Tsukuba

first: Motohiro

last: Sekiya

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

data_processing:
The raw read counts were normalized with transcripts per million (TPM). The downstream pathway analyses were performed using integrated Differential Expression & Pathway analysis (iDEP) software 2.01
Assembly: mm10
Supplementary files format and content: BigWig

source_name: hypothalamus

growth_protocol: normal chow

extract_protocol:
Total RNA was isolated using Sepazol Reagent (Nacalai) .
The sequencing library was constructed with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) and sequencing was performed using NovaSeq 6000 (Illumina). The following procedures such as quality check of the raw paired-end reads, trimming, and alignment to the mm10 mouse reference genome were performed

treatment_protocol: overnight starvation

value: hypothalamus

value: wild type

value: ad libitum fed


title: BC288 5hmC_Seal


title: HAM1Exo

description: Library name: HAM1Exo


title: BC286 5hmC_Seal


title: BC284 5hmC_Seal


title: hypothalamic tissue from control #3 [Flox_03]


title: healthy control 2

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: HC2

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

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.
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

value: Peripheral blood

tag: disease state

value: healthy control


title: BC282 5hmC_Seal

tag: tissue


title: hypothalamic tissue from control #2 [Flox_02]


title: BC278 5hmC_Seal

tag: population


title: BC275 5hmC_Seal

value: AA

tag: diagnosis


title: BC276 5hmC_Seal

tag: molecule


title: BC274 5hmC_Seal


title: AC1Minus

description: Library name: AC1Minus

value: PBMC


title: hypothalamic tissue from POMC neuron-specific CtBP2 knockout #4 [PCKO_4]

value: knockout


title: BC273 5hmC_Seal


title: hypothalamic tissue from control #1 [Flox_01]


title: AC1Exo

description: Library name: AC1Exo


title: BC272 5hmC_Seal


title: AC2Exo

description: Library name: AC2Exo


title: hypothalamic tissue from POMC neuron-specific CtBP2 knockout #3 [PCKO_3]


title: BC271 5hmC_Seal


title: LTL545 Apilimod 1424L

city: Ann Arbor

first: Arul

middle: M

last: Chinnaiyan

state: Michigan

address: 1500 E. Medical Center Dr

institute: University of Michigan

description:
Library name: SI_32989
RiboErase

data_processing:
Xenograft FASTQs were processed using xengsort. Then, the human FASTQs were trimmed using BBDuk. Transcripts were quantified by kallisto with human reference genome (GRCh38/hg38) and then summarized to obtain gene level counts and TPM.
Assembly: hg38
Supplementary files format and content: counts.tsv: Gene-level TPM counts obtained from kallisto.
Supplementary files format and content: tpm.tsv: Gene-level TPM values obtained from kallisto.

growth_protocol: 1. LTL331R-CL cells were maintained in modified RPMI-1640, supplemented with 1X ITS-G, 10 nM hydrocortisone, 10 nM beta-estradiol, extra 2mM Glutamax, and 5% FBS or 0.1% FBS overnight before treatment. 2. AR+ and NEPC tumors were maintained in SCID male mice. 3. NEPC tumors were maintained in SCID male mice.

extract_protocol:
Total RNA was extracted from cultured cells or tumor tissues using the RNeasy mini kit, following the manufacturer’s instructions. 1 μg of total RNA was used to construct the sequencing libraries.
For tumor samples, ribosomal RNA was depleted using the RiboErase selection kit (Kapa Biosystems, KK8561). For cell lines and other samples, polyadenylated transcripts were enriched using Sera-Mag Oligo(dT)-Coated Magnetic Particles (GE Healthcare Life Sciences, 38152103010150). RNA libraries were constructed using the KAPA RNA HyperPrep Kit (Roche Sequencing, KK8541) from 800 ng of total RNA. Following rRNA depletion and RNA fragmentation (200-300 bp), double-stranded cDNA was synthesized, ligated with NEB adapters, and PCR-amplified using KAPA HiFi HotStart ReadyMix and NEB dual-index barcodes.

treatment_protocol: 1. NEPC cells were treated with DMSO, ESK981, Apilimod, or PIK5-33d for 6 hours. 2. No treatment for basaline comparison. 3. NEPC tumor-bearing mice were treated with Vehicle, ESK981, or Apilimod for 5 days, once per day.

value: NEPC tumors

value: Apilimod


title: BC270 5hmC_Seal

value: Plasma


title: hypothalamic tissue from POMC neuron-specific CtBP2 knockout #2 [PCKO_2]


title: BC269 5hmC_Seal


title: BC267 5hmC_Seal

value: EA


title: LTL545 Apilimod 1424R

description:
Library name: SI_32988
RiboErase


title: BC268 5hmC_Seal

value: MM


title: hypothalamic tissue from POMC neuron-specific CtBP2 knockout #1 [PCKO_1]


title: LTL545 Apilimod 1412L

description:
Library name: SI_32987
RiboErase


title: hypothalamic tissue from control #4 [Flox_4]

treatment_protocol: ad libitum


title: BC266 5hmC_Seal


title: BC265 5hmC_Seal


title: LTL545 Apilimod 1412R

description:
Library name: SI_32986
RiboErase


title: BC264 5hmC_Seal


title: hypothalamic tissue from control #3 [Flox_3]


title: BC263 5hmC_Seal


title: LTL545 ESK981 1421L

description:
Library name: SI_32985
RiboErase


title: BC262 5hmC_Seal


title: hypothalamic tissue from control #2 [Flox_2]


title: BC241 5hmC_Seal


title: LTL545 ESK981 1421R

description:
Library name: SI_32984
RiboErase


title: BC240 5hmC_Seal


title: BC237 5hmC_Seal


title: BC238 5hmC_Seal


title: BC236 5hmC_Seal


title: hypothalamic tissue from control #1 [Flox_1]


title: hypothalamic tissue from AgRP neuron-specific CtBP2 knockout #4 [ACKO_4]


title: LTL545 ESK981 1408R

description:
Library name: SI_32982
RiboErase


title: BC235 5hmC_Seal


title: hypothalamic tissue from AgRP neuron-specific CtBP2 knockout #3 [ACKO_3]


title: AC2Minus

description: Library name: AC2Minus


title: BC234 5hmC_Seal


title: LTL545 Vehicle 1425L

description:
Library name: SI_32981
RiboErase

value: Vehicle


title: LTL545 ESK981 1408L

description:
Library name: SI_32983
RiboErase


title: BC231 5hmC_Seal


title: BC230 5hmC_Seal


title: hypothalamic tissue from AgRP neuron-specific CtBP2 knockout #2 [ACKO_2]


title: LTL545 Vehicle 1425R

description:
Library name: SI_32980
RiboErase


title: hypothalamic tissue from AgRP neuron-specific CtBP2 knockout #1 [ACKO_1]


title: LTL352 Apilimod 1497L

description:
Library name: SI_32536
RiboErase


title: BC226 5hmC_Seal


title: BC227 5hmC_Seal


title: LTL352 Apilimod 1497R

description:
Library name: SI_32535
RiboErase


title: normal mice hypothalamic tissue, control IgG ChIP

data_processing:
After trimming the low quality bases and adapter sequences by Trimmomatic software (version 0.38), the reads were aligned to the mouse reference genome mm10 using Bowtie2 (version 2.3.4.2), and 33,743,782 final reads were detected. Subsequently, the binding peaks were obtained by model-based analysis of ChIP-seq (MACS2, version 2.1.2).
Assembly: mm10
Supplementary files format and content: BigWig

extract_protocol:
Tissues were washed and fixed in 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched by adding glycine to a final concentration of 125 mM. Thereafter, ChIP was carried out using Magna ChIP HiSens Chromatin Immunoprecipitation system (EMD Millipore). Chromatin shearing was achieved by micrococcal nuclease (Cell Signaling) and sonication (Bronson sonifier 250). Chromatin was immunoprecipitated with either control IgG (Cell Signaling) or anti-CtBP2 (Active Motif, 61261).
The sequencing library was constructed with NEBNext Ultra II DNA Library Prep Kit (New England Biolabs). Paired-end sequencing was performed with an Illumina NovaSeq6000 system.

tag: antibody

value: control IgG (Cell Signaling)


title: BC225 5hmC_Seal


title: BC223 5hmC_Seal


title: BC222 5hmC_Seal


title: normal mice hypothalamic tissue, CtBP2 ChIP

value: anti-CtBP2 (Active Motif, 61261)


title: LTL352 Apilimod 1479L

description:
Library name: SI_32534
RiboErase

tag: cell type


title: BC221 5hmC_Seal

value: circulating cell-free DNA (cfDNA)


title: BC224 5hmC_Seal


title: D5-UV skin, CTRL, rep2

first: Khanh

last: Huynh

address: Winterthurerstrasse 190

institute: University of Zurich

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.2
Assembly: mm39 assembly (release M26 [2021-04-20]), plus the transgene tdTomato
Supplementary files format and content: the processed files consist of a compressed folder containing the filtered "barcodes.tsv.gz", "features.tsv.gz" and "matrix.mtax.gz" files for each sample

source_name: skin

extract_protocol:
2 cm x 2 cm tissue of day-5 irradiated skin was collected. Skin tissue was minced into small pieces, then digested with 10 ml of DMEM/F12 without phenol-red (Gibco, #21041025) containing 1.5 mg/ml collagenase I (Worthington, #LS0004194), 10% FBS, 100 U/ml Penicillin-Streptomycin (Gibco, #15140122) and 1:1000 Protector RNase Inhibitor (Roche, #3335399001) 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 (Gibco, #25200-256) and 2 mM EDTA (Thermo Fisher Scientific, #AM9261) for 5 minutes at 37°C with agitation. Trypsin was inactivated and the remaining skin pieces were passed three times through an 18G needle (Sterican, #4665120) and five times through a 21G needle (Sterican, #304432). 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 (STEMCELL Technologies, #17899), according to manufacturer’s instructions.
Single cell libraries were generated using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics).

