title: Mettl3 KO fetal liver LSK single-cell RNA-seq rep 2

description:
single cell RNA-seq from LSK cells sorted from E14.5 fetal liver of a Mettl3 deficient mouse, biological replicate 2
Mettl3_singlecell_RNAseq_counts.txt
scRNAseq_KO_2

value: METTL3 deficient

value: Vav-Cre Mettl3fl/fl mice


title: Mettl3 KO fetal liver LSK single-cell RNA-seq rep 1

status: Public on Jun 01 2020

type: SRA

city: New Haven, US & Trento, Italy

first: Toma

last: Tebaldi

state: CT

address: 300 George Street

department: CIBIO & Department of Internal Medicine, Yale Cancer Center

country: USA

institute: Yale University & University of Trento

description:
single cell RNA-seq from LSK cells sorted from E14.5 fetal liver of a Mettl3 deficient mouse, biological replicate 1
Mettl3_singlecell_RNAseq_counts.txt
scRNAseq_KO_1

library_source: transcriptomic

data_processing:
bulk RNA-seq: reads were aligned to the mouse genome (GRCm38.p5) with STAR (version 2.5.3a, –quantMode GeneCounts), using the Gencode M15 transcript annotation as transcriptome guide. Normalization with the TMM method and identification of differentially expressed genes were performed with the edgeR package in Bioconductor.
CUT&RUN: reads were aligned to the mouse genome (GRCm38.p5) with Bowtie2 v2.2.9, (--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700). Duplicated reads were removed with Picard tools v2.9.0. Using the Gencode M15 annotation and bedtools coverage function (v2.26.0), the number of reads aligned around known transcription start sites (TSS) was determined considering a window of 3k nucleotides. Differential changes in H3K4me3 occupancy between WT and Mettl3-deficient LSK cells were identified with edgeR.
J2-RIP RNA-seq: duplicated reads were removed with FastUniq (v1.1). Reads generated from J2 RIP and INPUT samples were aligned to the mouse genome (GRCm38.p5) with STAR (version 2.5.3a, –quantMode GeneCounts), using the Gencode M15 transcript annotation as transcriptome guide. Normalization with the TMM method and identification of J2 Mettl3-deficient enriched genes were performed with the edgeR package in Bioconductor.
single cell RNA-seq: single cell expression measurements (digital counts) were obtained from raw sequence data with Drop-seq tools v1.12. Reads were aligned to the mouse genome (GRCm38.p5) with STAR (version 2.5.3a) using the Gencode M15 transcript annotation as transcriptome guide. The final digital expression matrix was obtained selecting cells with at least 500 identified genes. Single cell expression data analysis was performed with Seurat 3.0.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Mettl3_bulk_RNAseq_counts.txt: tab-delimited text file including gene annotations (columns 1-4) and sample-specific counts of aligned reads (bulk RNA-seq, Mettl3 depleted and wild type).  Mettl3_H3K4me3_TSS_3k_counts.txt: tab-delimited text file including transcript annotations (columns 1-6) and sample specific counts of H3K4me3 CUT&RUN reads aligned in the TSS region, considering a window of 3kb (Mettl3 depleted and wild type).  Mettl3_J2_RNAseq_counts.txt: tab-delimited text file including gene annotations (columns 1-4) and sample-specific counts of aligned reads (for both J2-RIP and INPUT samples, Mettl3 depleted and wild type).  Mettl3_singlecell_RNAseq_counts.txt: tab-delimited text file containing gene-specific and cell-specific counts (single cell RNA-seq, Mettl3 depleted and wild type).

molecule: polyA RNA

organism: Mus musculus

source_name: Fetal Liver E14.5, Lin-Sca-1+c-Kit+ sorted cells

growth_protocol: Mice were bred and maintained under specific-pathogen-free conditions at the animal facility of Yale University School of Medicine. One male and one female mice were put in one cage for mating. The pregnant female mice were sacrificed at E14.5 for fetal liver analysis.

extract_protocol:
bulk RNA-seq: RNA were extracted from E14.5 LSK cells following QIAGEN RNeasy Plus Micro Kit protocol.
CUT&RUN: Nuclei from E14.5 LSK cells were isolated with NE buffer, captured with Bio-Mag Plus Concanavalin A coated beads (Polysciences) and incubated with primary antibody for 2 hours at 4°C. After washing away unbound antibody with wash buffer, protein A-MNase was added to a final concentration of 700 ng/ml and incubated for 1 hour at 4 °C. The nuclei were washed again and placed in a metal block at 0°C. To activate protein A-MNase, CaCl2 was added to a final concentration of 2 mM. The reaction was carried out for 45 min and stopped by addition of an equal volume of 2XSTOP buffer. The protein-DNA complex was released by incubation for 10 min at 37 °C and centrifugation. DNA was extracted by QIAGEN PCR MiniElute Kit.
J2-RIP RNA-seq: Fresh E14.5 fetal livers were harvested. One part of the fetal liver was extracted by TRIzol Reagent for input RNA, the other part of the fetal liver was lysed in dsRIP lysis buffer. The fetal liver lysate was incubated with 5 ug SCICONS J2 antibody for 2 hours at 4 ℃. Protein G Dynabeads were washed in dsRIP lysis buffer and added to the lysate to allow J2-RNA complex formation for 1 hour at 4 ℃. Beads were washed four times with dsRIP lysis buffer, and J2 antibody pull-down RNA was extracted with TRIzol Reagent.
single cell RNA-seq: Microfluidic devices were infused with PBS and pressurized to remove air bubbles inside the microwells using a manually operated syringe with a closed outlet. E14.5 LSK single cell suspensions with 20,000 cells/50 µl in PBS + 1%BSA were pipetted on the inlet and drawn into the device. Once the channel was completely filled with cell solution, the fluid flow was stopped, and cells were allowed to settle by gravity. Excess cells were washed out with PBS, and mRNA capture beads at concentrations of 30,000–120,000 beads/50–150 µl were similarly loaded into the cell-loaded wells. Microwells were sealed with fluorinated oil (Fluorinert FC-40), the tubing at the outlet was disconnected, and the microfluidic devices were exposed to three freeze-thaw cycles with 5 min freezing (–80°C) alternating with 5 min thawing at room temperature. Following lysis, the microfluidic device was incubated for one hour inside a wet chamber for mRNA capture onto beads. After incubation, beads were collected into 6x saline-sodium citrate (SSC) buffer and washed twice with 6x SSC buffer prior to reverse transcription.
Bulk RNA-seq: polyA RNA selection
CUT&RUN: NEBNext Ultra II DNA Library Prep Kit
J2-RIP RNA-seq: rRNA depletion
single cell RNA-seq: Library preparation steps follow the same steps as in the DropSeq and SeqWell methods

tag: sequencing method

value: single cell RNA-seq

tag: mouse genotype

tag: age

tag: mouse model

tag: tissue

value: liver

tag: cell type

value: Lin-Sca-1+c-Kit+ sorted cells


title: Sample 330_Single HEK293T cell

city: Stanford

first: Alina

last: Isakova

state: CA

address: 318 Campus drive

department: Bioengineering

institute: Stanford University

data_processing:
Sequences from the NovaSeq were de-multiplexed using bcl2fastq version 2.19.0.316. Reads were trimmed from polyA tails using cutadapt v 1.18 with the following parameters: -m 18 -j 4 -a AAAAAAAAAA -a TTTTTTTTTT. Reads were then aligned to the human (GRCh38) or mouse genome (GRCm38) using STAR v2.7.0d 37 with the following parameters --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 18 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0  --outMultimapperOrder Random. Reads mapping to multiple locations were assigned either to a location with the best mapping score or, in the case of equal multimapping score – to the genomic location randomly chosen as “primary”.
Genome_build: GRCm38, GRCh38
Supplementary_files_format_and_content: tab-delimited text files of count tables

molecule: total RNA

organism: Homo sapiens

source_name: Single HEK293T cell

growth_protocol: HEK293T cells were cultured in complete DMEM high glucose medium (Gibco, ThermoFisher 11965092) supplemented with 5% Fetal Bovine Serum (ThermoFisher 16000044), 1mM Sodium Pyruvate (ThermoFisher 11360070) and 100 μg/mL Pencillin/Streptomycin (ThermoFisher 15070063). They were collected 2h after passaging and sorted in either 96-well plates with 3uL lysis buffer or 384-well paltes with 0.3 uL of lysis buffer in each well.    Human primary dermal fibroblasts were obtained from ATCC (ATCC® PCS-201-012™). Cells were cultured and passaged four times in Fibroblast Basal Medium (ATCC® PCS-201-030™) supplemented with 5ng/mL rh FGF β, 7.5mM L-glutamine, 50 ug/mL Ascorbic acid, 5ug/mL rh Insulin, and 1% Fetal Bovine Serum (Fibroblast Growth kit- low serum, ATCC® PCS-201-041™).  MCF7 cells (ATCC® HTB¬22™) were cultured in complete DMEM high glucose medium (Gibco, ThermoFisher 11965092) supplemented with 10% Fetal Bovine Serum (ThermoFisher 16000044), 1mM Sodium Pyruvate (ThermoFisher 11360070) and 100 μg/mL Pencillin/Streptomycin (ThermoFisher 15070063).  mESCs were maintained and differentiated as described previously35,36. Briefly, mESCs were grown in serum-free 2i+LIF medium (complete medium: DMEM/F12 glutaMAX (Gibco, ThermoFisher  10565018) , 1% N2 supplement (Gemini Bio), 2% B27 supplement (Gemini Bio), 0.05% BSA fraction V (ThermoFisher, 15260037), 1% MEM-non-essential amino acids (c  11140050), and 110 μM 2-mercaptoethanol (Pierce); supplemeted with MEK inhibitor PD0325901 (0.8 μM), GSK3β inhibitor CHIR99021 (3.3 μM) and 10ng/mL mouse LIF (Gibco, PMC9484) in tissue culture (TC) dishes pretreated with 7.5 μg/ml polyL-ornithine (Sigma) and 5 μg/ml laminine (BD). To induce spontaneous embryoid body formation cells were washed with PBS, dissociated with StemPro Accutase (Gibco, ThermoFisher cat# A1110501), transferred to serum-rich medium (complete medium: DMEM/F12 glutaMAX (Gibco) , 1% N2 supplement (Gemini Bio), 2% B27 supplement (Gemini Bio), 0.05% BSA fraction V, 1% MEM-non-essential amino acids, and 110 μM 2-mercaptoethanol; supplemented with 10% FBS (ThermoFisher 10439001) and diluted to 10^6 cells/mL. Each 10 uL of cell suspension were plated as a hanging drop in 10 cm2 TC dishes (15-20 drops per dish). 10uL of fresh serum-rich media was added to each drop on day 4 of the culture. Primed mESCs were collected 6h after hanging drop culture. Embryoid bodies were collected and dissociated at days 4, 8 and 12 of culture.

extract_protocol:
Lysis plates were prepared by dispensing 0.3μL lysis buffer (4 U Recombinant RNase Inhibitor (RRI) (Takara Bio, 2313B), 0.12% TritonTM X-100 (Sigma, 93443-100ML), 1μM Smart-seq4 oligo-dT primer (5’-Biotin- /5BiosG/CATAGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGT30VN-3’;IDT) (see Supplementary Table 3 for a full list of oligos used in the present study) into 384-well hard-shell PCR plates (Bio-Rad HSP3901) using Mantis liquid handler (Formulatrix). 96-well lysis plates were prepared with 3 μl lysis buffer. All plates were sealed with AlumaSeal CS Films (Sigma-Aldrich Z722634), spun down and snap-frozen on dry ice.   Cells were stained with calcein-AM and ethidium homodimer-1 (LIVE/DEAD® Viability/Cytotoxicity Kit, ThermoFisher L3224) and individual live cells were sorted in 384 well lysis plates using SONY sorter (SH800S) with 100um nozzle chip. Plates were spun down and stored at -80 degrees immediately after sorting.
Smart-seq-total

tag: cell line

value: HEK293T cell

tag: day of differentiation


title: COGC-seq ADR-R2

city: panjin

first: bo

middle: yu

last: liu

state: liaoning

address: Dagong Road 2

country: China

institute: Dalian University of Technology

library_source: genomic

data_processing:
base-calling: in-house BGISEQ-500 software
Bowtie2 (version: v2.2.5) was used to map clean reads to reference gene
peak-calling: MACS2 for ChIP-Seq; FPKM method was used in calculated RNA-seq expression level.
ChIPseeker for the annotation of peaks.
Genome_build: Genome_build: ChIP-Seq: hg19; RNA-Seq: hg19;
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bigwig (bw): The signal intensity of binding.

