title: Ovcar8 cells, CCNE1 overexpression + shTMLHE #2, rep 2

first: Katherine

last: Aird

address: 5051 Centre Ave.

institute: University of Pittsburgh School of Medicine

description:
Library name: Sample 11
Ov8CCTkd2_2

data_processing:
Next generation sequencing was performed at Novogene using a NovaSeq 6000 Sequencing System  (Illumina)
Demultiplexed and quality-filtered mRNA-Seq reads were then aligned to human reference genome (GRCh38) using STAR (v.2.6.1)
Differential expression analysis was done using DESeq2 (v2_1.6.3)
Assembly: GRCh38
Supplementary files format and content: Tab delimited text file includes FPKMs for all samples

source_name: ovarian cancer

growth_protocol: Ovcar8 cells were cultured in RPMI-1640 + 5% FBS

extract_protocol:
RNA was harvested by Trizol followed by a Qiagen clean up column with a DNAse step.
The cDNA libraries were prepared using NEBNext Ultra 2 RNA Library Prep Kit for Illumina (New England Biolabs; Cat.# E7775)

treatment_protocol: Cells were transduced with lentivirus and selected with 3ug/ml puromycin for 2-3 days.

value: ovarian cancer

value: CCNE1 overexpression + shTMLHE #2


title: Ovcar8 cells, CCNE1 overexpression + shTMLHE #2, rep 3

status: Public on Feb 26 2025

type: SRA

city: Pittsburgh

state: PA

country: USA

description:
Library name: Sample 12
Ov8CCTkd2_3

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: genotype


title: blood leukocyte DNA from HCC control with metabolic liver disease [206260470001_R05C01]

type: genomic

city: Jacksonville

first: Samuel

middle: O

last: Antwi

state: FL

address: 4500 San Pablo Road South, 756N Stabile Building

department: Quantitative Health Sciences

institute: Mayo Clinic

hyb_protocol: Standard Illumina Protocol; Bisulphite converted DNA was amplified, fragmented and hybridized to Human Infinium MethylationEPIC BeadChip (Illumina)

scan_protocol: Standard Illumina Protocol; Arrays were imaged using BeadArray Reader (iScan) and standard recommended Illumina scanner setting

data_processing:
Data were processed via 'minfi' library and normalized via 'dasen' method in 'watermelon' R library in R environment (v4.2.2). Probes on chromosomes X and Y were excluded.
HCC_matrix_processed.txt contains normalized Beta

label: Cy3 and Cy5

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from leukocytes using the Maxwell RSC Instrument with appropriate kits (Promega) and quantitated using a Qubit fluorometer. DNA quantification was performed using the Invitrogen Qubit dsDNA Quantification Assay kit (ThermoFisher Scientific, Inc., Waltham, MA, USA). All sample processing, including DNA extraction and quantification were performed by the Mayo Clinic Special Studies Laboratory.

tag: Sex

value: Female

tag: age

tag: diseasestate

value: Control

value: peripheral blood leukocyte


title: blood leukocyte DNA from metabolic HCC case [206260470002_R01C01]

value: Male

value: Case


title: Collect STIC FT-12 | 010 | Stroma

first: Lan

last: Coffman

address: 5051 Centre Ave

institute: UPMC Hillman Cancer Center

description: Library name: Collect STIC FT-12 | 010 | Stroma

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

source_name: Stroma

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.

value: Stroma


title: Collect STIC FT-12 | 009 | Stroma

description: Library name: Collect STIC FT-12 | 009 | Stroma


title: Ovcar8 cells, CCNE1 overexpression + shTMLHE #2, rep 1

description:
Library name: Sample 10
Ov8CCTkd2_1


title: blood leukocyte DNA from metabolic HCC case [206260470001_R03C01]


title: blood leukocyte DNA from metabolic HCC case [206260470001_R01C01]


title: Ovcar8 cells, CCNE1 overexpression + shTMLHE #1, rep 3

description:
Library name: Sample 9
Ov8CCTkd1_3

value: CCNE1 overexpression + shTMLHE #1


title: Collect STIC FT-12 | 008 | Stroma

description: Library name: Collect STIC FT-12 | 008 | Stroma


title: Collect STIC FT-12 | 009 | STIC

description: Library name: Collect STIC FT-12 | 009 | STIC

source_name: STIC

value: STIC


title: blood leukocyte DNA from metabolic HCC case [206254910120_R05C01]


title: blood leukocyte DNA from metabolic HCC case [206260470001_R04C01]


title: Collect STIC FT-12 | 008 | STIC

description: Library name: Collect STIC FT-12 | 008 | STIC


title: Ovcar8 cells, CCNE1 overexpression + shTMLHE #1, rep 2

description:
Library name: Sample 8
Ov8CCTkd1_2


title: blood leukocyte DNA from metabolic HCC case [206254910120_R04C01]


title: blood leukocyte DNA from metabolic HCC case [206254910120_R03C01]


title: Ovcar8 cells, CCNE1 overexpression + shTMLHE #1, rep 1

description:
Library name: Sample 7
Ov8CCTkd1_1


title: Collect STIC FT-12 | 007 | Stroma

description: Library name: Collect STIC FT-12 | 007 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206260470001_R08C01]


title: Ovcar8 cells, CCNE1 overexpression, rep 3

description:
Library name: Sample 6
Ov8CC_3

value: CCNE1 overexpression


title: blood leukocyte DNA from metabolic HCC case [206254910120_R08C01]


title: blood leukocyte DNA from metabolic HCC case [206254910120_R01C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254910115_R03C01]


title: Collect STIC FT-12 | 007 | STIC

description: Library name: Collect STIC FT-12 | 007 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254910108_R06C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254910108_R05C01]


title: blood leukocyte DNA from metabolic HCC case [206254910108_R03C01]


title: Ovcar8 cells, CCNE1 overexpression, rep 2

description:
Library name: Sample 5
Ov8CC_2


title: Ovcar8 cells, CCNE1 overexpression, rep 1

description:
Library name: Sample 4
Ov8CC_1


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254910108_R07C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254910120_R06C01]


title: blood leukocyte DNA from metabolic HCC case [206254910108_R02C01]


title: blood leukocyte DNA from metabolic HCC case [206254910108_R01C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254910100_R08C01]


title: Collect STIC FT-12 | 005 | Stroma

description: Library name: Collect STIC FT-12 | 005 | Stroma


title: Ovcar8 cells, control, rep 2

description:
Library name: Sample 2
Ov8EV_2

value: control


title: Ovcar8 cells, control, rep 3

description:
Library name: Sample 3
Ov8EV_3


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254910100_R07C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254910100_R06C01]


title: Collect STIC FT-12 | 004 | Stroma

description: Library name: Collect STIC FT-12 | 004 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254910100_R04C01]


title: blood leukocyte DNA from metabolic HCC case [206254910100_R01C01]


title: blood leukocyte DNA from metabolic HCC case [206254580192_R04C01]


title: Collect STIC FT-12 | 006 | Stroma

description: Library name: Collect STIC FT-12 | 006 | Stroma


title: 35-day-old Arabidopsis rosettes exogenously mock treated with 0.01 % DMSO and 0.1 % ethanol

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
Library name: Arabidopsis_whole_rosette_Mock
10X genomics

data_processing:
Libraries were sequenced aligned to the Arabidopsis TAIR10 genome with Araport11 annotation. Transcriptional atlases from each experiment were assembled using Seurat.
Assembly: Arabidopsis TAIR10
Supplementary files format and content: Seurat object

molecule: nuclear RNA

organism: Arabidopsis thaliana

source_name: rosette

extract_protocol:
Nuclei isolation was performed upon whole rosettes. Frozen tissue was crushed using a mortar and pestle, and nuclei released from homogenate using a resuspension buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1% PBS, 1% Superase RNAse Inhibitor). The resulting homogenate was filtered using a 30mm filter. To enrich for nuclei, an Optiprep (Sigma) gradient was employed. Enriched nuclei were then purified using Fluorescent Activated Cell Sorting (FACS).
Purified nuclei were loaded directly onto the 10X machine 10X-Gene Expression v3.0 chemistry and sequenced on the Illumina Novaseq 6000 with 150 bp paired end chemistry.

treatment_protocol: 35 day old Col-0 rosettes were exogenously treated with hormone. 2 hours after subjective dawn, both roots (through replacing growth media) and shoots (through foliar spray) were treated with one of the following hormone treatments: 10   uM (±)-Abscisic acid, 25   uM 2,4-Dichlorophenoxyacetic acid, 50   uM Gibberellin A3, 300   uM Salicylic acid, 1   uM trans-Zeatin, 10 nM Brassinollide, 10   uM Methyl jasmonate, 50   uM 1-Aminocyclopropane-1-carboxylic acid (ACC). Each hormone solution contained 0.01 % DMSO and 0.1 % ethanol. A mock treatment control was also included. Plants were treated for ~3 h, before rosettes flash frozen in liquid nitrogen. ~ 15 plants were collected per treatment.