value: skin

tag: genotype

value: CTRL


title: BC323 5hmC_Seal


title: BC220 5hmC_Seal


title: LTL352 Apilimod 1479R

description:
Library name: SI_32533
RiboErase

tag: treatment


title: BC219 5hmC_Seal


title: D5-UV skin, Glia cKO, rep2

description: 10x Genomics

value: Glia cKO


title: BC218 5hmC_Seal


title: LTL352 ESK981 1491L

description:
Library name: SI_32532
RiboErase


title: EED-WT EGFR OFF tumor 1535

description:
Library name: CDN_1535
CDN_1535

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

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: BC216 5hmC_Seal


title: D5-UV skin, CTRL, rep1

description: 10x Genomics


title: BC215 5hmC_Seal


title: LTL352 ESK981 1491R

description:
Library name: SI_32531
RiboErase


title: D5-UV skin, Glia cKO, rep1

description: 10x Genomics


title: BC213 5hmC_Seal


title: LTL352 ESK981 1483L

description:
Library name: SI_32530
RiboErase


title: BC214 5hmC_Seal


title: BC210 5hmC_Seal


title: Ctsk positive, clcn7-/-, rep3

first: Katrin

last: Henke

address: 21 Ortho Lane

department: Orthopaedics

description:
Library name: clcn7-ctsk-pos-3
column name in DESeq2_output_clcn7_vs_wt.csv: clcn7mut_3

data_processing:
low-quality bases and adapter sequences were trimmed using TrimGalore
Trimmed reads were aligned to the GRCz11 version of the zebrafish genome using STAR (2.7.0a). For gene annotations an updated annotation file was retrieved from the Lawson Lab website (v4.3.2.gtf, Lawson, Li et al. 2020).
Transcript counts were generated with HTSeq (0.9.1) and differential gene expression analysis was performed using the DESeq2 option on the iDEP2.01 website (Love, Huber and Anders 2014, Anders, Pyl and Huber 2015, Ge, Son and Yao 2018).
Assembly: GRCz11
Supplementary files format and content: tab delimited text files with raw read counts generated with HTSeq, first column contains the Lawson lab gene IDs; second column contains gene names and third column the read counts
Supplementary files format and content: csv file with DESeq2 output (log2fold change, padj, normalized counts per sample)

organism: Danio rerio

source_name: skeletal tissue

growth_protocol: zebrafish were raised under standard conditions

extract_protocol:
Cell isolation and Fluorescent Activated Cell Sorting (FACS) was done as described before (Caetano-Lopes, Henke et al. 2020). Tissues were digested by vigorous shaking at 30°C in dissociation solution [0.21% trypsin-EDTA (Invitrogen), 16 mg/ml collagenase from Clostridium histolyticum, type IA (Sigma)] for 15 min. The cell suspension was removed and filtered through a 40 µm nylon mesh cell strainer. Fresh dissociation solution was added, and the remaining tissue was digested by vigorous shaking at 30°C for 15 min. The cell suspension was washed with Dulbecco's Modified Eagle Media (DMEM) supplemented with 10% of fetal bovine serum (FBS, Invitrogen) and filtered through a 40 µm nylon mesh. The filtered cell suspension was layered on Histopaque-1077 (Sigma) at a 2:1 ratio and centrifuged at 400 g, without acceleration or break, for 30 min in a swinging bucket rotor. Both the ring and the pellet were collected in PBS+2%FBS. Immediately prior to sorting, cells were stained with 1x SYTOX Blue (Invitrogen). After doublet exclusion, live cells were identified by the absence of SYTOX Blue staining. DsRed-positive cells were separated on an FACSAria II cell sorter (BD Biosciences) using an 85 µm nozzle at a flow rate of ∼2000 events/s. 5000 DsRed positive cells per fish were collected and cells from 2 fish were combined for each biological replicate. Sorted cells were collected directly in RNA lysis buffer and RNA was extracted using the Qiagen RNeasy Micro kit.
Ultra-low input library preparation and sequencing was performed at Genewiz/Azenta

value: skeletal tissue

value: ctsk positive osteoclast

tag: developmental stage


title: LTL352 ESK981 1483R

description:
Library name: SI_32529
RiboErase


title: BC212 5hmC_Seal

value: AA


title: Ctsk positive, clcn7-/-, rep2

description:
Library name: clcn7-ctsk-pos-2
column name in DESeq2_output_clcn7_vs_wt.csv: clcn7mut_2


title: BC208 5hmC_Seal


title: BC209 5hmC_Seal


title: Ctsk positive, clcn7-/-, rep1

description:
Library name: clcn7-ctsk-pos-1
column name in DESeq2_output_clcn7_vs_wt.csv: clcn7mut_1


title: LTL352 Vehicle 1484L

description:
Library name: SI_32528
RiboErase


title: LTL352 Vehicle 1484R

description:
Library name: SI_32527
RiboErase


title: BC204 5hmC_Seal


title: BC203 5hmC_Seal


title: BC205 5hmC_Seal


title: Ctsk positive, WT, rep3

description:
Library name: wt-ctsk-pos-3
column name in DESeq2_output_clcn7_vs_wt.csv: wt_3

value: WT


title: BC202 5hmC_Seal


title: LTL352 Vehicle 1478L

description:
Library name: SI_32526
RiboErase

value: NEPC tumors


title: BC201 5hmC_Seal


title: Ctsk positive, WT, rep2

description:
Library name: wt-ctsk-pos-2
column name in DESeq2_output_clcn7_vs_wt.csv: wt_2


title: BC200 5hmC_Seal


title: BC199 5hmC_Seal


title: Ctsk positive, WT, rep1

description:
Library name: wt-ctsk-pos-1
column name in DESeq2_output_clcn7_vs_wt.csv: wt_1


title: BC198 5hmC_Seal


title: NCI-H660 1332L

description:
Library name: SI_36987
RiboErase


title: BC196 5hmC_Seal


title: LTL352 Vehicle 1478R

description:
Library name: SI_32525
RiboErase


title: ECA109_shIGF2BP2_rep3

city: Guangzhou

first: XIAOHANG

last: GAO

state: Guangdong

address: the south of Xianlie Road

institute: Sun Yat-sen University Cancer Center

description:
Library name: SH3
Bulk RNA-seq of ECA109 cells transfected with IGF2BP2 shRNA, biological replicate 3.

data_processing:
Raw reads were processed to remove reads containing adapter sequences, reads with more than 10% ambiguous bases, and low-quality reads with more than 50% bases having Q <= 5.
Clean reads were used for downstream transcriptomic analysis.
Differential expression and pathway enrichment analyses were performed to identify transcriptomic changes associated with IGF2BP2 knockdown.
Assembly: GRCh38
Supplementary files format and content: Processed expression matrix files are being prepared and will include gene-level raw counts and normalized expression values for all six samples.

growth_protocol: ECA109 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted from ECA109 cells. RNA concentration and purity were assessed before library preparation.
RNA-seq libraries were constructed according to the manufacturer's instructions. Qualified libraries were pooled, circularized, amplified to generate DNA nanoballs, loaded onto the flow cell, and sequenced on the DNBSEQ-T7 platform.

treatment_protocol: ECA109 cells were stably transfected with IGF2BP2 shRNA or negative-control shRNA. Three biological replicates were prepared for each group.

tag: cell line

value: esophageal squamous cell carcinoma cell line

value: IGF2BP2 shRNA


title: BC195 5hmC_Seal

value: Plasma

value: EA


title: ECA109_shIGF2BP2_rep2

description:
Library name: SH2
Bulk RNA-seq of ECA109 cells transfected with IGF2BP2 shRNA, biological replicate 2.


title: NCI-H660 1331L

description:
Library name: SI_36985
RiboErase

value: Vehicle


title: BC193 5hmC_Seal

value: MM


title: BC192 5hmC_Seal


title: NCI-H660 1332R

description:
Library name: SI_36986
RiboErase


title: BC191 5hmC_Seal


title: ECA109_shIGF2BP2_rep1

description:
Library name: SH1
Bulk RNA-seq of ECA109 cells transfected with IGF2BP2 shRNA, biological replicate 1.


title: BC194 5hmC_Seal


title: BC190 5hmC_Seal


title: ECA109_shNC_rep3

description:
Library name: NC3
Bulk RNA-seq of ECA109 cells transfected with negative-control shRNA, biological replicate 3.

value: negative-control shRNA


title: BC189 5hmC_Seal

value: circulating cell-free DNA (cfDNA)


title: BC188 5hmC_Seal


title: LTL331R 1577L

description:
Library name: SI_36993
RiboErase


title: NCI-H660 1331R

description:
Library name: SI_36984
RiboErase


title: BC185 5hmC_Seal


title: ECA109_shNC_rep2

description:
Library name: NC2
Bulk RNA-seq of ECA109 cells transfected with negative-control shRNA, biological replicate 2.


title: BC184 5hmC_Seal


title: LTL331R 1577R

description:
Library name: SI_36992
RiboErase


title: BC183 5hmC_Seal


title: ECA109_shNC_rep1

description:
Library name: NC1
Bulk RNA-seq of ECA109 cells transfected with negative-control shRNA, biological replicate 1.


