title: Sample45.eRapa.205844020021_R03C02


title: Sample39.eRapa.205844020021_R03C01

status: Public on Aug 05 2022

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

country: USA

institute: University of California, Los Angeles

description: genomic DNA methylation from tissue=Liver species=Mouse

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

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

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

label: Cy3 and Cy5

molecule: genomic DNA

organism: Mus musculus

source_name: Liver

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

tag: age

tag: Sex

value: Male

tag: tissue

value: Liver

tag: agemonths

tag: treatment

value: eRapa

tag: platenumber

value: Plate 01

tag: welladdress


title: UMCG-esoph-P98t0-TR2694

type: SRA

city: Amsterdam

first: Myron

last: Best

address: De Boelelaan 1117

department: Neurosurgery

country: Netherlands

institute: VU University Medical Center

library_source: transcriptomic

data_processing:
Single-end 100 bp reads were subjected to pre-aligment 5'-end quality trimming and sequence adapter clipping using Trimmomatic.
Cleaned-up reads were mapped to the hg19 reference genome using STAR (version 2.3.0), using splice aware alignments and allowing for 10 mismatches.
Intron-spanning read summarization was performed using a samtools-based filtering step and HTSeq (version 0.6.1) using union-mode, unstranded reads and minimal mapping quality of 35, all guided by the Ensembl gene annotation version 75.
Genome_build: hg19
Supplementary_files_format_and_content: Samples in the Rdata-file were processed according to the described protocol (after filtering for low-abundent RNAs).

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing the EDTA anti-coagulant. The cells and aggregates were removed by centrifugation at room temperature for 20 minutes at 120g, resulting in platelet-rich plasma. The platelets were isolated from the platelet-rich plasma by centrifugation at room temperature for 20 minutes at 360g. The platelet pellet was collected in 30 μl RNAlater (Life Technologies), incubated overnight at 4°C and frozen at -80°C for further use. Frozen platelets were thawed on ice and total RNA was isolated using the mirVana RNA isolation kit (Life Technologies) according to the manufacturers’ protocol. Complementary purification of small RNAs was included in the isolation procedure by addition of miRNA homogenate (Life Technologies). Total RNA was dissolved in 30 μl Elution Buffer (Life Technologies) and RNA quality and quantity was measured using Bioanalyzer 2100 with RNA 6000 Picochip (Agilent).
100-500 pg of platelet total RNA diluted in nuclease free H2O was subjected to cDNA synthesis and amplification using the SMARTer Ultra Low RNA Kit for Illumina Sequencing v3 (Clontech, cat. nr. 634853) according to the manufacturers’ protocol. Conversion and efficient amplification of cDNA was quality-controlled using the Bioanalyzer 2100 with DNA High Sensitivity chip (Agilent). Samples with detectable fragments in the 300-7500 bp region were selected for further processing and Covaris shearing by sonication (Covaris Inc). Sample preparation for Illumina sequencing was performed using the Truseq DNA Sample Preparation Kit (Illumina, cat nr. FC-121-2001) or Truseq Nano DNA Sample Preparation Kit (Illumina, cat nr. FC-121-4001). Sample quality and quantity was measured using the DNA 7500 chip or DNA High Sensitivity chip (Agilent). High-quality samples with product sizes between 300-500 bp were pooled in equimolar concentrations and submitted for 100 bp Single Read sequencing on the Hiseq 2500 or 4000 platform (Illumina).

tag: cell type

value: Thrombocytes

tag: classification group

value: Malignant

tag: patient group

value: Esophageal Cancer


title: Sample42.Eudragit.205844020021_R06C01

value: Eudragit


title: Sample47.Eudragit.205844020021_R05C02

value: Female


title: Sample44.eRapa.205844020021_R02C02


title: Sample38.eRapa.205844020021_R02C01


title: NYU_GIST2_Vis 10x Genomics Visium

city: New York

first: Dalia

last: Barkley

state: NY

address: 435 E 30th st

department: Institute for Computational Medicine

institute: NYU Langone Health

data_processing:
Illumina RTA v2 software was used for basecalling and quality determination.
Raw sequencing data obtained from the inDrop scRNA-Seq method were processed using a custom-built pipeline, available online (https:__github.com_flo-compbio_singlecell). Briefly, the “W1” adapter sequence of the inDrop RT primer was located in the barcode read (the second read of each fragment), by comparing the 22-mer sequences starting at positions 9-12 of the read with the known W1 sequence (“GAGTGATTGCTTGTGACGCCTT”), allowing at most two mismatches. Reads for which the W1 sequence could not be located in this way were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read, which can range from 8-11 bp, as well as the start position of the second part of the inDrop cell barcode, which always consists of 8 bp. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read, allowing at most one mismatch. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally, the UMI sequence was extracted, and reads with low-confidence base calls for the six bases comprising the UMI sequence (minimum PHRED score less than 20) were discarded. The reads containing the mRNA sequence (the first read of each fragment) were mapped by STAR 2.5.1 with parameter “—outSAMmultNmax 1” and default settings otherwise36. Mapped reads were split according to their cell barcode and assigned to genes by testing for overlap with exons of protein-coding genes.
Raw sequencing data obtained from the 10x Genomics Visium method were processed using the SpaceRanger pipeline.
Raw sequencing data obtained from the 10x Gene Expression method were processed using the CellRanger pipeline.
Assembly: hg38, mm10
Supplementary files format and content: for inDrop single-cell RNA-Seq data: genes as rows and cells as columns. For 10x Genomics spatial transcriptomic data: output of SpaceRanger pipeline, including gene expression and spatial contents. For 10x Genomics single-cell RNA-Seq: output of CellRanger pipeline, including gene expression, features and barcodes.

source_name: Spatial transcriptomics of patient primary gastric stromal tumor

growth_protocol: For mouse pancreatic adenocarcinoma, Rag1-_- and WT C57BL_6 mice were obtained from Jackson Laboratories (Bar Harbor, ME). The KrasG12D;Tp53R172H;Pdx1Cre (KPC) derived cell line FC1242 was utilized for orthotopic injection of 100,000 cells into the tail of pancreata of 8-12 week old C57BL_6 or Rag mice. To model liver and peritoneal metastases, mice received FC1242 via splenic (1,000,000 cells) and intraperitoneal (100,000 cells) injection, respectively. Tumors were harvested 2-3 weeks after injection.

extract_protocol:
For inDrop single-cell RNA-Seq of patient tumor samples, cell suspension was generated from minced tumor tissue using human tumor dissociation kit (Miltenyi) prior to droplet encapsulation and individual barcoding of cells using the inDrop platform. Cell lysis was performed in droplets to release RNA, and reverse transcription and barcoding took place in droplets at 50C for 2h. For 10x Genomics spatial transcriptomics of patient tumor samples, 10 µm cryosections were mounted onto spatially barcoded arrays where reverse transcription of cellular transcripts took place in situ after tissue permeabilisation for 12 minutes. For 10x Genomics single-cell RNA-Seq of mouse tumors, cell suspension was generated from minced tumor tissue using the mouse tumor dissociation kit (Miltenyi) enzymes D and R prior to droplet encapsulation and individual barcoding of cells using the 10x Genomics platform.
For inDrop single-cell RNA-seq library construction, we followed the inDrop library construction protocol detailed by Klein et al,  Cell 2015, with minor changes. Briefly, RNA was reverse transcribed (RT) with SuperScript III (Invitrogen) in droplets. Droplet emulsions were broken, and post-RT material underwent second strand syntehsis and in vitro transcription using the T7 High Yield Enzyme mix (New England BiolaBS). RNA was fragmented for 105 seconds with 1X fragmentation reagent (1CellBio) prior to RT with random hexamers, eliminating the need for an adaptor ligation step. Cycles required for final library amplification was assessed by quantitative PCR (qPCR) with KAPA HiFi Hot Start PCR Mix (KAPA Biosystems) and EvaGreen dye (Biotium). Final libraries were amplified with KAPA HiFi Hot Start PCR mix for 9 to 13 cycles. inDrop library size assessed on a DNA BioAnalyzer chip following the manufacturer's instructions (Agilent).   For 10x Genomics spatial transcriptomic and single-cell RNA-Seq library construction, we followed the manufacturer's instructions.

