title: Whole larva, 24 h exposure, 0.19 uM fluticasone propionate, rep B

description: Library name: FCP_191_B

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

value: μM


title: Nvec_25hpf_GSK_ATACseq_rep2

status: Public on Apr 10 2026

type: SRA

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

country: United Kingdom

institute: Queen Mary University of London

description:
Library name: STELLA5mC10
ATACseq.all_peaks.counts.tsv

library_source: genomic

data_processing:
EM-seq data was mapped to the reference genome using BS-seeker2 with Bowtie2 as a back-end aligner. The resulting bam file was then deduplicated with Sambamba, and the methylation calling done with CGmapTools.
RNA-seq data was mapped against the reference transcriptome using Kallisto with default parameters.
ATAC-seq data was mapped to the reference genome using chromap (--preset atac), the resulting BEDPE was used as input for MACS3 callpeaks function (-g 2.7e8 -q 0.05 -B). All peaks were merged using BEDTOOLS merge function, and insert sites were counted using the featureCounts function in the SUBREAD package, requiring 20% read overlap (--fracOverlap 0.2).
Oxford Nanopore data was basecalled using Dorado (0.7.2) with the model 5mCG_5hmCG, sup model, mapped directly to the reference genome. Methylation calls where extracted using modkit with default parameters. Haplotype tags on the bam file were obtained using WhatsHap.
Raw CAGE reads were demultiplexed using standard Illumina processing pipelines. Adapter sequences and low-quality reads were trimmed and filtered using Trim Galore! (v0.6.7, Babraham Bioinformatics) with default settings, after which the G added during the reverse transcription step was removed with cutadapt (v4.6). Quality-filtered reads were aligned to the reference genome using STAR (v5.1.0), ensuring that the 5' end of each read was correctly mapped to its genomic location. Alignments were filtered to retain only primary, uniquely mapped reads with a mapping quality greater than 20.
Assembly: GCF_932526225.1
Supplementary files format and content: CGmap files are described in the BS-Seeker2 github repository: https://github.com/BSSeeker/BSseeker2?tab=readme-ov-file#44-bs_seeker2-call_methylationpy
Supplementary files format and content: Processed mRNA-seq data shows est_counts values obtained from Kallisto Quant function against the reference transcriptome, summarised per gene.
Supplementary files format and content: NarrowPeak files are described in MACS3 documentation (https://macs3-project.github.io/MACS/docs/narrowPeak.html). ATACseq.all_peaks.counts.tsv is the output of featureCounts, where each peak (defined as chr:start-end) is a row and each sample is a column.
Supplementary files format and content: Modkit bedmethyl format is described here: https://github.com/nanoporetech/modkit?tab=readme-ov-file#description-of-bedmethyl-output
Supplementary files format and content: TagCluster for CAGE seq data are described in the CAGEr package. Bigwigs are coverage normalised read counts divided per strand: plus or minus.

molecule: genomic DNA

organism: Nematostella vectensis

source_name: 25 hpf gastrulae

growth_protocol: Nematostella juveniles and adults were housed in glass dishes containing 15‰ artificial sea water at 19 °C and fed freshly hatched Artemia nauplii three to five times a week, with weekly water changes. Spawning induced following previously established protocols. The gelatinous mass surrounding the eggs was removed using 4% L-cysteine (Sigma-Aldrich, #1.02838), after which eggs were washed and fertilized. Embryos were cultured in 6-well plates at 22°C for consistent developmental staging. Primary polyps metamorphosed were initially fed mashed nauplii until they can ingest intact nauplii and then transferred to larger glass dishes for further growth and maturation.

extract_protocol:
Monarch Genomic DNA Purification Kit (New England Biolabs, #T1030)
mRNA-seq / EM-seq / OmniATAC-seq / Oxford Nanopore Ligation kit (SQK-LSK114) / CAGE-seq

treatment_protocol: For multi-omic profiling, fertilized zygotes produced by pooled gametes of multiple males and females were split into two wells containing either 5 μM GSK-3484862 (MedChemExpress, #HY-135146) or equivalent amount of DMSO (0.1%) as the control. Three independent biological replicates for both treatment and control were prepared using different broodstocks. After 25 hours, gastrula-stage embryos were washed and harvested for DNA, RNA, and nucleus extraction.

tag: tissue

value: 25 hpf gastrulae

tag: cell type

value: Whole embryo

tag: genotype

value: Massachussets

tag: treatment


title: Nvec_25hpf_GSK_EMseq_rep1

description: Library name: STELLA5mC12

data_processing:
EM-seq data was mapped to the reference genome using BS-seeker2 with Bowtie2 as a back-end aligner. The resulting bam file was then deduplicated with Sambamba, and the methylation calling done with CGmapTools.
RNA-seq data was mapped against the reference transcriptome using Kallisto with default parameters.
ATAC-seq data was mapped to the reference genome using chromap (--preset atac), the resulting BEDPE was used as input for MACS3 callpeaks function (-g 2.7e8 -q 0.05 -B). All peaks were merged using BEDTOOLS merge function, and insert sites were counted using the featureCounts function in the SUBREAD package, requiring 20% read overlap (--fracOverlap 0.2).
Oxford Nanopore data was basecalled using Dorado (0.7.2) with the model 5mCG_5hmCG, sup model, mapped directly to the reference genome. Methylation calls where extracted using modkit with default parameters. Haplotype tags on the bam file were obtained using WhatsHap.
Raw CAGE reads were demultiplexed using standard Illumina processing pipelines. Adapter sequences and low-quality reads were trimmed and filtered using Trim Galore! (v0.6.7, Babraham Bioinformatics) with default settings, after which the G added during the reverse transcription step was removed with cutadapt (v4.6). Quality-filtered reads were aligned to the reference genome using STAR (v5.1.0), ensuring that the 5' end of each read was correctly mapped to its genomic location. Alignments were filtered to retain only primary, uniquely mapped reads with a mapping quality greater than 20.
Assembly: GCF_932526225.1
Supplementary files format and content: CGmap files are described in the BS-Seeker2 github repository: https://github.com/BSSeeker/BSseeker2?tab=readme-ov-file#44-bs_seeker2-call_methylationpy
Supplementary files format and content: Processed mRNA-seq data shows est_counts values obtained from Kallisto Quant function against the reference transcriptome, summarised per gene.
Supplementary files format and content: NarrowPeak files are described in MACS3 documentation (https://macs3-project.github.io/MACS/docs/narrowPeak.html). ATACseq.all_peaks.counts.tsv is the output of featureCounts, where each peak (defined as chr:start-end) is a row and each sample is a column.
Supplementary files format and content: Modkit bedmethyl format is described here: https://github.com/nanoporetech/modkit?tab=readme-ov-file#description-of-bedmethyl-output
Supplementary files format and content: TagCluster for CAGE seq data are described in the CAGEr package. Bigwigs are coverage normalised read counts divided per strand: plus or minus.
Library strategy: EM-seq


title: SSB.Teniposide.100.B4

city: Xiamen

first: Huifen

last: Cao

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

country: China

institute: Huaqiao University

description: Library name: SSB.Teniposide.100.B4

data_processing:
SSiNGLe method: The genomic site mapping was performed the same way as in the SSiNGLe-ILM protocol (https://protocolexchange.researchsquare.com/article/pex-920/v2) with the two additional filtering steps. One, PCR duplicates were removed. Two, a read-pair was used only if the first base of the read 2 aligned to the reference sequence. The coordinate of  the first aligning base of the read 2 was assigned as the position of the SSB site.
Assembly: hg19(GRCh37) for the human reads mapping
Supplementary files format and content: All BED files contain coordinates of SSBs mapped to human genomes. The 5th columns show the number of reads representing the SSBs.

organism: Homo sapiens

extract_protocol:
Three million human chronic myeloid leukemia K562 cells were seeded at 1 million cells per 1 ml of culture medium in each well of 6-well plates. The cells were grown in RPMI 1640 (Gibco, Billings, MT, USA) supplemented with 10% heat-inactivated fetal bovine serum (ExCell Bio, Montevideo, Uruguay) and 1% penicillin-streptomycin (Gibco) at 37 oC in 5% CO2. After 16 h, the cells were separately treated with 0.1%DMSO, 100 μM etoposide (AbMole), 100 μM teniposide (Merck), 10 μM mitoxantrone (Merck), 10 μM m-amsacrine hydrochloride (Merck), 10 μM pixentrone, 0.1 μM, 1 μM, 10 μM, 20 μM or 100 μM doxorubicin (Merck), and 20 μM epirubicin (Selleck) for 1 hour. All drugs were dissolved in DMSO, and each treatment was done in three independent biological replicas. After the drug treatment, DNA was isolated with the TIANamp Genomic DNA Kit (TIANGEN Biotech, DP304) according to the manufacturer’s protocol
SSiNGLe method

