title: MS MS470

description: Library name: 194017-R81

tag: tissue

tag: disease

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Bronchopneumonia, Multiple Sclerosis

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Collect RD-LC-009 | 002 | Tumor

status: Public on Feb 26 2025

type: SRA

city: Pittsburgh

first: Lan

last: Coffman

state: PA

address: 5051 Centre Ave

country: USA

institute: UPMC Hillman Cancer Center

description: Library name: Collect RD-LC-009 | 002 | Tumor

library_source: other

data_processing:
RNA-seq; LOQ 2pct by target, 3rd quartile normalized.
Assembly: GRCh38.p13
Supplementary files format and content: Columns represent individual ROIs with descriptions designating tissue type, cell type, and sample ID. Rows represent genes.
Library strategy: Spatial Transcriptomics

molecule: other

organism: Homo sapiens

source_name: Tumor

growth_protocol: Slides were stored at 4C in a desiccator after sectioning, then DSP was performed within the timeframe specified by Nanostring.

extract_protocol:
Extract was performed according to UPMC Cytometry Facility, UPMC Health Sciences Sequencing Core and Nanostring GeoMx DSP protocols.
direct PCR. Read pattern: 27x27. 8bp index.

tag: tissue

value: Tumor


title: Subject UP20 R

type: protein

city: Stanford

first: Allan

last: Feng

state: CA

address: 269 Campus Dr

department: Imm/Rheum

institute: Stanford School of Medicine

description:
raw data file: CTD Array version 3 Platform Raw MFI.xlsx
Antibodies in samples bind to barcoded beads conjugated to antigens. Antibody reactivity was quantified by the fluorescence measured as MFI from the secondary antibody.

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

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

data_processing: Barebeed MFI values were subtracted from the MFI values for all analytes in each sample and  replicate MFI values were averaged.

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

molecule: protein

source_name: Serum/Plasma

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

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

tag: condition

value: iMCD patient


title: MS MS103

city: London

first: Carolina

last: Barcellos Machado

address: 4-8 Maple St

country: United Kingdom

institute: BenevolentAI

description: Library name: 194017-R79

library_source: transcriptomic

data_processing:
Reads were aligned to the GRCh38 (hg38) genome. The data were mapped to RefSeq gene model, using a professional website DNAnexus (https://dnanexus.com/).
sequencing QC was run with FastQC version 3.0.1
adaptors trimmed with Trim Galore version 0.6.0
alignment was run with STAR version 2.0.0
aligned sequencing reads were quantified with RSEM version 1.0.0
Assembly: GRCh38 (hg38)
Supplementary files format and content: csv file per sample including count, TPM and FPKM

molecule: total RNA

source_name: brain

extract_protocol:
Total RNA was isolsted from tissue using the RNeasy Plus Universal Mini Kit (Qiagen) according to the manufacturer's protocol with an additional DNAse digestion step using DNase I, RNase-free (Roche). 100ng of Total RNA was used for the construction of sequencing libraries.
rRNA depletion was performed using the NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB). RNA sequencing library preparation used the NEBNext Ultra II RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB).

value: brain

tag: disease

value: MS

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Pneumonia

tag: classification of_ms

value: SPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Spinal cord relapse

tag: first presented_symptom_category

value: Spinal cord

tag: history of_motor_weakness

value: Yes

value: No

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord


title: Subject UP41

description:
raw data file: ACA Array version 3 Platform Raw MFI.xlsx
Antibodies in samples bind to barcoded beads conjugated to antigens. Antibody reactivity was quantified by the fluorescence measured as MFI from the secondary antibody.

tag: condition

value: Hodgkin lymphoma patient control


title: Subject UP40


title: Collect RD-LC-009 | 002 | Stroma

description: Library name: Collect RD-LC-009 | 002 | Stroma

source_name: Stroma

tag: tissue

value: Stroma


title: MS MS407

description: Library name: 194017-R78

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Septicaemia, pneumonia

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Optic neuritis

tag: first presented_symptom_category

value: Visual

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Subject UP39

tag: condition


title: Subject UP18 R


title: MS MS050

description: Library name: 194017-R77

tag: tissue

tag: disease

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Bronchopneumonia, multiple sclerosis

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Optic neuritis, Muscle weakness

value: Visual, Motor

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord


title: Subject UP43

tag: condition


title: Subject UAMS45 F

value: iMCD patient


title: Collect RD-LC-009 | 001 | Stroma

description: Library name: Collect RD-LC-009 | 001 | Stroma

tag: tissue


title: Subject UP17 R


title: MS MS313

description: Library name: 194017-R76

value: brain

tag: disease

value: MS

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

value: male

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Gastrointestinal bleeding caused by peptic ulcer disease, MS

tag: classification of_ms

value: PPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Numbness

tag: first presented_symptom_category

value: Sensory

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Subject UAMS44 F

tag: condition


title: MS MS088

description: Library name: 194017-R75

tag: tissue

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Bronchopneumonia

tag: classification of_ms

value: SPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: history of_motor_weakness

value: Yes

value: No

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord


title: Co culture of KHYG-1 cells + a-NKp44 mAb + collection of mutant cells, round 2

city: Marseille

first: Bertrand

last: Escaliere

address: 163 avenue de Luminy

country: France

institute: CIML

library_source: genomic

data_processing:
Reads were aligned to the sgRNA library using Bowtie2. From these alignments, Protospacer count tables were generated using Python scripts and processed with MAGeCK. MAGeCK analysis was used to score and prioritize sgRNAs using the default settings of the algorithm (Li et al., 2014). MAGeCK scores were normalized to -log10 and values were plotted against FDR values
Assembly: GRCh38
Supplementary files format and content: Comparison_all.count.txt
Library strategy: DNA-seq

molecule: genomic DNA

extract_protocol:
genomic DNA was isolated from the cryopreserved cell pellet using the DNeasy Blood and Tissue Kit (Qiagen) and the genomic DNA concentration was determined using a NanoDrop spectrophotometer.
Library preparation requires a two-step PCR amplification, purification and quantification according to Webster et al. 2019. In a first PCR step, the sgRNA sequences are amplified with the PCR primers U6-F1 and Tracr-R1. A second PCR was performed to attach Illumina-compatible sequencing adapters for the NextSeq2000 sequencer (genomic platform at CIML). After purification on a 2% size-selective E-gel, the secondary PCR product was quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher) and qualified on the bioanalyzer (Agilent) using the High sensitivity DNA Assay (Agilent).