tag: cancer type

value: Gastric stromal tumor

tag: organ

value: Stomach

tag: method

value: 10x Genomics Visium


title: UMCG-esoph-P97t0-TR2693


title: Sample34.Eudragit.205844020032_R04C02


title: ID155075.SecondDraw.204221250015_R08C01

description: genomic DNA methylation from tissue=Blood species=Human

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium HumanMethylation850 BeadChip using standard Illumina protocol

data_processing: Noob normalization as implemented in the minfi R package M. Aryee et al 2014. PMID: 24478339

source_name: Blood

label_protocol: Bisulfite conversion was performed on 500 ng of DNA using the llumina Infinium Methylation Assay protocol in the EZ DNA Methylation kit (Zymo Research). Next the samples were loaded onto the Infinium Human MethylationEPIC BeadChip

extract_protocol: Genomic DNA of whole blood samples

value: Blood

tag: time

value: SecondDraw

tag: weight

tag: sampleID


title: Sample35.eRapa.205844020032_R05C02


title: Sample37.eRapa.205844020021_R01C01


title: NYU_GIST2  inDrop

source_name: Single-cell RNA-Seq of patient primary gastric stromal tumor

value: inDrop


title: Sample32.Eudragit.205844020032_R02C02


title: Sample36.eRapa.205844020032_R06C02


title: Sample33.Eudragit.205844020032_R03C02


title: UMCG-esoph-P95t0-TR2685


title: NYU_KIRC1  inDrop

source_name: Single-cell RNA-Seq of patient primary kidney renal cell carcinoma

value: Kidney renal cell carcinoma

value: Kidney


title: NYU_GIST1_Vis 10x Genomics Visium


title: ID73781.BaselineDraw.204221250112_R04C01

value: Male

value: BaselineDraw


title: RNAseq Trisomy21_stemcell_C03

city: Boston

first: VICTOR

last: BARRERA BURGOS

state: Massachusetts

address: Landmark 401 Park Drive 3 East

department: Biostatistics

institute: Harvard School of Public Health

description:
counts_raw-2019-12-06.csv
counts_tpm-2019-12-06.csv

data_processing:
Sequenced reads were assessed for low-quality sequence, then mapped against the GRCh38_98 transcriptome where reads were quantified at the transcript level using Salmon
Transcript-level abundance estimates  from Salmon were collapsed to gene-leve estimates and  converted to raw count values using the R Bioconductor package tximport
Differentially expressed genes were identified using the R Bioconductor package DESeq2
Genome_build: GRCh38.90
Supplementary_files_format_and_content: comma separated file of raw count matrix where columns correspond to samples and rows correspond to genes; comma separated file of transcript per million counts where columns correspond to samples and rows correspond to genes

source_name: hPSCs

growth_protocol: All hPSCs were grown and maintained in mTeSR medium on geltrex coated plates; hPSC derived neurons were generated by transduction with Ngn2 ectopic expression constructs with the addition of SMAD inhibitors, WNT inhibitors and neurotrophins.

extract_protocol:
For RNAseq, RNA was extracted using the AllPrep DNA/RNA/miRNA universal kit (Qiagen). For eCLIP-seq, cells were UV crosslinked, lysed, sonicated and treated with RNAse I followed by IP, processing and reverse transcripion using AffinityScript. cDNAs were adaptor ligated.
For RNAseq, libraries were prepared using the Illumina TruSeq HS Stranded Total RNA kit with Ribo-Zero Gold for rRNA depletion. For eCLIP-seq, libraries were generated using Q5 PCR mix.

value: iPSCs

tag: genotype/variation

value: Trisomy21 hPSCs


title: NYU_GIST1  inDrop


title: NYU_COAD1  inDrop

source_name: Single-cell RNA-Seq of patient primary colon adenocarcinoma

value: Colon adenocarcinoma

value: Colon


title: ID73781.SecondDraw.204221250112_R08C01

tag: age


title: Sample30.eRapa.205844020032_R06C01

tag: Sex

value: Liver

value: eRapa

value: Plate 01


title: Sample29.eRapa.205844020032_R05C01

tag: tissue


title: NYU_BRCA3  inDrop

source_name: Single-cell RNA-Seq of patient primary breast carcinoma

value: Breast carcinoma

value: Breast


title: RNAseq Trisomy21_stemcell_C01


title: ID29081.BaselineDraw.204221250105_R01C01


title: Sample31.Eudragit.205844020032_R01C02

tag: agemonths

value: Eudragit


title: RNAseq Trisomy21_neuron_G02

source_name: neurons

value: iPSC derived neurons

value: Trisomy21 neurons


title: RNAseq Trisomy21_neuron_G01


title: NYU_BRCA2_Vis 10x Genomics Visium

source_name: Spatial transcriptomics of patient primary breast carcinoma

value: 10x Genomics Visium


title: RNAseq Trisomy21_stemcell_C02


title: Sample28.Eudragit.205844020032_R04C01

tag: treatment


title: Sample27.Eudragit.205844020032_R03C01

tag: platenumber


title: Sample23.Eudragit.205844020049_R05C02

value: Female

tag: welladdress


title: NYU_BRCA1_Vis 10x Genomics Visium


title: RNAseq Trisomy21_neuron_F06

tag: cell type


title: Sample26.eRapa.205844020032_R02C01


title: NYU_BRCA1  inDrop

value: inDrop


title: Sample25.eRapa.205844020032_R01C01

value: Male


title: Sample24.eRapa.205844020049_R06C02


title: RNAseq Trisomy21_neuron_E05


title: ID155075.BaselineDraw.204221250015_R04C01

value: Blood

value: BaselineDraw


title: Sample21.Eudragit.205844020049_R03C02


title: NYU_BRCA2  inDrop


title: NYU_BRCA0_Vis 10x Genomics Visium


title: Sample17.eRapa.205844020049_R05C01


title: Sample19.eRapa.205844020049_R01C02


title: RNAseq Trisomy21_neuron_E03


title: Sample15.Eudragit.205844020049_R03C01


title: Sample20.eRapa.205844020049_R02C02


title: Sample18.Eudragit.205844020049_R06C01


title: Sample22.Eudragit.205844020049_R04C02


title: hFOB_G34W6_HA

city: London

first: Adrienne

middle: M

last: Flanagan

state: Middlesex

address: Huntley Street

country: United Kingdom

institute: University College London

library_source: genomic

data_processing:
Adaptors were removed by TrimGalore
Reads were aligned to hg19 and dm6 by Bowtie2 with default parameters
Bam files were filtered to contain normal chromosomes
Raw scaling factors were calculated for IP samples following Niu et al.(DOI:10.21769/BioProtoc.2981)
Raw scaling factors were justed for IP samples of the same histone modification by transforming the largest raw scaling factor to 1, and others were adjusted proportionally.
BAM files of IP samples were down-sampled by Picard and scaling factor.
BigWig files were created by bamCoverage from Deeptools with binSize=1
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

source_name: hFOB 1.19

growth_protocol: hFOB 1.19 were cultured according to ATCC guidelines (ATCC® CRL-11372™) at 34C.

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 minutes prior to quenching with excess glycine. Cells were resuspended on ice in a cell lysis buffer (10 mM Tris-HCL, 10 mM Nacl, 0.5 % NP-40, all reagents were from Sigma-Aldrich) for 15 minutes, centrifuged, and resuspended in nuclear lysis buffer (50 mM Tris-HCl, 10 mM EDTA, 1 % SDS, all from Sigma-Aldrich) for 10 minutes.  Samples were diluted with 2 volumes of dilution buffer (16.7 mM Tris-HCL, 167 mM NaCl, 1.2 mM EDTA, 0.01 % SDS, all from Sigma-Aldrich) and sonicated on a Bioruptor Pico (Diagenode, Belgium) for 10 cycles of 30 seconds on/30 seconds off. Sonication efficiency was checked by running a sample of de-crosslinked material on a 2 % agarose gel.
Libraries were prepared using the NEBNext Ultra 2 DNA Library Preparation Kit (New England Biolabs, MA, USA)

treatment_protocol: Cells were engineered to express H3.3-G34W, H3.3-WT or empty vector (EV).

tag: cell line

value: hFOB 1.19

value: osteoblastic cell line

tag: genotype

tag: chip antibody

value: HATag (Abcam, Ab9110)


title: UMCG-esoph-P96t0-TR2692

value: Thrombocytes

tag: classification group

value: Malignant

tag: patient group

value: Esophageal Cancer


title: RNAseq FMR1_WT_stemcell_A06

value: ESCs

value: FMR1y/+ hPSCs


title: Sample16.Eudragit.205844020049_R04C01

value: Liver

value: Eudragit

value: Plate 01


title: RNAseq FMR1_WT_stemcell_A04


title: ID29081.SecondDraw.204221250105_R05C01

tag: time

value: SecondDraw


title: RNAseq FMR1_WT_stemcell_A03


title: hFOB_WT6_HA


title: hFOB_G34W5_HA


title: Sample12.Eudragit.205844020029_R06C02


title: hFOB_WT5_HA


title: RNAseq FMR1_WT_stemcell_A02


title: hFOB_G34W6_Input


title: Donor2_1st-stimulatde_PRDM1_1

city: Philadelphia

first: Inyoung

last: Jung

state: PA

address: SPE, 9-304, 3400 Civic Center Blvd, Bldg. 421

institute: University of Pennsylvania

data_processing:
Reads were pseudoaligned to the human genome (GRCh38) transcriptomes using kallisto v0.46.0. Differential expression analyses between AAVS1 KO PSMA CAR T-cells and PRDM1 KO PSMA CAR T-cells were performed using the edgeR v3.34.0 and limma v3.48.0 packages. Briefly, expression data were normalized using a trimmed mean of log expression ratios method and transformed into log2(counts per million). Linear models were used to assess differential expression, and P values were adjusted using the Benjamini and Hochberg method.
Supplementary files format and content: tsv files include TPM values for each Sample
Assembly: GRCh38

source_name: blood

growth_protocol: Healthy donor T-cells were isolated from peripheral blood mononuclear cells (PBMC) using the Pan T Cell Isolation Kit according to the manufacturer’s instructions (Miltenyi Biotec). T-cells were activated with anti-CD3/CD28 antibody coated Dynabeads (Thermo Fisher Scientific) at 3:1 bead:cell ratio in T-cell media (OpTmizer CTS SFM media (Gibco) supplemented with 5% human AB serum and 100u/mL human IL-2). Following a 24-hour incubation, lentivirus encoding the PSMA CAR was added to the culture at a multiplicity of infection (MOI) of 2.5.  Following T-cell activation, beads were removed using a magnet on day 3 and electroporation was carried out with a P3 primary cell 4D-nucleofector kit (Lonza). 2 × 106 CAR T-cells were transfected with 12 µg TrueCutTM S. pyogenes Cas9 (Invitrogen) and 0.2nmol of chemically-modified tracrRNA and crRNA (Integrated DNA Technologies).