title: LTL331R 1572L

description:
Library name: SI_36991
RiboErase


title: BC182 5hmC_Seal


title: BC180 5hmC_Seal


title: BC181 5hmC_Seal


title: LTL331R 1572R

description:
Library name: SI_36990
RiboErase


title: SK-MEL-28, H2AZ, rep3

city: Shenzhen

first: Changbin

last: Sun

address: Dapeng

department: Agricultural Genomics Institute at Shenzhen

institute: Chinese Academy of Agricultural Sciences

data_processing:
Sequencing reads from mChIP-seq were demultiplexed to samples by the barcodes in the 5’ end of Read2 using fastq-multx (version 1.4.2) (https://github.com/brwnj/fastq-multx) with a mismatch setting of 0. Then, reads of each sample with adapter contamination and low quality were trimmed and filtered using fastp with parameters as -f 10 -t 5 -F 30 -T 5 --complexity_threshold=30 –n_base_limit=5  --length_required 60 (version 0.23.2) and aligned to the human reference genomes hg38, mouse reference genome mm10, or budding yeast genome sacCer3 using bowtie2 (version 2.2.5) with default parameters. Uniquely mapping reads with mapping quality more than 30 were kept using samtools (version 1.9) and duplicates were removed using picard MarkDuplicates (v2.26.10, http://broadinstitute.github.io/picard).
Assembly: BW25113 genome for E. coli, sacCer3 genome for yeast, GRCh38 genome for humans, mm10 genome for mice
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde at room temperature for 10 min and quenched by glycine with 0.125 M final concentration. sonicated using Covaris SE220 (75 W, 20% Duty factor, 1,000 cycles per burst) for 5 min at 4°C to obtain fragments with the peak size around 200 bp.
The tailing and ssDNA ligation method used to label sample chromatin, and then multiple barcoded samples were pooled and split for immunoprecipitation with relevant antibodies as standard ChIP-seq. After immunoprecipitation, the purified ChIPed DNA was resuspended in 18 µl of water and extended in an 40 µl reaction containing 1 × KAPA HiFi HotStart ReadyMix and 0.25 µM P7TruSeqHTRev at 98 for 30 sec and 63 °C for 5 min followed by purification with 1.2 × volume of SPRIselect™ beads. Then, the purified DNA was ligated to the second adapter in a 40 µl reaction (1× T4 DNA ligase buffer, 0.5 µM P5TruSeqHT/P5SPlint mixture (1:1), and 10 Weiss units of T4 DNA ligase) at 25 °C for 30 minutes and purified with 1.0 × volume of SPRIselect™ beads. Lastly, library was amplified in 50 μl of PCR reaction Mix containing eluted DNA, 0.5 μM of P5 index primer, 0.5 μM P7 index primers, and 25 μl of KAPA HiFi HotStart ReadyMix (2 ×) (Kapa Biosystems) for 12-16 cycles (each cycle with 20 s at 98°C, 30 s at 58°C, 1 min at 68°C). DNA of 200–700 bp was isolated using a double SPRIselect bead cleanup (0.6 × and 0.85 × volume).

value: Cutaneous melanoma

tag: chip antibody

value: H2A.Z (Abcam:#ab4174)


title: LTL610 1745L

description:
Library name: SI_36126
RiboErase


title: CCRF-CEM, H2AZ, rep3

source_name: CCRF-CEM

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia


title: BC178 5hmC_Seal


title: BC176 5hmC_Seal


title: LTL610 1745R

description:
Library name: SI_36125
RiboErase


title: BC179 5hmC_Seal


title: BC175 5hmC_Seal


title: K562, H2AZ, rep3

value: Chronic myeloid leukemia


title: MOLT-4, H2AZ, rep3

value: Adult T acute lymphoblastic leukemia


title: BC174 5hmC_Seal


title: BC171 5hmC_Seal

value: AA


title: BC170 5hmC_Seal


title: LTL610 1740R

description:
Library name: SI_36123
RiboErase


title: BC169 5hmC_Seal


title: LTL610 1320L

description:
Library name: SI_32993
RiboErase


title: BC166 5hmC_Seal


title: BC165 5hmC_Seal


title: SK-OV-3, H2AZ, rep3

value: Ovarian serous cystadenocarcinoma


title: SK-MEL-2, H2AZ, rep3

value: Melanoma


title: BC162 5hmC_Seal


title: LTL610 1320R

description:
Library name: SI_32992
RiboErase

value: NEPC tumors


title: BC161 5hmC_Seal


title: BC159 5hmC_Seal


title: BC158 5hmC_Seal


title: NCI-H522, H2AZ, rep3

value: Lung adenocarcinoma


title: LTL610 1307R

description:
Library name: SI_32990
RiboErase


title: NCI-H226, H2AZ, rep3

value: Pleural epithelioid mesothelioma


title: BC154 5hmC_Seal

value: Plasma

value: EA


title: LNCaP 537L

description:
Library name: SI_36712
RiboErase

source_name: LNCaP

value: LNCaP

value: AR+ tumors

value: Vehicle


title: BC152 5hmC_Seal

value: MM

value: circulating cell-free DNA (cfDNA)


title: MDA-MB-468, H2AZ, rep3

value: Breast adenocarcinoma

value: H2A.Z (Abcam:#ab4174)


title: BC156 5hmC_Seal


title: BC151 5hmC_Seal


title: T47D, H2AZ, rep3

value: Invasive breast carcinoma


title: BC150 5hmC_Seal


title: NCI-H460, H2AZ, rep3

value: Lung large cell carcinoma


title: CRPC VCaP 81R

description:
Library name: SI_36704
RiboErase

source_name: CRPC VCaP

value: CRPC VCaP


title: CRPC VCaP 81L

description:
Library name: SI_36705
RiboErase


title: BC143 5hmC_Seal


title: BC144 5hmC_Seal


title: A549, H2AZ, rep3


title: BC142 5hmC_Seal

value: AA


title: CRPC VCaP 79L

description:
Library name: SI_36703
RiboErase


title: BC141 5hmC_Seal


title: BC145 5hmC_Seal


title: NCI-H23, H2AZ, rep3


title: CRPC VCaP 79R

description:
Library name: SI_36702
RiboErase


title: BC139 5hmC_Seal


title: SNB19, H2AZ, rep3

value: Astrocytoma


title: BC138 5hmC_Seal


title: LTL331R-CL 0.1%FBS PIK5-33d 0.3µM 6h biol rep 2

description:
Library name: SI_36911
RiboErase

value: NEPC cells


title: BC137 5hmC_Seal


title: U251, H2AZ, rep3

value: Prostate carcinoma


title: BC135 5hmC_Seal


title: LTL331R-CL 0.1%FBS PIK5-33d 0.3µM 6h biol rep 1

description:
Library name: SI_36910
RiboErase


title: BC134 5hmC_Seal


title: LTL331R-CL 0.1%FBS Apilimod 1µM 6h biol rep 2

description:
Library name: SI_36909
RiboErase

value: Apilimod


title: LTL610 1740L

description:
Library name: SI_36124
RiboErase

value: NEPC tumors


title: RPMI-8226, H2AZ, rep3

value: Multiple myeloma


title: DU145, H2AZ, rep3


title: BC132 5hmC_Seal

value: Plasma

value: EA


title: BC131 5hmC_Seal


title: LTL331R-CL 0.1%FBS Apilimod 1µM 6h biol rep 1

description:
Library name: SI_36908
RiboErase


title: HCT116, H2AZ, rep3

value: Colon carcinoma


title: BC130 5hmC_Seal

value: MM


title: HL-60, H2AZ, rep3

value: Adult acute myeloid leukemia


title: LTL331R-CL 0.1%FBS ESK981 1µM 6h biol rep 2

description:
Library name: SI_36907
RiboErase


title: OVCAR-8, H2AZ, rep3

value: High grade ovarian serous adenocarcinoma


title: BC129 5hmC_Seal

value: circulating cell-free DNA (cfDNA)


title: BC146 5hmC_Seal


title: BC128 5hmC_Seal


title: LTL331R-CL 0.1%FBS ESK981 1µM 6h biol rep 1

description:
Library name: SI_36906
RiboErase


title: BC127 5hmC_Seal


title: PC-3, H2AZ, rep3

value: H2A.Z (Abcam:#ab4174)


title: BC126 5hmC_Seal


title: LNCaP 512L

description:
Library name: SI_36711
RiboErase

value: LNCaP

value: AR+ tumors

value: Vehicle


title: SW620, H2AZ, rep3

value: Colon adenocarcinoma


title: BC125 5hmC_Seal


title: LTL331R-CL 0.1%FBS DMSO 6h biol rep 1

description:
Library name: SI_36904
RiboErase

value: NEPC cells

value: DMSO


title: BC120 5hmC_Seal


title: BC124 5hmC_Seal


title: CCRF-CEM, H2AZ, rep2

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia


title: SK-MEL-28, H2AZ, rep2

value: Cutaneous melanoma


title: BC118 5hmC_Seal

value: Plasma

value: AA


title: LTL331R-CL 5%FBS PIK5-33d 0.3µM 6h biol rep 1

description:
Library name: SI_36902
RiboErase


title: BC117 5hmC_Seal


title: MOLT-4, H2AZ, rep2

value: Adult T acute lymphoblastic leukemia


title: LNCaP 512R

description:
Library name: SI_36710
RiboErase


title: LTL331R-CL 5%FBS Apilimod 1µM 6h biol rep 2

description:
Library name: SI_36901
RiboErase

value: Apilimod


title: BC115 5hmC_Seal

value: EA

value: MM


title: LTL331R-CL 5%FBS Apilimod 1µM 6h biol rep 1

description:
Library name: SI_36900
RiboErase


title: BC114 5hmC_Seal

value: circulating cell-free DNA (cfDNA)


title: BC113 5hmC_Seal


title: RPMI-8226, H2AZ, rep2

value: Multiple myeloma

value: H2A.Z (Abcam:#ab4174)


title: BC112 5hmC_Seal


title: LTL331R-CL 5%FBS ESK981 1µM 6h biol rep 2

description:
Library name: SI_36899
RiboErase


title: BC111 5hmC_Seal


title: BC110 5hmC_Seal


title: BC105 5hmC_Seal


title: SK-OV-3, H2AZ, rep2

value: Ovarian serous cystadenocarcinoma


title: BC104 5hmC_Seal


title: LTL331R-CL 5%FBS DMSO 6h biol rep 2

description:
Library name: SI_36897
RiboErase


title: BC102 5hmC_Seal


title: K562, H2AZ, rep2

value: Chronic myeloid leukemia


title: LTL331R-CL 5%FBS DMSO 6h biol rep 1

description:
Library name: SI_36896
RiboErase


title: BC103 5hmC_Seal


title: BC157 5hmC_Seal


title: BC101 5hmC_Seal


title: LTL610 1307L

description:
Library name: SI_32991
RiboErase

value: NEPC tumors

value: Vehicle


title: NCI-H522, H2AZ, rep2

value: Lung adenocarcinoma


title: BC155 5hmC_Seal


title: BC100 5hmC_Seal


title: SK-MEL-2, H2AZ, rep2

value: Melanoma


title: LTL331R-CL 5%FBS ESK981 1µM 6h biol rep 1

description:
Library name: SI_36898
RiboErase

value: NEPC cells


title: PCH84I-T4/IUGR

city: los angeles

first: Shubhamoy

last: Ghosh

state: CA

address: 650 Charles E Young  Dr East

department: Pediatrics

institute: University of California Los Angeles

description:
Library name: PCH84I-T4
Urine_countsT3nT4.txt

data_processing:
Raw reads obtained from sequencing were aligned to the human reference genome (hg38) using the STAR (v2.5.2b) software which retained unique alignments and those with up to 4 mismatches.
Read counts were obtained using featurecounts toll from subread package. Differential gene expressions were analyzed using DESeq2 (version v1.20.0) package in R.
Assembly: hg38
Supplementary files format and content: tab-delimited txt file includes raw counts for each samples