tag: cell line

tag: cell type

value: colon adenocarcinoma

tag: treatment

value: sgRNA Brunello library transduction & genome edition & NK cell cytotoxicity


title: Subject UP15 R

tag: condition


title: Control PDC034

description: Library name: 194017-R74

tag: tissue

tag: disease

value: Control

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Respiratory failure secondary to bronchial cancer

tag: classification of_ms

value: Non-MS control

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Subject UP19 R

tag: condition

value: iMCD patient


title: KHYG-1 NKp44 KO + collection of mutant cells, round 2.

tag: cell line

tag: cell type

tag: treatment


title: Subject UAMS43 F


title: Subject UP14 R


title: Subject UAMS42 F


title: Collect RD-LC-009 | 001 | Tumor

description: Library name: Collect RD-LC-009 | 001 | Tumor

tag: tissue

value: Tumor


title: Subject UP13 R


title: Control C032

description: Library name: 194017-R73

value: brain

tag: disease

tag: batch

tag: which cingulate_gyrus

value: Anterior

tag: age

tag: Sex

value: male

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Prostate cancer, bone metastases

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion


title: Subject UAMS41 R

tag: condition


title: MS MS390

description: Library name: 194017-R72

tag: tissue

tag: disease

value: MS

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Respiratory failure

tag: classification of_ms

value: PPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Foot drop, Bladder dysfunction

tag: first presented_symptom_category

value: Motor, Involuntary motor

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Subject UP12 R

tag: condition


title: Co culture KHYG-1 cells + collection of mutants,  round 2

tag: cell line

tag: cell type

value: colon adenocarcinoma

tag: treatment

value: sgRNA Brunello library transduction & genome edition & NK cell cytotoxicity


title: Subject UP16 R


title: Control C084

description: Library name: 194017-R71

tag: tissue

tag: disease

value: Control

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Old age

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion


title: Subject UAMS40 F

tag: condition


title: Subject UAMS39 R


title: Co culture of KHYG-1 cells + a-NKp44 mAb + collection of mutant cells,  round 1

tag: cell line

tag: cell type

tag: treatment


title: Control C092

description: Library name: 194017-R70

tag: tissue

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

tag: classification of_ms

value: Non-MS control

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Co culture KHYG-1 cells + collection of mutants,  round 1

tag: cell line

tag: cell type

tag: treatment


title: Subject UP10 R

tag: condition

value: iMCD patient


title: Subject UAMS38 F


title: Subject UP11 R


title: Subject UP09 R


title: Control PDC005

description: Library name: 194017-R68

tag: tissue

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion


title: MS MS264

description: Library name: 194017-R65

tag: tissue

tag: disease

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: E. Coli septicaemia

tag: classification of_ms

value: SPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Muscle weakness

tag: first presented_symptom_category

value: Motor

value: Yes

value: No

tag: history of_cognitive_function_loss

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: KHYG-1 NKp44 KO + collection of mutant cells, round 1

tag: cell line

tag: cell type

tag: treatment


title: Subject UP08 R

tag: condition


title: Subject UP07 F


title: Donor 15_Polyclonal stimulation_plate 2

city: Siena

first: Elisabetta

last: Soldaini

address: via Fiorentina, 1

country: Italy

institute: GSK

description: Library name: GSK-ES-s008

library_source: transcriptomic single cell

data_processing:
https://www.scdiscoveries.com/
Assembly: Human hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: Blood from healthy donor

extract_protocol:
PBMCs isolated from 6 healthy donors were separated via negative selection into CD4+ and CD4- fractions. After irradiation of CD4- cells, both fractions were re-mixed at a 1:1 ratio and stimulated with heat-killed S. aureus or  α-CD3/CD28 antibodies. After 24 h stimulation, for each stimulus CD4+ T cells co-expressing OX40 and CD137 (AIM+)  were sorted in single wells of 2 replicate 384-well plates from Single Cell Discoveries precast for SORT-seq. From each plate a library was generated by Single Cell Discoveries (https://www.scdiscoveries.com/).
https://www.scdiscoveries.com/

tag: tissue

value: Blood from healthy donor

value: primary cell

value: CD4+ T cell


title: Subject UAMS37 R


title: Subject UAMS36 F


title: Subject UAMS34 F


title: MS MS406

description: Library name: 194017-R63

value: brain

tag: disease

value: MS

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

value: male

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Chest infection, aspiration pneumonia, multiple sclerosis

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Vertigo

tag: first presented_symptom_category

value: Brainstem, Cerebellar

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion


title: Donor 05_Polyclonal stimulation_plate 2

description: Library name: GSK-ES-s002

tag: tissue

tag: cell line

tag: cell type

tag: treatment


title: Subject UP06

tag: condition

value: iMCD patient


title: Donor 04_Polyclonal stimulation_plate 1

description: Library name: GSK-ES-s019


title: MS MS485

description: Library name: 194017-R62

tag: disease

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Bronchopneumonia, advanced multiple sclerosis

tag: classification of_ms

value: PPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Optic neuritis

tag: first presented_symptom_category

value: Visual

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Subject UAMS33 R

tag: condition


title: Collection of mutant cells

tag: cell line

tag: cell type

value: colon adenocarcinoma

tag: treatment

value: sgRNA Brunello library transduction & genome edition


title: Subject UP04


title: MS MS094

description: Library name: 194017-R60

tag: tissue

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Bronchopneumonia, multiple sclerosis