tag: ecotype

value: rosette


title: 35-day-old Arabidopsis rosettes exogenously treated with 300uM Salicylic acid

description:
Library name: Arabidopsis_whole_rosette_SA
10X genomics


title: Collect STIC FT-12 | 003 | Stroma

description: Library name: Collect STIC FT-12 | 003 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580192_R05C01]


title: Collect STIC FT-12 | 004 | STIC

description: Library name: Collect STIC FT-12 | 004 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580192_R02C01]


title: blood leukocyte DNA from metabolic HCC case [206254580192_R01C01]


title: 35-day-old Arabidopsis rosettes exogenously treated with 10uM Methyl jasmonate

description:
Library name: Arabidopsis_whole_rosette_MJ
10X genomics


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580189_R08C01]


title: blood leukocyte DNA from metabolic HCC case [206254580189_R07C01]


title: Collect STIC FT-12 | 003 | STIC

description: Library name: Collect STIC FT-12 | 003 | STIC


title: Collect STIC FT-12 | 006 | STIC

description: Library name: Collect STIC FT-12 | 006 | STIC


title: 35-day-old Arabidopsis rosettes exogenously treated with 50uM Gibberellin A3

description:
Library name: Arabidopsis_whole_rosette_GA
10X genomics


title: blood leukocyte DNA from metabolic HCC case [206254580189_R06C01]


title: Collect STIC FT-12 | 002 | STIC

description: Library name: Collect STIC FT-12 | 002 | STIC


title: Collect STIC FT-12 | 005 | STIC

description: Library name: Collect STIC FT-12 | 005 | STIC


title: blood leukocyte DNA from metabolic HCC case [206254580189_R05C01]


title: 35-day-old Arabidopsis rosettes exogenously treated with 1uM trans-Zeatin

description:
Library name: Arabidopsis_whole_rosette_CK
10X genomics


title: Collect STIC FT-12 | 001 | Stroma

description: Library name: Collect STIC FT-12 | 001 | Stroma


title: 35-day-old Arabidopsis rosettes exogenously treated with 10nM Brassinollide

description:
Library name: Arabidopsis_whole_rosette_BR
10X genomics


title: blood leukocyte DNA from metabolic HCC case [206254580181_R08C01]


title: Ovcar8 cells, control, rep 1

description:
Library name: Sample 1
Ov8EV_1


title: Collect STIC FT-12 | 001 | STIC

description: Library name: Collect STIC FT-12 | 001 | STIC


title: blood leukocyte DNA from metabolic HCC case [206254580181_R06C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580181_R05C01]


title: 35-day-old Arabidopsis rosettes exogenously treated with 25uM 2,4-Dichlorophenoxyacetic acid

description:
Library name: Arabidopsis_whole_rosette_24D
10X genomics


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580181_R03C01]


title: Collect STIC FT-11 | 010 | Stroma

description: Library name: Collect STIC FT-11 | 010 | Stroma


title: Collect STIC FT-11 | 010 | STIC

description: Library name: Collect STIC FT-11 | 010 | STIC


title: blood leukocyte DNA from metabolic HCC case [206254580181_R04C01]


title: 35-day-old Arabidopsis rosettes exogenously treated with 10uM Abscisic acid

description:
Library name: Arabidopsis_whole_rosette_ABA
10X genomics


title: 35-day-old Arabidopsis rosettes exogenously treated with 50uM 1-Aminocyclopropane-1-carboxylic acid

description:
Library name: Arabidopsis_whole_rosette_ACC
10X genomics


title: blood leukocyte DNA from metabolic HCC case [206254580181_R02C01]


title: Collect STIC FT-11 | 009 | Stroma

description: Library name: Collect STIC FT-11 | 009 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580179_R05C01]


title: blood leukocyte DNA from metabolic HCC case [206254580179_R08C01]


title: Collect STIC FT-11 | 009 | STIC

description: Library name: Collect STIC FT-11 | 009 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580179_R07C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580179_R04C01]


title: Gata-3,VML,day7

city: Bethesda

first: Kaitlyn

last: Sadtler

state: Maryland

address: 50 S Drive, Room 4341

department: NIBIB

institute: NIH

data_processing:
Sequence reads were quality chekced for basecall accuracy greater than 30
Sequence reads were mapped to GRCm39 using Kalisto
Genes were annotated using EnsDb.Mmusculus.v79
Genes with less than 1 cpm in at least 3 samples were filtered out
Counts were log2 transformed and normalized using the TMM method
Assembly: mm39
Supplementary files format and content: filtered, log2 transformed, normalized counts for each gene across all samples

molecule: polyA RNA

organism: Mus musculus

source_name: Muscle

extract_protocol:
Total RNA isolation was performed at Azenta Life Sciences
Illumina library preperation for RNA with PolyA selection with ERCC spike in was performed at Azenta Life Sciences

treatment_protocol: Mice underwent volumetric muscle loss and did not receive any implants

value: Muscle

value: GATA-1 mutant

tag: treatment

value: Volumetric muscle loss


title: blood leukocyte DNA from metabolic HCC case [206254580179_R03C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580189_R03C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580179_R02C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580168_R06C01]


title: Collect STIC FT-11 | 008 | Stroma

description: Library name: Collect STIC FT-11 | 008 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580189_R04C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580168_R08C01]


title: Gata-1,VML,day7


title: Gata-2,VML,day7


title: blood leukocyte DNA from metabolic HCC case [206254580168_R05C01]


title: Collect STIC FT-11 | 008 | STIC

description: Library name: Collect STIC FT-11 | 008 | STIC


title: B6-3,VML,day7

value: WT


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580168_R04C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580168_R02C01]


title: B6-2,VML,day7


title: Collect STIC FT-11 | 007 | STIC

description: Library name: Collect STIC FT-11 | 007 | STIC


title: Collect STIC FT-11 | 007 | Stroma

description: Library name: Collect STIC FT-11 | 007 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580168_R01C01]


title: B6-1,VML,day7


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580167_R07C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580167_R06C01]


title: Collect STIC FT-11 | 006 | Stroma

description: Library name: Collect STIC FT-11 | 006 | Stroma


title: Wnt1, Cre-Dach1-flox-flox-E18-5-DRG, replicate 5

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422
STAR version 2.7.8a was used to align the reads to the GRCm39 genome using 2 mismatches within 50 bases
featureCounts version 2.0.1 was used to quantify reads for genes in GRCm39 version 105
Assembly: GRCm39 version 105
Supplementary files format and content: Tab-delimited gene counts

source_name: Dorsal root ganglia

extract_protocol:
Dorsal root ganglia were dissected in cold RNAse Free PBS and stored at −80°C in TRIZOL (ThermoFisher cat.# 15596026). RNAwas extracted using the illustra RNAspin MiniRNA isolationkit (GE Healthcare cat.# 25-0500-70)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Dorsal root ganglia

tag: developmental stage

tag: cell type

value: neurons and glia

value: Wnt1+/+Dach1 flox/flox


title: Collect STIC FT-11 | 006 | STIC

description: Library name: Collect STIC FT-11 | 006 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580167_R04C01]

value: Female

value: Control


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580167_R03C01]

value: Male

value: peripheral blood leukocyte


title: blood leukocyte DNA from metabolic HCC case [206254580167_R01C01]

value: Case


title: Wnt1, Cre-Dach1-flox-flox-E18-5-DRG, replicate 4


title: Wnt1, Cre-Dach1-flox-flox-E18-5-DRG, replicate 3


title: Collect STIC FT-11 | 005 | Stroma

description: Library name: Collect STIC FT-11 | 005 | Stroma

value: Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580166_R08C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580166_R06C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580166_R04C01]


title: Collect STIC FT-11 | 005 | STIC

description: Library name: Collect STIC FT-11 | 005 | STIC

value: STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580166_R03C01]


title: Wnt1, Cre-Dach1-flox-flox-E18-5-DRG, replicate 2


title: Collect STIC FT-11 | 004 | Stroma

description: Library name: Collect STIC FT-11 | 004 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580164_R08C01]


title: blood leukocyte DNA from metabolic HCC case [206254580164_R05C01]


title: Control, E18-5-DRG, replicate 5

value: Wnt1Cre/+Dach1 flox/flox


title: Collect STIC FT-11 | 003 | Stroma

description: Library name: Collect STIC FT-11 | 003 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580164_R04C01]


title: Control, E18-5-DRG, replicate 4


title: Collect STIC FT-11 | 003 | STIC

description: Library name: Collect STIC FT-11 | 003 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580164_R03C01]


title: blood leukocyte DNA from metabolic HCC case [206254580164_R01C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580160_R08C01]


title: Control, E18-5-DRG, replicate 3


title: Collect STIC FT-11 | 002 | Stroma

description: Library name: Collect STIC FT-11 | 002 | Stroma


title: Control, E18-5-DRG, replicate 2


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580160_R06C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580160_R05C01]


title: Control, E18-5-DRG, replicate 1


title: blood leukocyte DNA from metabolic HCC case [206254580160_R03C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580160_R04C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580166_R02C01]


title: blood leukocyte DNA from metabolic HCC case [206254580157_R08C01]


title: blood leukocyte DNA from metabolic HCC case [206254580157_R07C01]


title: Collect STIC FT-11 | 002 | STIC

description: Library name: Collect STIC FT-11 | 002 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580157_R05C01]


title: Collect STIC FT-11 | 004 | STIC

description: Library name: Collect STIC FT-11 | 004 | STIC


title: Control, E18-5-DRG, replicate 3


title: Control, E18-5-DRG, replicate 4


title: Wnt1, Cre-Dach1-flox-flox-E18-5-DRG, replicate 1


title: blood leukocyte DNA from metabolic HCC case [206254580164_R07C01]