tag: cell line

value: chronic myelogenous leukemia cell line

value: treated with 100 μM teniposide

tag: batch

value: 1 hr


title: Whole larva, 24 h exposure, 0.01 uM fluticasone propionate, rep A

city: Duluth

first: Peter

last: Schumann

state: MN

address: 6201 Congdon Blvd

country: USA

institute: United States Environmental Protection Agency

description: Library name: FCP_11_A

library_source: transcriptomic

data_processing:
Base calling: Base calling was done by Illumina Real Time Analysis (v3.4.4)
Demultiplex: Output was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0
Indexing: The fathead minnow reference genome (assembly GCA_016745375.1; Martinson et al., 2022) was indexed with STAR (v2.7.10a). The following sample specific parameters were used to generate the genome index: --genomeSAindexNbases 13 --sjdbOverhang 99.
Assign counts: HTSeq (v2.0.1) was used to assign counts to each gene. FastQC and MultiQC (v1.12) were used to assess quality control metrics of the processed reads.  Counts to each gene were parsed, and count data for each exposure condition written to a single tab-delimited matrix file with samples arranged as columns and genes arranged in rows.
Filter counts: Raw counts were first screened to see if any exhibited total counts <2M, and a boxplot of log10 raw counts (+1) for each sample was generated to look for samples with unusual counts distribution. Lowly expressed genes were removed from the raw count matrices using edgeR’s (Robinson et al., 2010) built-in filtering function, filterByExpr(), in version 3.40.2; namely, genes with < 15 reads across all samples and < 10 reads in 70% of samples in the smallest group (treatment or control) were filtered out.
Count normalization and filtering: Library normalization factors for the filtered count matrices were calculated using the trimmed mean of M-values method via the edgeR function calcNormFactors(). Filtered counts were then normalized by read depth using th counts per million (CPM) method. CPM values were then transformed with log2 with a pseudo-count of 1 added to prevent taking the log of a negative count value. PCA was performed on the normalized count values for outlier detection. Samples were removed as outliers based on visual inspection of the PCA plots as sample replicate size did not allow for robust statistical methods to be used.
Assembly: GCA_016745375.1
Supplementary files format and content: *.txt file raw count matrix
Supplementary files format and content: *.txt file count matrix with all filtering, normalization and quality control filters applied. Header rows provide unique sample ID and expsoure concentrations.

molecule: total RNA

organism: Pimephales promelas

source_name: whole body

extract_protocol:
Total RNA was extracted from pooled homogenates using the Zymo Research Direct-zol-96 RNA kit (Zymo Research). The protocol has been adapted to the Biomek i5 to yield 40 µL of total RNA. The quantity and quality of total RNA was observed using a NanoDrop Eight (Thermo Fisher Scientific; Waltham, MA, USA), prior to storage at -80 ºC.
Libraries were prepared using the Lexogen QuantSeq 3' mRNA-Seq V2 Library Prep Kit with Unique Dual Index (UDI) and QuantSeq Unique Molecular Identifier (UMI) module following manufacturer's recommendations.

tag: strain

tag: dev stage

value: larvae

value: whole body

tag: Sex

value: not determined

tag: store cond

value: -80 deg C

tag: collected by

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

value: Fluticasone Propionate (DTXSID8045511)


title: Whole larva, 24 h exposure, 0.01 uM fluticasone propionate, rep C

description: Library name: FCP_11_C

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: collection date

tag: geo loc_name

tag: biomaterial provider

tag: birth location

tag: breeding method


title: SSB.Teniposide.0.1.B5

description: Library name: SSB.Teniposide.0.1.B5

tag: cell line

tag: cell type

tag: treatment

value: treated with 0.1 μM teniposide

tag: batch


title: Nvec_25hpf_GSK_ATACseq_rep3

description:
Library name: STELLA5mC11
ATACseq.all_peaks.counts.tsv

tag: tissue

tag: genotype


title: Whole larva, 24 h exposure, 0.19 uM fluticasone propionate, rep A

description: Library name: FCP_191_A

tag: strain

tag: dev stage

tag: Sex

tag: store cond

value: USA:Minnesota, Duluth

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration


title: Nvec_25hpf_DMSO_RNAseq_rep1

description:
Library name: STELLA5mC6
Nvec_Complete_Gene_Counts.tsv

molecule: polyA RNA

value: 25 hpf gastrulae

value: Whole embryo

value: DMSO 0.1%


title: Nvec_25hpf_GSK_ATACseq_rep1

description:
Library name: STELLA5mC9
ATACseq.all_peaks.counts.tsv

value: Massachussets


title: Nvec_25hpf_DMSO_RNAseq_rep3

description:
Library name: STELLA5mC8
Nvec_Complete_Gene_Counts.tsv


title: SSB.Teniposide.0.1.B4

description: Library name: SSB.Teniposide.0.1.B4

value: chronic myelogenous leukemia cell line

value: 1 hr


title: SSB.Teniposide.0.1.B6

description: Library name: SSB.Teniposide.0.1.B6


title: Nvec_25hpf_DMSO_EMseq_rep2

description: Library name: STELLA5mC4


title: Nvec_25hpf_DMSO_RNAseq_rep2

description:
Library name: STELLA5mC7
Nvec_Complete_Gene_Counts.tsv


title: Nvec_25hpf_DMSO_EMseq_rep3

description: Library name: STELLA5mC5


title: Whole larva, 24 h exposure, 0.01 uM fluticasone propionate, rep B

description: Library name: FCP_11_B

tag: age

value: larvae

value: whole body

tag: collection date

tag: measured conc

tag: measured conc_units

value: μM

tag: nominal conc

tag: nominal conc_units


title: SSB.DMSO.B6

description: Library name: SSB.DMSO.B6

tag: cell line

tag: cell type

value: treated with DMSO


title: Nvec_25hpf_DMSO_EMseq_rep1

description: Library name: STELLA5mC3

tag: treatment


title: Whole larva, 24 h exposure, 0.1 uM fluticasone propionate, rep C

description: Library name: FCP_107_C

tag: tissue

value: not determined

value: -80 deg C

tag: geo loc_name

tag: biomaterial provider

tag: birth location

tag: breeding method

value: Great Lakes Toxicology & Ecology Division

value: Fluticasone Propionate (DTXSID8045511)


title: SSB.DMSO.B5

description: Library name: SSB.DMSO.B5

tag: batch


title: CosMx, slide_14

type: RNA

city: Houston

first: Salvador

last: Alonso

state: Texas

address: 1400 Holcombe Blvd, FC10.3030

department: GI Medical Oncology

institute: MD Anderson Cancer Center

description: FFPE tissue slides were submitted for in situ hybridization using the CosMx platform

hyb_protocol: The hybridized samples were then processed following the manufacturer’s protocol

scan_protocol: After hybridization, tissue slides were imaged using the CosMx system, capturing immunofluorescence images and individual RNA transcript location

data_processing:
Image processing and transcript localization were performed using NanoString’s pipeline, which includes cell segmentation, transcript quantification, and spatial mapping. Cell segmentation was performed based on nuclear and membrane staining
Cell clustering and cell typing, gene set enrichment analysis, differential gene expression, spatial transcriptomic images, heatmaps, and volcano plots were generated using Seurat, Prism and Illustrator
Processed Data File: expression_matrix_Alonso.csv

label: 1000-plex RNA panel

source_name: colorectal cancer

label_protocol: Antibodies used for immunofluorescence included CD298/B2M membrane marker mix, panCK, CD45, and DAPI (Nanostring).

growth_protocol: formalin-fixed, paraffin-embedded (FFPE) tissue sections (5 µm thick) were obtained from 30 patient samples and mounted onto glass slides.

extract_protocol: FFPE sections underwent deparaffinization and rehydration

value: colorectal cancer

tag: disease state

value: Metastatic


title: 417

city: Miami

first: Glaucia Maria

middle: de

last: Mendonça Fernandes

state: FL

address: 4060 SW 97th PL

department: HWCOM Cellular and Molecular Medicine

institute: Florida International University

description: Arraystar Human m6A Single Nucleotide resolution in microarray hybridization were performed based on the Arraystar’s standard protocols. total RNA was divided into two fractions. treated with RNA endoribonuclease MazF to cleave the unmodified m6A sites

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to Arraystar Human m6A Single Nucleotide Arrays (8x15K, Arraystar) at 60°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing:
Raw data was extracted using Agilent Feature Extraction software, retaining probe signals with "P" or "M" quality flags in at least 15 samples. Intensities from MazF-Digested (Cy5-labeled) and MazF-Undigested (Cy3-labeled) samples were normalized using RNA spike-in controls. The normalized MazF-Digested intensities represent the "m6A site abundance" for comparison across samples.
The m6A site abundance was calculated using the normalized intensity of MazF-Digested (Cy5-labeled) RNA, adjusted with spike-in controls. The percentage of m6A methylation (%Modified) was determined by comparing the normalized intensities of MazF-Digested (Cy5) and MazF-Undigested (Cy3) samples, incorporating a correction factor based on sample amounts.

label: MazF-Digested (Cy5-labelled), MazF-Undigested (Cy3-labelled)

source_name: pseudo Progression Disease

label_protocol: "MazF-Digested" and "MazF-Undigested" RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

growth_protocol: Tissue specimens for molecular analysis were selected based on clinical history as PD or psPD, determined by an interdisciplinary tumor board.

extract_protocol: The purity and amount of total RNA samples were determined with NanoDrop ND-1000. RNA integrity was assessed by Bioanalyzer 2100 or Mops electrophoresis. Results were provided in Sample QC report.

treatment_protocol: All samples were collected from the original second surgery and stored as archival formalin-fixed paraffin-embedded (FFPE) tissue.