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Ataxia

tag: first presented_symptom_category

tag: history of_motor_weakness

value: Yes

value: No

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion


title: Subject UP03

tag: condition


title: Donor 02_Polyclonal stimulation_plate 1

description: Library name: GSK-ES-s016

tag: tissue

value: Blood from healthy donor

tag: cell line

value: primary cell

tag: cell type

value: CD4+ T cell

tag: treatment


title: Donor 02_Polyclonal stimulation_plate 2

description: Library name: GSK-ES-s017


title: Subject UAMS32 F


title: Subject UP02


title: Subject UAMS35 R


title: Subject UAMS31 F


title: Subject UAMS30 R


title: Donor 04_Polyclonal stimulation_plate 2

description: Library name: GSK-ES-s020


title: Donor 15_Polyclonal stimulation_plate 1

description: Library name: GSK-ES-s007


title: Donor 05_Polyclonal stimulation_plate 1

description: Library name: GSK-ES-s001


title: MS MS517

description: Library name: 194017-R64

value: brain

tag: disease

value: MS

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Chest sepsis, MS

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Sensory

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Control PDC023

description: Library name: 194017-R56

tag: tissue

tag: disease

value: Control

tag: batch

tag: which cingulate_gyrus

value: Anterior

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

tag: classification of_ms

value: Non-MS control

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion


title: MS MS549

description: Library name: 194017-R52

tag: tissue

tag: disease

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

value: male

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: End stage of Multiple Sclerosis

tag: classification of_ms

value: SPMS

value: Numbness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: MS MS448

description: Library name: 194017-R61

tag: tissue

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Pulmonary Emboli

tag: classification of_ms

value: PPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Ataxia

tag: first presented_symptom_category

value: Brainstem, Cerebellar

tag: history of_motor_weakness

value: No

value: Yes

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion


title: Subject UP05

tag: condition

value: iMCD patient


title: Subject UAMS29 R


title: Clam UF98D-0400

type: genomic

city: Stony Brook

first: Denis

last: Grouzdev

address: 100 Nicolls Rd

institute: Stony Brook University

description: UF Phase I

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: Genotyping was performed at Neogen (Lincoln, Nebraska) on the Axiom 384HT arrays (Axiom HD Array [60K] Clam) following protocols outlined in the Axiom Assay 384HT Array Format Automated Workflow User Guide.

data_processing:
The raw genotyping data in CEL format was downloaded from the CAT website after the service and genotype annotation was analyzed using the Axiom software (v 5.4, Thermo Fisher) following the Best Practices Workflow with recommended threshold settings (DishQC ≥ 0.82, QC call rate ≥ 97%).
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

organism: Mercenaria mercenaria

source_name: Clam UF98D-0400

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Adults M. mercenaria (12-14 months old) were collected from three farms in Cedar Key, Florida with one whole bag from each farm (1000-1200 clams). The clam seeds of each farm were originally sourced from different hatcheries. After purchase, the quahogs from each bag were cleaned at the farms using fresh water to remove sediment before being transported to the laboratory in a cooler (1 hr driving). After arriving at the laboratory, all quahogs were maintained in an indoor recirculating artificial seawater system equipped with a bead filter (Endurance 4000, Aquaculture Systems Technologies, Baton Rouge, LA) at 24 ± 0.55°C, 25 ppt salinity, and pH = 8.35. Quahogs were fed daily with a combination of microalgae, including Tetraselmis spp., Isochrysis spp., and Chaetoceros spp., at 50,000 cells/ml supplemented with commercial algal paste (Instant algae, Reed Mariculture, San Jose, CA, USA). System water quality was checked daily using a saltwater combination kit (AQ-4, Lamotte, Maryland, USA) for ammonia (< 0.01 mg/L), nitrite (< 0.01 mg/L), and nitrate levels (< 10 mg/L).

extract_protocol: The quahogs that died earliest (n = 330) were categorized as “dead” under the dichotomous phenotype, and the quahogs that died latest (n = 144) and survivors (n =231) were considered as “survived”. Genotyping of samples was performed on the previously described SNP microarray chip (Grouzdev et al., 2024). Fixed samples were shipped to the Center for Aquaculture Technologies (CAT, https://aquatechcenter.com, San Diego, CA) for this service. The total genomic DNA was extracted from sample sources (adductor muscle or hemocytes) using a magnetic bead-based extraction protocol. Briefly, fixed tissues (~10-15 mg) were subsampled and processed using mag-bind blood and tissue DNA kits (Omega BioTek, Norcross, GA) according to the manufacturer’s guidelines. Automated processing and liquid handling steps associated with the extraction protocol were performed using PurePrep 96 units (Molgen, San Diego, CA) according to kit and instrument-specific guidelines. Extracted gDNAs were assessed for yields and quality by spectrophotometry (Nanodrop, ThermoFisher) and 2% agarose gels targeting a minimum of 35 µl at >20 ng/µl of largely intact DNA (minimum 5KB).

