title: EBV(-) exosome Tx, rep1

description:
Library name: sample7
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_43


title: M2c, rep1

status: Public on Nov 23 2024

type: SRA

city: Taoyuan

first: Tzu-Tung

last: Liu

address: Zhongda Rd,. Zhongli District

country: Taiwan

institute: National central university

description:
Library name: sample4
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_40

library_source: transcriptomic

data_processing:
Exosome-mediated effects on macrophages were evaluated using bulk RNA sequencing.
Quality control excluded genes detected in fewer than half of the samples with at least one UMI.  The expression matrix for the remaining cells was then normalized using the Relative Log Expression (RLE) method implemented in the DESeq2 R package (version 1.30.1)
Assembly: GRCh38
Supplementary files format and content: Matrix table with normalized counts for each gene of all individual cell

molecule: total RNA

organism: Homo sapiens

source_name: macrophage

extract_protocol:
Total RNA was extracted using Qiagen RNA purification kit  following manufacturer’s instructions.
QIAseq UPX 3' transcriptome kit (Qiagen, catalog# 333088) was used for library construction.

tag: tissue

value: macrophage

tag: phenotype


title: M0, rep1

description:
Library name: sample1
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_37


title: X1-16

city: Guangzhou

first: Ruixiang

last: Li

address: 56 Hengfu Road

country: China

institute: Guangzhou Institute of Dermatology

data_processing:
remove adapter
delete duplication reads
alignment
expression
different expression miRNA
Assembly: miRBase has 22.1
Supplementary files format and content: miRNA abundance table

source_name: plasma

extract_protocol:
the Micro RNA Isolation Kit was used to isolate miRNAs.
the miRNA Library Kit was used to miRNA library construction.

treatment_protocol: Not treated, sample collected from patient with Chronic Spontaneous Urticaria and health donor.

value: plasma

tag: genotype

value: Chronic Spontaneous Urticaria


title: X1-1


title: X1-12


title: X1-2


title: X1-8


title: X1-18


title: X1-24


title: M2a, rep1

description:
Library name: sample3
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_39


title: X1-29


title: X1-4


title: M1, rep2

description:
Library name: sample9
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_45


title: X1-22


title: X1-14


title: X1-20


title: X1-11


title: J2-35

value: health donor


title: J2-31


title: X1-5


title: J2-37


title: M2d, rep1

description:
Library name: sample5
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_41


title: J2-36


title: J2-38


title: M1, rep1

description:
Library name: sample2
MD0707_DKDL210006220-1a_HFTC5DSX2_cell_38


title: J2-34


title: J2-30


title: X1-19


title: J2-33


title: human_tonsil_EXP524

status: Public on Nov 24 2024

type: RNA

city: Seattle

first: Peiyao

middle: A

last: Zhao

state: WA

address: 615 Westlake Ave N

country: USA

institute: Allen Institute

scan_protocol: MERSCOPE was used to image target RNA positions and cell boundaries. Proprietary software was used to decode and return RNA positions along with raw images of cell nucleus and boundary stainings.

data_processing: Cell segmentation was performed on merFISH instrument using CellPose algorithm with cell-boundary stain 3 staining as input. Cell type inference and microenvironment zone delineation were performed using SPARROW (Zhao et al., 2024).

source_name: tonsil

extract_protocol: 5 um sections were cut from human tonsil and lymph node Formalin-Fixed Paraffin-Embedded (FFPE) blocks. Sections were floated in an RNAseq free, 41°C water bath and adhered to proprietary MERSCOPE slides. Sectioned tonsil and lymph node samples were processed in accordance with the Vizgen Formalin-Fixed Paraffin-Embedded Tissue Sample preparation protocol.