molecule: genomic DNA

source_name: human breast cancer cell MCF-7/ADR

extract_protocol:
MCF-7 and MCF-7/ADR cells were maintained in RPMI-1640 medium with 10% fetal calf serum. Approximately 2 x 10e7 cells were used for each COGC-seq or sWGA-seq assay. O-GlcNAz chromatin DNAs enriched by Streptavidin-magnetic beads were purified with the Qiagen PCR purification kit. For sWGA-seq, O-GlcNAc protein bound chromatin DNAs were enriched by sWGA-agarose beads. For RNA-seq, total RNA was extracted from the MCF-7 and MCF-7/ADR cells using Trizol reagent (Invitrogen). RNA quality was checked by Agilent 2100 Bioanalyzer (Agilent Technologies, USA). RNA libraries were prepared for sequencing using standard BGI protocols.
DNA-end repair, 3'-dA overhang and ligation of methylated sequencing adaptor. PCR amplification and size selection (usually 100-300bp, including adaptor sequence. Qualified library for sequencing. RNA-seq libraries were constructed using SMARTer cDNA library construction kit (Clontech, Takara Bio, CA, USA).

treatment_protocol: MCF-7 and MCF-7/ADR cells were cultured in RPMI-1640 medium with 10% fetal calf serum. MCF-7/ADR cells were cultured in the presence of a low concentration of Dox (1 µg/ml) and passaged for 1 week in drug-free medium before the experiments. For labeling, media was aspirated and the cells were washed with PBS. DMSO stocks of GalNAz was added to achieve the final treatment conditions and incubated for 48 h, with vehicle-only controls always included. ~2x107 S2 cells were used as a unit of cells for each experiment.

tag: morphology type

value: epithelial type of breast cancer cell

tag: chip antibody/selection

value: GalNAz feeding, Click reaction, and streptavidin purification


title: EORTC_Patient_81366

type: RNA

city: South San Francisco

first: Radia

last: Johnson

address: 1 DNA Way

country: United Kingdom

institute: Genentech

hyb_protocol: Per NanoString Total RNA Standard Protocol for formalin-fixed, paraffin-embedded (FFPE) samples.

data_processing:
Background correction was implemented using blank samples along with the global negative control probes. Sample-wise normalization was performed by transforming counts to the log2 scale and subtracting the sample-wise mean of housekeeping genes.
Water samples (used for the normalisation) and UHR control samples (used for cross-normalisation) using the NanoStringQCPro package on Bioconductor.

label: Nucleotide/fluorophore barcode

growth_protocol: Not applicable

extract_protocol: Not applicable

treatment_protocol: Not applicable

tag: Sex

value: Female

tag: corticosteroids

value: On

tag: surgical status

tag: treatment

value: BEVACIZUMAB+LOMUSTINE

tag: phillips subtype

value: Proliferative

tag: tcga subtype

value: Classical

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Non-methylated

tag: who category

tag: dataset

value: EORTC


title: COGC-seq ADR-R1

growth_protocol: RPMI-1640 medium with 10% fetal calf serum.


title: EORTC_Patient_81368

scan_protocol: Per NanoString Total RNA Standard Protocol for formalin-fixed, paraffin-embedded (FFPE) samples.

tag: age

value: Off

value: LOMUSTINE

value: Proneural

value: Methylated


title: EORTC_Patient_81364

label_protocol: Per NanoString Total RNA Standard Protocol for formalin-fixed, paraffin-embedded (FFPE) samples.


title: EORTC_Patient_81346

value: Male

value: Missing


title: Sample 329_Single HEK293T cell

tag: cell line

tag: day of differentiation


title: COGC-seq MCF_7 Input-R1

source_name: human breast cancer cell MCF-7

tag: morphology type

tag: chip antibody/selection


title: COGC-seq ADR Input-R2


title: Sample 328_Single HEK293T cell


title: COGC-seq MCF-7 Input-R2


title: Mettl3 WT fetal liver LSK  H3K4me3 CUT&RUN rep 1

description:
H3K4me3 CUT&RUN from LSK cells sorted from E14.5 fetal liver of a Mettl3 wild type mouse, biological replicate 1
Mettl3_H3K4me3_TSS_3k_counts.txt
H3K4me3_WT_1

data_processing:
Library strategy: CUT&RUN
bulk RNA-seq: reads were aligned to the mouse genome (GRCm38.p5) with STAR (version 2.5.3a, –quantMode GeneCounts), using the Gencode M15 transcript annotation as transcriptome guide. Normalization with the TMM method and identification of differentially expressed genes were performed with the edgeR package in Bioconductor.
CUT&RUN: reads were aligned to the mouse genome (GRCm38.p5) with Bowtie2 v2.2.9, (--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700). Duplicated reads were removed with Picard tools v2.9.0. Using the Gencode M15 annotation and bedtools coverage function (v2.26.0), the number of reads aligned around known transcription start sites (TSS) was determined considering a window of 3k nucleotides. Differential changes in H3K4me3 occupancy between WT and Mettl3-deficient LSK cells were identified with edgeR.
J2-RIP RNA-seq: duplicated reads were removed with FastUniq (v1.1). Reads generated from J2 RIP and INPUT samples were aligned to the mouse genome (GRCm38.p5) with STAR (version 2.5.3a, –quantMode GeneCounts), using the Gencode M15 transcript annotation as transcriptome guide. Normalization with the TMM method and identification of J2 Mettl3-deficient enriched genes were performed with the edgeR package in Bioconductor.
single cell RNA-seq: single cell expression measurements (digital counts) were obtained from raw sequence data with Drop-seq tools v1.12. Reads were aligned to the mouse genome (GRCm38.p5) with STAR (version 2.5.3a) using the Gencode M15 transcript annotation as transcriptome guide. The final digital expression matrix was obtained selecting cells with at least 500 identified genes. Single cell expression data analysis was performed with Seurat 3.0.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Mettl3_bulk_RNAseq_counts.txt: tab-delimited text file including gene annotations (columns 1-4) and sample-specific counts of aligned reads (bulk RNA-seq, Mettl3 depleted and wild type).  Mettl3_H3K4me3_TSS_3k_counts.txt: tab-delimited text file including transcript annotations (columns 1-6) and sample specific counts of H3K4me3 CUT&RUN reads aligned in the TSS region, considering a window of 3kb (Mettl3 depleted and wild type).  Mettl3_J2_RNAseq_counts.txt: tab-delimited text file including gene annotations (columns 1-4) and sample-specific counts of aligned reads (for both J2-RIP and INPUT samples, Mettl3 depleted and wild type).  Mettl3_singlecell_RNAseq_counts.txt: tab-delimited text file containing gene-specific and cell-specific counts (single cell RNA-seq, Mettl3 depleted and wild type).

tag: sequencing method

value: CUT&RUN

tag: mouse genotype

value: METTL3 wild type

tag: rip antibody

value: ChIP antibody:H3K4me3

tag: mouse model

value: Mettl3fl/fl mice without Vav-Cre

tag: tissue

value: liver

tag: cell type

value: Lin-Sca-1+c-Kit+ sorted cells


title: Sample 327_Single HEK293T cell

value: HEK293T cell


title: EORTC_Patient_81328

tag: Sex

value: Female

tag: corticosteroids

tag: surgical status

tag: treatment

value: BEVACIZUMAB+LOMUSTINE

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa


title: COGC-seq ADR Input-R1

tag: morphology type

value: epithelial type of breast cancer cell

value: GalNAz feeding, Click reaction, and streptavidin purification


title: EORTC_Patient_81330

tag: age

value: On

value: Mesenchymal

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Non-methylated

tag: who category

tag: dataset

value: EORTC


title: Sample 326_Single HEK293T cell

tag: cell line

tag: day of differentiation


title: Mettl3 KO fetal liver LSK  H3K4me3 CUT&RUN rep 2

description:
H3K4me3 CUT&RUN from LSK cells sorted from E14.5 fetal liver of a Mettl3 deficient mouse, biological replicate 2
Mettl3_H3K4me3_TSS_3k_counts.txt
H3K4me3_KO_2

tag: sequencing method

tag: mouse genotype

value: METTL3 deficient

tag: rip antibody

tag: mouse model

value: Vav-Cre Mettl3fl/fl mice

tag: tissue

tag: cell type


title: EORTC_Patient_81326

tag: Sex

tag: corticosteroids

value: Off

tag: surgical status

tag: treatment

tag: phillips subtype

value: Unclassified

tag: tcga subtype

tag: kps

tag: mmse


title: Mettl3 WT fetal liver LSK bulk RNA-seq rep 3

description:
bulk RNA-seq from LSK cells sorted from E14.5 fetal liver of a Mettl3 wild type mouse, biological replicate 3
Mettl3_bulk_RNAseq_counts.txt
bulkRNAseq_WT_3

value: bulk RNA-seq

value: METTL3 wild type

tag: age


title: Sample 325_Single HEK293T cell

tag: cell line


title: Mettl3 WT fetal liver LSK  H3K4me3 CUT&RUN rep 2

description:
H3K4me3 CUT&RUN from LSK cells sorted from E14.5 fetal liver of a Mettl3 wild type mouse, biological replicate 2
Mettl3_H3K4me3_TSS_3k_counts.txt
H3K4me3_WT_2

value: CUT&RUN

value: ChIP antibody:H3K4me3

value: Mettl3fl/fl mice without Vav-Cre

value: liver


title: Mettl3 WT fetal liver LSK bulk RNA-seq rep 2

description:
bulk RNA-seq from LSK cells sorted from E14.5 fetal liver of a Mettl3 wild type mouse, biological replicate 2
Mettl3_bulk_RNAseq_counts.txt
bulkRNAseq_WT_2

value: Lin-Sca-1+c-Kit+ sorted cells


title: EORTC_Patient_81324

value: Male

value: BEVACIZUMAB+LOMUSTINE

value: Proneural

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

tag: who category

tag: dataset


title: Sample 324_Single HEK293T cell

value: HEK293T cell

tag: day of differentiation


title: EORTC_Patient_81322

tag: Sex

value: Non-methylated


title: Mettl3 WT fetal liver LSK bulk RNA-seq rep 1

description:
bulk RNA-seq from LSK cells sorted from E14.5 fetal liver of a Mettl3 wild type mouse, biological replicate 1
Mettl3_bulk_RNAseq_counts.txt
bulkRNAseq_WT_1

tag: sequencing method

tag: mouse genotype

tag: mouse model

tag: tissue

tag: cell type


title: Sample 323_Single HEK293T cell


title: Mettl3 KO fetal liver LSK bulk RNA-seq rep 3

description:
bulk RNA-seq from LSK cells sorted from E14.5 fetal liver of a Mettl3 deficient mouse, biological replicate 3
Mettl3_bulk_RNAseq_counts.txt
bulkRNAseq_KO_3


title: EORTC_Patient_81320

value: Female

tag: corticosteroids

value: On

tag: surgical status

tag: treatment

tag: phillips subtype

value: Proliferative

tag: tcga subtype

value: Classical

tag: kps

value: Missing

value: EORTC


title: EORTC_Patient_81272

tag: age

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)


title: EORTC_Patient_81270

tag: Sex

value: LOMUSTINE

value: Unclassified

tag: mgmt status

tag: who category

tag: dataset


title: Mettl3 KO fetal liver LSK  H3K4me3 CUT&RUN rep 1

description:
H3K4me3 CUT&RUN from LSK cells sorted from E14.5 fetal liver of a Mettl3 deficient mouse, biological replicate 1
Mettl3_H3K4me3_TSS_3k_counts.txt
H3K4me3_KO_1