treatment_protocol: The heat shock challenge was applied by increasing water temperature at 1°C per day from 24°C to a final temperature of 35°C using a heat pump with a temperature controller (Model No. DC24S, Aqualogic, San Diego, CA, USA). When the total dead quahog numbers reached about 50% of the total initial clam number, the temperature decreased from 35°C to 27°C within 24 hr and gradually to 24°C within another 24 hr. For easy reading, the heat challenge was separated into three phases (Figure 1): Phase I (13 days) – temperature increased from 24°C to 35°C and stayed at 35°C; Phase II (9 days) – temperature decreased from 35°C to 24°C with more clams died, and Phase III – temperature was maintained at 24°C and no quahog mortality was found in two days. Two HOBO pendant temperature loggers (UA-001–64, Onset, MA, USA) were submerged in the tank to record the temperature changes. No feeding was conducted after the temperature reached 28°C, and water quality was monitored twice a day.

tag: tissue

value: Adductor muscle


title: MS MS422

description: Library name: 194017-R57

value: brain

tag: disease

value: MS

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Chest infection due to Multiple Sclerosis

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

value: Sensory

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Subject UP01

tag: condition


title: Subject UAMS27 R


title: Donor 09_Polyclonal stimulation_plate 2

description: Library name: GSK-ES-s004

tag: tissue

value: Blood from healthy donor

tag: cell line

value: primary cell

tag: cell type

value: CD4+ T cell

tag: treatment


title: Donor 01_Polyclonal stimulation_plate 2

description: Library name: GSK-ES-s012


title: Clam UF97D-0426

description: UF Phase I

source_name: Clam UF97D-0426


title: MS MS483

description: Library name: 194017-R51

tag: disease

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Bronchopneumonia, aspiration pneumonia, MS

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Optic neuritis

tag: first presented_symptom_category

value: Visual

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion


title: Donor 01_Polyclonal stimulation_plate 1

description: Library name: GSK-ES-s011

tag: tissue

tag: cell line

tag: cell type

tag: treatment


title: MS MS216

description: Library name: 194017-R50

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Breast cancer

tag: classification of_ms

value: PPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Ataxia

tag: first presented_symptom_category

value: Brainstem, Cerebellar

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Donor 09_Polyclonal stimulation_plate 1

description: Library name: GSK-ES-s003

tag: tissue

tag: cell line

tag: cell type

tag: treatment


title: Subject UAMS25 R

tag: condition

value: iMCD patient


title: Subject UAMS26 R


title: Clam UF96S-0608

description: UF Phase II

source_name: Clam UF96S-0608

value: Adductor muscle


title: Control PDC028

description: Library name: 194017-R49

value: brain

tag: disease

value: Control

tag: batch

tag: which cingulate_gyrus

value: Anterior

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Pancreatic cancer

tag: classification of_ms

value: Non-MS control

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion


title: HL-60 cells, DMSO treatment, 6 months, rep3

city: Busan

first: Ji-Eun

last: Lee

address: 2, Busandaehak-ro 63beon-gil

country: South Korea

institute: Pusan national university

data_processing:
Illumina bcl2fastq (v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastp), then mapped to GRCh38 (NCBI) whole genome using STAR.
Read count extraction using HTSeq-count.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

growth_protocol: HL-60 cells were cultured in the RPMI-1640 medium supplemented with 10% FBS, 1% L-glutamine, 1% HEPES and 1% penicilin/streptomycin at 37℃ in 5% CO2 incubator.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

treatment_protocol: HL-60 cells exposed to DMSO or corydalis incisa (Thunb.) Pers. (CIP) at slowly increasing concentrations from 2 μg/ml to 20 μg/ml over six months.

tag: cell line

tag: cell type

value: Human acute myeloid leukemia cell line

tag: genotype

value: WT

tag: treatment

value: DMSO treatment


title: Clam UF9D-0406

description: UF Phase I

source_name: Clam UF9D-0406

tag: tissue


title: Control C090

description: Library name: 194017-R53

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

value: male

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Pulmonary Fibrosis

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Subject UAMS28 R

tag: condition


title: Subject UAMS24 R


title: Clam UF99S-0630

description: UF Phase II

source_name: Clam UF99S-0630

tag: tissue


title: Clam UF94D-0399

description: UF Phase I

source_name: Clam UF94D-0399


title: Clam UF95D-0459

description: UF Phase I

source_name: Clam UF95D-0459


title: HL-60 cells, DMSO treatment, 6 months, rep2

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: MS MS125

description: Library name: 194017-R48

tag: disease

value: MS

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Multiple sclerosis

tag: classification of_ms

value: SPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Muscle weakness

tag: first presented_symptom_category

value: Motor

tag: history of_motor_weakness

value: Yes

tag: history of_sensory_loss

value: No

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: Clam UF93P-0491

description: UF Phase I

source_name: Clam UF93P-0491

tag: tissue

value: Adductor muscle


title: HL-60 cells, DMSO treatment, 6 months, rep1

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: HL-60 cells, CIP treatment, 6 months, rep3

value: CIP treatment (2μg/ml to 20μg/ml)


title: MS MS070

description: Library name: 194017-R46

value: brain

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

tag: classification of_ms

value: PPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: MS MS444

description: Library name: 194017-R47

tag: tissue

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Renal failure

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Spinal cord relapse

tag: first presented_symptom_category

value: Spinal cord

tag: history of_motor_weakness

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: Clam UF92D-0414

description: UF Phase I

source_name: Clam UF92D-0414

tag: tissue


title: Clam UF91S-0657

description: UF Phase III

source_name: Clam UF91S-0657


title: MS MS107

description: Library name: 194017-R45

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

value: male

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Aspiration pneumonia, pulmonary oedema