extract_protocol: On days 0, 5 and 20 of the CAR T-cell restimulation assay, before stimulation and after the fourth tumor challenge respectively, CD8+ CAR T-cells were isolated using CD8 microbeads (Miltenyi Biotec) and total mRNA was extracted with RNA Clean & Concentrator™ kits (Zymo Research). Bulk RNA-seq was conducted by Novogene using the Novaseq6000 system (paired-end 150bp) at 40 × 106 reads per sample.

treatment_protocol: AAVS1 KO and PRDM1 KO PSMA CAR-positive T-cells were isolated using a Biotin-goat anti-mouse IgG F(ab)2 fragment (Jackson ImmunoResearch #115-065-072) and anti-biotin kits (Miltenyi Biotech). Following isolation, CAR T-cell purity was confirmed by flow cytometric analysis and CAR T-cells were then serially exposed (i.e., every 5 days) to irradiated PC3-PSMA cells at an effector-to-target (E:T) ratio of 3:1. Restimulation assays were followed up for 25-30 days since cell counts and viability become largely unreliable beyond 5-6th  round of stimulation due to senescent proliferative arrest and a marked decrease in the viability of chronically stimulated CAR T cells.

value: blood

tag: cell subtype

value: T-cell

value: PRDM1 KO

tag: condition

tag: biological replicate

value: Normal donor 2_rep1


title: Donor2_1st-stimulated_PRDM1_2

value: Normal donor 2_rep2


title: Donor2_1st-stimulated_AAVS1_2

value: AAVS1 KO


title: Donor1_1st-stimulated_PRDM1_2

value: Normal donor 1_rep2


title: Donor2_1st-stimulated_AAVS1_1


title: Donor1_1st-stimulated_PRDM1_1

value: Normal donor 1_rep1


title: RNAseq FMR1_WT_stemcell_A01

tag: genotype/variation


title: Donor1_1st-stimulated_AAVS1_2


title: Sample9.eRapa.205844020029_R03C02

tag: age

tag: Sex

value: Female

value: eRapa


title: Sample10.eRapa.205844020029_R04C02

value: Male

tag: tissue

tag: agemonths


title: hFOB_G34W5_Input

value: hFOB 1.19

value: osteoblastic cell line


title: Donor1_1st-stimulated_AAVS1_1


title: Sample13.eRapa.205844020049_R01C01

value: Liver

tag: treatment

tag: platenumber


title: hFOB_WT6_Input

tag: cell type


title: RNAseq FMR1_WT_neuron_H01

value: ESC derived neurons

value: FMR1y/+ neurons


title: Multiplexing Capture

first: Seong Won

last: Kim

state: MA

address: 77 Ave Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, and aligning to the reference genome were done using CellRanger Software (ver 6.1.0)
Assembly: hg38
Supplementary files format and content: Tab separated matrix file, barcodes file, and feature files.
Supplementary files format and content: List of demultiplexed CellRanger barcodes and Genotype assignment

extract_protocol:
hiPSC-CMs were dissociated with Accutase and snap-frozen for snRNAseq
3' CellPlex Kit was used to barcode cell pellets. Nuclei was extracted, washed and pooled at equal amount. Library was constructed according to the manufacturer's instruction for Chromium 3’ v3.1 dual index kit.

tag: cell line

value: hiPSC derived cardiomyocytes

tag: sample type

value: Cell Multiplex Barcodes


title: Pooled Gene Expression of hiPSC-CM

description: 10X Genomics

value: snRNAseq


title: hFOB_WT5_Input

tag: genotype

tag: chip antibody


title: Sample7.Eudragit.205844020029_R01C02

value: Eudragit

value: Plate 01

tag: welladdress


title: IgG_ChIP_OCI_LY3_24h

city: Duarte

first: Alexey

last: Danilov

state: California

address: 1500 East Duarte Road

department: Toni Stephenson Lymphoma Center

institute: City of Hope

description: Only Replicate

data_processing:
The raw FASTQ files were trimmed with Trimmomatic (v0.39) to cut adapter and other Illumina-specific sequences from the read and only keep the reads longer than 36. Then, the trimmed FASTQ data was mapped to the human reference genome hg19 with Bowtie2 v2.2.9 with default settings. Mapped reads were further filtered to remove reads with a mapping quality (q score) less than 10 and duplicated reads using samtools (v1.3.1). To visualize occupancy, meta plots were generated using bamCompare, computeMatrix and plotProfile within deepTools2 (v3.5.1).
Assembly: hg19
Supplementary files format and content: bigWig files and bam files

source_name: cultured immortalized DLBCL cells

growth_protocol: Cell lines were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Chromatin immunoprecipitations were performed using the SimpleChIP Enzymatic Chromatin IP Kit with Magnetic Beads (Cell Signaling Technology #9003).
Sequencing libraries were prepared using the SimpleChIP ChIP-seq DNA Library Prep Kit for Illumina (Cell Signaling Technology #56795) with Dual Index Multiplex Oligos for Illumina (Cell Signaling Technology #47538).

treatment_protocol: Cells were treated with AZD4573 (30 nM) in singleplicate or duplicate for 0, 3 and 8 hours prior to harvest. After 8-hour exposure, drug was washed out and cells were harvested after 24 hours.

tag: time

value: 24 hours


title: IgG_ChIP_OCI_LY3_8h

description: Only Replicate

value: 8 hours


title: Sample11.eRapa.205844020029_R05C02


title: RNAseq FMR1_WT_neuron_G05


title: LAM1164-3

first: Yan

last: Tang

address: 20 Shattuck street

institute: Brigham and Women's Hospital

data_processing:
Raw sequencing data was aligned to GRCh38 reference genome using Cell Ranger (v 3.0.0) pipeline (10x Genomics) to generate gene counts matrix by cell barcodes.
Genome_build: GRCh38
Supplementary_files_format_and_content: gene-cell matrix

source_name: LAM lung

extract_protocol: Standard 10x genomics 5' library construction protocol

tag: disease

value: LAM lung


title: IgG_ChIP_OCI_LY3_0h

description: Only Replicate

value: 0 hours


title: RNAseq FMR1_WT_neuron_G03


title: BRD4_ChIP_OCI_LY3_24h

description: Only Replicate

value: BRD4 (Bethyl #A301-985a)