tag: sequencing method

value: CUT&RUN

tag: mouse genotype

value: METTL3 deficient

tag: rip antibody

value: ChIP antibody:H3K4me3

tag: mouse model

value: Vav-Cre Mettl3fl/fl mice

tag: tissue


title: Mettl3 KO fetal liver LSK bulk RNA-seq rep 2

description:
bulk RNA-seq from LSK cells sorted from E14.5 fetal liver of a Mettl3 deficient mouse, biological replicate 2
Mettl3_bulk_RNAseq_counts.txt
bulkRNAseq_KO_2

value: bulk RNA-seq

value: liver

tag: cell type

value: Lin-Sca-1+c-Kit+ sorted cells


title: Mettl3 KO fetal liver LSK bulk RNA-seq rep 1

description:
bulk RNA-seq from LSK cells sorted from E14.5 fetal liver of a Mettl3 deficient mouse, biological replicate 1
Mettl3_bulk_RNAseq_counts.txt
bulkRNAseq_KO_1


title: Sample 320_Single HEK293T cell

tag: cell line

value: HEK293T cell

tag: day of differentiation


title: Sample 321_Single HEK293T cell


title: Patient5_corifollitrophin alfa

city: Modena

first: Antonio

last: La Marca

state: Modena

address: Via del pozzo, 71

department: Mother-Infant Department, Institute of Obstetrics and Gynecology

country: Italy

institute: University of Modena and Reggio

hyb_protocol: not provided

scan_protocol: not provided

data_processing:
affymetrix-algorithm-name = sst-rma-gene-full
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

label_protocol: not provided

growth_protocol: hGCs were recovered from preovulatory ovarian follicles after the oocytes retrieval from the medium aspirated. Retrieved hGCs were cultured for 6 days in McCoy 5A medium (Carlo Erba, Italy) supplemented with 5% foetal bovine serum (FBS) South America (EU Approved, Carlo Erba, Italy), 2mM L-Glutamine, 1% Penicillin/Streptomicin and 1% Amphotericin B (Sigma Aldrich, St. Louis, MO, USA) at 37 °C under a controlled atmosphere of 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy mini kit (Qiagen) according to the manufacturer's protocol

treatment_protocol: hGCs primary cultures were maintained in starvation buffer for 12 hours. hGCs were treated with bioequivalent doses of corifollitrophin alfa or rec FSH. hGCs were evaluated after 24 hours from the removal of the unbound gonadotrophins.

value: Primary culture of human granulosa cells (hGCs)


title: Sample 319_Single HEK293T cell


title: Patien5_recFSH


title: 4823_B FGC1896_s_6

city: Miinneapolis

first: Jeffrey

middle: H

last: Albrecht

state: MN

address: One Veterans Drive

department: Medicine - Gastroenterology

institute: University of Minnesota

description:
ADV-D1-RD-FLAG_HNF4a_ChIP_Rep3
4823_B
ADV-D1-RD-FLAG_HNF4a_ChIP_Rep3.peaks.txt

data_processing:
Illumina's bcl2fastq-v2.17.1.14 software was used to convert BCL basecall files to fastq files.
RNA-Seq: Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to respective genomes and Refseq transcriptome. Differential expression analysis was carried out using a custom script implementing EdgeR software.
ChIP-Seq: Reads were aligned to mm9 genome using bowtie version 0.12.7 with parameters -v 3 -k 1 -m 1 --best --strata. Redundant reads were discarded before creating bedgraph profiles.
ChIP-Seq: Peak calling on HNF4a ChIP samples was done using HOMER in factor mode and FDR cut off of 0.01 with respect to corresponding Input. Bioconductor's diffBind package was used for differential binding analysis.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: Excel file with raw transcript counts
Supplementary_files_format_and_content: Tab-delimited peak files listing genomic coordinates and their respective scores and p-values. Scores represent fold-change with respect to Input.

source_name: ADV-D1-RD-FLAG HNF4a ChIP

growth_protocol:
RNA-Seq: AML12, HepG2, and Sk-Hep1 cells were cultured in the presence or absence of serum along with control or cyclin D1 siRNA (see PMID 27351284 and 22751438 for the culture conditions). HepG2 and SK-HEP-1 cells were cultured in the presence of control or cyclin D1 siRNA (see PMID 27351284 for the culture conditions)
ChIP-Seq: Male BALB/c mice were transduced with recombinant adenoviruses encoding cyclin D1-HA-FLAG or cyclin D1-RD-FLAG (see PMID: 22751438 and 27351284 for details). Livers were harvested 24 hours later for ChIP-seq.

extract_protocol:
RNA-Seq: RNA was extracted using Qiazol followed by purification using the miRNeasy kit (Qiagen)
ChIP-Seq: DNA was exgtracted from mouse liver as previously described (PMID: 18556755).
RNA-Seq: Libraries were prepared using TruSeq Stranded mRNA HT kit using standard Illumina protocols
ChIP-Seq: Libraries were prepared using NEBNext ChIP-seq library prep reagent kit according to Illumina's instructions.

treatment_protocol:
RNA-Seq: AML 12 cells were cultured in 10% FBS (FBS(+)) or had withdrawal of serum 24 hours before harvest (FBS(-)). 45 hours before harvest, AML 12, HepG2 and SK-Hep-1 cells were treated with control or cyclin D1 siRNA (Dharmacon On-Target plus SMARTpool, catalog # L-042441-00-0020).
ChIP-Seq:  Mice were treated with recombinant adenoviruses as above.

value: BALB/c


title: EORTC_Patient_81266

tag: age

value: Male

tag: corticosteroids

value: Off

tag: surgical status

tag: treatment

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

value: Proneural

tag: kps


title: 4823_B FGC1896_s_5


title: Patien4_recFSH


title: Sample 318_Single HEK293T cell


title: Sample 317_Single HEK293T cell


title: Sample 322_Single HEK293T cell


title: EORTC_Patient_81198

tag: Sex

value: Classical

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Missing

tag: who category

value: EORTC


title: 4826_B FGC1896_s_6

description:
ADV-D1-RD-FLAG_HNF4a_ChIP_Rep2
4826_B
ADV-D1-RD-FLAG_HNF4a_ChIP_Rep2.peaks.txt


title: Patient4_ctrl

tag: tissue


title: Patient4_corifollitrophin alfa


title: EORTC_Patient_81196

value: On

value: BEVACIZUMAB+LOMUSTINE

tag: dataset


title: EORTC_Patient_81194

value: Female

value: Methylated


title: 4826_B FGC1896_s_5

tag: cell line


title: 4649_B FGC1896_s_6

description:
Control-ADV_HNF4a_ChIP_Rep3
4649_B
Control-ADV_HNF4a_ChIP_Rep3.peaks.txt

source_name: Control-ADV HNF4a ChIP


title: EORTC_Patient_81268

tag: age


title: EORTC_Patient_81192

tag: corticosteroids

value: Proliferative

value: Non-methylated


title: Sample 315_Single HEK293T cell

tag: day of differentiation


title: Sample 314_Single HEK293T cell


title: 4649_B FGC1896_s_5


title: Patient3_corifollitrophin alfa


title: Patient3_recFSH


title: Patient5_ctrl


title: 4674_B FGC1896_s_6

description:
ADV-CyclinD1-FLAG-HA_HNF4a_ChIP_Rep3
4674_B
ADV-CyclinD1-FLAG-HA_HNF4a_ChIP_Rep3.peaks.txt

source_name: ADV-CyclinD1-FLAG-HA HNF4a ChIP


title: Sample 313_Single HEK293T cell


title: Patient3_ctrl


title: EORTC_Patient_81182

tag: surgical status

tag: treatment

value: LOMUSTINE


title: 4674_B FGC1896_s_5


title: EORTC_Patient_81186

tag: phillips subtype

tag: tcga subtype


title: Sample 316_Single HEK293T cell

value: HEK293T cell


title: Sample 311_Single HEK293T cell


title: Sample 310_Single HEK293T cell


title: 4647_B FGC1896_s_6

description:
Control-ADV_HNF4a_ChIP_Rep2
4647_B
Control-ADV_HNF4a_ChIP_Rep2.peaks.txt


title: 4647_B FGC1896_s_5


title: Patient2_corifollitrophin alfa

value: Primary culture of human granulosa cells (hGCs)


title: Patient2_recFSH


title: EORTC_Patient_81178

tag: Sex

tag: kps


title: EORTC_Patient_81188

tag: mmse

tag: rpa


title: EORTC_Patient_81172

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)


title: 113

city: Kongens Lyngby

first: Haja

middle: N

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

data_processing:
Reads were trimmed for quality and artificial sequences using trimmomatic version 0.39, using the default suggested setting for paired end reads: java -jar trimmomatic-0.39.jar PE input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 MINLEN:36
The read were mapped using STAR aligner version 2.7.1a. We generated and index from the Sus Scrofa genome version 11.1 using Ensembl annotation version 11.1.96 for splice reference. Read were mapped using default setting for paired end reads.
The reads were annotated and quantified to the Sus Scrofa Ensembl annotation version 11.1.96 by including the --quantMode GeneCounts command in the alignment step.
Genome_build: Sus Scrofa 11.1
Supplementary_files_format_and_content: The proceessed files include 4 colums: the first has the Ensembl gene names, the second column included the annotated readcounts assuming no strandedness and the 3rd and 4th columns assuming forward and reverse strand mapping respectively.

organism: Sus scrofa

source_name: psoas major muscle

growth_protocol: Pigs were fed ad libitum until ~100kg

extract_protocol:
Muscle tissue samples from the psoas major muscle were collected imediatly post slaughter and preserved RNAlater (Ambion, Austin, Texas). Samples were stored at -25.
All processing from extraction to sequencing was a service provided by BGI: https://www.bgi.com/global/

treatment_protocol: Feed intake and growth was measured from ~28 to ~100kg, and Feed Conversion Ratio and Residual feed intake was calculated

value: psoas major muscle

tag: breed

tag: rin

tag: feed conversion ratio

tag: sampling age(days)

tag: batch

tag: gender

value: male


title: 109

tag: tissue


title: EORTC_Patient_81174

tag: age

value: Male

tag: corticosteroids

value: Off

tag: surgical status

value: Unclassified

tag: mgmt status

tag: who category

tag: dataset


title: Sample 309_Single HEK293T cell

tag: cell line

tag: day of differentiation


title: 4675_B FGC1896_s_6

description:
ADV-CyclinD1-FLAG-HA_HNF4a_ChIP_Rep2
4675_B
ADV-CyclinD1-FLAG-HA_HNF4a_ChIP_Rep2.peaks.txt

value: BALB/c


title: Sample 308_Single HEK293T cell


title: 111


title: Sample 312_Single HEK293T cell


title: Patient2_ctrl


title: 4675_B FGC1896_s_5


title: EORTC_Patient_81168

tag: Sex

tag: treatment

tag: phillips subtype

value: Proneural

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

value: Missing


title: Sample 307_Single HEK293T cell


title: 4672_B FGC1896_s_6

description:
ADV-CyclinD1-FLAG-HA_HNF4a_ChIP_Rep1
4672_B
ADV-CyclinD1-FLAG-HA_HNF4a_ChIP_Rep1.peaks.txt


title: EORTC_Patient_81136

tag: os cnsr (event = 1, censor = 0)

value: EORTC


title: Sample 306_Single HEK293T cell


title: 100

tag: tissue

tag: breed

tag: rin

tag: feed conversion ratio

tag: sampling age(days)

tag: batch

tag: gender


title: 4672_B FGC1896_s_5

tag: cell line


title: Patient1_recFSH


title: 91


title: Patient1_ctrl


title: EORTC_Patient_81130

tag: age

tag: Sex

tag: corticosteroids

value: On

tag: surgical status

tag: mgmt status

tag: who category

tag: dataset


title: Patient1_corifollitrophin alfa


title: 4824_B FGC1896_s_5

description:
ADV-D1-RD-FLAG_HNF4a_ChIP_Rep1
4824_B
ADV-D1-RD-FLAG_HNF4a_ChIP_Rep1.peaks.txt