title: Collect STIC FT-11 | 001 | Stroma

description: Library name: Collect STIC FT-11 | 001 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580157_R03C01]


title: Collect STIC FT-11 | 001 | STIC

description: Library name: Collect STIC FT-11 | 001 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580157_R02C01]


title: Control, E18-5-DRG, replicate 2


title: blood leukocyte DNA from metabolic HCC case [206254580157_R01C01]


title: Collect STIC FT-10 | 004 | Stroma

description: Library name: Collect STIC FT-10 | 004 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580156_R08C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580156_R07C01]


title: Collect STIC FT-10 | 004 | STIC

description: Library name: Collect STIC FT-10 | 004 | STIC


title: Advillin, Cre-Dach1-E18-5-DRG, replicate 4


title: blood leukocyte DNA from metabolic HCC case [206254580156_R04C01]


title: Collect STIC FT-10 | 003 | Stroma

description: Library name: Collect STIC FT-10 | 003 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580156_R02C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580156_R03C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580155_R06C01]


title: blood leukocyte DNA from metabolic HCC case [206254580155_R04C01]


title: blood leukocyte DNA from metabolic HCC case [206254580155_R02C01]


title: Collect STIC FT-10 | 002 | STIC

description: Library name: Collect STIC FT-10 | 002 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580147_R08C01]


title: blood leukocyte DNA from metabolic HCC case [206254580155_R01C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580155_R08C01]


title: Advillin, Cre-Dach1-E18-5-DRG, replicate 3


title: Advillin, Cre-Dach1-E18-5-DRG, replicate 2


title: Collect STIC FT-10 | 005 | Stroma

description: Library name: Collect STIC FT-10 | 005 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580147_R07C01]


title: Advillin, Cre-Dach1-E18-5-DRG, replicate 1


title: PBS-Saline_5

city: Winston-Salem

first: Jonathon

middle: P

last: Sens

state: NC

address: 115 S Chestnut St

department: Physiology/Pharmacology

institute: Wake Forest Baptist Health

data_processing:
Raw FASTQs were trimmed and QC was performed using FASTQC (v 0.11.9). Reads were then aligned using STAR (v 2.7.0) to generate read counts.
Assembly: mm10
Supplementary files format and content: Raw gene read counts in a text tab deliminated file.

source_name: Brain, nucleus accumbens

extract_protocol:
RNA was extracted using a Qiagen Rneasy Mini Plus kit according to manufacturer's instructions (cat no #74134)
Total RNA was used and libraries were prepared using the NEBNext Ultra RNA Library Prep Kit according to manufacturer's instructions (cat no NEB #E7770)

treatment_protocol: Cocaine 7.5mg/kg/day +/- CSF2 10mcg/kg/day x 7 days --> sacrifice 24 hours after final

value: Brain, nucleus accumbens

value: Saline


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580155_R03C01]


title: Collect STIC FT-10 | 002 | Stroma

description: Library name: Collect STIC FT-10 | 002 | Stroma


title: PBS-Saline_6


title: Control, E18-5-DRG, replicate 1


title: Collect STIC FT-10 | 001 | Stroma

description: Library name: Collect STIC FT-10 | 001 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580147_R06C01]


title: blood leukocyte DNA from metabolic HCC case [206254580156_R05C01]


title: PBS-Saline_4


title: Collect STIC FT-10 | 001 | STIC

description: Library name: Collect STIC FT-10 | 001 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580147_R05C01]


title: Collect RD-LC-013-3C | 025 | Stroma

description: Library name: Collect RD-LC-013-3C | 025 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580143_R08C01]


title: PBS-Saline_2


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580143_R03C01]


title: Collect RD-LC-013-3C | 024 | Stroma

description: Library name: Collect RD-LC-013-3C | 024 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580143_R01C01]


title: PBS-Saline_1


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580142_R06C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580142_R03C01]


title: Collect RD-LC-013-3C | 024 | STIC

description: Library name: Collect RD-LC-013-3C | 024 | STIC


title: Collect RD-LC-013-3C | 023 | Stroma

description: Library name: Collect RD-LC-013-3C | 023 | Stroma


title: PBS-Cocaine_6

value: Cocaine


title: PBS-Cocaine_5


title: Collect RD-LC-013-3C | 023 | STIC

description: Library name: Collect RD-LC-013-3C | 023 | STIC


title: blood leukocyte DNA from metabolic HCC case [206254580141_R07C01]


title: blood leukocyte DNA from metabolic HCC case [206254580141_R04C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580142_R01C01]


title: Collect RD-LC-013-3C | 022 | Stroma

description: Library name: Collect RD-LC-013-3C | 022 | Stroma


title: PBS-Cocaine_3


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580141_R08C01]


title: PBS-Cocaine_4


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580141_R03C01]


title: blood leukocyte DNA from metabolic HCC case [206254580141_R02C01]


title: Collect RD-LC-013-3C | 022 | STIC

description: Library name: Collect RD-LC-013-3C | 022 | STIC


title: blood leukocyte DNA from metabolic HCC case [206254580141_R01C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580138_R07C01]


title: Collect RD-LC-013-3C | 021 | Stroma

description: Library name: Collect RD-LC-013-3C | 021 | Stroma


title: PBS-Cocaine_2


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580143_R04C01]


title: PBS-Cocaine_1


title: blood leukocyte DNA from metabolic HCC case [206254580138_R04C01]


title: Collect RD-LC-013-3C | 021 | STIC

description: Library name: Collect RD-LC-013-3C | 021 | STIC


title: GMCSF-Saline_6


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580142_R02C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580138_R01C01]


title: blood leukocyte DNA from metabolic HCC case [206254580134_R07C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580134_R06C01]


title: GMCSF-Saline_5


title: blood leukocyte DNA from metabolic HCC case [206254580134_R02C01]


title: GMCSF-Saline_4


title: Collect RD-LC-013-3C | 019 | Stroma

description: Library name: Collect RD-LC-013-3C | 019 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580134_R03C01]


title: Collect RD-LC-013-3C | 020 | STIC

description: Library name: Collect RD-LC-013-3C | 020 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580125_R06C01]


title: GMCSF-Saline_3


title: GMCSF-Saline_1


title: GMCSF-Saline_2


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580138_R06C01]


title: blood leukocyte DNA from metabolic HCC case [206254580134_R01C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580125_R01C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580125_R05C01]


title: blood leukocyte DNA from metabolic HCC case [206254580125_R04C01]


title: Collect RD-LC-013-3C | 019 | STIC

description: Library name: Collect RD-LC-013-3C | 019 | STIC


title: GMCSF-Cocaine_6


title: Collect RD-LC-013-3C | 017 | Stroma

description: Library name: Collect RD-LC-013-3C | 017 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580125_R02C01]


title: Collect RD-LC-013-3C | 018 | STIC

description: Library name: Collect RD-LC-013-3C | 018 | STIC


title: Collect RD-LC-013-3C | 020 | Stroma

description: Library name: Collect RD-LC-013-3C | 020 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580124_R08C01]


title: GMCSF-Cocaine_5


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580125_R08C01]


title: Collect RD-LC-013-3C | 018 | Stroma

description: Library name: Collect RD-LC-013-3C | 018 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580124_R07C01]


title: Collect STIC FT-10 | 003 | STIC

description: Library name: Collect STIC FT-10 | 003 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580124_R06C01]


title: Collect RD-LC-013-3C | 017 | STIC

description: Library name: Collect RD-LC-013-3C | 017 | STIC


title: GMCSF-Cocaine_4


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580117_R08C01]


title: blood leukocyte DNA from metabolic HCC case [206254580124_R02C01]


title: blood leukocyte DNA from metabolic HCC case [206254580117_R07C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580124_R01C01]


title: GMCSF-Cocaine_2


title: Collect RD-LC-013-3C | 015 | Stroma

description: Library name: Collect RD-LC-013-3C | 015 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580117_R04C01]


title: Collect RD-LC-013-3C | 016 | STIC

description: Library name: Collect RD-LC-013-3C | 016 | STIC


title: GMCSF-Cocaine_3


title: blood leukocyte DNA from metabolic HCC case [206254580117_R06C01]


title: GMCSF-Cocaine_1


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580116_R08C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580116_R07C01]


title: blood leukocyte DNA from metabolic HCC case [206254580117_R02C01]


title: Collect RD-LC-013-3C | 014 | Stroma

description: Library name: Collect RD-LC-013-3C | 014 | Stroma


title: ATAC-Seq Cdk6_K43M_1_p185_transformed

city: Vienna

first: Thorsten

last: Klampfl

address: Veterinaerplatz 1

country: Austria

institute: University of Veterinary Medicine Vienna

library_source: genomic

data_processing:
Raw reads were quality controlled using FASTQC
Trimmomatic (version 0.36) was used to perform adapter trimming and quality-based read filtering.
Filtered reads were mapped against the mm10 mouse reference genome (Gencode M13) using bwa-mem (v0.7.15) and blacklisted regions were removed with bedtools subtract (v2.26.0). Multimappers as well as reads with low mapping quality were removed using samtools (v1.3.1).
Peak calling was performed with MACS2 (v2.1.0)
Assembly: mm10
Supplementary files format and content: narrowPeak

source_name: Pre/Pro-B-cells

growth_protocol: Cells were cultured in RPMI incl. 10% FCS,50 μmol/l 2-mercaptoethanol, 100 u/ml penicillin and 100 μg/ml streptomycin

extract_protocol:
Cells were washed once in 50 μl PBS and resuspended in transposase reaction mix (12.5 μl 2 × TD buffer, 2 μl transposase (Illumina), 10.5 μl nuclease-free water and 0.01% NP-40)
Tagmentation was performed for 30 min at 37 °C.