tag: subject

value: Patient 92

value: Second

value: Glioblastoma

tag: status after 5 years

value: Deceased

tag: time survival

tag: Sex

value: Female

tag: side

value: Left

tag: lobe location

value: Frontal

tag: p53 mutation

value: Negative

tag: egfr

value: No

tag: mgmt

value: Hypermethylated/ Methylated

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: 411_3

tag: subject

value: Patient 90

tag: batch

tag: tissue

tag: status after 5 years

tag: age

value: Right

value: Temporal

value: Positive

value: Not Hypermethylated/ Unmethylated


title: Nvec_25hpf_DMSO_ATACseq_rep1

description:
Library name: STELLA5mC1
ATACseq.all_peaks.counts.tsv
ATACseq.all_peaks.bed

value: 25 hpf gastrulae

tag: cell type

value: Whole embryo

tag: genotype

value: Massachussets

tag: treatment

value: DMSO 0.1%


title: SSB.Amsacrine_hydrochloride.20.B6

description: Library name: SSB.Amsacrine_hydrochloride.20.B6

tag: cell line

value: chronic myelogenous leukemia cell line

value: treated with 20 μM amsacrine hydrochloride

value: 1 hr


title: SSB.Amsacrine_hydrochloride.20.B5

description: Library name: SSB.Amsacrine_hydrochloride.20.B5


title: Nvec_25hpf_DMSO_ATACseq_rep2

description:
Library name: STELLA5mC2
ATACseq.all_peaks.counts.tsv
ATACseq.all_peaks.bed


title: 411_2

value: Patient 89

value: Second

value: Glioblastoma

value: Deceased

tag: time survival

tag: Sex

value: Female

tag: side

tag: lobe location

tag: p53 mutation

tag: egfr

tag: mgmt

tag: wbc

tag: hemoglobin


title: Whole larva, 24 h exposure, 0.008 uM dexamethasone, rep C

description: Library name: DEX_8_C

tag: strain

value: GLTED-Duluth-wt

value: 5-6 dpf

tag: dev stage

value: larvae

value: whole body

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: μM

tag: nominal conc

tag: nominal conc_units

value: Dexamethasone (DTXSID3020384)


title: 387

tag: subject

value: Patient 87

tag: batch

tag: tissue

tag: status after 5 years

tag: time survival

tag: age

tag: Sex

tag: side

value: Left

tag: lobe location

value: Frontal

tag: p53 mutation

value: Negative

tag: egfr

value: Yes

tag: mgmt

value: Hypermethylated/ Methylated

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: Whole larva, 24 h exposure, 0.1 uM fluticasone propionate, rep B

description: Library name: FCP_107_B

tag: strain

value: GLTED-Duluth-wt

tag: dev stage

tag: tissue

tag: store cond

tag: collection date

tag: geo loc_name

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

tag: treatment

value: Fluticasone Propionate (DTXSID8045511)


title: Whole larva, 24 h exposure, 0.1 uM fluticasone propionate, rep A

description: Library name: FCP_107_A

tag: age

value: 5-6 dpf

value: larvae

value: whole body

tag: Sex


title: SSB.Amsacrine_hydrochloride.20.B4

description: Library name: SSB.Amsacrine_hydrochloride.20.B4

tag: cell line

tag: cell type

value: chronic myelogenous leukemia cell line

value: treated with 20 μM amsacrine hydrochloride

tag: batch

value: 1 hr


title: 366

tag: subject

value: Patient 86

value: Second

tag: tissue

value: Glioblastoma

tag: status after 5 years

value: Deceased

tag: time survival

value: Male

tag: side

tag: lobe location

tag: p53 mutation

tag: egfr

tag: mgmt

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: 331_3

tag: subject

value: Patient 85

tag: batch

tag: tissue

tag: age

tag: Sex

value: Right

value: Parietal

value: Positive

value: No


title: 411_1

value: Patient 88

tag: status after 5 years

tag: time survival

value: Female

tag: side

tag: lobe location

value: Temporal

tag: p53 mutation

value: Not Hypermethylated/ Unmethylated


title: 331_2

value: Patient 84

tag: egfr

tag: mgmt

value: Hypermethylated/ Methylated

tag: wbc

tag: hemoglobin

tag: platelets


title: SSB.DMSO.B4

description: Library name: SSB.DMSO.B4

tag: cell line

tag: cell type

value: chronic myelogenous leukemia cell line

tag: treatment

value: treated with DMSO

value: 1 hr


title: 331_1

tag: subject

value: Patient 83

tag: batch

value: Second

value: Glioblastoma

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: Whole larva, 24 h exposure, 0.008 uM dexamethasone, rep A

description: Library name: DEX_8_A

tag: strain

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

value: larvae

tag: tissue

value: whole body

tag: Sex

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: μM

tag: nominal conc

tag: nominal conc_units

value: Dexamethasone (DTXSID3020384)


title: 415

tag: subject

value: Patient 91

tag: batch

tag: status after 5 years

value: Deceased

tag: time survival

value: Female

tag: side

value: Left

tag: lobe location

value: Frontal

tag: p53 mutation

value: Positive

tag: egfr

value: No

tag: mgmt

value: Not Hypermethylated/ Unmethylated

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: 222

tag: subject

value: Patient 81

tag: batch

value: Second

tag: tissue

value: Glioblastoma

tag: age

tag: Sex

value: Male

value: Hypermethylated/ Methylated


title: CosMx, slide_9

treatment_protocol: FFPE sections underwent deparaffinization and rehydration

value: colorectal cancer

tag: disease state

value: Metastatic


title: SSB.Amsacrine_hydrochloride.1.B5

description: Library name: SSB.Amsacrine_hydrochloride.1.B5

tag: cell line

tag: cell type

value: chronic myelogenous leukemia cell line

tag: treatment

value: treated with 1 μM amsacrine hydrochloride

value: 1 hr


title: Whole larva, 24 h exposure, 0.8 uM dexamethasone, rep C

description: Library name: DEX_804_C

tag: strain

value: GLTED-Duluth-wt

value: 5-6 dpf

tag: dev stage

value: larvae

value: whole body

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: μM

tag: nominal conc

tag: nominal conc_units

value: Dexamethasone (DTXSID3020384)


title: 134

tag: subject

value: Patient 79

tag: batch

value: Second

tag: tissue

value: Glioblastoma

tag: status after 5 years

value: Alive

tag: time survival

tag: age

tag: Sex

value: Female

tag: side

value: Left

tag: lobe location

value: Frontal

tag: p53 mutation

value: Positive

tag: egfr

value: No

tag: mgmt

value: Hypermethylated/ Methylated

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: 92

source_name: Progression Disease

tag: subject

value: Patient 76

tag: batch

tag: tissue

tag: status after 5 years

value: Deceased

tag: time survival

value: Male

value: Parietal

value: Not Hypermethylated/ Unmethylated


title: 327

value: Patient 82

tag: age

tag: Sex

tag: side

value: Right

tag: lobe location

tag: p53 mutation

value: Negative

value: Yes


title: SSB.Amsacrine_hydrochloride.1.B6

description: Library name: SSB.Amsacrine_hydrochloride.1.B6

tag: cell line

tag: cell type

value: chronic myelogenous leukemia cell line

tag: treatment

value: treated with 1 μM amsacrine hydrochloride

value: 1 hr


title: 197

value: Patient 80

value: Second

value: Glioblastoma

value: Left

value: Temporal

tag: egfr

tag: mgmt

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort


title: SSB.Amsacrine_hydrochloride.1.B4

description: Library name: SSB.Amsacrine_hydrochloride.1.B4

tag: batch


title: Whole larva, 24 h exposure, 0.08 uM dexamethasone, rep A

description: Library name: DEX_80_A

tag: strain

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

value: larvae

tag: tissue

value: whole body

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: μM

tag: nominal conc

tag: nominal conc_units

value: Dexamethasone (DTXSID3020384)


title: Whole larva, 24 h exposure, 0.08 uM dexamethasone, rep B

description: Library name: DEX_80_B

tag: Sex

value: Great Lakes Toxicology & Ecology Division

tag: treatment


title: 94

tag: subject

value: Patient 77

tag: batch

tag: status after 5 years

value: Deceased

tag: time survival

tag: age

value: Male

tag: side

value: Right

tag: lobe location

value: Frontal

tag: p53 mutation

value: Negative

tag: egfr

tag: mgmt

value: Not Hypermethylated/ Unmethylated

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: 132

tag: subject

value: Patient 78

tag: batch

value: Second

tag: tissue

value: Glioblastoma

tag: status after 5 years

tag: Sex

value: Female

value: Positive

value: No

value: Hypermethylated/ Methylated


title: Multiome, 24hr Flu, GEX, Human

city: CINCINNATI

first: William

last: Zacharias

state: OH

address: 3333 BURNET AVE

institute: Cincinnati Children's Hospital Medical Center

description: Library name: 10X-Zacharias-William-Hufluganoid24hr-20240822-Multiv1-GEX-hg

library_source: transcriptomic single cell

data_processing:
Multiome files were demultiplexed using Cellranger mkfastq then processed using the Cell Ranger Arc pipeline.
Assembly: Custom - GRCm39 with PR8 IAV / GRCh38 with PR8 IAV
Supplementary files format and content: Cell Ranger Arc output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz
Supplementary files format and content: Seurat object: mouse_minseqe_submission_ready.rds, human_minseqe_submission_ready.rds

molecule: nuclear RNA

source_name: Lung

extract_protocol:
Nuclei isolated from flu-exposed and control AEOs at 8, 16, and 24hours were encapsulated in Gel-Beads-in emulsion (GEMs) using the Next-GEM Chromium Single Cell Multiome ATAC + Gene Expression Library & Gel Bead Kit v1 on the 10xChromium.
Standard institutional library preparation protocol for Illumina sequencing at CCMC