tag: classification of_ms

tag: age of_disease_onset

value: Ataxia

value: Brainstem, Cerebellar

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Subject UAMS20 F

tag: condition

value: iMCD patient


title: Subject UAMS22 R


title: Clam UF8P-0599

description: UF Phase II

source_name: Clam UF8P-0599

tag: tissue


title: Subject UAMS23 R


title: Subject UAMS19 R


title: Clam UF89D-0361

description: UF Phase I

source_name: Clam UF89D-0361


title: KELLY-H3K4me3-R1

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

country: Spain

institute: CNIO

data_processing:
*library strategy: CUT&RUN
Data were analyzed using cut and run nfcore pipeline: https://nf-co.re/cutandrun
Peak calling was performed using MACS2 software with mnase-treated chromatin as control sample. Only FDR-significant peaks <0.05 with signalValue > 3 were kept for analysis.
For down-stream analyses, regions found in at least 3 (KELLY) or 2 (LAN1, SK-N-AS, and KPNYN) replicates were used and annotated using the HOMER annotatePeaks.pl command.
Assembly: UCSC hg19
Supplementary files format and content: Bigwig files and called peaks output of MACS2 for each replicate.

source_name: Neuroblastoma

growth_protocol: KELLY and LAN-1 cells were cultured in RPMI  supplemented with 10% FBS and 1% sodium pyruvate. SK-N-AS cells were grown in DMEM  supplemented with 10% FBS and 0.1% non-essential amino acids. KP-N-YN cells expressing an inducible PRRX1 transgene were cultured in  control conditions or in the presence of doxycycline (0.5mg/ml)  in RPMI  supplemented with 10% FBS and 2mM L-glutamine. Cells were grown at 37 °C with 5% CO2.

extract_protocol:
500,000 cells/sample were harvested and bound to concanavalin A–coated magnetic beads. Cells were permeabilized with 5% digitonin. After overnight incubation with echa antibody, beads were washed and incubated with pAG-MNase produced at CNIO (Protein Production Unit). Cells were chilled to 0 °C and digestion was initiated by adding Ca2+. Reactions were stopped by chelation including spike-in DNA and the DNA fragments released by cleavage were extracted from the supernatant.
Library preparation and paired end sequencing for KELLY, LAN-1, and SK-N-AS  cells were performed at the CNIO Genomics Unit; experiments with the KP-N-YN inducible cells were performed at the Center for Applied Genomics (CHOP).
DNA samples were processed through subsequent enzymatic treatments for end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II DNA Library Prep Kit for Illumina" (NEB ref.E7645). Adapter-ligated libraries were completed by a limited-cycle PCR, with 63º T(ann/ext) for 10s, and extracted with a [single] double-sided SPRI size selection. Resulting average fragment size is 325 bp from which 120 bp correspond to adaptor sequences. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument by following manufacturer's recommendations.

value: Neuroblastoma

tag: cell line

value: KELLY

tag: cell type

value: Cancer cell

tag: antibody

value: H3K4me3-Abcam, ab8580

tag: antibody amount


title: Subject UAMS18 R

source_name: Serum/Plasma


title: Control C096

description: Library name: 194017-R43

source_name: brain

tag: disease

value: Control

tag: batch

tag: which cingulate_gyrus

value: Anterior

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Aspiration pneumonia, Parkinson’s disease, atherosclerosis

tag: classification of_ms

value: Non-MS control

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: KELLY-H3K27me3-R1

tag: tissue

tag: cell line

tag: cell type

tag: antibody

value: H3k27me3-Cell Signaling; #9377

tag: antibody amount


title: HL-60 cells, CIP treatment, 6 months, rep2

value: Human acute myeloid leukemia cell line

tag: genotype

value: WT

tag: treatment

value: CIP treatment (2μg/ml to 20μg/ml)


title: Clam UF88D-0425

description: UF Phase I

source_name: Clam UF88D-0425

value: Adductor muscle


title: MS MS263

description: Library name: 194017-R42

value: brain

tag: disease

value: MS

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Septicaemia, bronchopneumonia, urinary tract infection, small bowel obstruction, multiple sclerosis

tag: classification of_ms

value: SPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Numbness

tag: first presented_symptom_category

value: Sensory

tag: history of_motor_weakness

value: Yes

value: No

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Subject UAMS17 F

tag: condition

value: iMCD patient


title: HL-60 cells, CIP treatment, 6 months, rep1

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: MS MS301

description: Library name: 194017-R41

tag: tissue

tag: disease

tag: batch

tag: which cingulate_gyrus

value: Anterior

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Septicaemia, recurrent urinary tract infection, Hypokalaemia, multiple sclerosis

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Optic neuritis

tag: first presented_symptom_category

value: Visual

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: Subject UAMS21 R

tag: condition


title: KP-N-YN  PRRX1-induced cells-YAP1-R3

tag: tissue

value: Neuroblastoma

tag: cell line

value: KP-N-YN  PRRX1-induced cells

tag: cell type

value: Cancer cell

tag: antibody

value: YAP1-Cell Signaling; YAP (D8H1X) XP®

tag: antibody amount


title: MS MS102

description: Library name: 194017-R40

value: brain

tag: disease

value: MS

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

value: male

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Left ventricular failure, pneumonia, pleural effusion

tag: classification of_ms

value: PPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Pain

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: any periventricular_demyelination?