value: tonsil

tag: tissue type

value: FFPE block


title: J2-16


title: PDX004, Combi3

city: Shanghai

first: Ying

last: Cao

address: No.25/Ln 2200 Xie-Tu Road Xuhui District

institute: Shanghai Cancer Institute

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8)
Sequence quality was examined using the FastQC software(v0.11.7)
The trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt(v1.17)) were aligned to reference genome (GRCh37) using Hisat2 software(v2.1.0)
The transcript abundance for each sample was estimated with StringTie(v1.3.3), and the FPKM value for gene and transcript level was calculated with R package Ballgown(v2.10.0)
Assembly: GRCh37
Supplementary files format and content: the FPKM value of detected mRNA for each sample

source_name: liver cancer

extract_protocol:
RNA was harvested using Trizol reagent,and mRNA was purified by magnetic beads conjugated with oligo(dT).
RNA libraries for RNA-seq were prepared using KAPA Stranded RNA-Seq Library Prep Kit(illumina) following manufacturer's protocols.

value: liver cancer

tag: treatment


title: PDX004, Combi2


title: PDX004, HAR3

value: Harmine


title: X1-28


title: PDX004, HAR2


title: PDX004, Combi1


title: PDX004, IACS3


title: PDX004, CTL3


title: PDX004, IACS1


title: PDX004, IACS2


title: NPC, EBV_exo

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, alignment, barcode processing and gene expression matrices gerneration were performed by using Cell Ranger's pipelines (version 7.0.0; 10x Genomics).
We used Seurat R package (version 5.1.0) as the main tool for quality control, global-scaling normalization, dimensionality reduction, clustering and differential expression (DE) analysis. For quality control, cells with <200 feature counts or > 15% mitochondrial genes were excluded. Doublets were further filtered by using R package DoubletFinder (version 2.0.4)
Assembly: GRCh38
Supplementary files format and content: Matrix table with normalized counts for each gene in each cell

source_name: nasopharynx

extract_protocol:
Fresh tissue samples were immediately washed and cut into small pieces (< 2-mm3),followed by enzymatic digestion using a gentleMACS Dissociator (Miltenyi Biotec). The dissociated cells were neutralized by DMEM medium supplemented with 10% FBS and filtered through a 40 μm mesh to remove unwanted tissue and debris. Following RBC removal and wash steps (1100-1200 rpm, 6 minutes centrifugation), the processed cells were resuspended at the desired concentration. Additional debris removal (Miltenyi Biotec) was conducted if needed. Calcein-AM/PI double staining method was used to access the viability of collected cell populations. Cell suspensions with viability greater than 90% proceeded to library construction steps. Tissues and cells were kept on ice whenever possible during the entire procedure. For exosomal treatment experiments, processed cells were treated with 50μg exosomes for 2 hours under standard cell culture conditions (37°C and 5% CO2).
Library preparation was conducted using Chromium™ single cell 3’ v3.1 reagent kit (10x Genomics) following the manufacturer’s protocols.

value: nasopharynx

value: exosome treatment


title: PDX004, HAR1


title: Huh7 cells, OH

tag: cell line

tag: cell type

value: liver cancer cells

value: WT

value: Oligomycin+Harmine


title: PDX004, CTL2


title: NPC, Ctrl

description: 10x Genomics

value: control


title: CK_BS-seq_rep2

city: Nanjing

first: zhenyu

last: luo

state: Jiangsu

address: Xuanwu

department: College of Agricuture

institute: Nanjing Agricultural University

description: Methylation (5mc)

library_source: genomic

data_processing:
[RNA-seq]  The raw sequence data were processed using FastQC (v0.11.5) and fastp (v0.21.0) (--length_required=50) for removing low-quality reads. The filtered high-quality paired-end reads were aligned to the rice reference genome with MSU version 7.0 (http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/) using HISAT2 (v2.0.5) with default parameters.
[RNA-seq]  The cleaned reads were then aligned to the rice reference genome (MSU version 7.0) (http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/) using Bismark program (v0.23.0) (--bowtie2 -p 20 -N 0 -L 20), Reads with a mapping quality below twenty were excluded from further analyses using SAMtools (v1.9) (-q 20). FeatureCounts (v1.6.4) (-g gene_id) was used to obtain read counts for all annotated genes in the rice reference genome.
[RNA-seq]  To compare expression levels across samples and genes, the RNA-seq read density of each gene was normalized based on the gene length and the sequencing depth [i.e., transcripts per million (TPM)].
[BS-seq]  For data analyses, paired-end sequencing reads were first trimmed with fastp (v0.21.0) (--length_required=50) for removal of adapters and low-quality reads. The cleaned reads were then aligned to the rice reference genome (MSU version 7.0) (http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/) using Bismark program (v0.23.0) (--bowtie2 -p 20 -N 0 -L 20)
[BS-seq]  PCR duplicates were removed using the deduplicate_bismark implemented in the Bismark program.
[BS-seq]  The extent of the cytosine methylation was determined using the bismark_methylation_extractor implemented in the Bismark program.
Genome_build: Genome_build: http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/
Supplementary_files_format_and_content: [RNA-seq]  tab-delimited text files include TPM values  for each Sample.
Supplementary_files_format_and_content: [RNA-seq]  Matrix table with raw read counts for every gene and every sample
Supplementary_files_format_and_content: [RNA-seq]  bigwig
Supplementary_files_format_and_content: [BS-seq]  bigwig; gz for the extent of the cytosine methylation