value: Lung

tag: cell type

value: Organoid

tag: treatment

value: Flu

tag: timepoint


title: 88

value: Patient 75

tag: time survival

tag: age

tag: side

value: Left

tag: lobe location

value: Temporal

tag: p53 mutation

tag: egfr

tag: mgmt

tag: wbc


title: SSB.Amsacrine_hydrochloride.10.B6

description: Library name: SSB.Amsacrine_hydrochloride.10.B6

tag: cell line

value: chronic myelogenous leukemia cell line

value: treated with 10 μM amsacrine hydrochloride

value: 1 hr


title: Whole larva, 24 h exposure, 0.8 uM dexamethasone, rep B

description: Library name: DEX_804_B

tag: strain

value: GLTED-Duluth-wt

value: 5-6 dpf

tag: dev stage

value: larvae

value: whole body

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: μM

tag: nominal conc

tag: nominal conc_units

value: Dexamethasone (DTXSID3020384)


title: 78

tag: subject

value: Patient 74

tag: batch

value: Second

tag: tissue

value: Glioblastoma

tag: status after 5 years

value: Deceased

tag: time survival

tag: age

tag: Sex

value: Male

tag: side

value: Right

tag: lobe location

value: Frontal

tag: p53 mutation

value: Positive

tag: egfr

value: No

tag: mgmt

value: Not Hypermethylated/ Unmethylated

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: 75

tag: subject

value: Patient 73

tag: batch

tag: tissue

tag: status after 5 years

value: Temporal

value: Negative

tag: wbc


title: 45

value: Patient 70

tag: time survival

tag: age

tag: Sex

value: Female

tag: side

value: Left

tag: lobe location

value: Hypermethylated/ Methylated


title: SSB.Amsacrine_hydrochloride.100.B5

description: Library name: SSB.Amsacrine_hydrochloride.100.B5

tag: cell line

tag: cell type

value: chronic myelogenous leukemia cell line

tag: treatment

value: treated with 100 μM amsacrine hydrochloride

value: 1 hr


title: Whole larva, 24 h exposure, 8 uM dexamethasone, rep C

description: Library name: DEX_8044_C

tag: strain

value: GLTED-Duluth-wt

value: 5-6 dpf

tag: dev stage

value: larvae

value: whole body

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: μM

tag: nominal conc

tag: nominal conc_units

value: Dexamethasone (DTXSID3020384)


title: 475

tag: subject

value: Patient 72

tag: batch

value: Second

tag: tissue

value: Glioblastoma

tag: status after 5 years

value: Deceased

tag: time survival

tag: age

tag: Sex

value: Female

tag: side

tag: lobe location

value: Frontal

tag: p53 mutation

value: Positive

tag: egfr

value: No

tag: mgmt

value: Not Hypermethylated/ Unmethylated

tag: wbc

tag: hemoglobin

tag: platelets

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: 396

tag: subject

value: Patient 66

tag: batch

tag: tissue

value: Male

value: Left

tag: neutrophils

tag: lymohocytes


title: 343

value: Patient 65

tag: status after 5 years

tag: time survival

tag: age

tag: Sex

tag: side

value: Right

value: Hypermethylated/ Methylated


title: Whole larva, 24 h exposure, 8 uM dexamethasone, rep B

description: Library name: DEX_8044_B

tag: strain

value: GLTED-Duluth-wt

value: 5-6 dpf

tag: dev stage

value: larvae

value: whole body

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: μM

tag: nominal conc

tag: nominal conc_units

tag: treatment


title: SSB.Amsacrine_hydrochloride.100.B6

description: Library name: SSB.Amsacrine_hydrochloride.100.B6

tag: cell line

tag: cell type

value: chronic myelogenous leukemia cell line

value: treated with 100 μM amsacrine hydrochloride

tag: batch

value: 1 hr


title: Whole larva, 24 h exposure, 0.8 uM dexamethasone, rep A

description: Library name: DEX_804_A

tag: strain

tag: age

tag: dev stage

tag: tissue

tag: Sex

value: Great Lakes Toxicology & Ecology Division

value: Dexamethasone (DTXSID3020384)


title: 458

tag: subject

value: Patient 71

value: Second

value: Glioblastoma

tag: status after 5 years

value: Deceased

tag: time survival

value: Female

tag: side

value: Right

tag: lobe location

value: Frontal

tag: p53 mutation

value: Positive

tag: egfr

value: No

tag: mgmt

value: Not Hypermethylated/ Unmethylated

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: 401

tag: subject

value: Patient 68

tag: batch

tag: tissue

tag: age

tag: Sex

value: Male

value: Left

value: Temporal

value: Negative


title: SSB.Amsacrine_hydrochloride.100.B4

description: Library name: SSB.Amsacrine_hydrochloride.100.B4

tag: cell line

tag: cell type

value: chronic myelogenous leukemia cell line

tag: treatment

value: treated with 100 μM amsacrine hydrochloride

value: 1 hr


title: SSB.Amsacrine_hydrochloride.0.1.B5

description: Library name: SSB.Amsacrine_hydrochloride.0.1.B5

value: treated with 0.1 μM amsacrine hydrochloride


title: SSB.Amsacrine_hydrochloride.0.1.B6

description: Library name: SSB.Amsacrine_hydrochloride.0.1.B6


title: 440

value: Patient 69

value: Second

value: Glioblastoma

tag: status after 5 years

tag: time survival

tag: side

tag: lobe location

value: Parietal

tag: p53 mutation

tag: egfr

value: Yes

tag: mgmt

tag: wbc


title: Whole larva, 24 h exposure, 0.025 uM dexamethasone, rep C

description: Library name: DEX_25_C

tag: strain

value: GLTED-Duluth-wt

value: 5-6 dpf

tag: dev stage

value: larvae

value: whole body

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: μM

tag: nominal conc

tag: nominal conc_units

value: Dexamethasone (DTXSID3020384)


title: 34

tag: subject

value: Patient 64

tag: batch

tag: tissue

tag: status after 5 years

value: Deceased

tag: time survival

tag: age

tag: Sex

value: Female

tag: side

value: Left

tag: lobe location

value: Temporal

tag: p53 mutation

value: Positive

tag: egfr

value: Hypermethylated/ Methylated

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: Whole larva, 24 h exposure, 8 uM dexamethasone, rep A

description: Library name: DEX_8044_A

tag: strain

value: GLTED-Duluth-wt

value: 5-6 dpf

tag: dev stage

tag: tissue

tag: store cond

tag: collection date

tag: geo loc_name

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

tag: treatment


title: 30

tag: subject

value: Patient 63

tag: batch

value: Second

value: Glioblastoma

tag: status after 5 years

tag: time survival

tag: age

tag: Sex

value: Male

tag: side

tag: lobe location

value: Frontal

tag: p53 mutation

tag: egfr

value: Yes

tag: mgmt

value: Not Hypermethylated/ Unmethylated

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: SSB.Amsacrine_hydrochloride.0.1.B4

description: Library name: SSB.Amsacrine_hydrochloride.0.1.B4

tag: cell line

tag: cell type

value: chronic myelogenous leukemia cell line

tag: treatment

value: treated with 0.1 μM amsacrine hydrochloride

tag: batch

value: 1 hr


title: 277

description: Arraystar Human m6A Single Nucleotide resolution in microarray hybridization were performed based on the Arraystar’s standard protocols. total RNA was divided into two fractions. treated with RNA endoribonuclease MazF to cleave the unmodified m6A sites

tag: subject

value: Patient 62

tag: tissue

tag: status after 5 years

value: Deceased

tag: time survival

tag: age

tag: Sex

tag: side

value: Right

tag: lobe location

value: Negative


title: Whole larva, 24 h exposure, 0.025 uM dexamethasone, rep B

description: Library name: DEX_25_B

tag: strain

value: GLTED-Duluth-wt

tag: dev stage

value: larvae

value: whole body

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: μM

tag: nominal conc

tag: nominal conc_units

value: Dexamethasone (DTXSID3020384)


title: 248

tag: subject

value: Patient 60

tag: batch

value: Second

tag: tissue

value: Glioblastoma

tag: status after 5 years

tag: time survival

tag: age

tag: Sex

value: Male

value: Frontal

tag: p53 mutation

tag: egfr

value: No

tag: mgmt

value: Hypermethylated/ Methylated

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: 201

tag: subject

value: Patient 58

tag: batch

tag: tissue

value: Deceased

tag: side

value: Left

tag: lobe location

value: Temporal

value: Positive

value: Not Hypermethylated/ Unmethylated


title: GM12878 RNA-seq library, BRM014 (10uM) +Dex , 6h , replicate 2

city: Atlanta

first: Alexander

middle: O. D.

last: Gulka

state: Georgia

address: 1510 Clifton Rd NE

institute: Emory University

description: Library name: GM12878_RNA_BRM014_Dex_10uM_6h_rep2

data_processing:
Data were processed using the ENCODE RNA-seq pipeline (v1.2.4, https://github.com/ENCODE-DCC/rna-seq-pipeline), executed using Singularity containers. Reads were mapped to the hg38 reference genome using STAR and gene-level expression quantifications were produced using RSEM.
Assembly: hg38
Supplementary files format and content: RSEM gene-level expression quantifications for each biological replicate, provided as tab-separated value (TSV) files.