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: KP-N-YN  PRRX1-induced cells-YAP1-R4

tag: tissue

tag: cell line

tag: cell type

tag: antibody

tag: antibody amount


title: Subject UAMS15 R

tag: condition


title: Clam UF87P-0603

description: UF Phase II

source_name: Clam UF87P-0603

value: Adductor muscle


title: MS MS060

description: Library name: 194017-R39

tag: disease

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Aspiration of gastric contents, multiple sclerosis

tag: classification of_ms

value: SPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Muscle weakness, Spinal cord relapse

tag: first presented_symptom_category

value: Motor, Spinal cord

tag: history of_motor_weakness

value: Yes

value: No

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: Clam UF86S-0618

description: UF Phase II

source_name: Clam UF86S-0618

tag: tissue


title: KP-N-YN  PRRX1-induced cells-YAP1-R2

value: Neuroblastoma

tag: cell line

value: KP-N-YN  PRRX1-induced cells

tag: cell type

tag: antibody

tag: antibody amount


title: Subject UAMS16 R

tag: condition

value: iMCD patient


title: MS MS341

description: Library name: 194017-R44

value: brain

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Aspiration pneumonia, multiple sclerosis

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

value: Sensory

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Clam UF84P-0482

description: UF Phase I

source_name: Clam UF84P-0482

tag: tissue


title: Subject UAMS14 R

tag: condition


title: Control PDC022

description: Library name: 194017-R38

tag: disease

value: Control

tag: batch

tag: which cingulate_gyrus

value: Anterior

tag: age

tag: Sex

value: male

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Squamous cell carcinoma of the lung

tag: classification of_ms

value: Non-MS control

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: Clam UF82D-0398

description: UF Phase I

source_name: Clam UF82D-0398

tag: tissue

value: Adductor muscle


title: KP-N-YN control-YAP1-R4

tag: cell line

value: KP-N-YN control

tag: cell type

value: Cancer cell

tag: antibody

value: YAP1-Cell Signaling; YAP (D8H1X) XP®

tag: antibody amount


title: KP-N-YN  PRRX1-induced cells-YAP1-R1


title: Clam UF83S-0655

description: UF Phase III

source_name: Clam UF83S-0655

value: Hemocytes in ethanol


title: Subject UAMS12 R

tag: condition


title: Subject UAMS13 F


title: MS MS510

description: Library name: 194017-R35

tag: disease

value: MS

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Pneumonia, MS

tag: classification of_ms

value: SPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Numbness

tag: first presented_symptom_category

tag: history of_motor_weakness

value: Yes

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

value: No

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: KP-N-YN control-YAP1-R2

tag: tissue

value: Neuroblastoma

tag: cell line

tag: cell type

tag: antibody

tag: antibody amount


title: Clam UF81S-0654

description: UF Phase III

source_name: Clam UF81S-0654


title: Control PDC128

description: Library name: 194017-R34

value: brain

tag: disease

value: Control

tag: batch

tag: which cingulate_gyrus

value: Anterior

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Cardiac failure, hypotension, atrial fibrillation, aortic stenosis

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: Subject UAMS11 R

tag: condition

value: iMCD patient


title: Clam UF7D-0446

description: UF Phase I

source_name: Clam UF7D-0446

tag: tissue

value: Adductor muscle


title: Subject UAMS10 R


title: KP-N-YN control-YAP1-R1

tag: cell line

value: KP-N-YN control

tag: cell type

value: Cancer cell

tag: antibody

value: YAP1-Cell Signaling; YAP (D8H1X) XP®

tag: antibody amount


title: Clam UF79P-0602

description: UF Phase II

source_name: Clam UF79P-0602


title: Subject UAMS09 R


title: MS MS576

description: Library name: 194017-R33

tag: disease

value: MS

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

value: male

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

tag: classification of_ms

value: PPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Cerebellar relapse

tag: first presented_symptom_category

value: Cerebellar

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: MS MS049

description: Library name: 194017-R32

tag: tissue

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Aspiration pneumonia, cerebrovascular accident, multiple sclerosis

tag: classification of_ms

value: RRMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Blurred vision

tag: first presented_symptom_category

value: Visual

tag: history of_motor_weakness

value: Yes

value: No

tag: history of_sensory_loss

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: Subject UAMS08 R

tag: condition

value: iMCD patient


title: KP-N-YN  PRRX1-induced cells-GATA3-R4

tag: tissue

value: Neuroblastoma

tag: cell line

value: KP-N-YN  PRRX1-induced cells

tag: cell type

tag: antibody

value: GATA3-Cell Signaling; GATA-3 (D13C9) XP®

tag: antibody amount


title: Clam UF78D-0470

description: UF Phase I

source_name: Clam UF78D-0470

value: Adductor muscle


title: MS MS274

description: Library name: 194017-R36

value: brain

tag: disease

value: MS

tag: batch

tag: which cingulate_gyrus

value: Anterior

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Cancer of oesophagus

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Myokymia

tag: first presented_symptom_category

value: Brainstem

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Control C076

description: Library name: 194017-R31

tag: tissue

tag: disease

value: Control

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

value: male

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Pneumonia, Idiopathic pulmonary fibrosis

tag: classification of_ms

value: Non-MS control

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: KP-N-YN  PRRX1-induced cells-GATA3-R3

tag: tissue

tag: cell line

tag: cell type

value: Cancer cell

tag: antibody

tag: antibody amount


title: Subject UAMS07 R

tag: condition

value: iMCD patient


title: Clam UF77P-0481

description: UF Phase I

source_name: Clam UF77P-0481


title: Clam UF76D-0424

description: UF Phase I

source_name: Clam UF76D-0424


title: MS MS586

description: Library name: 194017-R30

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Respiratory failure, chest infection, MS, Asthma

tag: classification of_ms

value: SPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Numbness

tag: first presented_symptom_category

value: Sensory

tag: history of_motor_weakness

value: Yes

value: No

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Subject UAMS06 F

tag: condition


title: KP-N-YN control-YAP1-R3

tag: tissue

value: Neuroblastoma

tag: cell line

value: KP-N-YN control

tag: cell type

tag: antibody

value: YAP1-Cell Signaling; YAP (D8H1X) XP®

tag: antibody amount


title: Control PDC029

description: Library name: 194017-R29

value: brain

tag: disease

value: Control

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Metastatic liver and lung cancer