title: LAM1164-2


title: BRD4_ChIP_OCI_LY3_8h

description: Only Replicate


title: RNAseq FMR1_WT_neuron_E01


title: BRD4_ChIP_OCI_LY3_3h

description: Only Replicate

value: 3 hours


title: RNAseq FMR1_KO_stemcell_B05

value: ESCs

value: FMR1y/- hPSCs


title: LAM1164-1


title: BRD4_ChIP_OCI_LY3_0h

description: Only Replicate


title: Sample8.Eudragit.205844020029_R02C02

value: Female


title: RBP1_ChIP_OCI_LY3_24h

description: Only Replicate


title: LAM1163


title: RBP1_ChIP_OCI_LY3_8h

description: Only Replicate


title: Sample6.eRapa.205844020029_R06C01

value: Liver

value: eRapa


title: RBP1_ChIP_OCI_LY3_0h

description: Only Replicate


title: LAM1158


title: Input_VAL_8h

description: input DNA

value: VAL


title: RNAseq FMR1_KO_stemcell_B03


title: RNAseq FMR1_KO_stemcell_B02


title: LAM1110


title: Sample1.Eudragit.205844020029_R01C01


title: RBP1_ChIP_OCI_LY3_3h

description: Only Replicate


title: Input_VAL_24h

description: input DNA


title: Input_VAL_3h

description: input DNA


title: Sample2.Eudragit.205844020029_R02C01


title: RNAseq FMR1_WT_neuron_G06

value: ESC derived neurons

value: FMR1y/+ neurons


title: AML1172_Normal

source_name: Matched adjacent normal kideny

value: Matched adjacent normal kideny


title: Sample4.eRapa.205844020029_R04C01


title: Input_VAL_0h

description: input DNA


title: Sample5.eRapa.205844020029_R05C01


title: Sample14.eRapa.205844020049_R02C01


title: RNAseq FMR1_KO_stemcell_B01


title: Sample3.Eudragit.205844020029_R03C01

value: Eudragit


title: Input_LY3_24h

description: input DNA


title: AML1172

source_name: AML tumor

value: AML tumor


title: Input_LY3_8h

description: input DNA


title: Input_LY3_0h

description: input DNA


title: Input_LY3_3h

description: input DNA


title: RNAseq FMR1_KO_neuron_H04

value: FMR1y/- neurons


title: H3K27ac_ChIP_VAL_24h_r2

description: Replicate 2

value: 24 hours


title: AML1171


title: RNAseq FMR1_KO_neuron_H03


title: AML1167_Normal


title: H3K27ac_ChIP_VAL_8h_r2

description: Replicate 2

value: 8 hours


title: H3K27ac_ChIP_VAL_8h_r1

description: Replicate 1


title: RNAseq FMR1_KO_neuron_H02


title: H3K27ac_ChIP_VAL_3h_r2

description: Replicate 2


title: H3K27ac_ChIP_VAL_3h_r1

description: Replicate 1


title: AML1167-2


title: RNAseq FMR1_KO_neuron_E02


title: H3K27ac_ChIP_VAL_0h_r2

description: Replicate 2

value: 0 hours


title: H3K27ac_ChIP_VAL_0h_r1

description: Replicate 1


title: AML1167-1


title: RNAseq Euploid_stemcell_D05

value: iPSCs

value: Euploid control hPSCs


title: RNAseq FMR1_KO_neuron_H05


title: RNAseq FMR1_KO_stemcell_B04

value: ESCs


title: AML1166_Normal


title: AML1171_Normal


title: H3K27ac_ChIP_OCI_LY3_24h_r1

description: Replicate 1


title: AML1166


title: RNAseq Euploid_stemcell_D03


title: H3K27ac_ChIP_OCI_LY3_8h_r1

description: Replicate 1


title: H3K27ac_ChIP_OCI_LY3_3h_r2

description: Replicate 2

value: 3 hours


title: H3K27ac_ChIP_OCI_LY3_8h_r2

description: Replicate 2


title: AML1162


title: H3K27ac_ChIP_VAL_24h_r1

description: Replicate 1


title: H3K27ac_ChIP_OCI_LY3_3h_r1

description: Replicate 1


title: RNAseq Euploid_stemcell_D02


title: H3K27ac_ChIP_OCI_LY3_0h_r2

description: Replicate 2


title: H3K27ac_ChIP_OCI_LY3_0h_r1

description: Replicate 1


title: Input chromatin used for BNC2 ChIP-seq

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

country: France

institute: CNRS

description: Input chromatin used for BNC2 ChIP-seq

data_processing:
Reads were mapped to the human genome (hg38) using Bowtie 2
Input DNA was used as control, duplicate tags and those mapping to ENCODE blacklisted regions v2
Signal tracks corresponding to enrichment over input were obtained using MACS2 bdgcmp (Poisson pvalue)
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files for BNC2 ChIP-seq enrichment over input, H3K27ac ChIP-seq enrichment over input and CoP-seq enrichment over input. Bed file provides BNC2 peaks.

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 5% fetal bovine serum (FCS, Deutscher).

extract_protocol:
ChIP was performed using BNC2 (Sigma, HPA018525) or H3K27ac antibody (Active Motif ref 39685).
TruSeq ChIP Sample Preparation Kit (BNC2) or DNBseq involving Probe-Anchor Synthesis (cPAS), linear isothermal Rolling-Circle Replication  and DNA Nanoballs (DNBTM) technology, followed by high-resolution digital imaging.

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 10min at room temperature. Samples for ChIP were processed as in Dubois V. et al Mol Syst Biol 2020 while samples for CoP were processed as in Zhang et al Epigenetics & Chromatin 2020.

tag: antibody


title: RNAseq Euploid_stemcell_D01


title: H3K4me3_ChIP_VAL_24h_r1

description: Replicate 1


title: RNAseq Euploid_stemcell_D06


title: RNAseq Euploid_neuron_F04

value: iPSC derived neurons

value: Euploid control neurons


title: H3K27ac_ChIP_OCI_LY3_24h_r2

description: Replicate 2


title: BNC2 ChIP-seq for LX2 cells

description: BNC2 ChIP-seq LX2 cells

value: BNC2 from Sigma ref HPA018525


title: H3K4me3_ChIP_VAL_3h_r1

description: Replicate 1

value: VAL


title: H3K4me3_ChIP_VAL_8h_r1

description: Replicate 1


title: RNAseq Euploid_neuron_F02


title: H3K4me3_ChIP_OCI_LY3_8h_r2

description: Replicate 2


title: H3K4me3_ChIP_OCI_LY3_24h_r2

description: Replicate 2


title: RNAseq Euploid_neuron_F01


title: DCs, donor 8 HIV

city: Linkoping

first: Cecilia

last: Svanberg

address: Molecular Virology, lab1, plan 13, Medical Faculty, Linkoping University

department: Molecular virology

country: Sweden

institute: BKV

data_processing:
Illumina NextSeq System Suite v2.1.3 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low quality reads using trimmomatic
Reads were therafter mapped to the human reference genome using STAR.
To retrieve counts the reads were passed through the FeatureCounts program
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file with raw gene counts for every gene and every sample

source_name: DCs from DC-TC Coculture

growth_protocol: Cocultures were cultured in 5% pooled human serum and kept at 37°C for 8 days

extract_protocol:
Cell were lyzed and RNA extracted using the Bioline Isolate II RNA Micro Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mock vs HIV

tag: individual

value: donor 8

value: Monocyte derived dendritic cells (DCs)

tag: growth protocol

value: DCs from DC-TC Coculture

value: HIV treated


title: DCs, donor 8 mock

value: Mock treated


title: DCs, donor 7 HIV

value: donor 7


title: H3K4me3_ChIP_VAL_0h_r1

description: Replicate 1


title: H3K4me3_ChIP_OCI_LY3_3h_r2

description: Replicate 2


title: DCs, donor 7 mock


title: H3K4me3_ChIP_OCI_LY3_0h_r2

description: Replicate 2


title: RNAseq Euploid_neuron_E06

tag: genotype/variation


title: DCs, donor 6 HIV

value: donor 6


title: RNAseq Euploid_neuron_E04


title: MI+Cell Sheet_6_1wk_Infarct

city: Stanford

first: Albert

middle: James

last: Pedroza

state: CALIFORNIA

address: 870 Quarry Rd, Falk CVRB

department: Cardiothoracic Surgery

institute: Stanford University

data_processing:
Paired-end FASTQ files were input into STARAligner v.2.5.4 to simultaneously trim sequencing reads and align to the mRatBN7.2 genome assembly
Aligned reads were then mapped to the Rattus norvegicus Annotation Release 108 and individual sample count matrix files were generated
Downstream RNA sequencing analysis was performed using the DESeq2 package in R
All samples were merged into a single expression matrix dataframe and normalized by sequencing depth prior to differential expression testing
Assembly: mRatBN7.2
Supplementary files format and content: Text file with gene ID (column 1) and raw read counts (column 2) for individual samples.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: LV, infarct

extract_protocol:
Tissues were snap frozen then pulverized on dry ice and RNA was extracted using an RNeasy extraction kit.
polyA enrichment was performed pror to standard Illumina library preparation by third party vendor (Novogene)

tag: Sex

value: Female

tag: strain

value: Heart Left Ventricle

tag: stress

value: LAD Ligation (infarct)

value: Cell Sheet

tag: tissue region

value: infarct

tag: technical replicate


title: DCs, donor 6 mock

tag: cell type

tag: treatment


title: RT4, treated, 24h, biol rep 3

city: Ljubljana

first: Tadeja

last: Kuret

state: Slovenia

address: Vrazov trg 2

department: Faculty of Medicine

country: Slovenia

institute: University of Ljubljana

data_processing:
RNA-seq and data processing were performed by Novogene Co., Ltd. Downstream analysis was performed using a combination of programs including Hisat2, FeatureCounts and Novogene's wrapped scripts.
High quality reads were aligned to human (Ensembl GRCh38.p13) reference genome using Hisat2 (v2.0.5).
FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. The fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two groups (TNFα-treated vs. control; three replicates per group) was performed using DESeq2 R package (1.20.0). P value was calculated using the negative binomial distribution and the resulting p values were adjusted using the Benjamini-Hochberg’s approach for controlling the false discovery rate.
The clusterProfiler (v. 3.8.1) software was used for enrichment analysis of differentially expressed genes, including Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome database
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes counts for each gene for each sample (gene_count.txt)
Supplementary files format and content: tab-delimited text file includes FPKM values for each gene for each sample (gene_fpkm.txt)
Supplementary files format and content: tab-delimited text file includes FPKM values for each gene for each sample and diferential analysis of treated vs ctrl RT4 cells (treated_RT4vsCtrl_RT4_deg_all seq genes.txt)

growth_protocol: RT4 cells were grown in 75 cm2 cell culture flasks in basal media consisting of equal parts of advanced Dulbecco's modified Eagle's medium (A-DMEM) and F12 (HAM), supplemented with 5% fetal bovine serum (FBS), and 4 mM GlutaMAX  in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was isolated using Quick-RNA Microprep Kit (Zymo Research). Library preparation was performed by Novogene Co., Ltd, using at least 0.5 ug high-quality total RNA input per sample.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina following manufacturer’s recommendations

treatment_protocol: Cells were treated with 20 ng/ml human recombinant TNFα for 24h in serum-free basal media, untreated cells served as controls.

tag: cell line

value: urothelial cells

value: TNFa (20 ng/ml)


title: RT4, treated, 24h, biol rep 2


title: MI+Cell Sheet_5_1wk_Infarct

tag: tissue


title: RT4, control, 24h, biol rep 3


title: IgG_ChIP_OCI_LY3_3h

description: Only Replicate

value: 3 hours

tag: chip antibody


title: DCs, donor 5 HIV

value: donor 5


title: RT4, control, 24h, biol rep 2


title: RT4, control, 24h, biol rep 1


title: MI+Cell Sheet_4_1wk_Infarct


title: HaCaT cells_3 with HMW-HA and UVB exposure

city: Ube

first: Yoichi

last: Mizukami

state: Yamaguchi

department: Science Research Center

country: Japan

institute: Yamaguchi university

data_processing:
BCL files produced by Illimina NovaSeq 6000 were converted to FASTQ files using bcl2fastq tool. Created FASTQ files were imported to CLC Genomics Workbench software (ver.20.0.4).
Reads with more than 2 ambiguous nucleotides and reads with quality scores less  than 20 as calculated by the Phred program were removed using CLC Genomics Workbench software (ver.20.0.4). Long reads with more than 1000 nucleotides and short reads with fewer than 20 nucleotides were also discarded.
The trimmed reads were mapped to the human reference genome GRCh37 release-75 using CLC Genomics Workbench software (ver.20.0.4) with default setting.
Reads Per Kilobase of exon per Million mapped reads (RPKM) and Transcripts Per Million (TPM) were calculated using CLC Genomics Workbench software (ver.20.0.4).
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include RPKM and TPM values for each sample.