growth_protocol: GM12878 cells were cultured in suspension using RPMI-1640 medium (Thermo Scientific, A1049101) supplemented with 2 mM L-glutamine (Thermo Scientific, 25030081), 15% fetal bovine serum (FBS; Fisher Scientific, 10-082-147), and 100U/mL penicillin/streptomycin (Fisher Scientific, 15-140-122). HepG2 cells were cultured in Eagle’s Minimal Essential Medium (ATCC, 30-2003) supplemented with 10% FBS and 100U/mL penicillin/streptomycin.  HepG2 cells were passaged using Trypsin-EDTA (Fisher Scientific, 25-200-072). All cells were maintained at 37 °C in a humidified incubator with 5% CO₂.

extract_protocol:
Cells were harvested by centrifugation at 500 x g for 5 min, and after removing supernatant cell pellets were flash frozen in liquid nitrogen and stored at -80°C until use. Cells were disrupted using QIAshredder columns (Qiagen, 79656) and total RNA was prepared using RNeasy Mini kits (Qiagen, 74104) as per manufacturer protocol. RNA quality was assessed using High Sensitivity RNA ScreenTapes (Agilent, 5067-5580) run on an Agilent 4200 TapeStation system.
PolyA-enriched, stranded RNA-seq libraries were generated from 500ng total RNA for each sample using the Illumina Stranded mRNA prep kit (Illumina, 20040534) following manufacturer protocol. Completed libraries were quantified using a Qubit fluorometer (Thermo Fisher Scientific) with dsDNA High Sensitivity Assay reagents (Thermo Fisher Scientific, Q32854), and library size distributions was evaluated using High Sensitivity D1000 ScreenTapes on an Agilent 4200 TapeStation system.  Libraries were sequenced (150bp paired-end) on an Illumina NovaSeq platform.

treatment_protocol: BRM014 (MedChemExpress, HY-119374) was prepared as a 10mM stock in dimethyl sulfoxide (DMSO) and used at a final concentration of 10µM unless otherwise indicated. Vehicle controls were treated with an equivalent concentration of DMSO. For initial stimulus panel, cells were treated with lipopolysaccharide (Sigma L9641, 10ng/mL), tumor necrosis factor alpha (Genscript Z01001, 25ng/mL), interferon gamma (Genscript, Z02986, 100ng/mL), interleukin 2 (Sigma, 11011456001, 50U/mL), dexamethasone (MedChemExpress, HY-14648, 500nM), or doxorubicin (Selleck Chem, E2516, 500nM) for 6h. For BAFinh pretreatment experiments, 10µM BRM014 (or DMSO vehicle) was added to cells 30min prior to the addition of either 100ng/mL IFN-γ or 500nM Dex for 1h or 6h.

tag: cell line

tag: cell type

value: Lymphoblastoid cell line

tag: treatment

tag: timepoint

tag: inhibitor/protac concentration


title: 243

value: Patient 59

tag: status after 5 years

tag: time survival

tag: age

tag: Sex

value: Right

tag: p53 mutation

tag: egfr

value: Yes

tag: mgmt

tag: wbc

tag: hemoglobin

tag: platelets


title: Whole larva, 24 h exposure, 0.025 uM dexamethasone, rep A

description: Library name: DEX_25_A

tag: strain

value: GLTED-Duluth-wt

value: 5-6 dpf

tag: dev stage

value: larvae

tag: tissue

value: whole body

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: μM

tag: nominal conc

tag: nominal conc_units

value: Dexamethasone (DTXSID3020384)


title: GM12878 RNA-seq library, BRM014 (10uM) +Dex , 1h , replicate 2

description: Library name: GM12878_RNA_BRM014_Dex_10uM_1h_rep2

tag: cell line

tag: cell type

tag: treatment

tag: timepoint

tag: inhibitor/protac concentration


title: 185_2

tag: subject

value: Patient 56

tag: batch

value: Second

tag: tissue

value: Glioblastoma

tag: status after 5 years

value: Deceased

tag: time survival

tag: age

tag: Sex

value: Male

tag: side

value: Left

tag: lobe location

value: Temporal

tag: p53 mutation

value: Positive

tag: egfr

value: No

tag: mgmt

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: GM12878 RNA-seq library, BRM014 (10uM) +Dex , 6h , replicate 1

description: Library name: GM12878_RNA_BRM014_Dex_10uM_6h_rep1

tag: cell line

tag: cell type

value: Lymphoblastoid cell line

tag: treatment

tag: timepoint

tag: inhibitor/protac concentration


title: Whole larva, 24 h exposure, 0.25 uM dexamethasone, rep B

description: Library name: DEX_255_B

tag: strain

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

value: larvae

tag: tissue

value: whole body

tag: Sex

value: not determined

tag: store cond

tag: collection date

tag: geo loc_name

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units


title: Whole larva, 24 h exposure, 0.25 uM dexamethasone, rep C

description: Library name: DEX_255_C

tag: strain

value: -80 deg C

value: USA:Minnesota, Duluth

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

value: μM

tag: treatment

value: Dexamethasone (DTXSID3020384)


title: Whole larva, 24 h exposure, 0.25 uM dexamethasone, rep A

description: Library name: DEX_255_A

tag: age

tag: dev stage


title: 4

tag: subject

value: Patient 67

tag: batch

value: Second

tag: tissue

value: Glioblastoma

tag: status after 5 years

value: Deceased

tag: time survival

tag: Sex

value: Male

tag: side

value: Right

tag: lobe location

value: Parietal

tag: p53 mutation

value: Negative

tag: egfr

value: Yes

tag: mgmt

value: Not Hypermethylated/ Unmethylated

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: 165

tag: subject

value: Patient 52

tag: batch

tag: tissue

tag: status after 5 years

tag: age

value: Female

value: Positive

value: No


title: 185_3

value: Patient 57

tag: time survival

tag: Sex

tag: side

value: Left

tag: lobe location

value: Temporal

tag: p53 mutation


title: 18

value: Patient 54

tag: egfr

tag: mgmt

tag: wbc

tag: hemoglobin

tag: platelets


title: 185_1

value: Patient 55

value: Second

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions


title: 177

source_name: On a+F57

tag: subject

value: Patient 53

tag: batch

tag: tissue

value: Glioblastoma

tag: status after 5 years

value: Deceased

tag: cycles completed


title: GM12878 RNA-seq library, BRM014 (10uM) +Dex , 1h , replicate 1

description: Library name: GM12878_RNA_BRM014_Dex_10uM_1h_rep1

tag: cell line

tag: cell type

value: Lymphoblastoid cell line

tag: treatment

tag: timepoint

tag: inhibitor/protac concentration


title: GM12878 RNA-seq library, BRM014 (10uM) +IFNg , 6h , replicate 2

description: Library name: GM12878_RNA_BRM014_IFNg_10uM_6h_rep2


title: Whole larva, 24 h exposure, 2.5 uM dexamethasone, rep C

description: Library name: DEX_2545_C

tag: strain

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

value: larvae

value: whole body

tag: Sex

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: μM

tag: nominal conc

tag: nominal conc_units

value: Dexamethasone (DTXSID3020384)


title: GM12878 RNA-seq library, BRM014 (10uM) +IFNg , 6h , replicate 1

description: Library name: GM12878_RNA_BRM014_IFNg_10uM_6h_rep1

tag: cell line

tag: cell type

tag: treatment

tag: timepoint

tag: inhibitor/protac concentration


title: Whole larva, 24 h exposure, 2.5 uM dexamethasone, rep B

description: Library name: DEX_2545_B

tag: strain

tag: age

tag: dev stage

tag: tissue

tag: Sex

tag: store cond

value: Great Lakes Toxicology & Ecology Division


title: 142

tag: subject

value: Patient 47

tag: batch

value: Second

tag: status after 5 years

tag: time survival

value: Female

tag: side

value: Right

tag: lobe location

value: Temporal

tag: p53 mutation

value: Positive

tag: egfr

value: Yes

tag: mgmt

value: Not Hypermethylated/ Unmethylated

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: 126

tag: subject

value: Patient 44

tag: batch

tag: tissue

value: Glioblastoma

value: Deceased

tag: age

tag: Sex

value: No

value: Hypermethylated/ Methylated


title: GM12878 RNA-seq library, BRM014 (10uM) +IFNg , 1h , replicate 1

description: Library name: GM12878_RNA_BRM014_IFNg_10uM_1h_rep1

tag: cell line

tag: cell type

value: Lymphoblastoid cell line

tag: treatment

tag: timepoint

tag: inhibitor/protac concentration


title: 160

value: Patient 50

tag: status after 5 years

tag: time survival

tag: side

value: Left

tag: lobe location

value: Parietal

tag: p53 mutation

tag: egfr

tag: mgmt

tag: wbc

tag: hemoglobin

tag: platelets


title: 121_2

tag: subject

value: Patient 41

tag: batch

tag: tissue

tag: age

value: Male

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: GM12878 RNA-seq library, BRM014 (10uM) +Veh , 6h , replicate 2

description: Library name: GM12878_RNA_BRM014_Veh_10uM_6h_rep2

tag: cell line

tag: cell type

tag: treatment

tag: timepoint

tag: inhibitor/protac concentration


title: 16

value: Patient 49

value: Second

tag: status after 5 years

tag: time survival

tag: Sex

tag: side

tag: lobe location

tag: p53 mutation

tag: egfr

tag: mgmt

tag: wbc

tag: hemoglobin


title: Whole larva, 24 h exposure, 25 uM dexamethasone, rep B

description: Library name: DEX_25455_B

tag: strain

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

value: larvae

tag: tissue

value: whole body

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: μM

tag: nominal conc

tag: nominal conc_units

value: Dexamethasone (DTXSID3020384)