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: KP-N-YN  PRRX1-induced cells-GATA3-R2

tag: tissue

tag: cell line

value: KP-N-YN  PRRX1-induced cells

tag: cell type

tag: antibody

value: GATA3-Cell Signaling; GATA-3 (D13C9) XP®

tag: antibody amount


title: Clam UF75S-0653

description: UF Phase III

source_name: Clam UF75S-0653

value: Hemocytes in ethanol


title: Subject UAMS05

tag: condition

value: iMCD patient


title: KP-N-YN  PRRX1-induced cells-GATA3-R1

value: Cancer cell


title: Clam UF73D-0450

description: UF Phase I

source_name: Clam UF73D-0450

value: Adductor muscle


title: KP-N-YN control-GATA3-R4

source_name: Neuroblastoma


title: MS MS061

description: Library name: 194017-R28

tag: disease

value: MS

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Adenocarcinoma

tag: classification of_ms

value: PPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Muscle weakness

tag: first presented_symptom_category

value: Motor

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: MS MS499

description: Library name: 194017-R27

tag: tissue

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Bronchopneumonia, MS

tag: classification of_ms

value: SPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Brainstem relapse

tag: first presented_symptom_category

value: Brainstem

tag: history of_motor_weakness

value: Yes

tag: history of_sensory_loss

value: No

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: Clam UF71D-0458

description: UF Phase I

source_name: Clam UF71D-0458

tag: tissue


title: KP-N-YN control-GATA3-R3

value: Neuroblastoma

tag: cell line

value: KP-N-YN control

tag: cell type

tag: antibody

value: GATA3-Cell Signaling; GATA-3 (D13C9) XP®

tag: antibody amount


title: Subject UAMS04

source_name: Serum/Plasma

tag: condition

value: iMCD patient


title: Subject UAMS03


title: KP-N-YN control-GATA3-R2

value: Cancer cell


title: Clam UF70S-0617

description: UF Phase II

source_name: Clam UF70S-0617

value: Adductor muscle


title: Subject UAMS02


title: Control C064

description: Library name: 194017-R25

source_name: brain

value: brain

tag: disease

value: Control

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: multiple strokes, acute renal failure, pneumonia

tag: classification of_ms

value: Non-MS control

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: KP-N-YN control-GATA3-R1

tag: tissue

tag: cell line

tag: cell type

tag: antibody

tag: antibody amount


title: Clam UF6S-0642

description: UF Phase III

source_name: Clam UF6S-0642

value: Hemocytes in ethanol


title: Subject OU18 R

tag: condition


title: KP-N-YN  PRRX1-induced cells-Mnase

value: KP-N-YN  PRRX1-induced cells


title: Clam UF69D-0449

description: UF Phase I

source_name: Clam UF69D-0449


title: MS MS430

description: Library name: 194017-R24

tag: disease

value: MS

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Pneumonia, multiple sclerosis

tag: classification of_ms

value: SPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Spinal cord relapse

tag: first presented_symptom_category

value: Spinal cord

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: Clam UF68S-0652

description: UF Phase III

source_name: Clam UF68S-0652

tag: tissue


title: MS MS383

description: Library name: 194017-R23

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

value: male

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Aspiration pneumonia, multiple sclerosis

tag: classification of_ms

value: PPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Pain, Bladder dysfunction

tag: first presented_symptom_category

value: Sensory, Involuntary motor

tag: history of_motor_weakness

value: Yes

tag: history of_sensory_loss

value: No

tag: history of_cerebellar_malfunction

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: KP-N-YN  PRRX1-induced cells-BPTF-R4

tag: tissue

value: Neuroblastoma

tag: cell line

tag: cell type

value: Cancer cell

tag: antibody

tag: antibody amount


title: KP-N-YN  PRRX1-induced cells-BPTF-R3


title: Subject OU16 R

tag: condition

value: iMCD patient


title: Clam UF66D-0440

description: UF Phase I

source_name: Clam UF66D-0440

value: Adductor muscle


title: Subject OU17 R


title: MS MS086

description: Library name: 194017-R26

value: brain

tag: disease

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Cancer of the bladder, chest infection, multiple sclerosis

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Muscle weakness

tag: first presented_symptom_category

value: Motor

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: Clam UF65P-0601

description: UF Phase II

source_name: Clam UF65P-0601

tag: tissue


title: Control C045

description: Library name: 194017-R22

tag: disease

value: Control

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

value: male

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: cardio pulmonary degeneration, prostate cancer, old age, Alzheimers

tag: classification of_ms

value: Non-MS control

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Control C054

description: Library name: 194017-R21

tag: tissue

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Pancreatic cancer

tag: classification of_ms

tag: age of_disease_onset

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: Clam UF64S-0636

description: UF Phase II

source_name: Clam UF64S-0636

tag: tissue


title: Clam UF63S-0629

description: UF Phase II

source_name: Clam UF63S-0629


title: Subject OU14 R

tag: condition


title: Control C072

description: Library name: 194017-R20

tag: disease

tag: batch

tag: which cingulate_gyrus

value: Anterior

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Pneumonia, ischaemic bowel

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Subject OU15 R

tag: condition


title: Clam UF62D-0423

description: UF Phase I

source_name: Clam UF62D-0423

tag: tissue


title: MS MS352

description: Library name: 194017-R19

tag: disease

value: MS

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Bronchopneumonia, multiple sclerosis