molecule: genomic DNA

organism: Oryza sativa Japonica Group

source_name: Control (CK)

growth_protocol: For seedling growth, shelled rice seeds (Nipponbare, Oryza. sativa L. Japonica) were sterilized in 2% sodium hypochlorite containing 0.1% tween-20 for 15 min, followed by three times of washing using pure water.

extract_protocol:
For germination assay, rice seeds were soaked in pure water containing different concentrations of CDs for 48 h, then cultured in room temperature for another two days. The length of seminal root was statistically analyzed.
mRNA-seq libraries were prepared and sequenced on Illumina NovaSeq platform.
The BS-treated DNA was finally PCR-amplified and sequenced in paired-end 150 bp mode on Illumina NovaSeq 6000.

treatment_protocol: The sterilized rice seeds were seeded in 1/2 MS medium containing 0.56 mg/ml CDs. We used 1/2 MS as control. The seeds were grown in an artificial climate chest for three weeks.

tag: cultivar

value: Nipponbare

value: Leaves

value: ordinary hydroponic treatment

value: rice seedlings

tag: age

value: two-week-old rice seedlings


title: Huh7 cells, con


title: Huh7 cells, H


title: J2-20

value: plasma


title: CK_BS-seq_rep1

description: Methylation (5mc)


title: Huh7 cells, Combination-2

description: Huh7 combination-2


title: Huh7 cells, Combination-1

description: Huh7 combination-1


title: CD_BS-seq_rep2

description: Methylation (5mc)

source_name: Carbon dot (CD)

value: carbon dot nano-hydroponic treatment


title: Huh7 cells, Harmine-2

description: Huh7 Harmine-2


title: Huh7 cells, GABA bio rep 3

city: beijing

first: li

last: li

institute: pumc

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: Huh7 cells

growth_protocol: Huh7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TianGen kit (TianGen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with or without GABA for 24h

value: Huh7 cells


title: CD_BS-seq_rep1

description: Methylation (5mc)


title: Huh7 cells, Harmine-1

description: Huh7 Harmine-1


title: Huh7 cells, IACS-010759-2

description: Huh7 lACS-2


title: Huh7 cells, GABA bio rep 1


title: Huh7 cells, IACS-010759-1

description: Huh7 lACS-1


title: CK_RNA-seq_rep1


title: M15_KTSminus_rep2

city: Edinburgh

first: Silvia

last: Peluso

state: Midlothian

address: Western General Hospital, Crewe Road

country: United Kingdom

institute: MRC HGU at the University of Edinburgh

data_processing:
Library strategy: CUT&RUN
Quality of reads was verified using FASTQC 0.11.8 analysis
150bp paired-end Illumina reads in fastq format were mapped with bowtie2 2.2.6 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700"  to UCSC mm9.
Duplicates were removed  from the SAM files with picard 2.5.0 MarkDuplicates command. SAM files were converted to BAM files sorted and indexed using samtools 1.3 view, sort and index commands respectively.
Bedgraph files were generated by the BEDTools/2.23.0 genomecov command with options " -bg " and for visualisation (Supplementary file .bw ) bedgraph files were converted to .bw with ucsc v326 bedGraphToBigWig command.
enriched regions from bedgraph files were obtained using SEACR 1.3 with the options -norm -stringent (Supplementary file .bed ). As a control for the analysis IgG bedgraph has been used. For the final analysis, the peak file for each biological replicate has been merged using BEDOPS 2.4.26 -merge command.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig (.bw) files were generated usingwith ucsc v326 bedGraphToBigWig command.
Supplementary_files_format_and_content: peak text files (.bed files were generated with SEACR 1.3)

organism: Mus musculus

source_name: mesonephric cells

growth_protocol: M15 cells are mouse mesonephric cells that are maintained in DMEM with Sodium Pyruvate medium, supplemented with the 10% FBS and cultured in 5% CO2 and 37°C culture conditions.