source_name: HaCaT cell

growth_protocol: HaCaT cells were grown in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum (FBS), penicillin (100 IU/ml), and streptomycin (100 µg/ml). The cells were maintained in an incubator containing 5% CO2 at 37°C.

extract_protocol:
Total RNA was isolated from the HaCaT cells using the RNeasy Mini Kit (Qiagen). Polyadenylated  mRNA was purified with oligo dT beads (NEBNext Poly (A) mRNA magnet Isolation Module, New England Biolabs, NEB). Complementary DNA (cDNA) libraries for Illumina sequencing were generated with NEBNext Ultra II RNA library Prep kit (NEB) and NEBNext Multiplex Oligos for Illumina (NEB).
Extracted mRNA was incubated with NEBNext Random Primers in NEBNext First Strand Synthesis Reaction Buffer at 94°C for 15 min, and reverse transcription was performed with NEBNext Strand Synthesis Enzyme Mix. After reverse transcription, index sequences were inserted to cDNA fragments with PCR amplification using primers included in NEBNext Multiplex Oligos for Illumina. Following purification with AMPureXP beads (Beckman Coulter), the quality and the concentration of the libraries was evaluated using a Bioanalyzer. The confirmed libraries were mixed to equal molecular amounts against the clustering and sequencing on an Illumina NovaSeq 6000 DNA sequencer with 100 bp single-end cycle sequencing kit (Illumina).

treatment_protocol: HaCaT cells (5×105 cells/well) were seeded in 6-well plates and cultured overnight. Cells at 80% confluence were washed twice with 2 ml PBS before irradiation. The UVB source was a broadband UVB device, DERMARAY-200. The doses of UVB irradiation were determined with a UV radiometer, and the total energy of irradiation was 15 mJ/cm2 or 30 mJ/cm2. In HA treatment experiments, cells were treated with medium containing HA at the appropriate concentration after 15 mJ/cm2 irradiation.

value: Keratinocyte

value: treated with HMW-HA after UVB exposure


title: DCs, donor 4 HIV

value: donor 4

value: Monocyte derived dendritic cells (DCs)


title: HaCaT cells_2 with HMW-HA and UVB exposure


title: HaCaT cells_3 with uLMW-HA and UVB exposure

value: treated with uLMW-HA after UVB exposure


title: DCs, donor 4 mock

value: DCs from DC-TC Coculture

value: Mock treated


title: MI+Cell Sheet_2_1wk_Infarct


title: HaCaT cells_2 with uLMW-HA and UVB exposure


title: MI+Cell Sheet 1_1wk_Infarct


title: HaCaT cells_1 with uLMW-HA and UVB exposure


title: DCs, donor 5 mock


title: DCs, donor 3 mock

value: donor 3


title: HaCaT cells_2 irradiated by UVB

value: irradiated by UVB


title: DCs, donor 3 HIV

value: HIV treated


title: MI 6_1wk_Infarct

value: Female

value: Heart Left Ventricle

value: LAD Ligation (infarct)


title: HaCaT cells_1 with HMW-HA and UVB exposure


title: HaCaT cells_3 irradiated by UVB


title: MI 5_1wk_Infarct

value: infarct


title: RT4, treated, 24h, biol rep 1

value: urothelial cells

value: TNFa (20 ng/ml)


title: HaCaT cells_3 with HMW-HA

value: treated with HMW-HA


title: DCs, donor 2 mock

value: donor 2


title: HaCaT cells_2 with HMW-HA

value: Keratinocyte


title: MI+Cell Sheet_3_1wk_Infarct

value: Cell Sheet


title: HaCaT cells_3 with uLMW-HA

value: treated with uLMW-HA


title: DCs, donor 1 HIV

value: donor 1

value: Monocyte derived dendritic cells (DCs)


title: MI 3_1wk_Infarct


title: HaCaT cells_2 with uLMW-HA


title: HaCaT cells_3 without HAs

value: untreated


title: HaCaT cells_1 with uLMW-HA


title: MI 1_1 wk_Infarct


title: HaCaT cells_1 without HAs


title: DCs, donor 1 mock

value: DCs from DC-TC Coculture

value: Mock treated


title: HaCaT cells_2 without HAs


title: Sham 6_1 wk_Infarct

value: Sham surgery


title: K-562 SMART-seq stranded cell 8 [6minG1]

city: Grand Rapids

first: Benjamin

middle: K

last: Johnson

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Institute

data_processing:
Base calling was done by Illumina NextSeq or NovaSeq Control Software (NCS) v2.0 and output of NCS was demultiplexed and converted to FASTQ format with Illumina Bcl2fastq v1.9.0.
Subsampling was performed using seqtk (v1.3-r107-dirty) on the trimmed fastqs to the various read depths.
Demultiplexed fastqs were then trimmed using TrimGalore (v0.6.0) and cutadapt (v2.10) with the following parameters: --illumina, --trim-n, --length 36, --paired, --clip_R2 3, --fastqc. Pre- and post-trimming quality control was assessed using FastQC (v0.11.9).
Trimmed fastqs were processed using salmon quant (v1.3.0) to either a reference genome (K-562) or a spliced and unscpliced reference transcriptome (FTE; generated with eisaR v1.3.0) with the following parameters: -l ISR, --seqBias, --gcBias, --posBias, --softclip, --numBootstraps 100.
SummarizedExperiment objects were generated using tximeta (v1.6.3) in R (4.0.0). Gene counts were summarized using the tximeta function summarizeToGene with the argument countsFromAbundance = "lengthScaledTPM".
Genome_build: GRCh38 release 101
Supplementary_files_format_and_content: Tab-delimited TPM matrices

source_name: K-562 SMART-seq stranded cell

growth_protocol: The K562 cell line was purchased from the American Type Culture Collection (ATCC; CCL-243). Cells were cultured in RPMI 1640 medium supplemented with 10% FBS and 1% Penicillin/Streptomycin (Gibco). Cells were maintained at 37oC in 5% CO2 and sub-cultured at 1:5 ratio every 3-4 days.

extract_protocol:
BULK TOTAL RNA: Total RNA from 5 million K562 cells were isolated using TRIzol (Invitrogen). STORM-seq: total RNA extraction is integrated into the library preparation protocol with Takara Bio's lysis buffer that comes in the SMART-seq Stranded kit (Takara Bio, USA)
BULK TOTAL RNA: Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboseErase (v1.16) (Kapa Biosystems, Wilmington, MA USA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to Illumina UDIs. Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.) and QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA). SMART-seq STRANDED: Single-cell K562 libraries were prepared using the SSS Kit, following the manufacturer instructions with modifications. Following sorting into PBS, Takara Shearing Master Mix was added to all samples to a final concentration recommended by the kit. The samples underwent 6 minute fragmentation time at 85 °C. Section B step 4 in the protocol was modified to account for the incorporation of UDIs (Takara SMARTer RNA Unique Dual Index Kit-96A, Takara Bio, USA). A total of 2 uL of each UDI was used instead of the recommended 1 uL each of the 5’ and 3’ PCR primers. For PCR1, 10 cycles of amplification were performed, followed by pooling according to Appendix A. The remainder of the protocol was performed according to manufacturer recommendations. STORM-seq: Single cells were prepared using the SMART-Seq Stranded Kit (Takara USA) on the SPT Labtech Mosquito (HV) at 1:6, then 1:4 dilutions relative to the recommended volumes for subsequent steps in the protocol. In contrast to the manually prepared K562 libraries, for the miniaturized protocol, cells were sorted into a 384-well plate (Eppendorf twin-tec) containing a combination of Shearing Master Mix plus PBS and immediately transferred to a thermocycler and fragmented for 3 minutes at 85 °C. Following 1st Strand Synthesis, PCR1 (10 cycles of amplification) was performed with the addition of SMARTer RNA Unique Dual Index Set A (Takara SMARTer RNA Unique Dual Index Kit-96A) instead of Takara 5’ and 3’ PCR Primers. Samples were pooled across rows into groups of 12 cells according to Appendix A: Pooling Strategy for Single-Cell Applications and depletion of ribosomal cDNA was performed as indicated. 13 cycles of amplification were performed for PCR2 and the final library was eluted in 13ul 10mM Tris-HCl pH 8.0.

treatment_protocol: None.

tag: disease state

value: Chronic Myelogenous Leukemia

tag: tissue source

value: Bone marrow

tag: gender

value: Female

tag: experiment type

value: SMART-seq stranded


title: N2 CD4+ T cells

city: New Haven

first: jingjing

last: Ren

state: Connecticut

address: 200 S Frontage Rd, #0618: Hunter Building

institute: Yale University

description: CTCL with blood envolvement

data_processing:
Initial data processing was performed using the Cell Ranger version 3.0 pipeline (10X Genomics)
Post-processing, including filtering by number of genes expressed per cell, was performed using the Seurat package.
Following clustering and visualization with UMAP and PHATE.
Identification of cell clusters was performed on the final aligned object guided by marker genes.
Genome_build: GRCh38
Supplementary_files_format_and_content: "barcodes.tsv.gz" contains cell barcodes, "features.tsv.gz" contains metadata for genes, "matrix.mtx.gz" contains digital expression matrix

extract_protocol:
Total CD4+ T cells were purified via either MACS CD4+ negative selection kit (Miltenyi Biotec) or RosetteSep™ human CD4+ T cell enrichment cocktail kit (STEMCELL Technologies) under the manufacturer’s protocol.
Libraries were prepared by the Yale Center for Genome Analysis using 10x Genomics Chromium Next GEM Single Cell 5' Library and Gel Bead Kit V2 (1000263), Chromium Single Cell Human TCR Amplification Kit (1000252), Dual Index Kit TT Set A (1000215), and Chromium Next GEM Chip K Single Cell Kit (1000286) according to the manufacturer’s instructions.