title: 201


title: 4648_B FGC1896_s_6

description:
Control-ADV_HNF4a_ChIP_Rep1
4648_B
Control-ADV_HNF4a_ChIP_Rep1.peaks.txt


title: Sample 304_Single HEK293T cell

tag: day of differentiation


title: EORTC_Patient_81128

value: Female

tag: treatment

value: BEVACIZUMAB+LOMUSTINE

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)


title: Sample 305_Single HEK293T cell

tag: cell line


title: 93

tag: tissue

tag: breed

tag: rin

tag: feed conversion ratio

tag: sampling age(days)

tag: batch

tag: gender


title: 4648_B FGC1896_s_5


title: 90


title: 101


title: Sample 303_Single HEK293T cell

tag: day of differentiation


title: 200


title: EORTC_Patient_81018

tag: age

tag: Sex

tag: corticosteroids

tag: surgical status

tag: treatment

value: Mesenchymal

value: Classical

tag: mgmt status

tag: who category

tag: dataset


title: 4823 FGC1896_s_6

description:
ADV-D1-RD-FLAG_Input_Rep3
4823

source_name: ADV-D1-RD-FLAG Input

tag: cell line


title: 4824_B FGC1896_s_6


title: EORTC_Patient_81014

value: LOMUSTINE

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)


title: EORTC_Patient_81134


title: Sample 300_Single HEK293T cell

value: HEK293T cell

tag: day of differentiation


title: EORTC_Patient_81012

tag: age

value: Proliferative


title: EORTC_Patient_81008

tag: Sex


title: 78

tag: tissue

value: psoas major muscle

tag: breed

tag: rin

tag: feed conversion ratio

tag: sampling age(days)

tag: batch

tag: gender


title: Sample 302_Single HEK293T cell

tag: cell line


title: EORTC_Patient_81004

tag: corticosteroids

tag: surgical status

tag: treatment

tag: phillips subtype

tag: tcga subtype

tag: mgmt status

tag: who category

tag: dataset


title: Sample 299_Single HEK293T cell

tag: day of differentiation


title: Sample 301_Single HEK293T cell


title: 4826 FGC1896_s_6

description:
ADV-D1-RD-FLAG_Input_Rep2
4826


title: 4826 FGC1896_s_5

description:
ADV-D1-RD-FLAG_Input_Rep2
4826


title: Sample 298_Single HEK293T cell


title: EORTC_Patient_80860

tag: age

tag: Sex

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)


title: 4649 FGC1896_s_6

description:
Control-ADV_Input_Rep3
4649

source_name: Control-ADV Input

tag: cell line


title: 74

tag: tissue

tag: breed

tag: rin

tag: feed conversion ratio

tag: sampling age(days)

tag: batch

tag: gender

value: male


title: 72


title: 58


title: 63


title: 4823 FGC1896_s_5

description:
ADV-D1-RD-FLAG_Input_Rep3
4823


title: 4649 FGC1896_s_5

description:
Control-ADV_Input_Rep3
4649


title: Sample 296_Single HEK293T cell


title: EORTC_Patient_80858

value: Male

tag: corticosteroids

tag: surgical status

tag: treatment

tag: phillips subtype

tag: tcga subtype

tag: mgmt status

tag: who category

tag: dataset


title: Sample 297_Single HEK293T cell

tag: day of differentiation


title: Sample 295_Single HEK293T cell

tag: cell line


title: 86

tag: tissue


title: EORTC_Patient_80854

tag: age

tag: Sex

value: Off

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)


title: 4674 FGC1896_s_5

description:
ADV-CyclinD1-FLAG-HA_Input_Rep3
4674

source_name: ADV-CyclinD1-FLAG-HA Input


title: 60

tag: breed

tag: rin

tag: feed conversion ratio

tag: sampling age(days)

tag: batch

tag: gender


title: EORTC_Patient_80850

tag: corticosteroids

tag: surgical status

tag: treatment

tag: phillips subtype

tag: tcga subtype

tag: mgmt status

tag: who category

tag: dataset


title: Sample 294_Single HEK293T cell

tag: cell line

tag: day of differentiation


title: 70

tag: tissue


title: EORTC_Patient_80790

tag: age

tag: Sex

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)


title: 4647 FGC1896_s_6

description:
Control-ADV_Input_Rep2
4647


title: Sample 293_Single HEK293T cell


title: 64

tag: breed

tag: rin

tag: feed conversion ratio

tag: sampling age(days)

tag: batch

tag: gender


title: 4647 FGC1896_s_5

description:
Control-ADV_Input_Rep2
4647


title: Sample 292_Single HEK293T cell


title: 4674 FGC1896_s_6

description:
ADV-CyclinD1-FLAG-HA_Input_Rep3
4674


title: EORTC_Patient_80782

tag: corticosteroids

tag: surgical status

tag: treatment

tag: phillips subtype

tag: tcga subtype

tag: mgmt status

tag: who category

tag: dataset


title: 17

tag: tissue


title: 4675 FGC1896_s_6

description:
ADV-CyclinD1-FLAG-HA_Input_Rep2
4675

tag: cell line


title: 4675 FGC1896_s_5

description:
ADV-CyclinD1-FLAG-HA_Input_Rep2
4675


title: Sample 291_Single HEK293T cell

tag: day of differentiation


title: 27

tag: breed


title: EORTC_Patient_80778

tag: age

tag: Sex

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

value: Non-methylated


title: Sample 290_Single HEK293T cell


title: 4672 FGC1896_s_6

description:
ADV-CyclinD1-FLAG-HA_Input_Rep1
4672

value: BALB/c


title: EORTC_Patient_80776

tag: corticosteroids

tag: surgical status

tag: treatment


title: 25

tag: rin

tag: feed conversion ratio

tag: sampling age(days)

tag: batch

tag: gender


title: Sample 289_Single HEK293T cell

tag: cell line

tag: day of differentiation


title: 4672 FGC1896_s_5

description:
ADV-CyclinD1-FLAG-HA_Input_Rep1
4672


title: 15

tag: tissue

tag: breed


title: 19


title: Sample 288_Single HEK293T cell


title: 21


title: EORTC_Patient_80786

tag: age

tag: Sex

tag: phillips subtype

value: Proneural

tag: tcga subtype

tag: kps

tag: mgmt status

tag: who category

tag: dataset


title: EORTC_Patient_80774

tag: corticosteroids

tag: surgical status

tag: treatment

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)


title: Sample 287_Single HEK293T cell

tag: cell line

tag: day of differentiation


title: EORTC_Patient_80770

tag: age

value: Missing


title: Sample 286_Single HEK293T cell


title: EORTC_Patient_80772

tag: Sex

value: EORTC


title: 22

tag: tissue

tag: breed

tag: rin

tag: feed conversion ratio

tag: sampling age(days)

tag: batch

tag: gender


title: 4648 FGC1896_s_6

description:
Control-ADV_Input_Rep1
4648


title: Sample 285_Single HEK293T cell


title: EORTC_Patient_80734

tag: corticosteroids

tag: surgical status

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: mgmt status

value: Methylated

tag: who category

tag: dataset


title: 26


title: 4648 FGC1896_s_5

description:
Control-ADV_Input_Rep1
4648

tag: cell line


title: Sample 284_Single HEK293T cell

tag: day of differentiation


title: cage_275886_pup3_WT

city: Schwerzenbach

first: Katrien

last: De Bock

state: Zürich

address: Schorenstrasse 16

department: D-HEST

country: Switzerland

institute: ETH Zurich

data_processing:
Reads were aligned with STAR aligner with the options --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif
Alignments were counted with the featureCounts function
Genome_build: GRCm38
Supplementary_files_format_and_content: text files holding match counts per gene

source_name: P6 brain FACS isolated mouse endothelial cells

growth_protocol: Brain endothelial cells were isolated from GLUT1EC-/- mice and WT littermates using FACS sorting from neonates (P6). ECs were sorted directly into RLT plus RNeasy plus lysis buffer.

extract_protocol:
RNA was extracted using RNeasy Plus Micro Kit (Cat No. 74034, Qiagen, Hilden, Germany). RNA was stored  in -80 freezer till further processing for RNA-sequencing.
The libraries were prepared following Illumina TruSeq stranded mRNA protocol. The quality of the RNA and final libraries was determined using an Agilent 4200 TapeStation System. The libraries were pooled equimolecularly and sequenced in an Illumina NovaSeq sequencer (single-end 100 bp) with a depth of around 20 Mio reads per sample.
Illumina TruSeq stranded mRNA protocol

tag: cell type

value: Brain endothelial cells

tag: passages

value: primary uncultured endothelial cells

tag: strain

tag: age

value: post natal day 6

tag: genotype

value: WT


title: EORTC_Patient_80728

tag: Sex

value: Female

value: On

tag: treatment

value: BEVACIZUMAB+LOMUSTINE

value: Mesenchymal

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)


title: Sample 283_Single HEK293T cell

value: HEK293T cell


title: 14

tag: tissue

value: psoas major muscle

tag: breed

tag: rin

tag: feed conversion ratio

tag: sampling age(days)

tag: batch

tag: gender

value: male


title: EORTC_Patient_80726

tag: corticosteroids

value: Off

tag: surgical status

tag: phillips subtype

value: Proliferative

tag: tcga subtype

value: Classical

tag: kps

tag: mgmt status

tag: who category

tag: dataset


title: cage_275886_pup2_WT

tag: cell type

tag: passages

tag: strain

tag: age

tag: genotype


title: 4824 FGC1896_s_6

description:
ADV-D1-RD-FLAG_Input_Rep1
4824

tag: cell line

value: BALB/c


title: 4824 FGC1896_s_5

description:
ADV-D1-RD-FLAG_Input_Rep1
4824


title: 16

tag: tissue

tag: breed

tag: rin

tag: feed conversion ratio

tag: sampling age(days)


title: cage_275886_pup1_WT


title: 3

tag: batch

tag: gender


title: Sample 281_Single HEK293T cell

tag: day of differentiation


title: Sample 280_Single HEK293T cell


title: cage_275887_pup4_KO


title: EORTC_Patient_80722

tag: Sex

value: Male

tag: corticosteroids

tag: surgical status

tag: treatment

value: LOMUSTINE

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Missing

value: EORTC


title: cage_275887_pup5_WT

tag: cell type

value: Brain endothelial cells

tag: passages

value: primary uncultured endothelial cells

tag: strain

tag: age

value: post natal day 6

tag: genotype


title: EORTC_Patient_80768

tag: Sex

value: Non-methylated

tag: who category

tag: dataset


title: Sample 279_Single HEK293T cell

tag: cell line

tag: day of differentiation


title: 2

tag: tissue

tag: breed

tag: rin

tag: feed conversion ratio

tag: sampling age(days)

tag: batch

tag: gender


title: EORTC_Patient_80724

value: Female

tag: corticosteroids

tag: surgical status

tag: treatment

value: BEVACIZUMAB+LOMUSTINE

tag: phillips subtype

value: Proneural

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Methylated


title: EORTC_Patient_80718

tag: age

tag: Sex

value: On

value: Mesenchymal

tag: who category

tag: dataset


title: EORTC_Patient_80714

value: Proliferative


title: 9

tag: tissue

value: psoas major muscle

tag: breed

tag: rin

tag: feed conversion ratio

tag: sampling age(days)

tag: batch

value: male


title: 20

tag: gender


title: Sample 278_Single Dermal Fibroblast

source_name: Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: Sample 282_Single HEK293T cell

value: HEK293T cell


title: cage_275887_pup2_KO

tag: cell type

tag: passages

tag: strain

tag: genotype


title: Sample 277_Single Dermal Fibroblast


title: EORTC_Patient_80712

tag: age

value: Male

tag: corticosteroids

tag: surgical status

tag: treatment

value: LOMUSTINE

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: EORTC_Patient_80710

tag: Sex

tag: who category

tag: dataset

value: EORTC


title: 8

tag: tissue

tag: breed

tag: rin

tag: feed conversion ratio

tag: sampling age(days)

tag: batch

tag: gender


title: cage_275887_pup1_KO

tag: cell type

value: Brain endothelial cells

tag: passages

value: primary uncultured endothelial cells

tag: strain

tag: age

tag: genotype


title: EORTC_Patient_80708

tag: corticosteroids

tag: surgical status

tag: treatment

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

value: Non-methylated


title: Injured rep3

city: Philadelphia

first: G

middle: Scott

last: Worthen

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics

institute: Children's Hospital of Philadelphia

description:
170120_I283_FCHHL7JBBXX_L1_6
processed data file: injured_peaks.narrowPeak

data_processing:
Trimming the adapters with atactk (version 0.1.5)
Fastq files were aligned against the mouse reference genome (mm9) using the bowtie-1.1.2 aligner with the following flags:  “--chunkmbs 2000 --sam --best --strata -m1 -X 2000”
Duplicate reads and reads mapping to ChrM were excluded from further analysis.
MACS2 was used for peak calling with a q cutoff of 0.05.
Downstream analysis and visualization was done using HOMER and deepTools2.
Genome_build: mm9
Supplementary_files_format_and_content: MACS2 significant peaks

extract_protocol: Nuclei were exposed to Tn5 transposase (Illumina catalogue #FC-121-1030), and fractionated DNA was used for amplification and library preparation.