extract_protocol:
CUT&RUN was performed Mouse M15 and M15 KTS minus cells. Cells were gently washed twice in room temperature Wash buffer [20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and a Roche complete EDTA-free tablet (Sigma-Aldrich) per 50 ml], with 3 min centrifugation at 600 xg, mixed with activated Concanavalin A-coated magnetic beads (Bangs Laboratories) and rotated 5-10 min. Beads were captured by placing on a magnet stand, decanted and resuspended in Antibody buffer [2 mM EDTA and antibody at 1:100 in Dig-wash (Wash buffer supplemented with 0.05% digitonin (Calbiochem)]. Antibodies used were Anti-Wilms Tumor Protein antibody (Abcam, ab89901) and IgG (IgG (Bethyl, A60-111A guinea pig anti-rabbit). After overnight binding at 4 oC with rotation, beads were captured and washed once or twice in Dig-wash and incubated 1 hr at 4 oC and washed once in Dig-wash. Beads were resuspended in Protein A-MNase (kindly provided by Steven Henikoff lab, 360 µg/ml) 1:500 in Dig-wash, incubated 1 hr at 4 oC, washed twice in Dig-wash and resuspended in 100 µL Dig-wash. Tubes were placed 0 oC, mixed with 2 µL 100 mM CaCl2, incubated at 0 oC for 30 min, and reactions were stopped by addition of 100 µL 340 mM NaCl, 20 mM EDTA pH8, 4 mM EGTA, 0.05% digitonin, 50 µg/ml glycogen and 200 pg mono-nucleosomal S. cerevisiae (spike-in) DNA. Samples were incubated 10 min at 37 oC and centrifuged 5 min 16,000 xg at 4 oC and the supernatant was treated with 25 µg/ml RNAse A (Thermo) 10 min at 37 oC. After phenol-chloroform-isoamyl alcohol and chloroform extraction, DNA was precipitated by addition of 2.5 volumes 100% ethanol, chilled on ice, centrifuged 10 min at 4 oC at 16,000 xg and the pellets were rinsed in 100% ethanol and air-dried. Pellets were resuspended in 1 mM Tris pH8 0.1 mM EDTA and used for standard Illumina library preparation.
Libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S), according to the manufacturer's instructions. After adapter ligation, DNA was PCR amplified with Illumina primers for 14 cycles. The libraries were sequenced on Illumina sequencing PE150-Xten.

value: Mouse mesonephric epithelium, polyoma virus large T transformed

tag: chip antibody

value: WT1(Abcam, ab89901)

value: KTS-


title: PDX004, CTL1

value: liver cancer


title: Huh7 cells, O

value: Oligomycin


title: M15_KTSminus_rep1

value: KTS -


title: CD_RNA-seq_rep2


title: Huh7 cells, Control bio rep 3


title: Huh7 cells, Control-1

description: Huh7 control-1

value: liver cancer cells

value: WT


title: CD_RNA-seq_rep1


title: M15_rep2


title: Huh7 cells, Control-2

description: Huh7 control-2


title: Huh7 cells, Control bio rep 2


title: M15_rep1


title: Huh7 cells, Control bio rep 1


title: Huh7 cells, GABA bio rep 2


title: CK_RNA-seq_rep2


title: M15_IgG

value: IgG (Bethyl, A60-111A)


title: Newly diagnosed multiple myeloma_704

status: Public on Nov 22 2024

city: Little Rock

first: Yan

last: Cheng

state: Arkansas

address: 4301 W. Markham St.

department: Internal Medicine

institute: University of Arkansas for Medical Sciences

description: Bone marrow biopsy

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

source_name: Human bone marrow biopsy

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

growth_protocol: Bone marrow biopsies were harvested from the patient's iliac crest.