source_name: cell free RNA from Urine

growth_protocol: Urine samples were collected   in-person at three study visits during pregnancy and again at delivery

extract_protocol:
Urine samples were centrifuged immediately after collection at 16,000Xg for 10 min at 4°C to remove any residual debris and cells, aliquoted and stored at -80°C. Cell-free RNA was extracted from 4 ml of urine using the QIAmp MiniElute Virus Spin kit (Qiagen). Total RNA was quantified using the Qubit RNA HS Assay kit (Thermofisher Scientific) and RNA integrity verified using the Agilent High sensitivity RNA Screen Tape System (Agilent) on a 2200 TapeStation System (Agilent)
Ten µl of the extracted RNA (ranging from 2-4 ng of total RNA) was used to construct RNA-seq libraries with the NuGen Ovation SoLo RNA-Seq kit, along with the Human rRNA AnyDeplete kit (NuGen), following the manufacturer's instructions. The libraries were sequenced using 100 bp single-end reads on the HiSeq4000 System (Illumina).

value: cell free RNA from Urine

tag: trimester

value: Delivery

tag: study group

value: IUGR


title: BC81 5hmC_Seal

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

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


title: BC149 5hmC_Seal


title: NCI-H226, H2AZ, rep2

value: Pleural epithelioid mesothelioma


title: BC80 5hmC_Seal

value: EA


title: 786-O, H2AZ, rep3

value: Renal cell carcinoma


title: BC79 5hmC_Seal

value: MM

value: circulating cell-free DNA (cfDNA)


title: MDA-MB-468, H2AZ, rep2

value: Breast adenocarcinoma

value: H2A.Z (Abcam:#ab4174)


title: PSN78G-T4/IUGR

description:
Library name: PSN78G-T4
Urine_countsT3nT4.txt


title: PHC83M-T4/IUGR

description:
Library name: PHC83M-T4
Urine_countsT3nT4.txt


title: BC76 5hmC_Seal


title: BC78 5hmC_Seal


title: T47D, H2AZ, rep2

value: Invasive breast carcinoma


title: BC75 5hmC_Seal


title: PKK85B_T3/IUGR

description:
Library name: PKK85B_T3
Urine_countsT3nT4.txt

value: Third


title: BC74 5hmC_Seal


title: NCI-H460, H2AZ, rep2

value: Lung large cell carcinoma


title: PSN78G-T3/IUGR

description:
Library name: PSN78G-T3
Urine_countsT3nT4.txt


title: BC73 5hmC_Seal


title: BC140 5hmC_Seal


title: BC72 5hmC_Seal


title: 786-O, H2AZ, rep2


title: BC71 5hmC_Seal

value: AA


title: BC70 5hmC_Seal


title: HCT116, H2AZ, rep2

value: Colon carcinoma


title: PHC83M-T3/IUGR

description:
Library name: PHC83M-T3
Urine_countsT3nT4.txt


title: PCH84I-T3/IUGR

description:
Library name: PCH84I-T3
Urine_countsT3nT4.txt


title: A549, H2AZ, rep2

value: Lung adenocarcinoma


title: BC69 5hmC_Seal


title: BC136 5hmC_Seal


title: NCI-H23, H2AZ, rep2


title: BC68 5hmC_Seal


title: BC67 5hmC_Seal


title: PLH87K_T4/gHTN

description:
Library name: PLH87K_T4
Urine_countsT3nT4.txt

value: cell free RNA from Urine

value: gHTN


title: SNB19, H2AZ, rep2

value: Astrocytoma


title: A498, H2AZ, rep3


title: BC66 5hmC_Seal

value: Plasma


title: PTM93S-T4/gHTN

description:
Library name: PTM93S-T4
Urine_countsT3nT4.txt

value: Delivery


title: BC65 5hmC_Seal

value: EA


title: BC64 5hmC_Seal


title: BC133 5hmC_Seal


title: U251, H2AZ, rep2

value: Prostate carcinoma


title: BC63 5hmC_Seal

value: MM


title: BC62 5hmC_Seal

value: circulating cell-free DNA (cfDNA)


title: PPN84W-T4/gHTN

description:
Library name: PPN84W-T4
Urine_countsT3nT4.txt


title: A498, H2AZ, rep2

value: Renal cell carcinoma


title: PMM83E-T4/gHTN

description:
Library name: PMM83E-T4
Urine_countsT3nT4.txt


title: BC61 5hmC_Seal


title: BC59 5hmC_Seal


title: DU145, H2AZ, rep2

value: H2A.Z (Abcam:#ab4174)


title: PHR80H-T4/gHTN

description:
Library name: PHR80H-T4
Urine_countsT3nT4.txt


title: BC56 5hmC_Seal


title: HL-60, H2AZ, rep2

value: Adult acute myeloid leukemia


title: PDP82M-T4/gHTN

description:
Library name: PDP82M-T4
Urine_countsT3nT4.txt


title: BC55 5hmC_Seal


title: BC57 5hmC_Seal


title: BC54 5hmC_Seal


title: OVCAR-8, H2AZ, rep2

value: High grade ovarian serous adenocarcinoma


title: BC53 5hmC_Seal


title: PTM93S-T3/gHTN

description:
Library name: PTM93S-T3
Urine_countsT3nT4.txt

value: Third


title: BC52 5hmC_Seal

value: AA


title: PC-3, H2AZ, rep2


title: BC51 5hmC_Seal


title: BC50 5hmC_Seal


title: PSH87T-T3/gHTN

description:
Library name: PSH87T-T3
Urine_countsT3nT4.txt


title: SW620, H2AZ, rep2

value: Colon adenocarcinoma


title: LTL331R-CL 0.1%FBS DMSO 6h biol rep 2

description:
Library name: SI_36905
RiboErase

value: NEPC cells

value: DMSO


title: PPN84W-T3/gHTN

description:
Library name: PPN84W-T3
Urine_countsT3nT4.txt

value: cell free RNA from Urine

value: gHTN


title: BC49 5hmC_Seal

value: Plasma


title: BC47 5hmC_Seal


title: BC48 5hmC_Seal


title: CCRF-CEM, H3K4me1, rep2

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia


title: PJI84J-T3/gHTN

description:
Library name: PJI84J-T3
Urine_countsT3nT4.txt


title: BC46 5hmC_Seal

value: EA


title: SK-MEL-28, H3K4me1, rep2

value: Cutaneous melanoma


title: BC45 5hmC_Seal

value: MM

value: circulating cell-free DNA (cfDNA)


title: BC123 5hmC_Seal


title: BC44 5hmC_Seal


title: MOLT-4, H3K4me1, rep2

value: Adult T acute lymphoblastic leukemia


title: BC43 5hmC_Seal


title: PHR80H-T3/gHTN

description:
Library name: PHR80H-T3
Urine_countsT3nT4.txt


title: BC41 5hmC_Seal


title: PWZ84A_T4/PE

description:
Library name: PWZ84A_T4
Urine_countsT3nT4.txt

value: Delivery

value: PE


title: K562, H3K4me1, rep2

value: Chronic myeloid leukemia


title: BC40 5hmC_Seal


title: RPMI-8226, H3K4me1, rep2

value: Multiple myeloma


title: PDP82M-T3/gHTN

description:
Library name: PDP82M-T3
Urine_countsT3nT4.txt

value: Third


title: BC39 5hmC_Seal

value: AA


title: PHV89T_T4/PE

description:
Library name: PHV89T_T4
Urine_countsT3nT4.txt


title: SK-MEL-2, H3K4me1, rep2

value: Melanoma


title: BC38 5hmC_Seal


title: PET87Q_T4/PE

description:
Library name: PET87Q_T4
Urine_countsT3nT4.txt

value: cell free RNA from Urine


title: BC36 5hmC_Seal


title: BC35 5hmC_Seal


title: PBM86L_T4/PE

description:
Library name: PBM86L_T4
Urine_countsT3nT4.txt


title: BC34 5hmC_Seal


title: BC33 5hmC_Seal


title: PSC84U-T4/PE

description:
Library name: PSC84U-T4
Urine_countsT3nT4.txt


title: BC31 5hmC_Seal


title: BC29 5hmC_Seal


title: PCP81G-T4/PE

description:
Library name: PCP81G-T4
Urine_countsT3nT4.txt


title: HCT116, H3K4me1, rep2

value: Colon carcinoma


title: NCI-H226, H3K4me1, rep2

value: Pleural epithelioid mesothelioma


title: BC28 5hmC_Seal

value: Plasma


title: BC30 5hmC_Seal


title: PMG84U-T4/PE

description:
Library name: PMG84U-T4
Urine_countsT3nT4.txt


title: BC26 5hmC_Seal


title: MDA-MB-468, H3K4me1, rep2

value: Breast adenocarcinoma


title: PGR79F-T4/PE

description:
Library name: PGR79F-T4
Urine_countsT3nT4.txt


title: BC25 5hmC_Seal

value: EA


title: T47D, H3K4me1, rep2

value: Invasive breast carcinoma


title: BC24 5hmC_Seal

value: MM


title: PRE92W_T3/PE

description:
Library name: PRE92W_T3
Urine_countsT3nT4.txt


title: BC21 5hmC_Seal

value: circulating cell-free DNA (cfDNA)