treatment_protocol: AT2 cells were sorted from minced Right lung 24 hrs after Unilateral acid-induced lung injury or after PBS in control mice. Cells were washed and lysed to prepare nuclei

tag: strain background

tag: genotype/variation

value: WT

value: injured

tag: tissue

value: Lung

value: type II alveolar pneumocytes (AT2)

tag: sorting profile

value: DAPI- EpCAM+ CD45- CD31- Sca1-


title: EORTC_Patient_80342

tag: Sex

value: Female

value: On

value: BEVACIZUMAB+LOMUSTINE

value: Mesenchymal

tag: mgmt status

value: Methylated

tag: who category

tag: dataset


title: Sample 275_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: 10

value: psoas major muscle

tag: breed

tag: rin

tag: feed conversion ratio

tag: sampling age(days)

tag: batch

tag: gender

value: male


title: cage_275887_pup3_KO

tag: cell type

tag: passages

tag: strain

tag: age

value: post natal day 6

tag: genotype


title: 4

tag: tissue


title: Uninjured rep3

description:
170120_I283_FCHHL7JBBXX_L1_3
processed data file: control_peaks.narrowPeak

tag: strain background

tag: genotype/variation

tag: treatment

value: uninjured control

tag: sorting profile


title: 202


title: EORTC_Patient_80338

tag: Sex

tag: corticosteroids

value: Off

tag: surgical status

value: LOMUSTINE

tag: phillips subtype

value: Proliferative

tag: tcga subtype

value: Classical

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Missing

tag: who category

tag: dataset

value: EORTC


title: Injured rep1

description:
170120_I283_FCHHL7JBBXX_L1_4
processed data file: injured_peaks.narrowPeak

tag: strain background

value: WT

value: injured

tag: tissue

value: Lung

tag: cell type

value: type II alveolar pneumocytes (AT2)

value: DAPI- EpCAM+ CD45- CD31- Sca1-


title: 11

tag: breed

tag: rin

tag: feed conversion ratio

tag: sampling age(days)

tag: batch

tag: gender


title: Injured rep2

description:
170120_I283_FCHHL7JBBXX_L1_5
processed data file: injured_peaks.narrowPeak

tag: genotype/variation

tag: treatment

tag: sorting profile


title: 6


title: EORTC_Patient_80330

tag: age

tag: Sex

value: Male

tag: corticosteroids

tag: surgical status

tag: phillips subtype

value: Unclassified

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

value: Non-methylated


title: Sample 272_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: 48

tag: tissue

value: psoas major muscle

tag: breed

tag: rin

tag: feed conversion ratio

tag: sampling age(days)

tag: batch

value: male


title: Sample 271_Single Dermal Fibroblast


title: Sample 274_Single Dermal Fibroblast


title: Uninjured rep2

description:
170120_I283_FCHHL7JBBXX_L1_2
processed data file: control_peaks.narrowPeak

tag: strain background

tag: genotype/variation

tag: treatment

value: uninjured control

tag: cell type

tag: sorting profile


title: 42

tag: gender


title: EORTC_Patient_80084

tag: age

tag: Sex

tag: corticosteroids

value: On

tag: surgical status

value: BEVACIZUMAB+LOMUSTINE

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

tag: kps

tag: mmse

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

tag: who category

tag: dataset


title: Sample 273_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: Sample 276_Single Dermal Fibroblast


title: EORTC_Patient_80082

value: Off

tag: treatment

value: LOMUSTINE

tag: rpa

tag: os (diagnosis)


title: Sample 270_Single Dermal Fibroblast


title: EORTC_Patient_80080

tag: age

value: Female

value: Proneural

value: EORTC


title: mOSE_BRCA1_ko_3

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

description:
brca1_dge_results.csv
brca1_tpm_matrix.csv

data_processing:
Pseudoalignment and transcript quantification performed with Kallisto (0.44.0) with -b 50
Differential expression analysis performed with Sleuth (0.30.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV file containing TPM values for each gene across all samples

source_name: Ovarian surface epithelial cells

growth_protocol: mOSE cells were cultured in media consisting of a-Minimum Essential Medium (Corning) supplemented with 4% FBS, 0.01mg/mL ITSS (Roche), 2ug/mL EGF (R&D Systems). For spheroid cultures, cells were cultured on ultra low attachment plates

extract_protocol:
Total RNA was collected using the RNeasy Kit (Qiagen)
Libraries were generated from 250 ng of total RNA as following: mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were done using and the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument.

treatment_protocol: Spheroid Culture: TGFB1-treated cells were treated with 10ng/mL TGFB1 (R&D Systems) for 4 days prior to being cultured in low-attachment plates. Snail Overexpression: Cells were transduced with either a lentiviral vector control (WPI) or a Snail-overexpression construct. BRCA1 deletion: mOSE cells  harvested from BRCA fl/fl mice were infected with an adenoviral vector expression either GFP (control) or Cre recominase. RNA was collected after confirming BRCA1 deletion.

tag: cell type

value: Ovarian surface epithelial cells


title: Sample 269_Single Dermal Fibroblast


title: Uninjured rep1

description:
170120_I283_FCHHL7JBBXX_L1_1
processed data file: control_peaks.narrowPeak

tag: strain background

tag: genotype/variation

value: WT

tag: tissue

value: Lung

value: type II alveolar pneumocytes (AT2)

tag: sorting profile

value: DAPI- EpCAM+ CD45- CD31- Sca1-


title: EORTC_Patient_80078

tag: Sex

value: Male

tag: corticosteroids

tag: surgical status

tag: phillips subtype

tag: tcga subtype

tag: kps

value: Missing


title: Sample 268_Single Dermal Fibroblast

tag: cell line

value: primary cell


title: mOSE_BRCA1_ko_2


title: EORTC_Patient_80076

tag: mmse

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Non-methylated

tag: who category

tag: dataset


title: Sample 267_Single Dermal Fibroblast

tag: day of differentiation


title: mOSE_BRCA1_ko_1

tag: cell type

tag: treatment


title: Sample 266_Single Dermal Fibroblast


title: mOSE_BRCA1_wt_3


title: EORTC_Patient_79880

tag: age

tag: rpa

tag: os (diagnosis)

value: Methylated


title: EORTC_Patient_79878

tag: Sex

tag: corticosteroids

value: On


title: mOSE_BRCA1_wt_2


title: mOSE_BRCA1_wt_1


title: Sample 264_Single Dermal Fibroblast


title: Sample 265_Single Dermal Fibroblast


title: mOSE_Snail_3

description:
snail_dge_results.csv
snail_tpm_matrix.csv

value: Snail overexpression


title: EORTC_Patient_79758

value: Off

tag: surgical status

tag: phillips subtype

value: Mesenchymal


title: POAF_343_7

city: Lille

first: Sandro

last: Ninni

address: 1 rue du Professeur Calmette

country: France

institute: INSERM

description: epicardial adipose tissue biopsy

hyb_protocol: Following fragmentation, 5,5µg of ssDNA were hybridized for 16 hr at 45C on GeneChip® Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (protocol FS450_0002)

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

data_processing: Data were normalized using GIANT tools suite [Vandel et al 2018] on a local instance of Galaxy.  GIANT computes normalization via apt-probeset-summarize[ref APT tool]with : gc-correction,scale-intensities,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish as parameters and at probeset level.Data were processed using Genepattern software. Batch effect was corrected using COMBAT software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.

source_name: Patients developing postoperative atrial fibrillation after surgery

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

growth_protocol: Snap frozen samples

extract_protocol: Qiagen RNA mini kit (Dusseldorf, Germany)

tag: tissue

value: epicardial adipose tissue

tag: patient diagnosis

value: postoperative atrial fibrillation after surgery (POAF)


title: POAF_366_12

description: epicardial adipose tissue biopsy


title: POAF_340_6

description: epicardial adipose tissue biopsy


title: POAF_330_2

description: epicardial adipose tissue biopsy


title: POAF_415_7

description: epicardial adipose tissue biopsy


title: Sample 262_Single Dermal Fibroblast

tag: cell line


title: mOSE_Snail_2


title: EORTC_Patient_79744

value: LOMUSTINE

value: Proneural

tag: tcga subtype

value: Unclassified

tag: kps

tag: mmse

tag: os cnsr (event = 1, censor = 0)

value: EORTC


title: EORTC_Patient_79756

value: BEVACIZUMAB+LOMUSTINE

tag: mgmt status

tag: who category

tag: dataset


title: POAF_463_13

description: epicardial adipose tissue biopsy


title: mOSE_Snail_1

tag: cell type

value: Ovarian surface epithelial cells

tag: treatment


title: Sample 261_Single Dermal Fibroblast

tag: day of differentiation


title: EORTC_Patient_79742

tag: age

tag: Sex

value: Male

tag: rpa

tag: os (diagnosis)


title: mOSE_WPI_3

value: WPI vector control


title: Sample 260_Single Dermal Fibroblast

value: primary cell


title: EORTC_Patient_79740

value: Female

tag: corticosteroids

tag: surgical status

tag: phillips subtype

value: Proliferative

value: Classical


title: POAF_458_12

description: epicardial adipose tissue biopsy

tag: tissue

tag: patient diagnosis


title: EORTC_Patient_79586

value: On

tag: tcga subtype

tag: kps

tag: mmse

value: Non-methylated


title: Sample 259_Single Dermal Fibroblast

tag: cell line


title: mOSE_WPI_2


title: EORTC_Patient_79748

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

tag: who category

tag: dataset


title: Sample 258_Single Dermal Fibroblast

tag: day of differentiation


title: mOSE_WPI_1

tag: cell type

tag: treatment


title: TGFB1_spheroids_3

description:
sphere_dge_results.csv
sphere_tpm_matrix.csv

value: 10ng/mL TGFB1


title: EORTC_Patient_79576

tag: age

tag: Sex

value: Off

value: Mesenchymal

tag: rpa

tag: os (diagnosis)

value: Methylated


title: Sample 263_Single Dermal Fibroblast


title: POAF_419_8

description: epicardial adipose tissue biopsy

tag: tissue

value: epicardial adipose tissue

value: postoperative atrial fibrillation after surgery (POAF)


title: Sample 257_Single Dermal Fibroblast


title: EORTC_Patient_79460

tag: corticosteroids

tag: surgical status

value: LOMUSTINE

tag: phillips subtype

value: EORTC


title: EORTC_Patient_79570

tag: tcga subtype

tag: kps

tag: mmse


title: POAF_436_22

description: epicardial adipose tissue biopsy

tag: patient diagnosis


title: Sample 256_Single Dermal Fibroblast

tag: cell line


title: POAF_467_16

description: epicardial adipose tissue biopsy


title: POAF_444_1

description: epicardial adipose tissue biopsy


title: POAF_437_5

description: epicardial adipose tissue biopsy


title: TGFB1_spheroids_1

value: Ovarian surface epithelial cells


title: Sample 255_Single Dermal Fibroblast


title: EORTC_Patient_78810

value: Male

value: BEVACIZUMAB+LOMUSTINE

value: Proneural

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

tag: who category

tag: dataset


title: EORTC_Patient_78796

tag: age

tag: treatment


title: Sample 254_Single Dermal Fibroblast

value: primary cell

tag: day of differentiation


title: Sample 253_Single Dermal Fibroblast


title: EORTC_Patient_74616

tag: Sex

value: Female

tag: rpa

tag: os (diagnosis)