title: 161

tag: subject

value: Patient 51

tag: batch

value: Glioblastoma

tag: status after 5 years

value: Deceased

tag: time survival

tag: Sex

tag: side

value: Right

tag: lobe location

tag: p53 mutation

tag: egfr

tag: mgmt

value: Hypermethylated/ Methylated

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: Whole larva, 24 h exposure, 2.5 uM dexamethasone, rep A

description: Library name: DEX_2545_A

tag: strain

tag: age

tag: dev stage

tag: tissue

tag: store cond

tag: collection date

tag: geo loc_name

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

tag: treatment


title: Whole larva, 24 h exposure, 0.008 uM dexamethasone, rep B

description: Library name: DEX_8_B

tag: strain

value: GLTED-Duluth-wt

tag: Sex


title: 152

tag: subject

value: Patient 48

tag: batch

value: Second

tag: status after 5 years

tag: time survival

tag: age

value: Male

tag: side

value: Left

tag: lobe location

value: Parietal

tag: p53 mutation

value: Positive

tag: egfr

value: No

tag: mgmt

value: Not Hypermethylated/ Unmethylated

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: GM12878 RNA-seq library, BRM014 (10uM) +IFNg , 1h , replicate 2

description: Library name: GM12878_RNA_BRM014_IFNg_10uM_1h_rep2

tag: cell line

tag: cell type

value: Lymphoblastoid cell line

tag: treatment

tag: timepoint

tag: inhibitor/protac concentration


city: Yangzhou

first: Juan

last: Yang

address: 大学南路88号

department: College of Veterinary Medicine

institute: Yangzhou University

description:
Library name: PAM, SPI1 knockdown, RNA-seq, replicate 2
Column name in SPI1KD_vs_NC_PAM_merged_count.txt: si_3_24h.bam

data_processing:
Raw reads were trimmed with Trim Galore v0.6.5 Clean reads were aligned to the reference genome ((Sscrofa11.1) using STAR v2.7.3 Obtaining gene-level read counts using the featureCount function from subread v2.0.0 calculated TPM/FPKM value for each gene using RSEM v1.3.2 differentially expressed genes were identified with FDR<0.05 and fold change>1 using DESeq2 v1.36.0
Assembly: Sscrofa11.1
Supplementary files format and content: tab-delimited table, gene-level read counts

organism: Sus scrofa

source_name: PAM

extract_protocol:
Total RNA was extracted using RNAiso Plus (TaKaRa, 9109) with DNase digestion.
RNA-seq libraries were construction by using DNBSEQ Eukaryotic Strand-specific mRNA library sample preparation kit (BGI), and sequenced as 150 bp paired-end reads with DNBSEQ platform (DNBSEQ Technology).

value: PAM

value: porcine alveolar macrophages

value: SPI1-siRNA 24 hours


title: 121_3

tag: subject

value: Patient 42

tag: batch

tag: tissue

value: Glioblastoma

tag: status after 5 years

value: Deceased

tag: time survival

tag: age

tag: Sex

tag: side

tag: lobe location

tag: p53 mutation


title: 141

value: Patient 46

value: Female

value: Frontal

tag: egfr

tag: mgmt

value: Hypermethylated/ Methylated

tag: wbc

tag: hemoglobin

tag: platelets

tag: chemort

tag: number of gy admonistered

tag: number of fractions


title: GM12878 RNA-seq library, BRM014 (10uM) +Veh , 1h , replicate 2

description: Library name: GM12878_RNA_BRM014_Veh_10uM_1h_rep2

tag: cell line

tag: cell type

tag: treatment

tag: timepoint

tag: inhibitor/protac concentration


title: 133

tag: subject

value: Patient 45

tag: batch

value: Second

tag: tissue

tag: status after 5 years

tag: time survival

tag: age

tag: Sex

value: Right

value: Temporal

tag: neutrophils

tag: lymohocytes

tag: cycles completed


title: Whole larva, 24 h exposure, 25 uM dexamethasone, rep C

description: Library name: DEX_25455_C

tag: strain

value: GLTED-Duluth-wt

value: 5-6 dpf

tag: dev stage

value: larvae

value: whole body

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: μM

tag: nominal conc

tag: nominal conc_units

value: Dexamethasone (DTXSID3020384)


title: 123

tag: subject

value: Patient 43

tag: batch

tag: tissue

value: Glioblastoma

tag: status after 5 years

value: Deceased

tag: time survival

tag: age

tag: Sex

value: Female

tag: side

tag: lobe location

value: Frontal

tag: p53 mutation

value: Positive

tag: egfr

tag: mgmt

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: chemort

tag: number of gy admonistered

tag: number of fractions


title: Whole larva, 24 h exposure, 25 uM dexamethasone, rep A

description: Library name: DEX_25455_A

tag: strain

value: GLTED-Duluth-wt

tag: dev stage

tag: tissue

tag: store cond

tag: collection date

tag: geo loc_name

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

tag: treatment


title: GM12878 RNA-seq library, BRM014 (10uM) +Veh , 6h , replicate 1

description: Library name: GM12878_RNA_BRM014_Veh_10uM_6h_rep1

tag: cell line

tag: cell type

value: Lymphoblastoid cell line

tag: timepoint

tag: inhibitor/protac concentration


title: 121_1

tag: subject

value: Patient 40

tag: batch

value: Second

tag: tissue

tag: status after 5 years

tag: time survival

tag: age

tag: Sex

value: Male

tag: side

value: Right

tag: lobe location

value: Parietal

tag: p53 mutation

tag: egfr

tag: mgmt

value: Hypermethylated/ Methylated

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: 11

tag: subject

value: Patient 38

tag: batch

tag: tissue

tag: status after 5 years

tag: time survival

value: Left

value: Negative


title: PAM, NC, RNA-seq, replicate 2

description:
Library name: PAM, NC, RNA-seq, replicate 2
Column name in SPI1KD_vs_NC_PAM_merged_count.txt: nc_2_24h.bam

tag: cell line

value: PAM

tag: cell type

value: porcine alveolar macrophages

tag: treatment

value: NC 24 hours


title: 60a

value: Patient 36

value: First

value: Glioblastoma

value: Deceased

tag: age

tag: Sex

tag: side

tag: lobe location

value: Occipital

tag: p53 mutation

tag: egfr

value: Yes

tag: mgmt

value: Not Hypermethylated/ Unmethylated

tag: wbc


title: 57a

value: Patient 34

value: Female

value: Frontal

value: Positive

value: No

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: GM12878 RNA-seq library, DMSO+Dex , 6h , replicate 2

description: Library name: GM12878_RNA_DMSO_Dex_6h_rep2

tag: cell line

tag: cell type

value: Lymphoblastoid cell line

tag: treatment

tag: timepoint

tag: inhibitor/protac concentration


title: 114

tag: subject

value: Patient 39

tag: batch

value: Second

tag: tissue

tag: status after 5 years

tag: time survival

tag: age

tag: Sex

value: Male

tag: side

value: Left

tag: lobe location

tag: p53 mutation


title: 59a

value: Patient 35

value: Right

value: Parietal

value: Negative

tag: mgmt

value: Hypermethylated/ Methylated

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions


title: GM12878 RNA-seq library, DMSO+Dex , 6h , replicate 1

description: Library name: GM12878_RNA_DMSO_Dex_6h_rep1

tag: cell line

tag: cell type

tag: treatment

tag: timepoint

tag: inhibitor/protac concentration


description:
Library name: PAM, SPI1 knockdown, RNA-seq, replicate 1
Column name in SPI1KD_vs_NC_PAM_merged_count.txt: si_2_24h.bam

value: PAM

value: porcine alveolar macrophages

value: SPI1-siRNA 24 hours


title: 104

description: Arraystar Human m6A Single Nucleotide resolution in microarray hybridization were performed based on the Arraystar’s standard protocols. total RNA was divided into two fractions. treated with RNA endoribonuclease MazF to cleave the unmodified m6A sites

tag: subject

value: Patient 37

tag: batch

tag: tissue

value: Glioblastoma

tag: status after 5 years

value: Deceased

tag: time survival

tag: age

tag: Sex

value: Female

tag: side

tag: egfr

value: Yes

value: Not Hypermethylated/ Unmethylated

tag: cycles completed


title: 55a

value: Patient 32

value: First

tag: lobe location

value: Occipital

tag: p53 mutation

tag: mgmt

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered


title: PAM, NC, RNA-seq, replicate 1

description:
Library name: PAM, NC, RNA-seq, replicate 1
Column name in SPI1KD_vs_NC_PAM_merged_count.txt: nc_1_24h.bam