value: Pre/Pro-B-cells


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580117_R01C01]


title: Collect RD-LC-013-3C | 014 | STIC

description: Library name: Collect RD-LC-013-3C | 014 | STIC


title: Collect RD-LC-013-3C | 015 | STIC

description: Library name: Collect RD-LC-013-3C | 015 | STIC


title: blood leukocyte DNA from metabolic HCC case [206254580116_R05C01]


title: ATAC-Seq Cdk6_WT_2_p185_transformed


title: blood leukocyte DNA from metabolic HCC case [206254580116_R06C01]


title: Collect RD-LC-013-3C | 013 | Stroma

description: Library name: Collect RD-LC-013-3C | 013 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580116_R04C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580124_R04C01]


title: Collect RD-LC-013-3C | 016 | Stroma

description: Library name: Collect RD-LC-013-3C | 016 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580125_R07C01]


title: blood leukocyte DNA from metabolic HCC case [206254580116_R03C01]


title: blood leukocyte DNA from metabolic HCC case [206254580116_R01C01]


title: Collect RD-LC-013-3C | 013 | STIC

description: Library name: Collect RD-LC-013-3C | 013 | STIC


title: blood leukocyte DNA from metabolic HCC case [206254580114_R07C01]


title: blood leukocyte DNA from metabolic HCC case [206254580114_R08C01]


title: MC38 shControl, 10 tumors, SMCs

city: Stanford

first: Caitlin

last: Bell

state: California

address: 241 Pasteur Drive

department: Medicine

institute: Stanford University School of Medicine

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation performed using CellRanger v 7.2 (https://www.10xgenomics.com/support/software/cell-ranger/7.2)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Tumor tissue harvested from mice was placed in cold PBS prior to tissue digestion. Tumor tissue was mechanically dissociated into 2-4mm pieces and then digested in 2.5 mg/mL Liberase and 0.1 mg/mL Dnase (Roche) for 1 hour at 37C. Digested tissue was then passed through 70um filters and incubated with red blood cell lysis buffer for 10 minutes prior to neutralization with PBS. Cells were stained with a viability dye, spun down, and resuspended PBS +1% BSA. The first 3 libraries were composed of all live single cells from one dissociated tumor. Otherwise, live cells sorted for presence of fluorescent lineage tracer (either eGFP or tdTomato depending on mouse line). Fluorescent negative cells added back to final samples for sequencing as needed to ensure manufacturer-recommended concentration of 500 cells/uL minimum.
Library was constructed according to the manufacturer's protocol (single cell 3' v3.1, 10X Genomics) by the Stanford Genome Sequencing Core. Briefly, cells were resuspended in the master mix and loaded together with the partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every GEM was reverse transcribed to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI), and the 10X barcode. The pooled and barcoded cDNA was then cleaned with Silane DynaBeads, amplified by PCR, and the appropriate sized fragments were selected with SPRIselect for library construction. During library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences, and a sample index were added.

value: Tumor

value: Smooth muscle cell

value: Myh11-ERT-creT2 ROSA-STOP-flox-tdT


title: Collect RD-LC-013-3C | 012 | Stroma

description: Library name: Collect RD-LC-013-3C | 012 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580114_R04C01]


title: Collect RD-LC-013-3C | 012 | STIC

description: Library name: Collect RD-LC-013-3C | 012 | STIC


title: MC38 55L

description: 10X Genomics

value: tdT Myh11-ERT-creT2 ROSA-STOP-flox-eGFP


title: Collect RD-LC-013-3C | 011 | Stroma

description: Library name: Collect RD-LC-013-3C | 011 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580114_R03C01]


title: MC38 47L

description: 10X Genomics


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580114_R01C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580112_R05C01]


title: blood leukocyte DNA from metabolic HCC case [206254580112_R07C01]


title: blood leukocyte DNA from metabolic HCC case [206254580112_R08C01]


title: MC38 44R

description: 10X Genomics


title: ATAC-Seq Cdk6_K43M_2_p185_transformed


title: Collect RD-LC-013-3C | 010 | Stroma

description: Library name: Collect RD-LC-013-3C | 010 | Stroma


title: CT2_IP

city: Beijing

first: Dongdong

last: Jian

address: 38 Xueyuan Road

department: Biochemistry and Molecular Biology

country: China

institute: Peking University Health Science Center

data_processing:
Raw sequencing data was first filtered by fastp (version 0.23.4), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster.
After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
The de-duplicated consensus sequences were mapped to the reference genome of Mus musculus from GRCm39 using STAR software (version 2.5.3a) with default parameters. The exomePeak（Version 3.8）software was used for peak calling. The m5C peaks were annotated using bedtools（Version 2.25.0）.
The differentially m5C peaks were identified by QNB (version 1.0). Sequence motifs enriched in m5C peak regions were identified using Homer（version 4.10）. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for annotated genes were both implemented by KOBAS software (version: 2.1.1) with a corrected p-value cutoff of 0.05 to judge statistically significant enrichment.
Assembly: GRCm39
Supplementary files format and content: bigWig

source_name: left ventricular myocytes

extract_protocol:
Total RNAs were extracted from langendorf isolated cardiomyocytes using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999). DNA digestion was carried out after RNA extraction by DNase I. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity (RQN) was confirmed by Qsep 100 (BIOptic Inc).
200 μg total RNAs were used for polyadenylated RNA enrichment by VAHTS mRNA Capture Beads（VAHTS, cat. NO. N401-01/02）. 20 mM ZnCl2 was added to mRNA and incubated at 95℃ for 5min-10min until the RNA fragments were mainly distributed in 100-200 nt. Then 10% RNA fragments was saved as “Input” and the rest was used for m5C immunoprecipitation（IP）.The specific anti-m5C antibody (Abcam, ab10805) was applied for m5C immunoprecipitation. RNA samples of both input and IP were prepared using TRIzol reagent(Invitrogen, cat. NO 15596026). The stranded RNA sequencing library was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and fnally sequenced on a MGISEQ-T7 instrument (MGI) in PE150 mode.

tag: group

value: CT

value: left ventricular myocytes

value: TAC

tag: rip antibody

value: anti-m5C antibody (Abcam, ab10805)


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580112_R04C01]

value: Female

value: Control

value: peripheral blood leukocyte


title: MC38 shBST2, 10 tumors, SMCs

description: 10X Genomics


title: Collect RD-LC-013-3C | 010 | STIC

description: Library name: Collect RD-LC-013-3C | 010 | STIC

value: STIC


title: blood leukocyte DNA from metabolic HCC case [206254580095_R07C01]

value: Case


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580095_R08C01]


title: blood leukocyte DNA from metabolic HCC case [206254580095_R06C01]

value: Male


title: MC38, 10 tumors, SMCs

description: 10X Genomics


title: Collect RD-LC-013-3C | 009 | Stroma

description: Library name: Collect RD-LC-013-3C | 009 | Stroma

value: Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580114_R02C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580095_R02C01]


title: CT2_Input


title: Collect RD-LC-013-3C | 009 | STIC

description: Library name: Collect RD-LC-013-3C | 009 | STIC


title: Collect RD-LC-013-3C | 011 | STIC

description: Library name: Collect RD-LC-013-3C | 011 | STIC


title: Collect RD-LC-013-3C | 008 | Stroma

description: Library name: Collect RD-LC-013-3C | 008 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580087_R07C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580087_R05C01]


title: FT2_IP

value: FT


title: CT1_Input


title: blood leukocyte DNA from metabolic HCC case [206254580087_R04C01]


title: Collect RD-LC-013-3C | 008 | STIC

description: Library name: Collect RD-LC-013-3C | 008 | STIC


title: FT1_IP


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580087_R01C01]


title: Collect RD-LC-013-3C | 007 | Stroma

description: Library name: Collect RD-LC-013-3C | 007 | Stroma


title: FT2_Input


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580087_R02C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580085_R06C01]


title: Collect RD-LC-013-3C | 007 | STIC

description: Library name: Collect RD-LC-013-3C | 007 | STIC


title: blood leukocyte DNA from metabolic HCC case [206254580085_R05C01]


title: CT1_IP


title: Collect RD-LC-013-3C | 006 | Stroma

description: Library name: Collect RD-LC-013-3C | 006 | Stroma


title: FT1_Input


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580085_R03C01]


title: blood leukocyte DNA from metabolic HCC case [206254580095_R03C01]


title: blood leukocyte DNA from metabolic HCC case [206254580083_R08C01]


title: blood leukocyte DNA from metabolic HCC case [206254580085_R02C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580087_R08C01]


title: cKO2_IP

value: cKO

value: sham


title: blood leukocyte DNA from metabolic HCC case [206254580087_R06C01]


title: cKO1_IP


title: Collect RD-LC-013-3C | 005 | Stroma

description: Library name: Collect RD-LC-013-3C | 005 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580083_R07C01]


title: blood leukocyte DNA from metabolic HCC case [206254580083_R06C01]


title: Collect RD-LC-013-3C | 006 | STIC

description: Library name: Collect RD-LC-013-3C | 006 | STIC


title: cKO2_Input


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580083_R03C01]