title: BC22 5hmC_Seal


title: BC20 5hmC_Seal


title: NCI-H460, H3K4me1, rep2

value: Lung large cell carcinoma


title: PGR79F-T3/PE

description:
Library name: PGR79F-T3
Urine_countsT3nT4.txt


title: BC19 5hmC_Seal


title: 786-O, H3K4me1, rep2

value: Renal cell carcinoma


title: BC17 5hmC_Seal


title: A549, H3K4me1, rep2

value: Lung adenocarcinoma


title: PBM86L-T3/PE

description:
Library name: PBM86L-T3
Urine_countsT3nT4.txt

value: PE


title: NCI-H23, H3K4me1, rep2


title: SNB19, H3K4me1, rep2

value: Astrocytoma


title: BC12 5hmC_Seal


title: BC11 5hmC_Seal


title: PVA80N-T4/GDM

description:
Library name: PVA80N-T4
Urine_countsT3nT4.txt

value: Delivery

value: GDM


title: BC10 5hmC_Seal

value: AA


title: BC9 5hmC_Seal


title: U251, H3K4me1, rep2

value: Prostate carcinoma


title: BC8 5hmC_Seal


title: A498, H3K4me1, rep2


title: PRA77U-T4/GDM

description:
Library name: PRA77U-T4
Urine_countsT3nT4.txt

value: cell free RNA from Urine


title: BC7 5hmC_Seal


title: PFP80Z-T4/GDM

description:
Library name: PFP80Z-T4
Urine_countsT3nT4.txt


title: BC5 5hmC_Seal


title: PCJ88V-T4/GDM

description:
Library name: PCJ88V-T4
Urine_countsT3nT4.txt


title: BC4 5hmC_Seal


title: HL-60, H3K4me1, rep2

value: Adult acute myeloid leukemia


title: BC3 5hmC_Seal

value: Plasma


title: PVA80N_T3/GDM

description:
Library name: PVA80N_T3
Urine_countsT3nT4.txt

value: Third


title: BC2 5hmC_Seal

value: EA


title: OVCAR-8, H3K4me1, rep2

value: High grade ovarian serous adenocarcinoma


title: BC1 5hmC_Seal

value: MM


title: PLJ81T_T3/GDM

description:
Library name: PLJ81T_T3
Urine_countsT3nT4.txt


title: SLE.2911.2209.rN

value: blood

tag: patient id

value: rN

tag: disease

value: SLE

tag: sledai

tag: Sex

value: F

tag: race

tag: batch


title: SLE.2932.3240.rN

tag: tissue

tag: sorting markers


title: HCD.796.1235.T1T2

value: HC


title: Non-ICU patient #17, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

city: Heidelberg

first: Dominik

last: Schaack

address: Im Neuenheimer Feld 420

country: Germany

institute: Heidelberg University Hospital

description: Library name: Non-ICU17, T1, H3Pan, Lane001

data_processing:
ChIP-seq data was trimmed and clipped by Trimmomatic 0.39. Technical replicates were merged.
Short and low-quality reads were discarded. For reads alignment Bowtie 2 2.3.5.1 mapping software was used with the pre-compiled H. sapiens UCSC hg19 reference genome (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Ambiguous and duplicate reads were separated before building ChIP-seq sequence alignment maps.
SAMtools 1.9 was used to generate binary alignment maps required for the following downstream processing steps.
In preparation of the peak calling procedure, anomalous, unstructured, or high signal regions, recommended to be blacklisted by the ENCODE project, were removed sample-wise by utilizing the intersect functionality of BEDTools 2.29.2 based on the ENCODE provided hg19 blacklist (https://github.com/Boyle-Lab/Blacklist/tree/master/lists).
The signal tracks of H3K4me3 histone modifications were subsequently analyzed by MACS2 2.2.7.1 in comparison to H3Pan sequencing reads originating from the same sample which were used as control (Input). narrowPeak files were generated using default settings.
Assembly: hg19
Supplementary files format and content: narrowPeak (except for H3Pan/Input samples)

extract_protocol:
Blood samples anticoagulated with lithium heparin were drawn at the time of study inclusion (T1), in both groups, and after 7 days (T2), only in the ICU group, and were processed immediately. For peripheral blood mononuclear cell (PBMC) separation, density gradient centrifugation was used with Leucosep tubes prefilled with separation medium (greiner bio-one, Kremsmuenster, Austria). Following centrifugation, the PBMC layer was aspirated and washed with ice-cold isolation buffer (phosphate-buffered saline supplemented with 2 mM ethylenediaminetetraacetic acid (Thermo Fisher Scientific Inc, Waltham, USA) and 0.5% protease-free bovine serum albumin (Carl Roth, Karlsruhe, Germany)). To perform a hypotonic lysis to remove remaining erythrocytes, cells were resuspended in 20mL 0.2% sodium chloride (Merck KGaA, Darmstadt, Germany) for 20 seconds before 20mL of 1.6% sodium chloride was added for restoration of isotonic conditions. Subsequently, cells were centrifuged), washed with ice-cold isolation buffer. The isolated PBMCs were counted using a ScepterTM 2.0 Cell Counter (Merck Millipore, Burlington, USA) that operates via impedance-based particle detection.
Prior to chromatin immunoprecipitation (ChIP), 7x10^6 PBMCs were crosslinked using formaldehyde at a final concentration of 1% for 8 min at 22°C. To stop the fixation of proteins linked to the DNA 0.125 M glycine was added to the mix. After washing the cells for three times (500xg, 5min) and cell lysis (106 cells per 1mL lysis buffer) DNA-shearing was performed using the Bioruptor Pico® (Diagenode, Liège, Belgium) to achieve fragments of 150-200 base pairs. Next, we used an automated system (IP-Star® Compact) for immunoprecipitation, reverse cross-linking, DNA purification, and tagmentation with specific reagent kit (Auto ChIPmentation Kit for Transcription Factors, Diagenode, Liège, Belgium) as well as antibodies against histone 3 (H3 Pan) and trimethylated lysine 4 of histone 3 (both Diagenode, Liège, Belgium), all according to manufacturer`s instructions. The enriched chromatin was stripped prior to end repair and reverse cross link according to the ChIPmentation kit guidelines. Unique dual indexes (UDI) (Diagenode, Liège, Belgium) were used for ChIP DNA library amplification and AMPure XP beads (Beckman Coulter, Brea, USA) for purification. Each library’s quality was analyzed using a High Sensitivity DNA chip for Bioanalyzer (Agilent Technologies. Santa Clara, USA) and Qubit™ assay (Qubit Fluorometric Quantitation, Thermo Fisher Scientific, Waltham, USA) was used for quantification of the amount of obtained ChIP-DNA. ChIP-seq libraries were sequenced on a NextSeq 500 Sequencing System using 150-cycle NextSeq 500/550 v2.5 sequencing reagent kits (Illumina, San Diego, USA).

treatment_protocol: Patient allocation to the ICU or normal ward was performed according to hospital standard operating procedure. Individuals had to meet the following criteria to be administered to the hospital: (1) C-Reactive Protein ≥20 mg/dl; (2) Ferritin >400mg/dl; (3) abnormal white blood cell count; (4) peripheral oxygen saturation <95%. Patients with a peripheral oxygen saturation ≤ 93% on room air as well as patients with supplemental oxygen of at least 4 L/min were administered to the ICU. Patients with a peripheral oxygen saturation ≥ 94% on room air and no hypotension were administered to the normal ward (`non-ICU-group´). None of the patients received vaccination against SARS-CoV-2 prior to enrolment.

tag: disease state

value: Normal ward

tag: time

tag: lane

value: PBMC


title: PC-3, H3K4me1, rep2

tag: cell type


title: Non-ICU patient #17, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: Non-ICU17, T1, H3K4me3, Lane001


title: PRL80T_T3/GDM

description:
Library name: PRL80T_T3
Urine_countsT3nT4.txt

value: GDM


title: Non-ICU patient #16, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: Non-ICU16, T1, H3Pan, Lane001


title: Non-ICU patient #16, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: Non-ICU16, T1, H3K4me3, Lane001


title: Non-ICU patient #15, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: Non-ICU15, T1, H3Pan, Lane001


title: CCRF-CEM, H3K18ac, rep2

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia

value: H3K18ac (Abcam:#ab1191)


title: Non-ICU patient #15, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: Non-ICU15, T1, H3K4me3, Lane001


title: PSN79O-T3/GDM

description:
Library name: PSN79O-T3
Urine_countsT3nT4.txt

value: cell free RNA from Urine


title: Non-ICU patient #14, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: Non-ICU14, T1, H3Pan, Lane001


title: SK-MEL-28, H3K18ac, rep2

value: Cutaneous melanoma


title: patient with sepsis-associated ARDS 1

description: Library name: SA1

value: Peripheral blood

value: patient with sepsis-associated ARDS


title: IGROV1 DARPP-32 knockdown (replicate 1)

city: Nottingham

first: Sarah

middle: Joanne

last: Storr

state: Nottinghamshire

address: Biodiscovery Institute

institute: University of Nottingham

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

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

tag: treatment

value: DARPP-32 KD


title: MOLT-4, H3K18ac, rep2

tag: cell line

value: Adult T acute lymphoblastic leukemia


title: Non-ICU patient #13, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: Non-ICU13, T1, H3K4me3, Lane001

tag: chip antibody


title: PRA77U-T3/GDM

description:
Library name: PRA77U-T3
Urine_countsT3nT4.txt

tag: trimester

value: Third


title: PFP80Z-T3/GDM

description:
Library name: PFP80Z-T3
Urine_countsT3nT4.txt

tag: study group


title: Non-ICU patient #12, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: Non-ICU12, T1, H3Pan, Lane001


title: PCJ88V-T3/GDM

description:
Library name: PCJ88V-T3
Urine_countsT3nT4.txt


title: RPMI-8226, H3K18ac, rep2

value: Multiple myeloma


title: Non-ICU patient #11, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: Non-ICU11, T1, H3K4me3, Lane001


title: Osteosarcoma tumor sample 5

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-5
Condition: Osteosarcoma; source folder: 20171010_5; 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: osteosarcoma tumor 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: osteosarcoma tumor tissue

value: Osteosarcoma


title: BC391 5hmC_Seal

city: Chicago

first: Zhou

last: Zhang

address: 680 North Lake Shore Drive, Suite 1400

institute: Northwestern University

source_name: Plasma

value: Plasma

tag: population

value: EA

tag: diagnosis

value: MM

tag: molecule

value: circulating cell-free DNA (cfDNA)


title: IGROV1 DDR1 knockdown (replicate 3)