title: POAF_383_16

description: epicardial adipose tissue biopsy

tag: tissue


title: SR_332_3

description: epicardial adipose tissue biopsy

source_name: Patients in sinus rhythm after surgery

value: sinus rhythm after surgery


title: TGFB1_spheroids_2

tag: cell type


title: Control_spheroids_1

value: Untreated


title: Sample 252_Single Dermal Fibroblast


title: TGFB1_mOSE_3_re-analyzed

description:
GSM3450299
sphere_dge_results.csv
sphere_tpm_matrix.csv


title: Control_spheroids_2


title: Sample 251_Single Dermal Fibroblast


title: POAF_409_20

description: epicardial adipose tissue biopsy


title: SR_374_14

description: epicardial adipose tissue biopsy


title: Sample 250_Single Dermal Fibroblast


title: Sample 249_Single Dermal Fibroblast


title: TGFB1_mOSE_2_re-analyzed

description:
GSM3450298
sphere_dge_results.csv
sphere_tpm_matrix.csv


title: Control_spheroids_3


title: EORTC_Patient_74600

tag: corticosteroids

tag: surgical status

tag: phillips subtype

tag: tcga subtype

value: Non-methylated


title: POAF_344_8

description: epicardial adipose tissue biopsy

tag: patient diagnosis


title: EORTC_Patient_74602

tag: kps

tag: mmse

tag: os cnsr (event = 1, censor = 0)

value: Missing


title: SR_433_4

description: epicardial adipose tissue biopsy


title: EORTC_Patient_74088

value: On

value: Classical

tag: mgmt status

tag: who category

tag: dataset


title: EORTC_Patient_74614

tag: age

tag: treatment

value: Mesenchymal


title: TGFB1_mOSE_1_re-analyzed

description:
GSM3450297
sphere_dge_results.csv
sphere_tpm_matrix.csv

tag: cell line

value: 10ng/mL TGFB1


title: Control_mOSE_3_re-analyzed

description:
GSM3450296
sphere_dge_results.csv
sphere_tpm_matrix.csv


title: SR_465_14

description: epicardial adipose tissue biopsy

value: epicardial adipose tissue


title: Sample 248_Single Dermal Fibroblast

tag: day of differentiation


title: EORTC_Patient_73112

tag: Sex

value: Off

tag: rpa

tag: os (diagnosis)

value: Methylated


title: SR_454_6

description: epicardial adipose tissue biopsy

tag: tissue


title: Sample 247_Single Dermal Fibroblast


title: SR_466_15

description: epicardial adipose tissue biopsy


title: Control_mOSE_2_re-analyzed

description:
GSM3450294
sphere_dge_results.csv
sphere_tpm_matrix.csv

tag: cell type

value: Ovarian surface epithelial cells


title: Sample 246_Single Dermal Fibroblast


title: Sample 245_Single Dermal Fibroblast


title: Control_mOSE_1_re-analyzed


title: Sample 244_Single Dermal Fibroblast


title: SR_440_11

description: epicardial adipose tissue biopsy


title: Sample 243_Single Dermal Fibroblast


title: EORTC_Patient_73110

tag: corticosteroids

tag: surgical status

tag: phillips subtype

value: Proliferative

tag: tcga subtype

value: EORTC


title: EORTC_Patient_73104

value: LOMUSTINE

value: Proneural

tag: kps

tag: mmse

tag: os cnsr (event = 1, censor = 0)


title: Sample_25_fl/fl Fxr fl/fl Shp + Cholic Acid diet 2

city: Urbana

first: Waqar

last: Arif

state: IL

address: 506 S. Mathews Avenue

department: Biochemistry

institute: UIUC

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina)
Adaptors were trimmed from the reads using trimmomatic
Reads were mapped to the genome using STAR_2.4.2a
Insert distribution calculated with Picard_1.119
Gene read_count values were calculated using htseq-counts along with the GRCm38 vM9 annotation file (.gff3).
Genome_build: GRCm38 vM9 mm10 (mus musculus)
Supplementary_files_format_and_content: consists of read_count values calculated for all genes annotated in vM10 for all samples submitted

source_name: fl/fl Fxr fl/fl Shp + Cholic Acid diet

growth_protocol: Organisms were housed in flow cages, following the standard 12 hour light/dark cycle

extract_protocol:
Whole livers or hepatocytes were isolated, flash frozen on Liquid nitrogen, and RNA was harvested using RNeasy tissue mini-kit (Qiagen, Cat No./ID: 74104)
RNA libraries were prepared for sequencing using standard Illumina protocols for “TruSeq Stranded mRNAseq Sample Prep kit”

tag: strain background

tag: genotype/variation

value: fl/fl Fxr fl/fl Shp

value: 10-12 weeks

tag: fed state

value: 8-10 hour fast

tag: tissue/cell type

value: Whole Liver


title: Sample_24_fl/fl Fxr fl/fl Shp + Cholic Acid diet 1

tag: age


title: EORTC_Patient_73086

tag: Sex

value: Male

tag: treatment

tag: mgmt status

value: Non-methylated

tag: who category

tag: dataset


title: SR_394_18

description: epicardial adipose tissue biopsy

tag: tissue

tag: patient diagnosis

value: sinus rhythm after surgery


title: Sample 242_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: Sample_26_fl/fl Fxr fl/fl Shp + Cholic Acid diet 3


title: Sample_23_fl/fl Fxr fl/fl Shp + Chow 3

source_name: fl/fl Fxr fl/fl Shp + Chow


title: EORTC_Patient_73082

tag: corticosteroids

value: On

tag: surgical status

value: BEVACIZUMAB+LOMUSTINE

tag: phillips subtype

tag: tcga subtype

value: Classical

tag: kps

tag: rpa

tag: os (diagnosis)


title: SR_445_10

description: epicardial adipose tissue biopsy

value: epicardial adipose tissue


title: SR_407_19

description: epicardial adipose tissue biopsy


title: Sample_22_fl/fl Fxr fl/fl Shp + Chow 2

tag: strain background

tag: genotype/variation

tag: age

tag: fed state

tag: tissue/cell type


title: EORTC_Patient_73100

tag: Sex

tag: treatment

tag: mmse

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Methylated

tag: who category

tag: dataset


title: Sample 241_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: EORTC_Patient_73052

value: Female

tag: corticosteroids

value: Off

tag: surgical status

tag: phillips subtype

tag: tcga subtype

tag: kps


title: Sample_21_fl/fl Fxr fl/fl Shp + Chow 1

tag: strain background

tag: genotype/variation

tag: age


title: EORTC_Patient_73058

tag: Sex

value: Mesenchymal

tag: rpa

tag: os (diagnosis)

value: EORTC


title: Sample 240_Single Dermal Fibroblast


title: SR_335_5

description: epicardial adipose tissue biopsy

tag: tissue

tag: patient diagnosis


title: Sample_20_Wild Type + 60% High Fat Diet 2

source_name: Wild Type + 60% High Fat Diet

value: wild type

value: 16 weeks

tag: fed state

value: 10 Hour Fast

tag: tissue/cell type

value: Hepatocytes


title: SR_381_15

description: epicardial adipose tissue biopsy


title: SR_364_11

description: epicardial adipose tissue biopsy


title: Sample 239_Single Dermal Fibroblast

tag: cell line


title: SR_391_17

description: epicardial adipose tissue biopsy


title: Sample 237_Single Dermal Fibroblast

tag: day of differentiation


title: EORTC_Patient_73040

value: Male

tag: corticosteroids

tag: treatment

value: LOMUSTINE

tag: mmse

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

tag: who category

tag: dataset


title: Sample 236_Single Dermal Fibroblast


title: EORTC_Patient_73074

tag: age

tag: surgical status

tag: phillips subtype

value: Proneural

tag: tcga subtype

tag: kps

value: Non-methylated


title: Sample 238_Single Dermal Fibroblast

value: primary cell


title: N205

city: Boston

first: Kamil

last: Krawczynski

state: MA

address: 60 Fenwood Rd

department: Neurosurgery

institute: Brigham and Womens Hospital

description: circ RNA expression

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven

scan_protocol: The Agilent Scanner G2505C was used to scan the slides

data_processing: Agilent Feature Extraction software was applied to asses the array images. Quantile normalization and subsequent data processing were performed with the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, circRNAs that have flags at least 6 out of 9 samples  in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed circRNAs with statistical significance were identified through Volcano Plot filtering.

source_name: neural progenitor cells

label_protocol: Rnase R (Epicentre, Madison, WI) was used to remove linear RNAs. The enriched circRNAs were amplified and transcribed into fluorescent cRNA by random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000

growth_protocol: 3D culture in Neurobasal medium supplemented with gluatmine, B27, EGF and FGF

extract_protocol: Total RNA was extracted from cells using TRIzol Reagent (Invitrogen, Carlsbad, USA) according to the manufacturer’s protocol. The purity and concentration of RNA was evaluated with the NanoDrop ND-1000 (Thermo Fisher Scientific, Wilmington, DE).

treatment_protocol: Cells  harvested after 72h in culture

tag: disease state

value: glioblastoma

tag: tissue

value: brain

tag: molecule

value: circRNA


title: SR_435_9

description: epicardial adipose tissue biopsy

value: epicardial adipose tissue

tag: patient diagnosis

value: sinus rhythm after surgery


title: Sample_19_Wild Type + 60% High Fat Diet 1

tag: strain background

tag: genotype/variation

tag: fed state

tag: tissue/cell type


title: Sample_18_Wild Type + Chow 2

source_name: Wild Type + Chow


title: Sample 235_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: G088

description: circ RNA expression

source_name: glioblastoma patient derived cells


title: Sample_17_Wild Type + Chow 1


title: EORTC_Patient_73028

tag: Sex

tag: corticosteroids

value: Off

tag: treatment

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Methylated

tag: who category


title: EORTC_Patient_73010

tag: age

value: Female

tag: surgical status

tag: phillips subtype

value: Proliferative

tag: tcga subtype

value: Classical

tag: kps

tag: dataset

value: EORTC


title: EORTC_Patient_73048

value: Mesenchymal


title: N708

description: circ RNA expression

tag: disease state

tag: tissue

tag: molecule


title: Sample 234_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: Sample_15_48 hour post PHx 2

source_name: 48 hour post PHx

tag: strain background

value: 8-10 weeks

tag: fed state

value: Ad libitum

tag: tissue/cell type

value: Whole Liver


title: G081

description: circ RNA expression


title: EORTC_Patient_73032

tag: Sex

tag: corticosteroids

tag: treatment

value: BEVACIZUMAB+LOMUSTINE

value: Unclassified

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

value: Non-methylated


title: EORTC_Patient_73008

tag: age

value: Male

tag: surgical status

value: LOMUSTINE

tag: phillips subtype

value: Proneural

tag: tcga subtype

tag: kps

tag: mgmt status

tag: who category


title: Sample 233_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: Sample_13_0 hour Sham 3

source_name: 0 hour Sham

tag: strain background

tag: fed state

tag: tissue/cell type


title: EORTC_Patient_73006

tag: Sex

tag: corticosteroids

value: On

tag: treatment

tag: dataset


title: Sample 232_Single Dermal Fibroblast


title: Sample_16_48 hour post PHx 3


title: Sample_12_0 hour Sham 2


title: G062

description: circ RNA expression

tag: disease state

value: glioblastoma

tag: tissue

value: brain

tag: molecule

value: circRNA


title: EORTC_Patient_72996

tag: age

value: Off

tag: surgical status

tag: phillips subtype

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)