tag: disease

value: Healthy Control


title: HaCaT cells_1 irradiated by UVB

value: irradiated by UVB


title: K-562 SMART-seq stranded cell 6 [6minE1]


title: DCs, donor 2 HIV

tag: individual

tag: growth protocol

value: HIV treated


title: N3 CD4+ T cells

description: CTCL with blood envolvement


title: N1 CD4+ T cells

description: CTCL with blood envolvement


title: P11 CD4+ T cells

description: CTCL with blood envolvement

value: Cutaneous T Cell Lymphoma


title: Sham 5_1 wk_Infarct

tag: Sex

value: Heart Left Ventricle

value: infarct


title: HaCaT cells_1 with HMW-HA

value: Keratinocyte

value: treated with HMW-HA


title: Sham 4_1 wk_Infarct

tag: strain


title: P10 CD4+ T cells

description: CTCL with blood envolvement


title: MI 4_1wk_Infarct

tag: stress

value: LAD Ligation (infarct)


title: K-562 SMART-seq stranded cell 5 [6minD1]


title: MI 2_1wk_Infarct

tag: tissue region


title: Sham 3_1 wk_Infarct

tag: technical replicate


title: K-562 SMART-seq stranded cell 4 [6minC1]


title: Sham 2_1 wk_Infarct


title: K-562 SMART-seq stranded cell 7 [6minF1]


title: P6 CD4+ T cells

description: CTCL with blood envolvement


title: P7 CD4+ T cells

description: CTCL with blood envolvement


title: Sham 1_1 wk_Infarct


title: P5 CD4+ T cells

description: CTCL with blood envolvement


title: K-562 SMART-seq stranded cell 3 [6minB2]


title: P3 CD4+ T cells

description: CTCL with blood envolvement


title: MI+Cell Sheet 6_1wk_Borderzone

source_name: LV, Borderzone

value: Cell Sheet

value: Borderzone


title: K-562 SMART-seq stranded cell 2 [6minB1]


title: K-562 SMART-seq stranded cell 1 [6minA2]


title: MI+Cell Sheet 5_1wk_Borderzone


title: P2 CD4+ T cells

description: CTCL with blood envolvement


title: MI+Cell Sheet 4_1wk_Borderzone


title: hFOB_G34W2_H3K36me3

data_processing:
Adaptors were removed by TrimGalore
Reads were aligned to hg19 and dm6 by Bowtie2 with default parameters
Raw scaling factors were calculated for IP samples following Niu et al.(DOI:10.21769/BioProtoc.2981)
Raw scaling factors were justed for IP samples of the same histone modification by transforming the largest raw scaling factor to 1, and others were adjusted proportionally.
BAM files of IP samples were down-sampled by Picard and scaling factor.
BigWig files were created by bamCoverage from Deeptools with binSize=1
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

treatment_protocol: Cells were engineered to express H3.3-G34W, H3.3-WT or EV.

value: hFOB 1.19

tag: cell type

value: osteoblastic cell line

tag: genotype


title: K-562 STORM-seq cell 69 [H7]

source_name: K-562 STORM-seq cell

tag: cell line

value: Chronic Myelogenous Leukemia

tag: treatment

value: STORM-seq


title: hFOB_G34W1_H3K36me3

tag: chip antibody


title: K-562 STORM-seq cell 70 [H8]

tag: disease state

value: Bone marrow

value: Female


title: P9 CD4+ T cells

description: CTCL with blood envolvement


title: MI+Cell Sheet 3_1wk_Borderzone

tag: tissue


title: P8 CD4+ T cells

description: CTCL with blood envolvement


title: K-562 STORM-seq cell 68 [H6]

tag: tissue source

tag: gender


title: K-562 STORM-seq cell 67 [H5]

tag: experiment type


title: hFOB_WT3_H3K36me3


title: MI+Cell Sheet 2_1wk_Borderzone


title: hFOB_WT2_H3K36me3


title: K-562 STORM-seq cell 65 [H3]


title: P4 CD4+ T cells

description: CTCL with blood envolvement

tag: disease


title: P1 CD4+ T cells

description: CTCL with blood envolvement


title: K-562 STORM-seq cell 64 [H2]


title: MI 6_1wk_Borderzone


title: Patient 1 Fallopian Tube Epithelium

source_name: Fallopian Tube Epithelium

value: Healthy

value: Fallopian Tube Epithelium


title: K-562 bulk total RNA sample 1 [K5621]

source_name: K-562 bulk total RNA sample

value: Kapa Hyper Prep


title: K-562 bulk total RNA sample 2 [K5622]


title: K-562 STORM-seq cell 63 [H1]


title: crypts, WT, DSS+CA, Day5 [CA3]

city: Shanghai

first: Tingying

last: Jiao

state: Shanghai

address: 501 Haike Road, Pudong New Area

country: China

institute: SIMM

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence/length<25/species ribosome RNA using CLC genomic benchwork (parameter- Quality limit: 0.01)
Trimmed sequence reads were mapped to GrCM38/mm10 using Hisat2（version:2.0.4）
Read count extraction and normalization were performed using Stringtie（version:1.3.0）and TMM（trimmed mean of M values）
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: crypts

extract_protocol:
RNA was harvested using RNeasy Micro Kit- QIAGEN#74004. 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Sample Preparation kit following manufacturer's protocols.

tag: strain background

value: crypts

value: WT

value: DSS+CA

tag: time

value: Day 5


title: crypts, WT, DSS+CA, Day5 [CA4]


title: hFOB_EV1_H3K36me3

source_name: hFOB 1.19_EV_H3K36me3

value: Empty vector (EV)


title: crypts, WT, DSS+CA, Day5 [CA2]


title: MI 4_1wk_Borderzone

tag: Sex

tag: strain

value: Heart Left Ventricle

value: LAD Ligation (infarct)


title: K-562 STORM-seq cell 62 [G9]


title: crypts, WT, DSS+CA, Day5 [CA1]


title: hFOB_G34W2_H3K27ac

value: H3K27ac (Abcam, Ab4729)


title: MI 5_1wk_Borderzone

tag: stress

tag: tissue region

value: Borderzone


title: K-562 STORM-seq cell 61 [G8]


title: K-562 STORM-seq cell 66 [H4]


title: MI 3_1wk_Borderzone

tag: technical replicate


title: crypts, WT, DSS, Day5 [DSS4]

tag: cell type

tag: genotype

value: DSS


title: MI 2_1wk_Borderzone

tag: treatment


title: K-562 STORM-seq cell 60 [G7]

tag: cell line

value: Chronic Myelogenous Leukemia


title: MI+Cell Sheet 1_1wk_Borderzone

value: Cell Sheet


title: crypts, WT, DSS, Day5 [DSS3]


title: hFOB_WT3_H3K27ac

value: hFOB 1.19

value: osteoblastic cell line

tag: chip antibody


title: MI 1_1wk_Borderzone

value: Female

tag: tissue


title: K-562 STORM-seq cell 59 [G6]

tag: disease state

tag: tissue source

value: Bone marrow

value: STORM-seq


title: hFOB_WT1_H3K36me3


title: hFOB_EV2_H3K36me3


title: hFOB_WT2_H3K27ac


title: crypts, WT, DSS, Day5 [DSS2]

value: crypts


title: K-562 STORM-seq cell 58 [G5]

tag: gender

tag: experiment type


title: crypts, WT, DSS, Day5 [DSS1]

tag: strain background

value: WT


title: hFOB_WT1_H3K27ac


title: Sham 6 1wk_Borderzone

value: Sham surgery


title: 1h

city: wuhan

first: Jian

last: Wu

address: donghu road

institute: wuhan university

data_processing:
Cells were washed using Dig-Wash buffer to remove unbound antibodies.
A dilution of pA-Tn5 adapter complex was prepared and added to the nucleus with gentle vortexing,The nucleus incubated at RT for 1 h.
Nucleus were washed in wash Buffer to remove unbound pA-Tn5 protein.Next, nucleus were resuspended in Tagmentation buffer and incubated at 37℃ for 1 h.
To stop tagmentation, STOP buffer was added to sample, which was incubated at 55℃ for 30 min , and then at 70℃ for 20 min.
The library DNA was purified and amplified for sequencing with the Illumina NovaSeq 6000.
Assembly: mm10

extract_protocol:
Cells were harvested, counted and centrifuged for 3 min at 600 × g at room temperature.Aliquots of cells (60-500,000 cells), were washed twice in Wash Buffer by gentle pipetting.Cell nucleus were prepared and resuspended.Primary antibody incubation was pe
To increase the number of Protein A binding sites for each bound antibody, an appropriate secondary antibody (such as Guinea Pig anti-Rabbit IgG antibody for a rabbit primary antibody) was diluted in Dig-Wash buffer and cells were incubated at RT for 30 m
CUT&Tag

value: mouse macrophage

value: Myc antibody (10828-2-AP, Proteintech, China)