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

value: DDR1 KD


title: IGROV1 DDR1 knockdown (replicate 2)

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


title: BC387 5hmC_Seal


title: Non-ICU patient #10, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: Non-ICU10, T1, H3Pan, Lane001

value: Normal ward

value: PBMC


title: Non-ICU patient #10, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: Non-ICU10, T1, H3K4me3, Lane001


title: SK-MEL-2, H3K18ac, rep2

value: Melanoma

value: H3K18ac (Abcam:#ab1191)


title: Non-ICU patient #9, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: Non-ICU09, T1, H3Pan, Lane001


title: PMY86E-T4/NORM

description:
Library name: PMY86E-T4
Urine_countsT3nT4.txt

value: cell free RNA from Urine

value: Delivery

value: Normal pregnancy


title: Non-ICU patient #8, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: Non-ICU08, T1, H3Pan, Lane001


title: HCT116, H3K18ac, rep2

value: Colon carcinoma


title: PJP90Y-T4/NORM

description:
Library name: PJP90Y-T4
Urine_countsT3nT4.txt


title: Non-ICU patient #8, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: Non-ICU08, T1, H3K4me3, Lane001


title: NCI-H522, H3K18ac, rep2

value: Lung adenocarcinoma


title: Non-ICU patient #7, timepoint 1, ChIP with H3Pan antibody (Input), Lane002

description: Library name: Non-ICU07, T1, H3Pan, Lane002


title: PGN82S-T4/NORM

description:
Library name: PGN82S-T4
Urine_countsT3nT4.txt


title: Non-ICU patient #7, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: Non-ICU07, T1, H3K4me3, Lane001


title: SW620, H3K4me1, rep2

value: Colon adenocarcinoma


title: PRN85I_T3/GDM

description:
Library name: PRN85I_T3
Urine_countsT3nT4.txt

value: Third

value: GDM


title: Non-ICU patient #6, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: Non-ICU06, T1, H3K4me3, Lane001


title: Non-ICU patient #14, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: Non-ICU14, T1, H3K4me3, Lane001


title: MDA-MB-468, H3K18ac, rep2

value: Breast adenocarcinoma


title: Non-ICU patient #13, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: Non-ICU13, T1, H3Pan, Lane001


title: Non-ICU patient #5, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: Non-ICU05, T1, H3Pan, Lane001


title: PAA85E-T4/NORM

description:
Library name: PAA85E-T4
Urine_countsT3nT4.txt


title: Non-ICU patient #5, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: Non-ICU05, T1, H3K4me3, Lane001


title: K562, H3K18ac, rep2

value: Chronic myeloid leukemia


title: T47D, H3K18ac, rep2

value: Invasive breast carcinoma


title: Non-ICU patient #11, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: Non-ICU11, T1, H3Pan, Lane001


title: Non-ICU patient #12, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: Non-ICU12, T1, H3K4me3, Lane001


title: Non-ICU patient #4, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: Non-ICU04, T1, H3Pan, Lane001


title: PTG80I_T3/NORM

description:
Library name: PTG80I_T3
Urine_countsT3nT4.txt


title: Non-ICU patient #4, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: Non-ICU04, T1, H3K4me3, Lane001


title: NCI-H460, H3K18ac, rep2

value: Lung large cell carcinoma


title: Non-ICU patient #3, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: Non-ICU03, T1, H3Pan, Lane001


title: Non-ICU patient #3, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: Non-ICU03, T1, H3K4me3, Lane001


title: PGN82S-T3/NORM

description:
Library name: PGN82S-T3
Urine_countsT3nT4.txt


title: 786-O, H3K18ac, rep2

value: Renal cell carcinoma


title: Non-ICU patient #2, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: Non-ICU02, T1, H3Pan, Lane001

value: Normal ward


title: PJP90Y-T3/NORM

description:
Library name: PJP90Y-T3
Urine_countsT3nT4.txt


title: Non-ICU patient #2, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: Non-ICU02, T1, H3K4me3, Lane001

value: PBMC


title: Non-ICU patient #1, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: Non-ICU01, T1, H3Pan, Lane001


title: PBH84C-T3/NORM

description:
Library name: PBH84C-T3
Urine_countsT3nT4.txt


title: A549, H3K18ac, rep2


title: Non-ICU patient #1, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: Non-ICU01, T1, H3K4me3, Lane001


title: PPF87I_T4/NORM

description:
Library name: PPF87I_T4
Urine_countsT3nT4.txt


title: SK-OV-3, H3K18ac, rep2

value: Ovarian serous cystadenocarcinoma


title: Non-ICU patient #9, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: Non-ICU09, T1, H3K4me3, Lane001


title: ICU patient #27, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU27, T1, H3Pan, Lane001

value: Admission to ICU


title: NCI-H23, H3K18ac, rep2

value: H3K18ac (Abcam:#ab1191)


title: PAV82H-T3/NORM

description:
Library name: PAV82H-T3
Urine_countsT3nT4.txt

value: cell free RNA from Urine


title: ICU patient #27, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU27, T1, H3K4me3, Lane001


title: ICU patient #26, timepoint 2, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU26, T2, H3Pan, Lane001


title: SNB19, H3K18ac, rep2

value: Astrocytoma


title: PAA85E-T3/NORM

description:
Library name: PAA85E-T3
Urine_countsT3nT4.txt

value: Normal pregnancy


title: ICU patient #26, timepoint 2, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU26, T2, H3K4me3, Lane001


title: U251, H3K18ac, rep2

value: Prostate carcinoma


title: ICU patient #26, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU26, T1, H3Pan, Lane001


title: ICU patient #26, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU26, T1, H3K4me3, Lane001


title: PTG80I_T4/NORM

description:
Library name: PTG80I_T4
Urine_countsT3nT4.txt

value: Delivery


title: A498, H3K18ac, rep2


title: PSN78G_T2/IUGR

description:
Library name: PSN78G_T2
Urine_counts_T1nT2.txt

value: Second

value: IUGR


title: ICU patient #25, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU25, T1, H3Pan, Lane001


title: PML88R_T2/IUGR

description:
Library name: PML88R_T2
Urine_counts_T1nT2.txt


title: ICU patient #25, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU25, T1, H3K4me3, Lane001


title: DU145, H3K18ac, rep2


title: ICU patient #24, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU24, T1, H3Pan, Lane001


title: PKK85B_T2/IUGR

description:
Library name: PKK85B_T2
Urine_counts_T1nT2.txt


title: ICU patient #24, timepoint 1, ChIP with H3K4me3 antibody, Lane002

description: Library name: ICU24, T1, H3K4me3, Lane002


title: Non-ICU patient #7, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: Non-ICU07, T1, H3Pan, Lane001


title: HL-60, H3K18ac, rep2

value: Adult acute myeloid leukemia


title: NCI-H226, H3K18ac, rep2

value: Pleural epithelioid mesothelioma


title: OVCAR-8, H3K18ac, rep2

value: High grade ovarian serous adenocarcinoma


title: ICU patient #23, timepoint 2, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU23, T2, H3Pan, Lane001


title: PKK81U_T2/IUGR

description:
Library name: PKK81U_T2
Urine_counts_T1nT2.txt


title: ICU patient #24, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU24, T1, H3K4me3, Lane001


title: ICU patient #23, timepoint 2, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU23, T2, H3K4me3, Lane001


title: PHC83M_T2/IUGR

description:
Library name: PHC83M_T2
Urine_counts_T1nT2.txt


title: ICU patient #23, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU23, T1, H3Pan, Lane001


title: PC-3, H3K18ac, rep2


title: ICU patient #23, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU23, T1, H3K4me3, Lane001


title: Non-ICU patient #6, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: Non-ICU06, T1, H3Pan, Lane001


title: ICU patient #22, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU22, T1, H3Pan, Lane001


title: PCH84I_T2/IUGR

description:
Library name: PCH84I_T2
Urine_counts_T1nT2.txt


title: SW620, H3K18ac, rep2

value: Colon adenocarcinoma


title: PAV82H-T4/NORM

description:
Library name: PAV82H-T4
Urine_countsT3nT4.txt


title: ICU patient #21, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU21, T1, H3Pan, Lane001


title: ICU patient #22, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU22, T1, H3K4me3, Lane001


title: ICU patient #21, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU21, T1, H3K4me3, Lane001


title: CCRF-CEM-Input, rep2

source_name: CCRF-CEM-Input

value: CCRF-CEM-Input

value: Childhood T acute lymphoblastic leukemia


title: PSN78G_T1/IUGR

description:
Library name: PSN78G_T1
Urine_counts_T1nT2.txt

value: First


title: ICU patient #20, timepoint 2, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU20, T2, H3Pan, Lane001

value: PBMC


title: PML88R_T1/IUGR

description:
Library name: PML88R_T1
Urine_counts_T1nT2.txt


title: SK-MEL-28-Input, rep2

value: Cutaneous melanoma


title: PKK85B_T1/IUGR

description:
Library name: PKK85B_T1
Urine_counts_T1nT2.txt


title: ICU patient #20, timepoint 2, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU20, T2, H3K4me3, Lane001

value: Admission to ICU


title: MOLT-4-Input, rep2

value: Adult T acute lymphoblastic leukemia


title: ICU patient #20, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU20, T1, H3Pan, Lane001