title: Sample 231_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: N007

description: circ RNA expression


title: Sample_11_0 hour Sham 1

tag: strain background

tag: fed state

tag: tissue/cell type


title: EORTC_Patient_72990

tag: Sex

tag: corticosteroids

tag: treatment

tag: tcga subtype

tag: kps

tag: mgmt status

value: Missing

tag: who category

value: EORTC


title: EORTC_Patient_72978

tag: age

value: Female

tag: surgical status

tag: phillips subtype

value: Proliferative

value: Classical

value: Methylated

tag: dataset


title: Sample 230_Single Dermal Fibroblast


title: Sample 229_Single Dermal Fibroblast


title: G816

description: circ RNA expression

tag: disease state

tag: tissue

tag: molecule


title: G157

description: circ RNA expression


title: G146

description: circ RNA expression


title: Sample_14_48 hour post PHx 1

tag: strain background

value: 8-10 weeks

value: Ad libitum

value: Whole Liver


title: Sample_10_Fxr-/- Shp-/- 3

source_name: Fxr-/- Shp-/-

tag: genotype/variation

value: Fxr-/- Shp-/-

value: 12 weeks

tag: fed state


title: EORTC_Patient_72974

tag: Sex

value: Male

value: BEVACIZUMAB+LOMUSTINE

value: Proneural

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

value: Non-methylated


title: RPF (45-140 nts) T4 infection

city: Cork

first: John

last: Atkins

address: Western GateWay Building, Western Road, UCC, Cork

department: School of Biochemistry and Cell Biology

country: Ireland

institute: UCC

data_processing:
The adapter sequence at the 5'end of the the reads has being clipped with Cutadapt. Those which mapped to rRNA have being discarded.
Reads were mapped to reference  genomes of E. coli sub-strain MG1655 (accession number NC_000913.2 ) and T4 ( NC_000866.4). The single end reads were mapped with Bowtie with parameters (-m 1) i.e. allowing of no ambigous mapped reads. The  paired-end reads associated with the longer fragments were aligned with Bowtie2 with parameters (-M 10 -I 0 --no-unal --no-discordant --no-mixed –dovetail). Reads less than 45 nucleotides were discarded when processing the “long fragments” fractions.

organism:
Escherichia coli
Tequatrovirus T4

source_name: RPF (45-140 nts) T4 infection

growth_protocol: The method for ribosome profiling used was described by Ingolia et al. 2009 and modified for E. coli (Oh et al. 2011). Three 200 ml cultures of E. coli strain MC4100 (OD600 ~ 0.5) were each infected with bacteriophage T4 at a multiplicity of infection (MOI) of 10 and harvested at different time points (2.5, 4 or 5 min) post-infection In parallel, a 200 ml culture (uninfected) was also harvested as a control. In addition, ribosome profiling was also performed on 200 ml cultures of E. coli containing a plasmid-borne cassette with the gp60 sequence. E. coli cells (OD600 ~ 0.5) were induced for 10 min with IPTG.   References  Ingolia, N.T., Ghaemmaghami, S., Newman, J.R. & Weissman, J.S. (2009). Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 324, 218-223.    Oh, E., Becker, A.H., Sandikci, A., Huber, D., Chaba, R., Gloge, F., Nichols, R.J., Typas, A., Gross, C.A., Kramer, G. et al. (2011). Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo. Cell, 147, 1295-1308.

extract_protocol: Lysates were then loaded onto 10-55% sucrose gradients (gradient buffer: 100 mM NH4Cl, 10 mM MgCl2, 20 mM Tris pH 8.0 and 100 µg/ml choramphenicol) and centrifuged at 35,000 rpm for 2.5 hr at 4˚ C. Monosomes fractions were collected and ribosome-protected mRNAs were isolated by acid phenol extraction and isopropanol precipitation. Following dephosphorylation, RNAs (20 µg each) were fractionated on 15% TBE-urea gels and the appropriate size ranges, 30-40 nt or 45-150 nt, were excised. RNAs were eluted from the gel slices.

treatment_protocol: Cells were collected by fast filtration and immediately frozen in liquid nitrogen. Cells were lysed by mechanical disruption while frozen to prevent further translation elongation during sample preparation. Clarified lysates, corresponding to 20 OD260, (in 100 mM NH4Cl, 10 mM MgCl2, 20 mM Tris pH 8.0, 0.4% Triton X-100, 0.1% NP40, 5 mM CaCl2, 100 units/ml RNase-free DNase, and 100 µg/ml chloramphenicol) were treated with micrococcal nuclease (MNase) (60 units/OD260) for 1 hr at 25˚ C. Nuclease digestion was stopped by the addition of EGTA.

tag: polyacrylamide gel size selection

tag: viral infection


title: Sample_9_Fxr-/- Shp-/- 2

tag: age

tag: tissue/cell type


title: G044

description: circ RNA expression

value: glioblastoma

value: brain

value: circRNA


title: RPF (30-40 nts) T4 infection

source_name: RPF (30-40 nts) T4 infection


title: Sample_8_Fxr-/- Shp-/- 1


title: EORTC_Patient_72970

tag: corticosteroids

value: Off

tag: surgical status

tag: treatment

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: mgmt status

tag: who category

value: EORTC


title: Sample 227_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: EORTC_Patient_72966

tag: Sex

value: Female

value: Proliferative

value: Classical

tag: mmse

tag: rpa

tag: dataset


title: Sample_7_Wild Type 3

source_name: Wild Type

tag: strain background

tag: genotype/variation

value: wild type

tag: fed state

value: Ad libitum


title: AAP5, high carbon, light, Replicate 3

city: Trebon

first: Karel

middle: Vaclav

last: Kopejtka

address: Novohradska

department: Centre Algatech

country: Czech Republic

institute: Institute of Microbiology Czech Acad. Sci.

data_processing:
The demultiplexed raw fastq-files were quality-controlled using the FASTQ-mcf suite (https://github.com/ExpressionAnalysis/ea-utils). Low quality bases (Phred-score < 30) and Illumina adaptors were clipped. Reads were mapped to the reference genome using bowtie2 (Langmead et al., 2012) with default parameters for single end reads. Ambiguously mapping reads were randomly distributed between all regions to which they could be assigned. The resulting sam-files were converted to indexed binary format and pile-up format using samtools (Li et al., 2009). The program featureCounts (Liao et al., 2014) was used to count the reads mapping to genes.
Genome_build: NZ_CP037913.1, NZ_CP037915.1, NZ_CP037914.1, NZ_CP037916.1
Supplementary_files_format_and_content: tab-delimited text file contains reads per gene

organism: Sphingomonas sp. AAP5

source_name: AAP5 cultivated in liquid organic medium

extract_protocol:
For isolation and purification the RNeasy-kit (Qiagen) was used according to the manufacturer’s manual. Modifications are listed below. Cells lysis was performed enzymatically using 15 mg/mL lysozyme in Tris-EDTA-buffer (ph 8.0) and mechanically by vortexing for 3 min with acid washed glass beads. A first digestion of genomic DNA was performed on the column, using RNase-free DNase I (Qiagen) according to the manufacturer’s protocol. Total RNA was eluted in 88 µL RNase-free H2O and a second DNase I-digestion of genomic DNA was performed in solution, followed by a second RNeasy purification step. In this second purification an additional washing step with 80 % ethanol was performed prior to elution with 30µl RNase-free water. The concentration of the RNA was quantified using a NanoDrop spectrophotometer (Peqlab, Erlangen, Germany) and the RNA integrity was assessed using Bioanalyzer 2100 (Agilent, Santa Clara, USA). Ribosomal RNA depletion:  The Ribo-Zero (gram-negative) kit to remove the prokaryotic rRNA, according to the manufacturer’s instructions.
Single end, strand specific cDNA libraries were prepared using the Scriptseq v2 RNA-Seq Library Preparation Kit (Illumina, San Diego, CA, USA) following the manufacturers protocol. For sequencing equal volumes of libraries (12 pM) were multiplexed on a single lane. Sequencing was done on the HiSeq 2500 (Illumina, San Diego, CA, USA) using TruSeq SBS Kit v3 - HS (Illumina, San Diego, CA, USA) for 50 cycles resulting in 50 bp reads. Image analysis and base calling were performed using the Illumina pipeline v 1.8 (Illumina, San Diego, CA, USA).

value: growth in full medium, harvested in light

tag: time (day)

tag: replicate


title: Sample_6_Wild Type 2

tag: age

value: 12 weeks

tag: tissue/cell type

value: Whole Liver


title: Sample 226_Single Dermal Fibroblast

source_name: Single Dermal Fibroblast


title: EORTC_Patient_72956

value: Male

tag: corticosteroids

value: On

tag: surgical status

tag: treatment

value: BEVACIZUMAB+LOMUSTINE

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)


title: AAP5, high carbon, light, Replicate 2


title: EORTC_Patient_72958

tag: Sex

value: LOMUSTINE

tag: kps

tag: mmse

tag: mgmt status

value: Methylated

tag: who category


title: Sample 224_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: EORTC_Patient_72954

value: Unclassified

tag: rpa

value: Non-methylated

tag: dataset


title: AAP5, low carbon, light, Replicate 3

source_name: AAP5 cultivated in liquid 0.1 organic medium

value: growth in diluted medium, harvested in light

tag: time (day)

tag: replicate


title: G035

description: circ RNA expression

tag: disease state

value: glioblastoma

tag: tissue

value: brain

tag: molecule

value: circRNA


title: Sample_5_Wild Type 1

tag: strain background

tag: genotype/variation

value: wild type

tag: age

tag: fed state

tag: tissue/cell type


title: AAP5, low carbon, light, Replicate 2

tag: treatment


title: EORTC_Patient_72846

tag: Sex

tag: corticosteroids

value: Off

tag: surgical status

tag: phillips subtype

tag: tcga subtype

value: Classical

tag: kps

tag: mmse

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: EORTC


title: Sample_3_Wild Type + 36 hours post TCPOBOP injection 1

source_name: Wild Type +6 hours post TCPOBOP injection

value: 8 weeks

value: Ad libitum

value: Whole Liver


title: Sample_4_Wild Type + 36 hours post TCPOBOP injection 2


title: Sample 222_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: Sample 223_Single Dermal Fibroblast


title: EORTC_Patient_72842

value: Female

value: BEVACIZUMAB+LOMUSTINE

value: Proneural

tag: rpa

tag: who category

tag: dataset


title: EORTC_Patient_72342

tag: age

value: Proliferative


title: AAP5, low carbon, light, Replicate 1

tag: treatment

tag: time (day)

tag: replicate


title: Sample 221_Single Dermal Fibroblast


title: AAP5, high carbon, dark, Replicate 3

value: growth in full medium, harvested in dark


title: Sample_1_Wild Type + Cornoil 1

source_name: Wild Type + Cornoil

tag: strain background

tag: genotype/variation

tag: fed state

tag: tissue/cell type


title: Sample_2_Wild Type + Cornoil 2


title: EORTC_Patient_72340

tag: Sex

tag: corticosteroids

tag: surgical status

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: mmse

value: Non-methylated


title: Sample 225_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: AAP5, high carbon, dark, Replicate 2


title: AAP5, high carbon, light, Replicate 1

value: growth in full medium, harvested in light


title: Sample 220_Single Dermal Fibroblast


title: Sample 219_Single Dermal Fibroblast


title: 28331

city: Burlington

first: Travis

last: Sullivan

address: 41 Mall Rd.

institute: Lahey Hospital & Medical Center

description: FFPE

data_processing:
Non-normalized data are the Cq values computed by the Bio-Rad CFX themal cycler software, no adjustment to baseline backgrounds were made
Each microRNA of interest was normalized to the average of the insignificant control miRNA: miRs-28-5p, -125-5p, and -191-5p, selected from the screening array dataset using NormFinder©.  Prior to normalization each target value was scaled to the internal plate calibrator (IPC) by dividing the samples IPC by the grand average of all the IPCs and then multiplying the resulting value by the target Cq.  The global mean was calculated only using microRNA with a Cq<35 detected in all 20 samples.   2^-deltaCq, where deltaCq = (Cq_Target − Cq_global_mean).  All Cq values >37 were set to 40.
Fold change (delta delta Ct) values were not computed for this dataset
The file normalized_data.txt  reports normalized signal (against each samples global mean).