title: K-562 STORM-seq cell 57 [G4]


title: Sham 5 1wk_Borderzone

value: Heart Left Ventricle


title: K-562 STORM-seq cell 56 [G3]


title: hFOB_EV2_H3K27ac

source_name: hFOB 1.19_EV_H3K27ac

value: Empty vector (EV)


title: Sham 4 1wk_Borderzone


title: hFOB_EV1_H3K27ac

value: H3K27ac (Abcam, Ab4729)


title: hFOB_G34W1_H3K27ac


title: Sham 3 1wk_Borderzone

value: Borderzone


title: K-562 STORM-seq cell 55 [G2]


title: 0h

value: Myc antibody (10828-1-AP, Proteintech, China)


title: hFOB_G34W2_Input


title: hFOB_G34W1_Input


title: K-562 STORM-seq cell 53 [F9]

value: Chronic Myelogenous Leukemia


title: Sham 2 1wk_Borderzone


title: K-562 STORM-seq cell 54 [G1]


title: Sham 1 1wk_Borderzone


title: hFOB_WT3_Input


title: MI+Cell Sheet 6_1wk_Remote

source_name: LV, Remote

value: LAD Ligation (infarct)

value: Cell Sheet

value: Remote


title: Prj161-L3-54

city: East Lansing

first: Tim

last: Zacharewski

state: Michigan

address: 1129 Farm Ln

department: Biochemistry and Molecular Biology, Integrative Toxicological Sciences

institute: Michigan State University

description:
Adult male mouse dosed every 4 days for 28 days
54

data_processing:
Read quality was assessed using FastQC v0.11.7 and adapter trimming was performed using Trimmomatic v0.39.
Alignment was performed with STAR v2.7.3a. Genome indices were created using Mus_musculus.GRCm39.dna.chromosome.fa and Mus_musculus.GRCm39.104.gtf.
Gene counts were determined using STAR v2.7.3a.
Assembly: mm10 (build 39)
Supplementary files format and content: Transformed counts were normalized using a semi-parametric approach (Eckel et al., 2004) and analyzed using an empirical Bayes method (Eckel et al., 2005).
Supplementary files format and content: Tab-delimited text files represent the number of aligned PE reads to each gene.

source_name: Liver

extract_protocol:
Frozen liver (~100 mg) was homogenized in 1 mL of TriZOL with chrome-steel beads using a Mixer Mill 300 (Life Sciences, Carlsbad, CA) for 4 minutes. Following, total RNA was extracted per the manufacturer’s instructions with an additional 5:1 phenol:chloroform extraction step (Sigma Aldrich, St. Louis, MO). RNA purity (260/280 ratio) and concentration (ng/µL) were assessed with a NanoDrop 1000 spectrophotometer. RNA quality was determined using an Agilent 2100 Bioanalyzer. All RNA samples had RNA integrity numbers (RINs) ≥7.
Library preparation was performed using a Ultra2 NEB RNA kit.

treatment_protocol: Mice were orally gavaged with TCDD in sesame oil vehicle every 4 days for 28 days.

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

tag: vehicle substance

value: sesame oil

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

value: milliliter

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

value: oral gavage

tag: administration route ontology

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

value: Carbon dioxide euthanasia

tag: euthaniasia method ontology

tag: library kit

value: NEBNext Ultra II


title: Prj161-L3-53

description:
Adult male mouse dosed every 4 days for 28 days
53

tag: tissue

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

tag: Sex

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

tag: vehicle substance

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit


title: Prj161-L3-52

description:
Adult male mouse dosed every 4 days for 28 days
52

tag: tissue

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

tag: Sex

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

tag: administration route ontology

tag: dose

tag: dose unit

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

tag: euthaniasia method ontology

tag: library kit


title: K-562 STORM-seq cell 51 [F7]

tag: cell line

tag: disease state

value: Chronic Myelogenous Leukemia

tag: treatment

tag: tissue source

value: Bone marrow

tag: gender

value: Female

tag: experiment type

value: STORM-seq


title: Prj161-L3-51

description:
Adult male mouse dosed every 4 days for 28 days
51

tag: tissue

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

tag: Sex

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

tag: vehicle substance

value: sesame oil

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

value: milliliter

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route


title: MI+Cell Sheet 5_1wk_Remote

tag: Sex

tag: strain

tag: tissue

value: Heart Left Ventricle

tag: stress

value: LAD Ligation (infarct)

tag: treatment

value: Cell Sheet

tag: tissue region

value: Remote

tag: technical replicate


title: Prj161-L3-50

description:
Adult male mouse dosed every 4 days for 28 days
50

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

tag: vehicle substance

value: oral gavage

tag: administration route ontology

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

value: Carbon dioxide euthanasia

tag: euthaniasia method ontology

tag: library kit

value: NEBNext Ultra II


title: hFOB_WT1_Input

tag: cell line

value: hFOB 1.19

tag: cell type

value: osteoblastic cell line

tag: genotype

tag: chip antibody


title: K-562 STORM-seq cell 50 [F6]

tag: disease state

value: Chronic Myelogenous Leukemia

tag: treatment

tag: tissue source

value: Bone marrow

tag: gender

value: Female

tag: experiment type

value: STORM-seq


title: MI+Cell Sheet 4_1wk_Remote

tag: Sex

tag: strain

tag: tissue

value: Heart Left Ventricle

tag: stress

value: LAD Ligation (infarct)

value: Cell Sheet

tag: tissue region

value: Remote

tag: technical replicate


title: K-562 STORM-seq cell 49 [F5]


title: hFOB_EV2_Input

value: Empty vector (EV)


title: Prj161-L3-49

description:
Adult male mouse dosed every 4 days for 28 days
49

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

tag: vehicle substance

value: sesame oil

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

value: milliliter

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

tag: administration route ontology

tag: dose

tag: dose unit

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

tag: euthaniasia method ontology


title: Prj161-L3-48

description:
Adult male mouse dosed every 4 days for 28 days
48

tag: tissue

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

tag: Sex

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

tag: vehicle substance

tag: vehicle substance ontology

tag: administration volume

value: oral gavage

value: microgram per kilogram

value: Carbon dioxide euthanasia

tag: library kit

value: NEBNext Ultra II


title: hFOB_EV1_Input

tag: cell line

value: hFOB 1.19

tag: cell type

value: osteoblastic cell line

tag: genotype

value: Empty vector (EV)

tag: chip antibody


title: K-562 STORM-seq cell 48 [F4]

tag: disease state

value: Chronic Myelogenous Leukemia

tag: treatment

tag: tissue source

value: Bone marrow

tag: gender

value: Female

tag: experiment type

value: STORM-seq


title: MI+Cell Sheet 2_1wk_Remote

tag: Sex

tag: strain

tag: tissue

value: Heart Left Ventricle

tag: stress

value: LAD Ligation (infarct)

value: Cell Sheet

tag: tissue region

value: Remote

tag: technical replicate


title: Prj161-L3-47

description:
Adult male mouse dosed every 4 days for 28 days
47

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

tag: vehicle substance

value: sesame oil

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

value: milliliter

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

tag: administration route ontology

tag: dose

tag: dose unit

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

tag: euthaniasia method ontology


title: K-562 STORM-seq cell 47 [F3]

tag: cell line

tag: disease state

value: Chronic Myelogenous Leukemia

tag: treatment

tag: tissue source

value: Bone marrow

tag: gender

value: Female

tag: experiment type

value: STORM-seq


title: MI+Cell Sheet 1_1wk_Remote

tag: Sex

tag: strain

tag: tissue

value: Heart Left Ventricle

tag: stress

value: LAD Ligation (infarct)

value: Cell Sheet

tag: tissue region

value: Remote

tag: technical replicate


title: K-562 STORM-seq cell 52 [F8]


title: Prj161-L3-44

description:
Adult male mouse dosed every 4 days for 28 days
44

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

tag: vehicle substance

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

value: oral gavage

tag: administration route ontology

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit ontology

tag: time point

value: Carbon dioxide euthanasia

tag: library kit

value: NEBNext Ultra II


title: MI 6_1wk_Remote

tag: Sex

value: Female

tag: strain

tag: tissue

tag: stress

tag: treatment

tag: tissue region

tag: technical replicate


title: K-562 STORM-seq cell 46 [F2]

tag: cell line

tag: disease state

value: Chronic Myelogenous Leukemia

tag: tissue source

value: Bone marrow

tag: gender

tag: experiment type

value: STORM-seq


title: K-562 STORM-seq cell 45 [F1]


title: Prj161-L3-43

description:
Adult male mouse dosed every 4 days for 28 days
43

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain ontology

tag: organism supplier

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

tag: vehicle substance

value: sesame oil

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

value: milliliter

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

tag: administration route ontology

tag: dose

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

tag: euthaniasia method ontology


title: MI 5_1wk_Remote

tag: Sex

tag: strain

tag: tissue

value: Heart Left Ventricle

tag: stress

value: LAD Ligation (infarct)

tag: treatment

tag: tissue region

value: Remote

tag: technical replicate


title: Prj161-L3-42

description:
Adult male mouse dosed every 4 days for 28 days
42

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

tag: vehicle substance

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

value: oral gavage

tag: dose unit

value: microgram per kilogram

tag: dose unit ontology

tag: time point

value: Carbon dioxide euthanasia

tag: library kit


title: K-562 STORM-seq cell 44 [E9]