title: ICU patient #20, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU20, T1, H3K4me3, Lane001


title: PKK81U_T1/IUGR

description:
Library name: PKK81U_T1
Urine_counts_T1nT2.txt

value: cell free RNA from Urine


title: ICU patient #19, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU19, T1, H3Pan, Lane001


title: K562-Input, rep2

value: Chronic myeloid leukemia


title: ICU patient #18, timepoint 2, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU18, T2, H3Pan, Lane001


title: PHC83M_T1/IUGR

description:
Library name: PHC83M_T1
Urine_counts_T1nT2.txt


title: RPMI-8226-Input, rep2

value: Multiple myeloma


title: ICU patient #19, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU19, T1, H3K4me3, Lane001


title: ICU patient #18, timepoint 2, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU18, T2, H3K4me3, Lane001


title: PCH84I_T1/IUGR

description:
Library name: PCH84I_T1
Urine_counts_T1nT2.txt


title: ICU patient #18, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU18, T1, H3Pan, Lane001


title: SK-MEL-2-Input, rep2

value: Melanoma


title: ICU patient #18, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU18, T1, H3K4me3, Lane001


title: PTM93S_T2/gHTN

description:
Library name: PTM93S_T2
Urine_counts_T1nT2.txt

value: Second

value: gHTN


title: ICU patient #17, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU17, T1, H3Pan, Lane001


title: SK-OV-3-Input, rep2

value: Ovarian serous cystadenocarcinoma


title: ICU patient #17, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU17, T1, H3K4me3, Lane001


title: PSH87T_T2/gHTN

description:
Library name: PSH87T_T2
Urine_counts_T1nT2.txt


title: HCT116-Input, rep2

value: Colon carcinoma


title: ICU patient #16, timepoint 2, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU16, T2, H3Pan, Lane001


title: BC42 5hmC_Seal

value: Plasma

value: EA

value: MM

value: circulating cell-free DNA (cfDNA)


title: PPN84W_T2/gHTN

description:
Library name: PPN84W_T2
Urine_counts_T1nT2.txt


title: ICU patient #16, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU16, T1, H3Pan, Lane001


title: ICU patient #16, timepoint 2, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU16, T2, H3K4me3, Lane001


title: NCI-H522-Input, rep2

value: Lung adenocarcinoma


title: ICU patient #16, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU16, T1, H3K4me3, Lane001

value: PBMC


title: ICU patient #15, timepoint 2, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU15, T2, H3Pan, Lane001


title: PNC75Z_T2/gHTN

description:
Library name: PNC75Z_T2
Urine_counts_T1nT2.txt


title: NCI-H226-Input, rep2

value: Pleural epithelioid mesothelioma


title: ICU patient #15, timepoint 2, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU15, T2, H3K4me3, Lane001

value: Admission to ICU


title: PMM83E_T2/gHTN

description:
Library name: PMM83E_T2
Urine_counts_T1nT2.txt


title: ICU patient #15, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU15, T1, H3Pan, Lane001


title: MDA-MB-468-Input, rep2

value: Breast adenocarcinoma


title: ICU patient #14, timepoint 2, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU14, T2, H3Pan, Lane001


title: ICU patient #15, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU15, T1, H3K4me3, Lane001


title: T47D-Input, rep2

value: Invasive breast carcinoma


title: ICU patient #14, timepoint 2, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU14, T2, H3K4me3, Lane001


title: PJD88L_T2/gHTN

description:
Library name: PJD88L_T2
Urine_counts_T1nT2.txt

value: cell free RNA from Urine


title: ICU patient #14, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU14, T1, H3Pan, Lane001


title: PLH87K_T2/gHTN

description:
Library name: PLH87K_T2
Urine_counts_T1nT2.txt


title: ICU patient #14, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU14, T1, H3K4me3, Lane001


title: ICU patient #13, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU13, T1, H3Pan, Lane001


title: NCI-H460-Input, rep2

value: Lung large cell carcinoma


title: 786-O-Input, rep2

value: Renal cell carcinoma


title: ICU patient #12, timepoint 1, ChIP with H3Pan antibody (Input), Lane002

description: Library name: ICU12, T1, H3Pan, Lane002


title: PHR80H_T2/gHTN

description:
Library name: PHR80H_T2
Urine_counts_T1nT2.txt

value: Second


title: PJB84J_T2/gHTN

description:
Library name: PJB84J_T2
Urine_counts_T1nT2.txt

value: gHTN


title: ICU patient #13, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU13, T1, H3K4me3, Lane001


title: ICU patient #12, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU12, T1, H3K4me3, Lane001


title: A549-Input, rep2


title: ICU patient #12, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU12, T1, H3Pan, Lane001


title: NCI-H23-Input, rep2


title: ICU patient #11, timepoint 2, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU11, T2, H3Pan, Lane001


title: PDP82M_T2/gHTN

description:
Library name: PDP82M_T2
Urine_counts_T1nT2.txt


title: PGC81D_T2/gHTN

description:
Library name: PGC81D_T2
Urine_counts_T1nT2.txt


title: ICU patient #11, timepoint 2, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU11, T2, H3K4me3, Lane001


title: SNB19-Input, rep2

value: Astrocytoma


title: PTM93S_T1/gHTN

description:
Library name: PTM93S_T1
Urine_counts_T1nT2.txt

value: First


title: ICU patient #11, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU11, T1, H3Pan, Lane001


title: ICU patient #11, timepoint 1, ChIP with H3Pan antibody (Input), Lane002

description: Library name: ICU11, T1, H3Pan, Lane002


title: U251-Input, rep2

value: Prostate carcinoma


title: PSH87T_T1/gHTN

description:
Library name: PSH87T_T1
Urine_counts_T1nT2.txt


title: ICU patient #10, timepoint 2, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU10, T2, H3Pan, Lane001


title: ICU patient #11, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU11, T1, H3K4me3, Lane001


title: BC18 5hmC_Seal

value: Plasma

value: AA


title: A498-Input, rep2


title: ICU patient #10, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU10, T1, H3Pan, Lane001


title: DU145-Input, rep2


title: ICU patient #10, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU10, T1, H3K4me3, Lane001


title: PNC75Z_T1/gHTN

description:
Library name: PNC75Z_T1
Urine_counts_T1nT2.txt


title: PPN84W_T1/gHTN

description:
Library name: PPN84W_T1
Urine_counts_T1nT2.txt


title: ICU patient #9, timepoint 2, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU09, T2, H3Pan, Lane001


title: ICU patient #10, timepoint 2, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU10, T2, H3K4me3, Lane001


title: PCP81G-T3/PE

description:
Library name: PCP81G-T3
Urine_countsT3nT4.txt

value: Third

value: PE


title: HL-60-Input, rep2

value: Adult acute myeloid leukemia


title: BC16 5hmC_Seal

value: EA

value: MM

value: circulating cell-free DNA (cfDNA)


title: ICU patient #9, timepoint 2, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU09, T2, H3K4me3, Lane001

value: Admission to ICU

value: PBMC


title: PMM83E_T1/gHTN

description:
Library name: PMM83E_T1
Urine_counts_T1nT2.txt

value: cell free RNA from Urine


title: BC15 5hmC_Seal


title: OVCAR-8-Input, rep2

value: High grade ovarian serous adenocarcinoma


title: ICU patient #9, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU09, T1, H3Pan, Lane001


title: PLH87K_T1/gHTN

description:
Library name: PLH87K_T1
Urine_counts_T1nT2.txt


title: ICU patient #9, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU09, T1, H3K4me3, Lane001


title: ICU patient #8, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU08, T1, H3Pan, Lane001


title: ICU patient #8, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU08, T1, H3K4me3, Lane001


title: ICU patient #7, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU07, T1, H3Pan, Lane001


title: SW620-Input, rep2

value: Colon adenocarcinoma


title: PJB84J_T1/gHTN

description:
Library name: PJB84J_T1
Urine_counts_T1nT2.txt

value: gHTN


title: PJD88L_T1/gHTN

description:
Library name: PJD88L_T1
Urine_counts_T1nT2.txt


title: PC-3-Input, rep2


title: ICU patient #7, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU07, T1, H3K4me3, Lane001


title: ICU patient #6, timepoint 2, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU06, T2, H3Pan, Lane001


title: ICU patient #6, timepoint 2, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU06, T2, H3K4me3, Lane001


title: CCRF-CEM, H3K36me3, rep3

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia


title: PHR80H_T1/gHTN

description:
Library name: PHR80H_T1
Urine_counts_T1nT2.txt

value: First


title: ICU patient #6, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU06, T1, H3Pan, Lane001


title: ICU patient #6, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU06, T1, H3K4me3, Lane001


title: PGC81D_T1/gHTN

description:
Library name: PGC81D_T1
Urine_counts_T1nT2.txt


title: SK-MEL-28, H3K36me3, rep3

value: Cutaneous melanoma


title: MOLT-4, H3K36me3, rep3

value: Adult T acute lymphoblastic leukemia


title: ICU patient #5, timepoint 2, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU05, T2, H3K4me3, Lane001


title: PDP82M_T1/gHTN

description:
Library name: PDP82M_T1
Urine_counts_T1nT2.txt


title: ICU patient #5, timepoint 2, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU05, T2, H3Pan, Lane001


title: ICU patient #5, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU05, T1, H3Pan, Lane001


title: K562, H3K36me3, rep3

value: Chronic myeloid leukemia


title: ICU patient #5, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU05, T1, H3K4me3, Lane001


title: PWZ84A_T2/PE

description:
Library name: PWZ84A_T2
Urine_counts_T1nT2.txt

value: Second

value: PE


title: ICU patient #4, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU04, T1, H3Pan, Lane001


title: ICU patient #4, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU04, T1, H3K4me3, Lane001


title: RPMI-8226, H3K36me3, rep3

value: Multiple myeloma


title: ICU patient #3, timepoint 2, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU03, T2, H3Pan, Lane001