title: Collect RD-LC-013-3C | 005 | STIC

description: Library name: Collect RD-LC-013-3C | 005 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580082_R04C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580083_R02C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580082_R03C01]


title: Collect RD-LC-013-3C | 004 | Stroma

description: Library name: Collect RD-LC-013-3C | 004 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580082_R02C01]


title: Collect RD-LC-013-3C | 004 | STIC

description: Library name: Collect RD-LC-013-3C | 004 | STIC


title: blood leukocyte DNA from metabolic HCC case [206254580079_R07C01]


title: FF1_IP

value: FF


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580079_R06C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580079_R03C01]


title: Collect RD-LC-013-3C | 003 | Stroma

description: Library name: Collect RD-LC-013-3C | 003 | Stroma


title: FF2_Input


title: Collect RD-LC-013-3C | 003 | STIC

description: Library name: Collect RD-LC-013-3C | 003 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580079_R02C01]


title: blood leukocyte DNA from metabolic HCC case [206254580079_R01C01]


title: FF1_Input


title: blood leukocyte DNA from metabolic HCC case [206254580075_R07C01]


title: Collect RD-LC-013-3C | 002 | Stroma

description: Library name: Collect RD-LC-013-3C | 002 | Stroma


title: cKO1_Input


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580075_R05C01]


title: FF2_IP


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580075_R08C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580075_R04C01]


title: Collect RD-LC-013-3C | 001 | Stroma

description: Library name: Collect RD-LC-013-3C | 001 | Stroma


title: Collect RD-LC-013-3C | 002 | STIC

description: Library name: Collect RD-LC-013-3C | 002 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580075_R01C01]


title: blood leukocyte DNA from metabolic HCC case [206254580082_R01C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580083_R05C01]


title: blood leukocyte DNA from metabolic HCC case [206254580075_R02C01]


title: Collect RD-LC-013-3C | 001 | STIC

description: Library name: Collect RD-LC-013-3C | 001 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580073_R08C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580073_R06C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580075_R06C01]


title: Collect RD-LC-012-1M | 025 | Stroma

description: Library name: Collect RD-LC-012-1M | 025 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580073_R07C01]


title: Collect RD-LC-012-1M | 025 | STIC

description: Library name: Collect RD-LC-012-1M | 025 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580073_R05C01]


title: MSTO 211H miRNA503 inhibitor treated_biological rep 2

type: RNA

city: Napoli

first: Stefania

last: Crispi

address: Via Pietro Castellino,111

department: DISBA

country: Italy

institute: CNR

hyb_protocol: Total RNA was converted in labelled ssDNA and used to hybridize microarrays. All the procedures including wash and staining of array were performed following the manufacturer's instructions. Hybridization was performed by incubation with rotation at 60 rpm for 16 hours at 45°C.

scan_protocol: Clariom S arrays were scanned using the GeneChip™ Scanner 3000 7G using GCOS

data_processing: Samples data registration and primary analisys was performed using GeneChip™ Command Console™ (GCC). After laser scanning .CEL files from array were used for data analysis. Primary data analysis was performed with the Transcriptome Analysis Console software (Thermofisher version 4.0) including the Robust Multiarray Average module for normalization. Expression cut off selected was Fold change <-2 >2 and pvalue <0.05 and transcriptional modifications were detected comparing AGS treated cells to untreated cells. Differentially expressed genes were selected applying as cut-off criteria log2-fold change ≥+/−2 and a P-value≤0.05.

label: Biotin

source_name: MSTO-211H cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Applied Biosystem protocol from 100 ng total RNA (Whole Transcript Expression Array User Guide).

growth_protocol: Cells were grown in RPMI 1640 at 37°C with 5% CO2

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were treated with miRNA503 inhibitor or with vehicle (0.1% DMSO) for 48 hours. After cells were detached collected and placed in Trizol for RNA extreaction

value: mesothelioma cells


title: blood leukocyte DNA from metabolic HCC case [206254580073_R03C01]


title: Collect RD-LC-012-1M | 024 | Stroma

description: Library name: Collect RD-LC-012-1M | 024 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580069_R03C01]


title: Collect RD-LC-012-1M | 023 | STIC

description: Library name: Collect RD-LC-012-1M | 023 | STIC


title: blood leukocyte DNA from metabolic HCC case [206254580073_R01C01]


title: MSTO 211H miRNA503 inhibitor treated_biological rep 3


title: MSTO 211H miRNA503 inhibitor treated_biological rep 1


title: blood leukocyte DNA from metabolic HCC case [206254580068_R04C01]


title: blood leukocyte DNA from metabolic HCC case [206254580069_R08C01]


title: MSTO 211H untread_biological rep 3


title: Subject HC30

type: protein

first: Allan

last: Feng

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: Healthy control


title: Collect RD-LC-012-1M | 024 | STIC

description: Library name: Collect RD-LC-012-1M | 024 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580069_R06C01]


title: MSTO 211H untread_biological rep 1


title: blood leukocyte DNA from metabolic HCC case [206254580069_R05C01]


title: Subject HC29


title: MSTO 211H untread_biological rep 2


title: blood leukocyte DNA from metabolic HCC case [206254580069_R01C01]


title: Collect RD-LC-012-1M | 023 | Stroma

description: Library name: Collect RD-LC-012-1M | 023 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580069_R07C01]


title: Collect RD-LC-012-1M | 022 | STIC

description: Library name: Collect RD-LC-012-1M | 022 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580068_R02C01]


title: Collect RD-LC-012-1M | 022 | Stroma

description: Library name: Collect RD-LC-012-1M | 022 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580067_R08C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580068_R03C01]


title: blood leukocyte DNA from metabolic HCC case [206254580068_R06C01]


title: Subject HC27


title: blood leukocyte DNA from metabolic HCC case [206254580067_R06C01]


title: Collect RD-LC-012-1M | 021 | Stroma

description: Library name: Collect RD-LC-012-1M | 021 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580067_R05C01]


title: Subject HC25


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580067_R04C01]


title: Subject HC28


title: Subject HC24


title: Collect RD-LC-012-1M | 021 | Immune

description: Library name: Collect RD-LC-012-1M | 021 | Immune

source_name: Immune

value: Immune


title: Subject HC26


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580059_R04C01]


title: Subject HC23


title: Collect RD-LC-012-1M | 021 | STIC

description: Library name: Collect RD-LC-012-1M | 021 | STIC


title: Collect RD-LC-012-1M | 019 | STIC

description: Library name: Collect RD-LC-012-1M | 019 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580059_R07C01]


title: blood leukocyte DNA from metabolic HCC case [206254580067_R03C01]


title: blood leukocyte DNA from metabolic HCC case [206254580059_R08C01]


title: Collect RD-LC-012-1M | 020 | Immune

description: Library name: Collect RD-LC-012-1M | 020 | Immune


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580059_R05C01]


title: Collect RD-LC-012-1M | 019 | Stroma

description: Library name: Collect RD-LC-012-1M | 019 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580055_R06C01]


title: blood leukocyte DNA from metabolic HCC case [206254580059_R03C01]


title: blood leukocyte DNA from metabolic HCC case [206254580059_R02C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580055_R08C01]


title: Subject HC22


title: Subject HC21


title: blood leukocyte DNA from metabolic HCC case [206254580055_R03C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580055_R07C01]


title: Subject HC20


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580053_R08C01]


title: Collect RD-LC-012-1M | 017 | Stroma

description: Library name: Collect RD-LC-012-1M | 017 | Stroma


title: Collect RD-LC-012-1M | 018 | Stroma

description: Library name: Collect RD-LC-012-1M | 018 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580053_R07C01]


title: Subject HC19


title: blood leukocyte DNA from metabolic HCC case [206254580055_R05C01]


title: blood leukocyte DNA from metabolic HCC case [206254580053_R06C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580055_R04C01]


title: Subject HC18


title: Subject HC17


title: Subject HC16


title: Collect RD-LC-012-1M | 017 | STIC

description: Library name: Collect RD-LC-012-1M | 017 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580053_R05C01]


title: blood leukocyte DNA from metabolic HCC case [206254580053_R03C01]


title: Collect RD-LC-012-1M | 018 | STIC

description: Library name: Collect RD-LC-012-1M | 018 | STIC


title: Collect RD-LC-012-1M | 016 | Immune

description: Library name: Collect RD-LC-012-1M | 016 | Immune


title: blood leukocyte DNA from metabolic HCC case [206254580053_R02C01]


title: Subject HC14


title: Collect RD-LC-012-1M | 015 | Immune

description: Library name: Collect RD-LC-012-1M | 015 | Immune


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580050_R06C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580050_R08C01]


title: Collect RD-LC-012-1M | 014 | Immune

description: Library name: Collect RD-LC-012-1M | 014 | Immune


title: blood leukocyte DNA from metabolic HCC case [206254580050_R05C01]


title: Subject HC13

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.