tag: classification of_ms

value: SPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Optic neuritis

tag: first presented_symptom_category

value: Visual

value: Yes

value: No

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: KP-N-YN control-Mnase

tag: tissue

value: Neuroblastoma

tag: cell line

value: KP-N-YN control

tag: cell type

value: Cancer cell


title: KP-N-YN control-BPTF-R4

tag: antibody

tag: antibody amount


title: Subject OU13 F

tag: condition

value: iMCD patient


title: Subject UAMS01


title: Subject OU12 F


title: Clam UF61S-0651

description: UF Phase III

source_name: Clam UF61S-0651

value: Hemocytes in ethanol


title: KP-N-YN  PRRX1-induced cells-BPTF-R2

value: KP-N-YN  PRRX1-induced cells


title: Control PDC087

description: Library name: 194017-R17

value: brain

tag: disease

value: Control

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

tag: classification of_ms

value: Non-MS control

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: KP-N-YN control-BPTF-R3

tag: tissue

tag: cell line

tag: cell type

tag: antibody

tag: antibody amount


title: KP-N-YN control-BPTF-R2


title: Control C039

description: Library name: 194017-R16

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

value: male

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Myelodysplastic Syndrome, Rheumatoid Arthritis

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: Clam UF5D-0420

description: UF Phase I

source_name: Clam UF5D-0420

tag: tissue

value: Adductor muscle


title: Subject OU11 F

tag: condition


title: Control PDC123

description: Library name: 194017-R15

tag: disease

tag: batch

tag: which cingulate_gyrus

value: Anterior

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Bronchopneumonia

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: macroscopic lesions_at_meninges

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: KP-N-YN  PRRX1-induced cells-BPTF-R1

tag: tissue

tag: cell line

tag: cell type

tag: antibody

tag: antibody amount


title: KP-N-YN control-BPTF-R1


title: Clam UF58S-0650

description: UF Phase III

source_name: Clam UF58S-0650


title: SK-N-AS-Mnase

value: SK-N-AS


title: Subject OU10 F

tag: condition


title: Clam UF59D-0413

description: UF Phase I

source_name: Clam UF59D-0413


title: Control PDC035

description: Library name: 194017-R18

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Advanced cancer of uterus, renal failure

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: Subject OU09 F

tag: condition


title: Subject OU08


title: Control C046

description: Library name: 194017-R14

tag: tissue

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: End stage renal failure, multiple myeloma

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Subject OU07

tag: condition


title: MS MS527

description: Library name: 194017-R13

tag: tissue

tag: disease

value: MS

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Pneumonia, MS

tag: classification of_ms

value: SPMS

tag: age of_disease_onset

tag: age of_progressive_disease

value: Optic neuritis

value: Visual

value: Yes

value: No

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: Control C028

description: Library name: 194017-R12

tag: tissue

value: brain

tag: disease

value: Control

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Ovarian cancer

tag: classification of_ms

tag: age of_disease_onset

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Clam UF53D-0410

description: UF Phase I

source_name: Clam UF53D-0410

tag: tissue

value: Adductor muscle


title: SK-N-AS-BPTF-R1

source_name: Neuroblastoma

value: Neuroblastoma

tag: cell line

tag: cell type

value: Cancer cell

tag: antibody

tag: antibody amount


title: SK-N-AS-BPTF-R3

value: SK-N-AS


title: Subject OU05

source_name: Serum/Plasma

tag: condition

value: iMCD patient


title: Clam UF51S-0647

description: UF Phase III

source_name: Clam UF51S-0647

value: Hemocytes in ethanol


title: Clam UF50D-0457

description: UF Phase I

source_name: Clam UF50D-0457


title: Control PDC131

description: Library name: 194017-R09

source_name: brain

tag: disease

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Bronchopneumonia, COPD, cerebrovascular disease

tag: classification of_ms

value: Non-MS control

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: Subject OU06

tag: condition


title: LAN-1-BPTF-R4

tag: tissue

tag: cell line

tag: cell type

tag: antibody

tag: antibody amount


title: Control PDC068

description: Library name: 194017-R08

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Pneumonia and chronic kidney disease

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Subject OU04

tag: condition


title: MS MS098

description: Library name: 194017-R10

tag: tissue

tag: disease

value: MS

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

value: male

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Multiple sclerosis, sepsis secondary to urinary tract infection

tag: classification of_ms

value: RRMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Pain

tag: first presented_symptom_category

value: Sensory

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: LAN-1-Mnase

tag: tissue

tag: cell line

tag: cell type


title: Clam UF4D-0397

description: UF Phase I

source_name: Clam UF4D-0397


title: Clam UF54D-0376

description: UF Phase I

source_name: Clam UF54D-0376


title: LAN-1-BPTF-R2

tag: antibody

tag: antibody amount


title: Clam UF49P-0480

description: UF Phase I

source_name: Clam UF49P-0480


title: MS MS497

description: Library name: 194017-R07

value: brain

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Aspiration pneumonia

tag: classification of_ms

value: SPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Numbness

tag: first presented_symptom_category

tag: history of_motor_weakness

value: Yes

tag: history of_sensory_loss

tag: history of_depression

value: No

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Clam UF47D-0646

description: UF Phase I

source_name: Clam UF47D-0646

tag: tissue

value: Adductor muscle


title: SK-N-AS-BPTF-R2

value: Neuroblastoma

tag: cell line

value: SK-N-AS

tag: cell type

value: Cancer cell

tag: antibody

tag: antibody amount


title: Subject OU02

tag: condition

value: iMCD patient


title: LAN-1-BPTF-R3


title: MS MS547

description: Library name: 194017-R06

tag: disease

value: MS

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Multiple Myeloma, MS

tag: classification of_ms

value: PPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Optic neuritis

tag: first presented_symptom_category

value: Visual

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: Subject OU01

tag: condition


title: LAN-1-BPTF-R1

tag: tissue

tag: cell line

tag: cell type

tag: antibody

tag: antibody amount


title: KELLY-Mnase

value: KELLY


title: Subject UP38 F