tag: cell line

tag: cell type

tag: treatment

value: NC 24 hours


title: 56a

tag: subject

value: Patient 33

tag: batch

tag: tissue

tag: status after 5 years

tag: time survival

tag: age

tag: Sex

value: Male

value: Right

value: Temporal

value: Positive

tag: number of fractions


title: GM12878 RNA-seq library, DMSO+Dex , 1h , replicate 2

description: Library name: GM12878_RNA_DMSO_Dex_1h_rep2

value: Lymphoblastoid cell line

tag: timepoint

tag: inhibitor/protac concentration


title: GM12878 RNA-seq library, BRM014 (10uM) +Veh , 1h , replicate 1

description: Library name: GM12878_RNA_BRM014_Veh_10uM_1h_rep1


title: CTCF - NPC neurons rep2

city: Cambridge

first: Bongmin

last: Bae

state: MA

address: 16 Divinity Ave

institute: Harvard University

description:
Library name: CTCF_NPCneuron_2
CTCF - NPC neurons rep2

library_source: other

data_processing:
Adapters sequences were automatically detected and trimmed using TrimGalore. Reads were mapped to CAST SNP-masked GRCm39 genome using bowtie2 --local -X 2000. PCR duplicates were removed using Picard MarkDuplicates. Allele-specific reads were parsed using SNPsplit (v 0.6.0). For visualization purposes, bam files were converted to bigwig files with CPM normalization.
Assembly: GRCm39
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

molecule: other

organism: Mus musculus

source_name: NPC-derived neuron

growth_protocol: Cortices from E16 embryos were carefully collected into cortical neuron plating media (Neurobasal supplemented with 2% B27, 2% FBS and 1X glutamine). Tissues were mechanically triturated into the plating media by pipetting up and down with 1000μL micropipette tips. Cell suspensions were filtered through a 40 μm cell strainer. Dissociated cells were plated onto Poly-D-lysine coated plates with plating media. Next day, media was replaced with cortical neuron maintenance media (Neurobasal supplemented with 2% B27 and 1X glutamine) and kept at 37°C with 5% CO2 until use. / NPCs were plated onto Geltrex coated plates at a density of 50,000 cells/mL (e.g. in 12 well plates 50,000 cells with 1 mL media, and in 6 well plates 100,000 cells in 2 mL media), and incubated for 3-4 hours to allow cell adherence. Transduction was performed at 7500 genomic particles per cell. Next day, NPC media was fed to keep multipotent state of the NPCs. After 48h of transduction, cells were replated onto new Geltrex coated plates with blasticidin-supplemented media. The next day, neuron differentiation was induced by replating NPCs onto PDL coated plates with cortical neuron media with blasticidin. The following day, cell culture media was optionally replaced to fresh cortical neuron media to enhance neuronal differentiation.

extract_protocol:
Cells were gently washed with PBS and scraped into 1 ml PBS. An aliquot equivalent of 600,000 cells were used for each CUT&Tag sample. Cells were collected by centrifugation for 4 min at 300xg and supernatant was discarded.
Cells were resuspended in lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 0.5 mM spermidine, 1.5 mM MgCl, 0.1 mM EDTA, and 0.25% IGEPAL CA-630) and incubated for 5 min on ice. Lysis was assisted mechanically by gently pipetting up and down 10 times with 1000 μL tips. Successful lysis was confirmed by Typan blue staining and inspection under a light microscope. Nuclei were collected by centrifugation for 4 min at 800xg. Nuclei pellet was washed with CUT&Tag wash buffer and resuspended in 1.5 mL wash buffer. All the procedures were performed according to manufacturer’s guides. Concanavalin A beads were conditioned by washing with 1.6 mL 1X CUT&Tag binding buffer two times. Prepared beads were resuspended in binding buffer and slowly added to the nuclei suspension. For each sample, 20 μL of beads were used. Nuclei binding was performed for 10 min at room temperature in a rotator. Beads-bound nuclei were collected using a magnetic stand and clear supernatant was discarded. Beads were resuspended in 50 μL ice-cold CUT&Tag antibody buffer and desired amount of antibody was added. Suspension was gently mixed by vortexing. Primary antibody binding was performed overnight at 4°C. After a quick spin, beads were cleared on a magnetic stand and supernatant was discarded. Beads were resuspended in 100 μL of 1:100 diluted secondary antibody in CUT&Tag Dig-Wash buffer and incubated for 1h at room temp with rotation. After secondary antibody binding, three washes with 1 mL CUT&Tag Dig-Wash buffer were performed. Beads were resuspended in 1:100 diluted CUT&Tag transposomes in CUT&Tag Dig-300 buffer and incubated on an orbital rotator for 60 min at room temperature. After transposome binding, beads were washed three times with Dig-300 buffer. Tagmentation was induced by incubating beads in 125 μL of CUT&Tag tagmentation buffer for 1h at 37°C. After tagmentation, total DNA was extracted using columns. Purified DNA was PCR amplified using proper index primers. Then, the PCR reaction was purified using SPRI beads. Samples were pooled equimolar. Sequencing was performed PE150.

value: NPC-derived neuron

tag: genotype


title: GM12878 RNA-seq library, DMSO+Dex , 1h , replicate 1

description: Library name: GM12878_RNA_DMSO_Dex_1h_rep1


title: CTCF - NPC neurons rep1

description:
Library name: CTCF_NPCneuron_1
CTCF - NPC neurons rep1


title: 51a

value: Patient 30

tag: side

tag: lobe location

value: Parietal

tag: p53 mutation

tag: egfr

value: No

tag: mgmt

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: cycles completed


title: 50a

tag: subject

value: Patient 29

tag: batch

tag: tissue

value: Glioblastoma

tag: status after 5 years

value: Deceased

tag: time survival

tag: age

value: Left

value: Hypermethylated/ Methylated

tag: chemort

tag: number of gy admonistered


title: 52a

value: Patient 31

value: First

value: Alive

tag: Sex

tag: side

tag: lobe location

tag: p53 mutation

tag: number of fractions


title: GM12878 RNA-seq library, DMSO+IFNg , 6h , replicate 2

description: Library name: GM12878_RNA_DMSO_IFNg_6h_rep2

tag: cell line

tag: cell type

tag: treatment

tag: timepoint

tag: inhibitor/protac concentration


title: 45a

tag: subject

value: Patient 27

tag: batch

value: Female

value: Frontal

tag: egfr

value: Yes

tag: mgmt

value: Not Hypermethylated/ Unmethylated

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: cycles completed


title: 49a

value: Patient 28

tag: tissue

tag: status after 5 years

tag: time survival

tag: age

tag: Sex

value: Male

tag: side

value: Right

tag: lobe location

tag: p53 mutation

value: Positive

tag: chemort

tag: number of gy admonistered


title: CTCF - NPC rep1

description:
Library name: CTCF_NPC_1
CTCF - NPC rep1

source_name: NPC

tag: cell type

value: NPC

tag: genotype


title: 44a

tag: subject

value: Patient 26

tag: batch

value: Glioblastoma

value: Occipital

value: Negative

tag: egfr

tag: mgmt

tag: wbc

tag: hemoglobin

tag: number of fractions


title: CTCF - NPC rep2

description:
Library name: CTCF_NPC_2
CTCF - NPC rep2


title: 41a

value: Patient 24

tag: tissue

tag: status after 5 years

value: Deceased

tag: time survival

value: Temporal

value: No

value: Hypermethylated/ Methylated

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: cycles completed


title: GM12878 RNA-seq library, DMSO+IFNg , 1h , replicate 1

description: Library name: GM12878_RNA_DMSO_IFNg_1h_rep1

tag: cell line

value: Lymphoblastoid cell line

tag: treatment

tag: timepoint

tag: inhibitor/protac concentration


title: GM12878 RNA-seq library, DMSO+IFNg , 6h , replicate 1

description: Library name: GM12878_RNA_DMSO_IFNg_6h_rep1

tag: cell type


title: SSB.Amsacrine_hydrochloride.10.B4

description: Library name: SSB.Amsacrine_hydrochloride.10.B4

value: chronic myelogenous leukemia cell line

value: treated with 10 μM amsacrine hydrochloride

tag: batch

value: 1 hr


title: 38a

tag: subject

value: Patient 22

value: First

tag: age

tag: Sex

value: Female

tag: side

value: Left

tag: lobe location

tag: p53 mutation

tag: egfr

tag: mgmt

tag: chemort

tag: number of gy admonistered


title: GM12878 RNA-seq library, DMSO+IFNg , 1h , replicate 2

description: Library name: GM12878_RNA_DMSO_IFNg_1h_rep2


title: H3K9me3 - NPC neuron treated with LV-E111 rep2

description:
Library name: H3K9me3_E111_2
H3K9me3_E111_2

value: NPC-derived neuron

tag: genotype

value: E111 gRNA


title: 40a

value: Patient 23

tag: tissue

value: Glioblastoma

tag: status after 5 years

tag: time survival

value: Male

value: Right

value: Occipital

value: Positive

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: number of fractions

tag: cycles completed


title: Multiome, 24hr Control, GEX, Human

description: Library name: 10X-Zacharias-William-Huganoidcon24hr-20240822-Multiv1-GEX-hg

value: Lung

tag: cell type

value: Organoid

tag: treatment

value: Control

tag: timepoint


title: GM12878 RNA-seq library, DMSO+Veh , 6h , replicate 2

description: Library name: GM12878_RNA_DMSO_Veh_6h_rep2

tag: cell line

value: Lymphoblastoid cell line

tag: inhibitor/protac concentration


title: Whole larva, 24 h exposure, 0.08 uM dexamethasone, rep C

description: Library name: DEX_80_C

tag: strain

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

value: larvae

value: whole body

tag: Sex

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: μM

tag: nominal conc

tag: nominal conc_units

value: Dexamethasone (DTXSID3020384)