title: blood leukocyte DNA from metabolic HCC case [206254580050_R03C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580050_R04C01]


title: Collect RD-LC-012-1M | 013 | Immune

description: Library name: Collect RD-LC-012-1M | 013 | Immune


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580050_R02C01]


title: Subject HC12


title: Collect RD-LC-012-1M | 012 | Stroma

description: Library name: Collect RD-LC-012-1M | 012 | Stroma


title: Subject HC11


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580049_R07C01]


title: Collect RD-LC-012-1M | 012 | STIC

description: Library name: Collect RD-LC-012-1M | 012 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580049_R04C01]


title: Subject HC10


title: Collect RD-LC-012-1M | 011 | Stroma

description: Library name: Collect RD-LC-012-1M | 011 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580049_R03C01]


title: Subject HC09


title: blood leukocyte DNA from metabolic HCC case [206254580053_R01C01]


title: Subject HC08


title: Collect RD-LC-012-1M | 011 | STIC

description: Library name: Collect RD-LC-012-1M | 011 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580048_R08C01]


title: blood leukocyte DNA from metabolic HCC case [206254580048_R07C01]


title: blood leukocyte DNA from metabolic HCC case [206254580048_R06C01]


title: Subject HC07


title: Collect RD-LC-012-1M | 010 | Stroma

description: Library name: Collect RD-LC-012-1M | 010 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580048_R03C01]


title: Subject HC15


title: blood leukocyte DNA from metabolic HCC case [206254580048_R05C01]


title: Collect RD-LC-012-1M | 010 | STIC

description: Library name: Collect RD-LC-012-1M | 010 | STIC


title: blood leukocyte DNA from metabolic HCC case [206254580048_R01C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580049_R06C01]


title: Subject HC06


title: Collect RD-LC-012-1M | 009 | Stroma

description: Library name: Collect RD-LC-012-1M | 009 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580038_R06C01]


title: Collect RD-LC-012-1M | 009 | STIC

description: Library name: Collect RD-LC-012-1M | 009 | STIC


title: Subject HC05


title: Subject HC04


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580038_R02C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580037_R08C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580049_R02C01]


title: Subject HC03


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580037_R07C01]


title: blood leukocyte DNA from metabolic HCC case [206254580037_R06C01]


title: Collect RD-LC-012-1M | 008 | STIC

description: Library name: Collect RD-LC-012-1M | 008 | STIC


title: Subject HC02


title: blood leukocyte DNA from metabolic HCC case [206254580037_R05C01]


title: Collect RD-LC-012-1M | 007 | Stroma

description: Library name: Collect RD-LC-012-1M | 007 | Stroma


title: Subject HC01


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580048_R02C01]


title: blood leukocyte DNA from metabolic HCC case [206254580037_R04C01]


title: Collect RD-LC-012-1M | 007 | STIC

description: Library name: Collect RD-LC-012-1M | 007 | STIC


title: blood leukocyte DNA from metabolic HCC case [206254580035_R08C01]


title: blood leukocyte DNA from metabolic HCC case [206254580037_R02C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580038_R03C01]


title: Collect RD-LC-012-1M | 006 | Stroma

description: Library name: Collect RD-LC-012-1M | 006 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580035_R07C01]


title: Subject UP57

value: Hodgkin lymphoma patient control


title: Subject UP58


title: Collect RD-LC-012-1M | 008 | Stroma

description: Library name: Collect RD-LC-012-1M | 008 | Stroma


title: paneth cells, zinc depleted diet, replicate 3

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
Reads were quality checked with fastqc and quality filtered with trimmomatic (v0.39; parameters:SLIDINGWINDOW:4:30 MINLEN:50)
Reads were aligned to the mm39 reference genome with the STAR aligner (v2.7.10a) and read counts were directly obtained using the "--quantMode GeneCounts" parameter for STAR
Differential expression analysis was done using the DESeq2 package, with the FDR set at 5%
Assembly: mm39
Supplementary files format and content: A tab delimited text file with raw counts for each sample

source_name: small intestine

extract_protocol:
The small intestine was isolated and a single cell suspension was prepared from the material. Cells were sorted using FACS and paneth cells were collected for RNA isolation. RNA was isolated using an aurum total RNA mini kit accorting to the manufacturers instructions
RNA was used to generate a sequencing libary for the Element AVITI accoring to the manufacturers instructions from the AVITI 150 cycles Cloudbreak sequencing kit single-end reads

treatment_protocol: Mice were given standard chow or zinc depleted chow at libitum for 7 weeks, afterwards thay were treated with TNF for 3 hours

value: small intestine

value: purified paneth cells

value: WT

value: zinc depletion + 3h TNF


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580035_R03C01]

value: Control

value: peripheral blood leukocyte


title: Subject UP56


title: Collect RD-LC-012-1M | 005 | Stroma

description: Library name: Collect RD-LC-012-1M | 005 | Stroma


title: paneth cells, zinc depleted diet, replicate 2


title: Collect RD-LC-012-1M | 005 | STIC

description: Library name: Collect RD-LC-012-1M | 005 | STIC

value: STIC


title: paneth cells, zinc depleted diet, replicate 1


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580035_R01C01]

value: Male


title: Subject UP54

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.


title: blood leukocyte DNA from metabolic HCC case [206254580026_R06C01]

value: Female

value: Case


title: Subject UP55


title: Collect RD-LC-012-1M | 004 | Stroma

description: Library name: Collect RD-LC-012-1M | 004 | Stroma

value: Stroma


title: paneth cells, standard diet, replicate 3

value: control diet + 3h TNF


title: Collect RD-LC-012-1M | 006 | STIC

description: Library name: Collect RD-LC-012-1M | 006 | STIC


title: blood leukocyte DNA from metabolic HCC case [206254580037_R01C01]


title: Subject UP53


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580026_R05C01]


title: paneth cells, standard diet, replicate 2


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580026_R03C01]


title: Subject UP52


title: Collect RD-LC-012-1M | 004 | STIC

description: Library name: Collect RD-LC-012-1M | 004 | STIC


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580026_R01C01]


title: Collect RD-LC-012-1M | 003 | Stroma

description: Library name: Collect RD-LC-012-1M | 003 | Stroma


title: Subject UP51


title: paneth cells, standard diet, replicate 1


title: blood leukocyte DNA from metabolic HCC case [206254580022_R07C01]


title: Collect RD-LC-012-1M | 003 | STIC

description: Library name: Collect RD-LC-012-1M | 003 | STIC


title: Subject UP50


title: Subject UP49


title: Collect RD-LC-012-1M | 002 | Stroma

description: Library name: Collect RD-LC-012-1M | 002 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580022_R06C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580022_R05C01]


title: Prototype Histones

description:
raw data file: CTD Array version prototype 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.

extract_protocol: Blood was collected from autoimmune disease patients healthy controls. Blood was then processed into serum or plasma.

value: Autoimmune Disease Patient


title: Subject UP48


title: blood leukocyte DNA from metabolic HCC case [206254580022_R03C01]


title: Prototype La


title: Collect RD-LC-012-1M | 001 | Stroma

description: Library name: Collect RD-LC-012-1M | 001 | Stroma


title: Subject UP47


title: Prototype Scl-70


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580022_R01C01]


title: Prototype Ro


title: Subject UP45


title: Prototype TG


title: Subject UP46


title: Collect RD-LC-012-1M | 001 | STIC

description: Library name: Collect RD-LC-012-1M | 001 | STIC


title: Collect RD-LC-012-1M | 002 | STIC

description: Library name: Collect RD-LC-012-1M | 002 | STIC


title: blood leukocyte DNA from metabolic HCC case [206254580017_R08C01]


title: blood leukocyte DNA from metabolic HCC case [206254580022_R02C01]


title: Collect RD-LC-011 | 021 | Stroma

description: Library name: Collect RD-LC-011 | 021 | Stroma


title: Collect RD-LC-011 | 021 | Tumor

description: Library name: Collect RD-LC-011 | 021 | Tumor

value: Tumor


title: Subject UP44


title: blood leukocyte DNA from metabolic HCC case [206254580017_R06C01]


title: Subject HC30

value: Healthy Control


title: blood leukocyte DNA from metabolic HCC case [206254580017_R07C01]


title: Collect RD-LC-011 | 019 | Tumor

description: Library name: Collect RD-LC-011 | 019 | Tumor


title: Collect RD-LC-011 | 020 | Tumor

description: Library name: Collect RD-LC-011 | 020 | Tumor


title: Subject HC27


title: Subject HC29


title: Subject UP42


title: Subject HC28


title: Subject UP41


title: Collect RD-LC-011 | 020 | Stroma

description: Library name: Collect RD-LC-011 | 020 | Stroma


title: Subject HC31


title: Subject HC25


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580017_R05C01]


title: Subject UP39


title: Collect RD-LC-011 | 019 | Stroma

description: Library name: Collect RD-LC-011 | 019 | Stroma


title: Subject HC24


title: Collect RD-LC-011 | 018 | Tumor

description: Library name: Collect RD-LC-011 | 018 | Tumor


title: Subject UP43

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.


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580017_R04C01]


title: Subject UP40


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580017_R03C01]


title: Collect RD-LC-011 | 018 | Stroma

description: Library name: Collect RD-LC-011 | 018 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580017_R01C01]


title: Subject HC21


title: blood leukocyte DNA from metabolic HCC case [206254580016_R07C01]


title: Collect RD-LC-011 | 017 | Tumor

description: Library name: Collect RD-LC-011 | 017 | Tumor


title: Subject HC18


title: Collect RD-LC-011 | 017 | Stroma

description: Library name: Collect RD-LC-011 | 017 | Stroma


title: Subject UAMS44 F

value: iMCD patient


title: Subject HC17


title: Subject UAMS43 F


title: blood leukocyte DNA from metabolic HCC case [206254580016_R04C01]


title: Collect RD-LC-011 | 016 | Tumor

description: Library name: Collect RD-LC-011 | 016 | Tumor


title: Subject UAMS42 F


title: Subject HC16


title: Subject UAMS41 R


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580016_R01C01]


title: Collect RD-LC-011 | 016 | Stroma

description: Library name: Collect RD-LC-011 | 016 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580016_R02C01]


title: Subject HC15

description:
raw data file: CTD Array version prototype 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.