tag: cell line

tag: disease state

value: Chronic Myelogenous Leukemia

tag: treatment

tag: tissue source

value: Bone marrow

tag: gender

value: Female

tag: experiment type

value: STORM-seq


title: MI+Cell Sheet 3_1wk_Remote

tag: Sex

tag: strain

tag: tissue

value: Heart Left Ventricle

tag: stress

value: LAD Ligation (infarct)

value: Cell Sheet

tag: tissue region

tag: technical replicate


title: MI 4_1wk_Remote

value: Remote


title: MI 3_1wk_Remote


title: K-562 STORM-seq cell 43 [E8]


title: Prj161-L3-41

description:
Adult male mouse dosed every 4 days for 28 days
41

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

tag: vehicle substance

value: sesame oil

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

value: milliliter

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

tag: administration route ontology

tag: dose

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

tag: euthaniasia method ontology

value: NEBNext Ultra II


title: Prj161-L3-40

description:
Adult male mouse dosed every 4 days for 28 days
40

tag: tissue

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain

tag: strain ontology

tag: organism supplier

tag: Sex

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: oral gavage

tag: dose unit

value: microgram per kilogram

tag: dose unit ontology

tag: time point

value: Carbon dioxide euthanasia

tag: library kit


title: MI 2_1wk_Remote

tag: Sex

value: Female

tag: strain

tag: tissue

value: Heart Left Ventricle

tag: stress

value: LAD Ligation (infarct)

tag: treatment

tag: tissue region

value: Remote

tag: technical replicate


title: K-562 STORM-seq cell 42 [E7]

tag: cell line

tag: disease state

value: Chronic Myelogenous Leukemia

tag: tissue source

value: Bone marrow

tag: gender

tag: experiment type

value: STORM-seq


title: Prj161-L3-39

description:
Adult male mouse dosed every 4 days for 28 days
39

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

tag: vehicle substance

value: sesame oil

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

value: milliliter

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

tag: administration route ontology

tag: dose

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

tag: euthaniasia method ontology


title: MPiFR_3

type: RNA

city: Odense M

first: Carla

last: Alves

address: Fioniavej 36, 2. sal

country: Denmark

institute: SDU

description: Gene expression data from combined PI3Ki and fulvestrant- resistant cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on human transcriptome array 2.0 (HTA). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Data analysis was conducted in Transcriptome Analysis Console (Thermo Fisher Scientific). A fold change ≤ -3 or ≥3, p-value < 0.05, and false discovery rate (FDR) < 0.05 cutoffs were set to select differentially expressed genes between MCF-7 and MPiF-R cells

label: biotin

source_name: MPiFR cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MCF-7 cells were cultured in phenol red-free Dulbecco’s modified Eagle medium (D-MEM)/F-12 (Gibco) supplemented with 1% heat-inactivated fetal bovine serum (FBS, Gibco), 2 mM glutamine (Gibco) and 6 ng/ml insulin (Sigma-Aldrich). MPiF-R cells were maintained in the same growth media supplemented with 10 µM PI3Ki and 100 nM fulvestrant.

extract_protocol: Total RNA was extracted and purified with RNeasy Mini kit (Qiagen) according to the manufacturer´s instructions.

treatment_protocol: The combined PI3Ki, alpelisib, and fulvestrant-resistant cell line, MPiFR, was established through long-term treatment with 100 nM fulvestrant and increasing concentrations of PI3Ki (0.5-10 µM) over a period of 4 months.

tag: cell line source

value: MCF-7 cells

tag: cell type

value: Combined PI3Ki and fulvestrant resistant cells


title: MPiFR_2


title: MPiFR_1


title: K-562 STORM-seq cell 41 [E6]

tag: cell line

tag: disease state

tag: treatment

tag: tissue source

tag: gender

value: Female

tag: experiment type


title: MI 1_1wk_Remote

tag: Sex

tag: strain

tag: tissue

value: Heart Left Ventricle

tag: stress

value: LAD Ligation (infarct)

tag: tissue region

value: Remote

tag: technical replicate


title: Prj161-L3-38

description:
Adult male mouse dosed every 4 days for 28 days
38

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain ontology

tag: organism supplier

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

tag: vehicle substance

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

value: oral gavage

tag: administration route ontology

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

value: Carbon dioxide euthanasia

tag: library kit

value: NEBNext Ultra II


title: Sham 6_1 wk_Remote

tag: Sex

tag: strain

tag: tissue

tag: stress

value: Sham surgery

tag: treatment

tag: tissue region

tag: technical replicate


title: MCF-7_2

description: Gene expression data from parental sensitive MCF-7 cells

source_name: MCF-7 cells

tag: cell line source

value: MCF-7 cells

tag: cell type

value: Parental sensitive cells


title: K-562 STORM-seq cell 40 [E5]

tag: cell line

tag: disease state

value: Chronic Myelogenous Leukemia

tag: tissue source

value: Bone marrow

tag: gender

value: Female

tag: experiment type

value: STORM-seq


title: Prj161-L3-37

description:
Adult male mouse dosed every 4 days for 28 days
37

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

tag: vehicle substance

value: sesame oil

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

value: milliliter

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

tag: administration route ontology

tag: dose

tag: dose unit

tag: dose unit ontology

tag: time point

tag: time point unit

tag: euthaniasia method

tag: euthaniasia method ontology


title: Sham 5_1 wk_Remote

tag: Sex

tag: strain

tag: tissue

value: Heart Left Ventricle

tag: stress

value: Sham surgery

tag: treatment

tag: tissue region

value: Remote

tag: technical replicate


title: K-562 STORM-seq cell 39 [E4]

tag: cell line

tag: disease state

value: Chronic Myelogenous Leukemia

tag: tissue source

value: Bone marrow

tag: gender

tag: experiment type


title: MCF-7_3

tag: cell line source

value: MCF-7 cells

tag: cell type

value: Parental sensitive cells


title: Prj161-L3-36

description:
Adult male mouse dosed every 4 days for 28 days
36

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

tag: vehicle substance

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

value: oral gavage

tag: administration route ontology

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

value: Carbon dioxide euthanasia

tag: library kit

value: NEBNext Ultra II


title: Sham 4_1 wk_Remote

tag: Sex

value: Female

tag: strain

tag: tissue

value: Heart Left Ventricle

tag: stress

value: Sham surgery

tag: treatment

tag: tissue region

tag: technical replicate


title: K-562 STORM-seq cell 38 [E3]

tag: cell line

tag: disease state

value: Chronic Myelogenous Leukemia

tag: tissue source

value: Bone marrow

tag: gender

tag: experiment type

value: STORM-seq


title: Sham 3_1 wk_Remote

value: Remote


title: hFOB_WT2_Input

value: hFOB 1.19

tag: cell type

value: osteoblastic cell line

tag: genotype

tag: chip antibody


title: Prj161-L3-34

description:
Adult male mouse dosed every 4 days for 28 days
34

value: Liver

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain ontology

tag: organism supplier

value: Charles Rivers Laboratories

value: Male

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

value: day

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

value: degree celsius

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

tag: humidity unit ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

value: Aquavive water (Innovive)

tag: feed name

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: feed description

tag: feed source

value: Harlan Teklad

tag: feed catalog no

tag: ad lib feeding

value: Yes

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

value: Accustandard

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

value: Room temperature

tag: vehicle substance

value: sesame oil

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

value: milliliter

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

tag: administration route ontology

tag: dose

tag: dose unit

tag: dose unit ontology

tag: time point

tag: time point unit

tag: time point unit ontology

tag: euthaniasia method

tag: euthaniasia method ontology


title: Sham 2_1 wk_Remote

tag: Sex

value: Female

tag: strain

tag: tissue

value: Heart Left Ventricle

tag: stress

value: Sham surgery

tag: treatment

tag: tissue region

tag: technical replicate


title: Prj161-L3-29

description:
Adult male mouse dosed every 4 days for 28 days
29

tag: metadata template url

tag: source ontology

tag: organism ontology

tag: strain ontology

tag: organism supplier

tag: sex ontology

tag: acclimation period

tag: acclimation period unit

tag: acclimation period unit ontology

tag: study start age

tag: study end age

tag: age unit

tag: age unit ontology

tag: average vivarium temperature

tag: temperature unit

tag: temperature unit ontology

tag: average vivarium humidity

tag: humidity unit

value: percent

tag: humidity unit ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

tag: feed name

tag: feed description

tag: feed source

tag: feed catalog no

tag: ad lib feeding

tag: toxic substance

tag: toxic substance ontology

tag: cas number

tag: smile string

tag: formula

tag: inchi code

tag: toxic substance molecular weight

tag: toxic substance vendor

tag: toxic substance catalog number

tag: toxic substance purity

tag: toxic substance lot

tag: toxic substance storage

tag: vehicle substance

tag: vehicle substance ontology

tag: administration volume

tag: administration volume unit

tag: administration volume unit ontology

tag: administration interval

tag: administration interval unit

tag: administration interval unit ontology

tag: administration number

tag: administration route

value: oral gavage

value: microgram per kilogram

value: Carbon dioxide euthanasia

tag: library kit

value: NEBNext Ultra II


title: Sham 1_1 wk_Remote

tag: Sex

tag: strain

tag: tissue

tag: stress

tag: treatment

tag: tissue region

value: Remote

tag: technical replicate


title: K-562 STORM-seq cell 35 [D8]

tag: cell line

tag: disease state

value: Chronic Myelogenous Leukemia

tag: tissue source

value: Bone marrow

tag: gender

tag: experiment type

value: STORM-seq


title: K-562 STORM-seq cell 36 [E1]


title: K-562 STORM-seq cell 37 [E2]