title: H3K9me3 - NPC neuron treated with LV-E111 rep1

description:
Library name: H3K9me3_E111_1
H3K9me3_E111_1

tag: cell type

value: NPC-derived neuron

tag: genotype

tag: treatment

value: E111 gRNA


title: H3K9me3 - NPC neuron treated with LV-E105 rep2

description:
Library name: H3K9me3_E105_2
H3K9me3_E105_2

value: E105 gRNA


title: 42a

description: Arraystar Human m6A Single Nucleotide resolution in microarray hybridization were performed based on the Arraystar’s standard protocols. total RNA was divided into two fractions. treated with RNA endoribonuclease MazF to cleave the unmodified m6A sites

tag: subject

value: Patient 25

tag: batch

value: First

tag: tissue

value: Glioblastoma

tag: status after 5 years

value: Deceased

tag: time survival

tag: age

value: Female

tag: side

value: Right

tag: lobe location

value: Temporal

tag: p53 mutation

value: Positive

tag: egfr

value: No

tag: mgmt

value: Not Hypermethylated/ Unmethylated

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: 34a

tag: subject

value: Patient 20

tag: batch

tag: tissue

tag: status after 5 years

tag: Sex

value: Male

value: Left

value: Parietal

value: Yes


title: 37a

value: Patient 21

tag: time survival

tag: age

tag: side

tag: lobe location

tag: p53 mutation


title: 8a

value: Patient 17

tag: egfr

tag: mgmt

value: Hypermethylated/ Methylated

tag: wbc

tag: hemoglobin

tag: platelets


title: GM12878 RNA-seq library, DMSO+Veh , 6h , replicate 1

description: Library name: GM12878_RNA_DMSO_Veh_6h_rep1

tag: cell line

tag: cell type

value: Lymphoblastoid cell line

tag: treatment

tag: timepoint

tag: inhibitor/protac concentration


title: H3K9me3 - NPC neuron treated with LV-E105 rep1

description:
Library name: H3K9me3_E105_1
H3K9me3_E105_1

value: NPC-derived neuron

tag: genotype

value: E105 gRNA


title: 9a

tag: subject

value: Patient 18

tag: batch

value: First

tag: tissue

value: Glioblastoma

tag: status after 5 years

value: Deceased

tag: Sex

value: Female

value: Frontal

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: GM12878 RNA-seq library, DMSO+Veh , 1h , replicate 2

description: Library name: GM12878_RNA_DMSO_Veh_1h_rep2

tag: cell line


title: 7a

value: Patient 16

tag: time survival

tag: age

tag: side

tag: lobe location

tag: p53 mutation

value: Positive

tag: egfr

tag: mgmt

value: Not Hypermethylated/ Unmethylated

tag: wbc

tag: hemoglobin

tag: platelets


title: Whole larva, 24 h exposure, 0.019 uM fluticasone propionate, rep B

description: Library name: FCP_19_B

tag: strain

value: GLTED-Duluth-wt

value: 5-6 dpf

tag: dev stage

value: larvae

tag: tissue

value: whole body

tag: Sex

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: μM

tag: nominal conc

tag: nominal conc_units

tag: treatment

value: Fluticasone Propionate (DTXSID8045511)


title: H3K9me3 - NPC neuron treated with LV-E104 rep2

description:
Library name: H3K9me3_E104_2
H3K9me3_E104_2

tag: cell type

value: NPC-derived neuron

tag: genotype

value: E104 gRNA


title: 4a

tag: subject

value: Patient 14

tag: batch

value: First

tag: tissue

value: Glioblastoma

tag: status after 5 years

value: Deceased

tag: time survival

tag: age

value: Female

tag: side

value: Left

tag: lobe location

value: Parietal

tag: p53 mutation

value: Negative

tag: egfr

value: Yes

tag: mgmt

value: Hypermethylated/ Methylated

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: GM12878 RNA-seq library, Dex , 6h , replicate 2

description: Library name: GM12878_RNA_Dex_6h_rep2

tag: cell line

tag: cell type

value: Lymphoblastoid cell line

tag: treatment

value: Dex

tag: timepoint

tag: inhibitor/protac concentration


title: H3K9me3 - NPC neuron treated with LV-E104 rep1

description:
Library name: H3K9me3_E104_1
H3K9me3_E104_1

tag: genotype


title: 2a

tag: subject

value: Patient 12

tag: batch

tag: tissue

tag: status after 5 years

tag: time survival

tag: age

tag: Sex

tag: side

tag: lobe location

value: Frontal

tag: p53 mutation

value: Positive

tag: egfr

value: No


title: 28a

value: Patient 10

value: Male

value: Right

tag: mgmt

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: 5a

tag: subject

value: Patient 15

tag: batch

value: First

tag: tissue

value: Glioblastoma

tag: status after 5 years

tag: time survival

value: Not Hypermethylated/ Unmethylated


title: H3K9me3 - NPC neuron treated with LV-Scrb rep1

description:
Library name: H3K9me3_Scrb_1
H3K9me3_Scrb_1

tag: cell type

value: NPC-derived neuron

tag: genotype

tag: treatment

value: Scrb gRNA


title: tumor-infiltrating type 1 conventional dendritic cells,  Wild type, Day13, rep3

first: Hongjiao

last: Wang

address: xiangannanlu

institute: xiamen university

description:
Library name: Sample 6
WT_DC1_3

data_processing:
Data quality control: Raw data (raw reads) of fastq format were firstly processed throughfastpsoftware. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-Nandlowquality reads from raw data. At the same time, Q20, Q30 and GCcontent the clean data were calculated. All the downstreamanalyses were basedon the clean data with high quality.                                                                                Reads mapping to the reference genome: Reference genome and gene model annotation files were downloadedfrom genome website. Use HISAT2 (2.2.1) to build the index of thereference genome, and use HISAT2 to align paired-end clean reads to the reference genome. HISAT2 can use the gene model annotationfiletocreate splice-aware alignments, providing better alignment accuracycompared to other non-splice alignment tools.                     Quantification of gene expression level: featureCounts (2.0.6) was used to count the reads numbers mappedtoeach gene. And then FPKM of each gene was calculated based onthelength of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequenceper Millions base pairs sequenced, considers the effect of sequencingdepthand gene length for the reads count at the same time, and is currentlythe most commonly used method for estimating gene expressionlevels.                         Differential expression analysis: Differential expression analysis for two conditions/groups was performed using the DESeq2 R package(1.42.0). DESeq2 provides statistical programs for determining differential expression in digital gene expression data using models based on negative binomial distribution. The resulting P-value is adjusted using the Benjamini and Hochberg’s methods to control theerror discovery rate. The threshold of significant differential expression：padj <= 0.05 ＆ |log2(foldchange)| >= 1.
Assembly: mm10
Supplementary files format and content: CSV file includes raw counts for each sample.

source_name: B16-F10 subcutaneous tumor

extract_protocol:
Total RNA were extracted using Life-Trizol. A total amount of 500 ng RNA per sample was used as input material for the RNA sample preparations.
Messenger RNA (mRNA) was enriched from total RNA using oligo(dT) magnetic beads. Following fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. Subsequently, the cDNA fragments underwent end repair, A-tailing, adapter ligation, size selection, PCR amplification, and purification to generate the final sequencing library.

value: B16-F10 subcutaneous tumor


title: 24a

value: Patient 7

value: Deceased

tag: age

tag: Sex

tag: side

value: Left

tag: lobe location

value: Temporal

tag: p53 mutation

value: Negative

tag: egfr

tag: mgmt

value: Hypermethylated/ Methylated

tag: wbc


title: GM12878 RNA-seq library, Dox , 6h , replicate 1

description: Library name: GM12878_RNA_Dox_6h_rep1

tag: cell line

value: Lymphoblastoid cell line

value: Dox

tag: timepoint

tag: inhibitor/protac concentration


title: GM12878 RNA-seq library, DMSO+Veh , 1h , replicate 1

description: Library name: GM12878_RNA_DMSO_Veh_1h_rep1


title: H3K9me3 - NPC neuron treated with LV-Scrb rep2

description:
Library name: H3K9me3_Scrb_2
H3K9me3_Scrb_2


title: 27a

tag: subject

value: Patient 9

tag: batch

tag: tissue

value: Male

value: Positive

value: Yes

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered

tag: number of fractions

tag: cycles completed


title: 29a

value: Patient 11

value: First

value: Glioblastoma

tag: status after 5 years

tag: time survival

tag: age

tag: Sex

tag: side

tag: lobe location

tag: p53 mutation

tag: egfr

value: No


title: GM12878 RNA-seq library, Dex , 6h , replicate 1

description: Library name: GM12878_RNA_Dex_6h_rep1

tag: cell line

tag: cell type

tag: treatment

value: Dex

tag: timepoint

tag: inhibitor/protac concentration


title: GM12878 RNA-seq library, IFNg , 6h , replicate 2

description: Library name: GM12878_RNA_IFNg_6h_rep2

value: IFNg


title: tumor-infiltrating type 1 conventional dendritic cells,  Wild type, Day13, rep2

description:
Library name: Sample 5
WT_DC1_2

tag: tissue

value: B16-F10 subcutaneous tumor


title: 26a

tag: subject

value: Patient 8

tag: batch

value: Deceased

value: Female

value: Left

value: Frontal

tag: mgmt

tag: wbc

tag: hemoglobin

tag: platelets

tag: neutrophils

tag: lymohocytes

tag: chemort

tag: number of gy admonistered