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580016_R05C01]


title: Collect RD-LC-011 | 015 | Tumor

description: Library name: Collect RD-LC-011 | 015 | Tumor


title: Collect RD-LC-011 | 014 | Stroma

description: Library name: Collect RD-LC-011 | 014 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580014_R08C01]


title: Subject HC13


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580014_R07C01]


title: Subject UAMS37 R


title: blood leukocyte DNA from metabolic HCC case [206254580014_R06C01]


title: Subject HC14


title: Collect RD-LC-011 | 013 | Stroma

description: Library name: Collect RD-LC-011 | 013 | Stroma


title: Subject HC11


title: Collect RD-LC-011 | 012 | Stroma

description: Library name: Collect RD-LC-011 | 012 | Stroma


title: Subject HC12


title: Collect RD-LC-011 | 013 | Tumor

description: Library name: Collect RD-LC-011 | 013 | Tumor


title: Subject UAMS36 F


title: Subject UAMS38 F


title: Subject UAMS40 F


title: Subject UAMS45 F


title: Subject HC10


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580014_R03C01]


title: Collect RD-LC-011 | 011 | Tumor

description: Library name: Collect RD-LC-011 | 011 | Tumor


title: Subject UAMS35 R


title: Subject HC09


title: blood leukocyte DNA from metabolic HCC case [206254580014_R01C01]


title: Subject UAMS34 F


title: Collect RD-LC-011 | 008 | Stroma

description: Library name: Collect RD-LC-011 | 008 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580012_R08C01]


title: Subject UAMS32 F


title: Collect RD-LC-011 | 007 | Tumor

description: Library name: Collect RD-LC-011 | 007 | Tumor


title: Subject UAMS33 R


title: Subject HC07


title: Subject UAMS31 F


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580012_R05C01]


title: blood leukocyte DNA from metabolic HCC case [206254580014_R02C01]


title: Collect RD-LC-011 | 006 | Stroma

description: Library name: Collect RD-LC-011 | 006 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580012_R04C01]


title: Subject UAMS30 R


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580012_R02C01]


title: AMI Patient

description:
raw data file: ACA Array version prototype 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.

extract_protocol: Blood was collected from an autoimmune disease patient and healthy controls. Blood was then processed into serum or plasma.


title: Collect RD-LC-011 | 005 | Full ROI

description: Library name: Collect RD-LC-011 | 005 | Full ROI

source_name: Full ROI

value: Full ROI


title: Subject HC31


title: Subject HC30


title: Collect RD-LC-011 | 004 | Stroma

description: Library name: Collect RD-LC-011 | 004 | Stroma


title: Subject HC29


title: Subject UAMS39 R

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.


title: Collect RD-LC-011 | 009 | Tumor

description: Library name: Collect RD-LC-011 | 009 | Tumor


title: Subject UAMS28 R


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580012_R06C01]


title: Collect RD-LC-011 | 010 | Stroma

description: Library name: Collect RD-LC-011 | 010 | Stroma


title: Subject HC08


title: Subject UAMS29 R


title: blood leukocyte DNA from metabolic HCC case [206254580009_R08C01]


title: Subject HC27


title: Subject UAMS27 R


title: blood leukocyte DNA from metabolic HCC case [206254580009_R07C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580009_R06C01]


title: Collect RD-LC-011 | 002 | Tumor

description: Library name: Collect RD-LC-011 | 002 | Tumor


title: Collect RD-LC-011 | 001 | Tumor

description: Library name: Collect RD-LC-011 | 001 | Tumor


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580009_R04C01]


title: Subject UAMS25 R


title: Collect RD-LC-010 | 017 | Tumor

description: Library name: Collect RD-LC-010 | 017 | Tumor


title: Subject HC24


title: Subject HC28


title: Subject HC21


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580009_R02C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580009_R03C01]


title: Subject UAMS24 R


title: Subject UAMS23 R


title: Collect RD-LC-010 | 017 | Stroma

description: Library name: Collect RD-LC-010 | 017 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254580004_R06C01]


title: Collect RD-LC-010 | 016 | Tumor

description: Library name: Collect RD-LC-010 | 016 | Tumor


title: Collect RD-LC-010 | 016 | Stroma

description: Library name: Collect RD-LC-010 | 016 | Stroma


title: Subject HC17


title: blood leukocyte DNA from metabolic HCC case [206254580004_R04C01]


title: Subject HC18


title: Subject UAMS21 R


title: Subject HC16


title: Subject UAMS22 R


title: Collect RD-LC-011 | 003 | Stroma

description: Library name: Collect RD-LC-011 | 003 | Stroma


title: Subject UAMS26 R


title: Subject HC15


title: Collect RD-LC-010 | 015 | Tumor

description: Library name: Collect RD-LC-010 | 015 | Tumor


title: Subject HC25


title: Collect RD-LC-010 | 015 | Stroma

description: Library name: Collect RD-LC-010 | 015 | Stroma


title: Subject UAMS19 R


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580004_R02C01]


title: blood leukocyte DNA from metabolic HCC case [206254580004_R03C01]


title: Subject HC14


title: Collect RD-LC-010 | 014 | Tumor

description: Library name: Collect RD-LC-010 | 014 | Tumor


title: Subject UAMS18 R


title: Collect RD-LC-010 | 014 | Stroma

description: Library name: Collect RD-LC-010 | 014 | Stroma


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254580004_R01C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254440093_R08C01]


title: Collect RD-LC-010 | 013 | Tumor

description: Library name: Collect RD-LC-010 | 013 | Tumor


title: Subject HC13

description:
raw data file: ACA Array version prototype 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.


title: Subject UAMS17 F


title: Subject UAMS20 F


title: Subject HC11


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254440093_R07C01]


title: Subject UAMS16 R


title: Collect RD-LC-010 | 013 | Stroma

description: Library name: Collect RD-LC-010 | 013 | Stroma


title: Subject UAMS15 R

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.


title: Subject HC10


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254440093_R06C01]


title: blood leukocyte DNA from metabolic HCC case [206254440093_R03C01]


title: blood leukocyte DNA from metabolic HCC case [206254440093_R04C01]


title: Collect RD-LC-010 | 012 | Tumor

description: Library name: Collect RD-LC-010 | 012 | Tumor


title: Subject UAMS11 R


title: Subject UAMS13 F


title: Subject UAMS14 R


title: Subject HC09


title: Subject HC12


title: Collect RD-LC-010 | 011 | Stroma

description: Library name: Collect RD-LC-010 | 011 | Stroma


title: Collect RD-LC-010 | 012 | Stroma

description: Library name: Collect RD-LC-010 | 012 | Stroma


title: Subject HC08


title: blood leukocyte DNA from metabolic HCC case [206254440074_R04C01]


title: Collect RD-LC-010 | 010 | Stroma

description: Library name: Collect RD-LC-010 | 010 | Stroma


title: Collect RD-LC-010 | 010 | Tumor

description: Library name: Collect RD-LC-010 | 010 | Tumor


title: Subject HC07


title: Subject UAMS12 R


title: Subject UAMS10 R


title: Subject UAMS08 R


title: Subject UAMS09 R


title: blood leukocyte DNA from metabolic HCC case [206254440074_R03C01]


title: Collect RD-LC-010 | 011 | Tumor

description: Library name: Collect RD-LC-010 | 011 | Tumor


title: blood leukocyte DNA from metabolic HCC case [206254440074_R08C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254440074_R05C01]


title: Collect RD-LC-010 | 009 | Tumor

description: Library name: Collect RD-LC-010 | 009 | Tumor


title: Subject HC30

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.

value: Healthy control


title: Subject HC29


title: Subject HC27


title: Subject HC28


title: Collect RD-LC-010 | 008 | Tumor

description: Library name: Collect RD-LC-010 | 008 | Tumor


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254440074_R01C01]


title: blood leukocyte DNA from metabolic HCC case [206254440064_R07C01]


title: Collect RD-LC-010 | 009 | Stroma

description: Library name: Collect RD-LC-010 | 009 | Stroma


title: Subject HC26


title: Subject HC25


title: Collect RD-LC-010 | 007 | Tumor

description: Library name: Collect RD-LC-010 | 007 | Tumor


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254440064_R04C01]


title: Collect RD-LC-010 | 007 | Stroma

description: Library name: Collect RD-LC-010 | 007 | Stroma


title: Subject UAMS05


title: Collect RD-LC-010 | 008 | Stroma

description: Library name: Collect RD-LC-010 | 008 | Stroma


title: Subject HC24


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254440074_R02C01]


title: Subject UAMS07 R


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254440064_R03C01]


title: Subject HC22


title: Subject UAMS04


title: Subject UAMS02


title: Subject UAMS06 F


title: blood leukocyte DNA from metabolic HCC case [206254440064_R02C01]


title: Collect RD-LC-010 | 006 | Tumor

description: Library name: Collect RD-LC-010 | 006 | Tumor


title: Subject UAMS03


title: Collect RD-LC-010 | 006 | Stroma

description: Library name: Collect RD-LC-010 | 006 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254440064_R05C01]


title: Subject UAMS01


title: Subject HC23


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254440053_R08C01]


title: Subject HC21


title: blood leukocyte DNA from metabolic HCC case [206254440053_R06C01]


title: Collect RD-LC-010 | 005 | Tumor

description: Library name: Collect RD-LC-010 | 005 | Tumor


title: Subject OU18 R

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.