label: SYBR Green

source_name: clear cell renal cell carcinoma primary tumor

label_protocol: cDNA and RT-PCR were performed using miRCURY LNA custom miRnome PCR panel, currently provided by Qiagen formerly from Exiqon, following the manufacturer's recommendations. Catalog number 339317

extract_protocol: Total RNA was isolated using the Ambion RecoverAll Total Nucleic Acid Isolation Kit for FFPE following the manufacturer's recommendations

tag: tissue

tag: institution

value: PSU

tag: group

value: survival analysis only

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

value: A

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: EORTC_Patient_72336

tag: age

tag: Sex

value: Male

tag: corticosteroids

value: On

tag: surgical status

tag: treatment

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

tag: who category

tag: dataset


title: 5931_9

description: FFPE

tag: tissue

value: clear cell renal cell carcinoma primary tumor

tag: institution

value: LHMC

tag: group

value: validation and survival analyses

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause


title: AAP5, high carbon, dark, Replicate 1

tag: time (day)

tag: replicate


title: Sample 218_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: 22554

description: FFPE

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: AAP5, low carbon, dark, Replicate 3

tag: treatment

value: growth in diluted medium, harvested in dark


title: 24547

description: FFPE


title: EORTC_Patient_72332

tag: age

tag: Sex

tag: corticosteroids

value: Off

tag: surgical status

value: LOMUSTINE

tag: phillips subtype

tag: tcga subtype

value: Classical

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

tag: who category

value: EORTC


title: AAP5, low carbon, dark, Replicate 2

tag: time (day)

tag: replicate


title: EORTC_Patient_72334

value: Proliferative

value: Missing

tag: dataset


title: 7438

description: FFPE

tag: tissue

tag: institution

tag: group

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: Sample 228_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: EORTC_Patient_72328

tag: age

tag: Sex

tag: corticosteroids

tag: surgical status

tag: treatment

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Non-methylated


title: Sample 215_Single Dermal Fibroblast


title: Sample 216_Single Dermal Fibroblast


title: 30824

description: FFPE

tag: tissue

tag: institution

tag: group

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs


title: AAP5, late plate, day 8, Replicate 3

source_name: AAP5 cultivated on solid 0.5 organic medium

tag: treatment

value: growth on solid medium

tag: time (day)

tag: replicate


title: 21628

description: FFPE

value: survival analysis only

value: A

tag: grade


title: Sample 214_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: AAP5, late plate, day 8, Replicate 1


title: 20163

description: FFPE


title: EORTC_Patient_72338

tag: age

tag: Sex

value: Male

tag: corticosteroids

tag: surgical status

value: BEVACIZUMAB+LOMUSTINE

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

value: Methylated

tag: who category

tag: dataset


title: AAP5, late plate, day 8, Replicate 2

tag: treatment

tag: time (day)

tag: replicate


title: EORTC_Patient_72320

value: Female

value: On

value: Proneural

tag: mgmt status


title: AAP5, early plate, day 4, Replicate 3


title: Sample 211_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: EORTC_Patient_71842

tag: age

tag: Sex

tag: corticosteroids

value: Off

value: LOMUSTINE


title: AAP5, low carbon, dark, Replicate 1

value: growth in diluted medium, harvested in dark


title: Sample 217_Single Dermal Fibroblast


title: 7505

description: FFPE

tag: tissue

value: clear cell renal cell carcinoma primary tumor

tag: institution

value: LHMC

tag: group

value: validation and survival analyses

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: EORTC_Patient_71952

tag: surgical status

tag: treatment

tag: phillips subtype

value: Proliferative

tag: tcga subtype

value: Classical

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: who category

tag: dataset

value: EORTC


title: 9671

description: FFPE

tag: tissue

tag: institution

tag: group

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause


title: 5931_7

description: FFPE

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: Sample 210_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: EORTC_Patient_71838

tag: age

tag: Sex

tag: corticosteroids

tag: surgical status

tag: treatment

tag: phillips subtype

value: Unclassified

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: mgmt status

value: Non-methylated


title: AAP5, early plate, day 4, Replicate 2

value: growth on solid medium

tag: time (day)

tag: replicate


title: AAP5, bottle, day 2, Replicate 3

source_name: AAP5 cultivated in liquid 0.5 organic medium

value: growth in liquid medium


title: Sample 209_Single Dermal Fibroblast


title: AAP5, early plate, day 4, Replicate 1


title: EORTC_Patient_71372

value: Male

value: Mesenchymal

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: who category

tag: dataset


title: 5389

description: FFPE

tag: tissue

tag: institution

tag: group

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

value: A

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: EORTC_Patient_72062

tag: age

tag: Sex

tag: corticosteroids

value: On

tag: surgical status

tag: treatment

value: BEVACIZUMAB+LOMUSTINE

tag: phillips subtype

value: Proneural

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: mgmt status


title: EORTC_Patient_71260

value: Off

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: who category

tag: dataset


title: Sample 213_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: Sample 208_Single Dermal Fibroblast


title: EORTC_Patient_70872

tag: age

value: Female


title: AAP5, bottle, day 2, Replicate 2

tag: time (day)

tag: replicate


title: Sample 212_Single Dermal Fibroblast


title: 4386

description: FFPE

tag: tissue

value: clear cell renal cell carcinoma primary tumor

tag: institution

value: LHMC

tag: group

value: validation and survival analyses

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: AAP5, bottle, day 2, Replicate 1

tag: treatment


title: 24965

description: FFPE


title: 11661

description: FFPE


title: EORTC_Patient_70868

tag: Sex

tag: corticosteroids

tag: surgical status

tag: phillips subtype

tag: tcga subtype

value: Classical

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

tag: who category

tag: dataset

value: EORTC


title: Sample 205_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: 22 µM DO_2

city: Iowa City

first: Timothy

middle: E

last: Mattes

address: 4105 Seamans Center

institute: University of Iowa

data_processing:
Raw sequencing data was processed online with software available on the Galaxy server (usegalaxy.org). First, fastq data files were converted to fastqsanger format with the fastq groomer tool. The quality of transcriptomic sequence reads was assessed with FastQC.
Forward strand transcriptomic reads were then mapped to the T. autotrophicus strain EF1 genome sequence (Genbank accession no. CP010552) using HISAT2. This resulted in 6.97×105– 1.38×106 reads mapped to the EF1genome per treatment. Similarly, forward strand reads were also mapped to the internal mRNA standards, yielding 1.41×105 – 2.48×105 mRNA standard reads per treatment (9-22% of total reads).
HISAT2-generated BAM files for each treatment were loaded into ReadXplorer 2.2.3 where differential gene expression analyses were performed. First, a transcript count table was generated. The percent recovery of internal mRNA standards was used to estimate the absolute number of EF1 transcripts per treatment and subsequently normalized to the number of EF1 cells per RNA extraction to obtain absolute “transcript per cell” values
Differential gene expression analysis among the three different DO treatments was performed with the DeSeq2 algorithm. Genes that were differentially expressed at a statistically significant level (p<0.05) were considered for further analysis
Genome_build: T. autotrophicus strain EF1 genome sequence (Genbank accession no. CP010552)
Supplementary_files_format_and_content: excel files inlcude transcript counts, cell counts and transcript per cell values for each gene in the genome. DeSeq2 output provided in excel files.

organism: Candidatus Thioglobus autotrophicus

source_name: cells

growth_protocol: Filter-sterilized Puget Sound seawater (PS media; collected June 2017) was used as bacterial growth media with filter-sterilized thiosulfate (1 mM) added as the energy source. The PS media initially contained 13.5 ± 0.58 μM nitrate. No additional nitrate was added to the media. PS media (100 mL) was placed into acid-washed (10% HCl) and autoclaved 160 mL glass serum bottles and sealed with 20 mm blue butyl rubber stoppers and aluminum crimp caps (DWK Life Sciences, Millville, NJ). Sealed serum bottles were subsequently purged (7 minutes liquid, followed by 5 min headspace) with a mixture of nitrogen gas containing 1000 ppm carbon dioxide to remove dissolve oxygen (DO). Purged anoxic PS media bottles were prepared in triplicate.

extract_protocol:
When EF1 cell density reached approximately 1-3x106 cells/ml, bottles were sacrificed for RNA extraction. Cultures (~100 mL) were vacuum filtered onto 47 mm 0.2 μm IsoporeTM membrane filters (Millipore Inc., Billerica, MA, USA) under a nitrogen headspace to limit oxygen diffusion. Filters were placed into a 50 ml conical tube containing Trizol reagent (3 mL), 375 μL glass and zirconia bead mixture, and 12.5 μl (6.79×109 copies) internal mRNA standards. Bead-beating was performed for 5 minutes on a vortexer. After a 1 min centrifugation step at 3,220 xg, RNA was extracted from the supernatant with the Zymo Direct-zol RNA MiniPrep Plus kit (Zymo Research Corporation, Irvine, CA) according to the manufacturer’s protocol (including on-column DNase I treatment). To further minimize DNA contamination, RNA extracts were subjected to a separate DNase I treatment step with the TURBO DNA-freeTM kit (Thermofisher Scientific, Waltham, MA). RNA concentrations were estimated with the QubitTM fluorometer and HS RNA assay kit (Thermofisher Scientific,Waltham, MA)
rRNA was depleted from the extractions with the Ribozero rRNA removal kit for bacteria (Illumina, Inc.San Diego, CA). Libraries were prepared from the depleted RNA using the Illumina Truseq library prep kit v2, normalized and loaded at equal concentration on the Illumina MiSeq using V2 chemistry and then subjected to PE150 sequencing at the University of Washington

treatment_protocol: One set of triplicate bottles was kept anoxic. A second set of bottles received 1 mL of filtered-sterilized air (approximate initial aqueous DO concentration = 3.8 μM), and a third set received 5 mL of filter-sterilized air (approximate initial aqueous DO concentration = 22 μM). All bottles were incubated without shaking at 13ºC during the experiments.

tag: strain

tag: dissolved oxygen (do) um


title: EORTC_Patient_70748

tag: age

tag: Sex

tag: treatment

value: LOMUSTINE

value: Proliferative

value: Missing


title: 11325

description: FFPE

tag: tissue

tag: institution

tag: group

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: 22 µM DO_1


title: EORTC_Patient_70744

tag: corticosteroids

tag: surgical status

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Methylated

tag: who category

tag: dataset


title: 3.8 µM DO_2

tag: strain

tag: dissolved oxygen (do) um


title: 25799

description: FFPE

tag: tissue

tag: institution

tag: group

tag: obese_1 is bmi>=30

tag: death_a=alive, c=died of ccrcc, o=death from other cause

tag: time_months to last fu or death

tag: Stage

tag: tumor size_cm


title: 3.8 µM DO_1


title: 6431

description: FFPE

tag: _1=progress to metastatic disease in 5yrs

tag: grade


title: EORTC_Patient_70742

tag: age

tag: Sex

tag: corticosteroids

tag: surgical status

tag: treatment

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

value: Non-methylated


title: anoxic_2

tag: strain

tag: dissolved oxygen (do) um


title: Sample 207_Single Dermal Fibroblast

data_processing:
Sequences from the NovaSeq were de-multiplexed using bcl2fastq version 2.19.0.316. Reads were trimmed from polyA tails using cutadapt v 1.18 with the following parameters: -m 18 -j 4 -a AAAAAAAAAA -a TTTTTTTTTT. Reads were then aligned to the human (GRCh38) or mouse genome (GRCm38) using STAR v2.7.0d 37 with the following parameters --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 18 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0  --outMultimapperOrder Random. Reads mapping to multiple locations were assigned either to a location with the best mapping score or, in the case of equal multimapping score – to the genomic location randomly chosen as “primary”.
Genome_build: GRCm38, GRCh38
Supplementary_files_format_and_content: tab-delimited text files of count tables

tag: cell line

tag: day of differentiation