title: PSC84U_T2/PE

description:
Library name: PSC84U_T2
Urine_counts_T1nT2.txt


title: PRE92W_T2/PE

description:
Library name: PRE92W_T2
Urine_counts_T1nT2.txt


title: SK-MEL-2, H3K36me3, rep3

value: Melanoma


title: ICU patient #3, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU03, T1, H3Pan, Lane001


title: SK-OV-3, H3K36me3, rep3

value: Ovarian serous cystadenocarcinoma


title: PMG84U_T2/PE

description:
Library name: PMG84U_T2
Urine_counts_T1nT2.txt


title: ICU patient #2, timepoint 2, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU02, T2, H3Pan, Lane001

value: Admission to ICU


title: ICU patient #3, timepoint 2, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU03, T2, H3K4me3, Lane001

value: PBMC


title: HCT116, H3K36me3, rep3

value: Colon carcinoma


title: ICU patient #3, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU03, T1, H3K4me3, Lane001


title: ICU patient #2, timepoint 2, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU02, T2, H3K4me3, Lane001


title: PMD88R_T2/PE

description:
Library name: PMD88R_T2
Urine_counts_T1nT2.txt

value: cell free RNA from Urine


title: ICU patient #2, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU02, T1, H3Pan, Lane001


title: ICU patient #2, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU02, T1, H3K4me3, Lane001


title: PKO84D_T2/PE

description:
Library name: PKO84D_T2
Urine_counts_T1nT2.txt


title: ICU patient #1, timepoint 1, ChIP with H3Pan antibody (Input), Lane001

description: Library name: ICU01, T1, H3Pan, Lane001


title: NCI-H522, H3K36me3, rep3

value: Lung adenocarcinoma


title: NCI-H226, H3K36me3, rep3

value: Pleural epithelioid mesothelioma


title: ICU patient #1, timepoint 1, ChIP with H3K4me3 antibody, Lane001

description: Library name: ICU01, T1, H3K4me3, Lane001


title: GeoMx-DSP-1001660022457-B-H12

city: Rochester

first: Alexandra

last: Krivonos

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description: Library name: GeoMx-DSP-1001660022457-B-H12

data_processing:
The samples were sequenced on an Illumina NextSeq 2000 P3 instrument at PE50. Sequencing depth was calculated based on a total area of 9,002,857 μm2 and 900 million read pairs determined from the GeoMx GeoMx-DSP generated Lab Worksheet.
Sequencing-generated FASTQ files were processed using the NanoString GeoMx NGS pipeline to generate DCC files used in downstream data analysis.
Assembly: mm10
Supplementary files format and content: GeoMx_sample_metadata.csv includes the samples metadata
Supplementary files format and content: vwf+_VWF+_DE_analysis.xlsx Differential expression results from NanoString GeoMx WTA analysis; log₂ fold change, FDR, p-value, and mean expression values for genes in one tissue segment subset
Supplementary files format and content: cd68+_CD68+_DE_analysis.xlsx - Differential expression results from NanoString GeoMx WTA analysis; log₂ fold change, FDR, p-value, and mean expression values for genes in one tissue segment subset
Supplementary files format and content: ela2+_ELA+_DE_analysis.xlsx - Differential expression results from NanoString GeoMx WTA analysis; log₂ fold change, FDR, p-value, and mean expression values for genes in one tissue segment subset
Supplementary files format and content: else_ELSE_DE_analysis.xlsx - Differential expression results from NanoString GeoMx WTA analysis; log₂ fold change, FDR, p-value, and mean expression values for genes in one tissue segment subset
Library strategy: Spatial Transcriptomics

source_name: liver

growth_protocol: human liver FFPE

extract_protocol:
Fresh tissues from surgery were processed for FFPE embedding, 5um section were cut.
Slides were flourensently labeled with  endothelial cell marker Von Willebrand Factor (VWF), macrophage and monocyte marker CD68, and neutrophil marker Elastase (ELA2). Regions of interest (ROIs) were manually draw based on their zonal location within the liver lobule: periportal zone 1, midzonal zone 2, and pericentral zone 3. Each ROI consisted of four segments: segment 4 for VWF+ area, segment 1 for CD68+ area, segment 2 for ELA2+ area, and segment 3 was called ‘else’ to refer to non-stained areas within the ROI. Photo-cleaved oligonucleotide tags were collected from 377 AOI. PCR amplification and liabrary pprepareation were done using GeoMx Human Whole Transcriptome Atlas (WTA) accorrding to manufacture's instruction.

treatment_protocol: 3 patients with normal, 3 patients with steatosis and 4 patients with MASH

value: liver

tag: condition

tag: segment

tag: zone


title: PHV89T_T2/PE

description:
Library name: PHV89T_T2
Urine_counts_T1nT2.txt

tag: tissue


title: MDA-MB-468, H3K36me3, rep3

value: Breast adenocarcinoma


title: GeoMx-DSP-1001660022457-B-H11

description: Library name: GeoMx-DSP-1001660022457-B-H11

tag: batch


title: PGR79F_T2/PE

description:
Library name: PGR79F_T2
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022457-B-H10

description: Library name: GeoMx-DSP-1001660022457-B-H10


title: T47D, H3K36me3, rep3

value: Invasive breast carcinoma


title: GeoMx-DSP-1001660022457-B-H08

description: Library name: GeoMx-DSP-1001660022457-B-H08


title: PEW80F_T2/PE

description:
Library name: PEW80F_T2
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022457-B-H07

description: Library name: GeoMx-DSP-1001660022457-B-H07


title: GeoMx-DSP-1001660022457-B-H06

description: Library name: GeoMx-DSP-1001660022457-B-H06


title: PET67Q_T2/PE

description:
Library name: PET67Q_T2
Urine_counts_T1nT2.txt


title: NCI-H460, H3K36me3, rep3

value: Lung large cell carcinoma


title: GeoMx-DSP-1001660022457-B-H02

description: Library name: GeoMx-DSP-1001660022457-B-H02


title: 786-O, H3K36me3, rep3

value: Renal cell carcinoma


title: PCP81G_T2/PE

description:
Library name: PCP81G_T2
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022457-B-G12

description: Library name: GeoMx-DSP-1001660022457-B-G12


title: PBM86L_T2/PE

description:
Library name: PBM86L_T2
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022457-B-G11

description: Library name: GeoMx-DSP-1001660022457-B-G11


title: GeoMx-DSP-1001660022457-B-G10

description: Library name: GeoMx-DSP-1001660022457-B-G10


title: PSC84U_T1/PE

description:
Library name: PSC84U_T1
Urine_counts_T1nT2.txt

value: First


title: PWZ84A_T1/PE

description:
Library name: PWZ84A_T1
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022457-B-G04

description: Library name: GeoMx-DSP-1001660022457-B-G04


title: PMG84U_T1/PE

description:
Library name: PMG84U_T1
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022457-B-F11

description: Library name: GeoMx-DSP-1001660022457-B-F11


title: GeoMx-DSP-1001660022457-B-F09

description: Library name: GeoMx-DSP-1001660022457-B-F09


title: GeoMx-DSP-1001660022457-B-F05

description: Library name: GeoMx-DSP-1001660022457-B-F05

value: Portal-Periportal


title: GeoMx-DSP-1001660022457-B-F04

description: Library name: GeoMx-DSP-1001660022457-B-F04


title: PKO84D_T1/PE

description:
Library name: PKO84D_T1
Urine_counts_T1nT2.txt

value: PE


title: HL-60, H3K36me3, rep3

value: Adult acute myeloid leukemia


title: GeoMx-DSP-1001660022457-B-F03

description: Library name: GeoMx-DSP-1001660022457-B-F03


title: OVCAR-8, H3K36me3, rep3

value: High grade ovarian serous adenocarcinoma


title: PHV89T_T1/PE

description:
Library name: PHV89T_T1
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022457-B-E12

description: Library name: GeoMx-DSP-1001660022457-B-E12


title: GeoMx-DSP-1001660022457-B-F01

description: Library name: GeoMx-DSP-1001660022457-B-F01


title: PC-3, H3K36me3, rep3

value: Prostate carcinoma


title: GeoMx-DSP-1001660022457-B-E10

description: Library name: GeoMx-DSP-1001660022457-B-E10


title: SW620, H3K36me3, rep3

value: Colon adenocarcinoma


title: PGR79F_T1/PE

description:
Library name: PGR79F_T1
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022457-B-E09

description: Library name: GeoMx-DSP-1001660022457-B-E09


title: A549, H3K36me3, rep3


title: CCRF-CEM, H3K36me3, rep2

value: CCRF-CEM

value: Childhood T acute lymphoblastic leukemia


title: PEW80F_T1/PE

description:
Library name: PEW80F_T1
Urine_counts_T1nT2.txt

value: cell free RNA from Urine


title: GeoMx-DSP-1001660022457-B-E08

description: Library name: GeoMx-DSP-1001660022457-B-E08


title: GeoMx-DSP-1001660022457-B-G08

description: Library name: GeoMx-DSP-1001660022457-B-G08


title: GeoMx-DSP-1001660022457-B-G07

description: Library name: GeoMx-DSP-1001660022457-B-G07


title: GeoMx-DSP-1001660022457-B-E07

description: Library name: GeoMx-DSP-1001660022457-B-E07


title: PRE92W_T1/PE

description:
Library name: PRE92W_T1
Urine_counts_T1nT2.txt


title: PET67Q_T1/PE

description:
Library name: PET67Q_T1
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022457-B-E06

description: Library name: GeoMx-DSP-1001660022457-B-E06


title: SK-MEL-28, H3K36me3, rep2

value: Cutaneous melanoma


title: PMD88R_T1/PE

description:
Library name: PMD88R_T1
Urine_counts_T1nT2.txt


title: GeoMx-DSP-1001660022457-B-E04

description: Library name: GeoMx-DSP-1001660022457-B-E04


title: GeoMx-DSP-1001660022457-B-E03

description: Library name: GeoMx-DSP-1001660022457-B-E03


title: MOLT-4, H3K36me3, rep2

value: Adult T acute lymphoblastic leukemia


title: PBM86L_T1/PE

description:
Library name: PBM86L_T1
Urine_counts_T1nT2.txt