title: Subject HC19


title: Subject OU17 R


title: Collect RD-LC-010 | 005 | Stroma

description: Library name: Collect RD-LC-010 | 005 | Stroma


title: Subject HC18


title: blood leukocyte DNA from metabolic HCC case [206254440053_R03C01]


title: Collect RD-LC-010 | 004 | Stroma

description: Library name: Collect RD-LC-010 | 004 | Stroma


title: Collect RD-LC-010 | 004 | Tumor

description: Library name: Collect RD-LC-010 | 004 | Tumor


title: Subject OU16 R


title: blood leukocyte DNA from metabolic HCC case [206254440047_R08C01]


title: Subject OU15 R


title: Subject HC17


title: Subject HC20


title: Collect RD-LC-010 | 003 | Tumor

description: Library name: Collect RD-LC-010 | 003 | Tumor


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254440053_R02C01]


title: Subject HC16


title: Collect RD-LC-010 | 003 | Stroma

description: Library name: Collect RD-LC-010 | 003 | Stroma


title: Subject OU14 R


title: Subject HC15


title: Collect RD-LC-010 | 002 | Tumor

description: Library name: Collect RD-LC-010 | 002 | Tumor


title: blood leukocyte DNA from metabolic HCC case [206254440047_R05C01]


title: Subject HC14


title: Subject OU12 F


title: Subject OU11 F


title: blood leukocyte DNA from metabolic HCC case [206254440047_R04C01]


title: Collect RD-LC-010 | 002 | Stroma

description: Library name: Collect RD-LC-010 | 002 | Stroma


title: Subject HC13

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.


title: Subject HC12


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254440053_R05C01]


title: Subject OU10 F


title: Collect RD-LC-010 | 001 | Tumor

description: Library name: Collect RD-LC-010 | 001 | Tumor


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254440047_R03C01]


title: Subject HC11


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254440047_R07C01]


title: Collect RD-LC-010 | 001 | Stroma

description: Library name: Collect RD-LC-010 | 001 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254440047_R02C01]


title: Subject OU09 F


title: Collect RD-LC-009 | 016 | Tumor

description: Library name: Collect RD-LC-009 | 016 | Tumor


title: Subject HC10


title: Collect RD-LC-009 | 016 | Stroma

description: Library name: Collect RD-LC-009 | 016 | Stroma


title: Subject OU13 F


title: blood leukocyte DNA from metabolic HCC case [206254440032_R08C01]


title: blood leukocyte DNA from metabolic HCC case [206254440047_R01C01]


title: Collect RD-LC-009 | 015 | Tumor

description: Library name: Collect RD-LC-009 | 015 | Tumor


title: blood leukocyte DNA from metabolic HCC case [206254440032_R07C01]


title: Subject OU07


title: Subject HC06


title: Collect RD-LC-009 | 015 | Stroma

description: Library name: Collect RD-LC-009 | 015 | Stroma


title: Subject OU06


title: blood leukocyte DNA from metabolic HCC case [206254440032_R06C01]


title: Collect RD-LC-009 | 014 | Tumor

description: Library name: Collect RD-LC-009 | 014 | Tumor


title: Subject OU05


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254440032_R03C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254440032_R04C01]


title: Subject HC05


title: Subject OU04


title: Collect RD-LC-009 | 014 | Stroma

description: Library name: Collect RD-LC-009 | 014 | Stroma


title: Subject HC07


title: Subject HC04


title: Subject OU08

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.


title: Subject OU03


title: Subject HC09


title: Subject OU02


title: Collect RD-LC-009 | 013 | Tumor

description: Library name: Collect RD-LC-009 | 013 | Tumor


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254440032_R01C01]


title: Subject HC08


title: Subject HC03


title: Collect RD-LC-009 | 013 | Stroma

description: Library name: Collect RD-LC-009 | 013 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254440024_R08C01]


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254440024_R07C01]


title: Subject OU01


title: Collect RD-LC-009 | 012 | Tumor

description: Library name: Collect RD-LC-009 | 012 | Tumor


title: Subject HC02


title: Subject HC01


title: Collect RD-LC-009 | 012 | Stroma

description: Library name: Collect RD-LC-009 | 012 | Stroma


title: blood leukocyte DNA from metabolic HCC case [206254440024_R04C01]


title: Subject UP38 F


title: blood leukocyte DNA from metabolic HCC case [206254440024_R03C01]


title: Collect RD-LC-009 | 011 | Tumor

description: Library name: Collect RD-LC-009 | 011 | Tumor


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254440024_R02C01]


title: Subject UP37 F


title: Subject UP57

value: Hodgkin lymphoma patient control


title: Collect RD-LC-009 | 010 | Tumor

description: Library name: Collect RD-LC-009 | 010 | Tumor


title: Subject UP35 F


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254440024_R01C01]


title: Collect RD-LC-009 | 011 | Stroma

description: Library name: Collect RD-LC-009 | 011 | Stroma


title: Subject UP36 F


title: blood leukocyte DNA from metabolic HCC case [206254440013_R08C01]


title: Subject UP55

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.


title: blood leukocyte DNA from metabolic HCC case [206254440013_R07C01]


title: Subject UP54


title: Collect RD-LC-009 | 010 | Stroma

description: Library name: Collect RD-LC-009 | 010 | Stroma


title: Subject UP56


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

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


title: Subject UP33 F


title: Subject UP53


title: Subject UP32 F


title: blood leukocyte DNA from metabolic HCC case [206254440013_R05C01]


title: Subject UP31 R


title: Subject UP58


title: Subject UP52


title: Collect RD-LC-009 | 008 | Tumor

description: Library name: Collect RD-LC-009 | 008 | Tumor


title: Subject UP30 R


title: blood leukocyte DNA from metabolic HCC case [206254440013_R01C01]


title: Subject UP34 F


title: blood leukocyte DNA from HCC control with metabolic liver disease [206254440013_R02C01]


title: Subject UP50


title: Collect RD-LC-009 | 008 | Stroma

description: Library name: Collect RD-LC-009 | 008 | Stroma


title: Collect RD-LC-009 | 007 | Stroma

description: Library name: Collect RD-LC-009 | 007 | Stroma


title: Control C094

city: London

first: Carolina

last: Barcellos Machado

address: 4-8 Maple St

country: United Kingdom

institute: BenevolentAI

description: Library name: 194017-R90

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

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

tag: batch

tag: which cingulate_gyrus

value: Posterior

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Pulmonary embolism, metastatic ovarian 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

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 UP28 R

tag: condition


title: Subject UP49


title: Subject UP29 R


title: Subject UP48


title: Subject UP27 F


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

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

tag: tissue


title: Control C074

description: Library name: 194017-R89

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: Acute myocardial infarction, CKD

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


title: Collect RD-LC-009 | 006 | Stroma

description: Library name: Collect RD-LC-009 | 006 | Stroma

tag: tissue


title: MS MS126

description: Library name: 194017-R87

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: Pneumonia

tag: classification of_ms

value: SPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Sensory

value: Yes

value: No

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 UP47

tag: condition


title: Subject UP26 R

value: iMCD patient


title: Collect RD-LC-009 | 005 | Tumor

description: Library name: Collect RD-LC-009 | 005 | Tumor

tag: tissue

value: Tumor


title: MS MS500

description: Library name: 194017-R86

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: Urinary Sepsis

tag: classification of_ms

value: PPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Headache

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


title: Collect RD-LC-009 | 005 | Stroma

description: Library name: Collect RD-LC-009 | 005 | Stroma

tag: tissue

value: Stroma


title: Subject UP51

tag: condition

value: Hodgkin lymphoma patient control


title: Subject UP24 F

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.


title: Subject UP25 R


title: Control PDC086

description: Library name: 194017-R85

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: Bronchopneumonia

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: 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 UP46

tag: condition


title: Subject UP45


title: Collect RD-LC-009 | 004 | Tumor

description: Library name: Collect RD-LC-009 | 004 | Tumor

tag: tissue


title: Control PDC027

description: Library name: 194017-R84

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: pneumonia

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


title: Subject UP23 F

tag: condition


title: Collect RD-LC-009 | 004 | Stroma

description: Library name: Collect RD-LC-009 | 004 | Stroma

tag: tissue


title: Subject UP22 R


title: Subject UP44


title: MS MS439

description: Library name: 194017-R82

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: Aspiration pneumonia, Multiple Sclerosis, metastatic breast cancer

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

value: Yes

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 | 003 | Tumor

description: Library name: Collect RD-LC-009 | 003 | Tumor

tag: tissue

value: Tumor


title: Subject UP21 R

tag: condition

value: iMCD patient


title: Collect RD-LC-009 | 003 | Stroma

description: Library name: Collect RD-LC-009 | 003 | Stroma

value: Stroma


title: Subject UP42

value: Hodgkin lymphoma patient control


title: Collect RD-LC-009 | 006 | Tumor

description: Library name: Collect RD-LC-009 | 006 | Tumor


title: MS MS528

description: Library name: 194017-R80

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

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

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