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

treatment_protocol: Bone marrow biopsies were used directly for RNA extraction.

value: Newly diagnosed multiple myeloma


title: Newly diagnosed multiple myeloma_702

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_700

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_697

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_695

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_696

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_699

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_703

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_698

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_692

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_690

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_691

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_694

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_689

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_688

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_685

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_693

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_684

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_686

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_701

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_681

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_682

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_679

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_677

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_675

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_676

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_674

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_683

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_678

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_687

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_671

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_659

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_664

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_663

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_667

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_656

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_658

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_670

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_666

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_672

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_669

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_657

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_673

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_665

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_668

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_655

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_652

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_662

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_649

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_661

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_653

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_650

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_651

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_654

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_660

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_647

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_648

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_644

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_639

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_645

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_634

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_632

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_635

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_636

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_628

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_643

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_633

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_646

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_629

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_630

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_631

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_642

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_638

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_627

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_640

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_637

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_623

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_625

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_619

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_620

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_617

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_621

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_618

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_626

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_622

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_624

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_615

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_616

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_614

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_611

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_607

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_609

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_613

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_610

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_612

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_600

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_602

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_606

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_598

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_608

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_590

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_588

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_596

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_595

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_599

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_641

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_605

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_601

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_603

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_597

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_593

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_594

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_589

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_592

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_591

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_585

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_583

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_584

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_582

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_581

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_604

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_579

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_576

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_577

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_569

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_575

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_562

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_571

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_570

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_573

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_566

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_565

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_578

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_561

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_574

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_560

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_559

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_563

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_572

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_567

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_564

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_580

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_568

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_557

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_556

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_554

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_558

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_555

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_553

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_548

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_535

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_544

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_542

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_552

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_540

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_551

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_546

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_533

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_532

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_547

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_541

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_539

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_531

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_536

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_537

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_545

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_538

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_549

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_534

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_587

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_530

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_543

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_528

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_526

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_529

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_550

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_527

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_524

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_525

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_523

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_586

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_520

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_511

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_519

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_515

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_512

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_514

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_522

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_513

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_507

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_510

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_504

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_499

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_501

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_516

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_517

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_503

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_497

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_498

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_509

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_505

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_521

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_496

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_508

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_500

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_502

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_506

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_494

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_491

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_495

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_492

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_493

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_490

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_486

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_484

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_488

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_489

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_485

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_483

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_476

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_472

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_475

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_478

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_473

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_474

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_479

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_477

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_469

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_480

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_470

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_482

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_465

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_453

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_459

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_456

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_455

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_468

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_454

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_464

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_458

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_467

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_457

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_460

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_471

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_461

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_463

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_462

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_446

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_450

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_441

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_445

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_448

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_451

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_443

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_447

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_444

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_449

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_440

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_452

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_435

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_438

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_442

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_428

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_432

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_439

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_436

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_433

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_429

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_430

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_425

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_431

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_437

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_434

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_426

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_427

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_424

description: Bone marrow biopsy


title: 75.11_IW1A12_8w

first: Kathryn

middle: R

last: Bowles

address: 49 Little France Crescent

institute: University of Edinburgh

data_processing:
Raw sequencing reads were passed through the ISOseq3 pipeline to detect full-length transcripts
Single consensus sequences were generated for each MAPT amplicon with a SMRT adapter on both ends of the molecule
SMRT adapter sequences were removed and MAPT-specific primer sequences were identified to orient isoforms
Isoforms were trimmed of poly(A) tails, and concatemers identified and removed.
Isoform consensus sequences were predicted using hierarchical alignment and iterative cluster merging to align imcomplete reads to longer sequences
Clustered isoform sequences were polished using the arrrow model and binned into groups, then aligned to hg38 with GMAP aligner
Assembly: hg38
Supplementary files format and content: csv fille of isoform counts per sample
Library strategy: Targeted MAPT ISO-seq

source_name: iPSC-neuron

growth_protocol: Neurons and astrocytes were differentiated as previously published (Bowles et al, 2019; TCW et al, 2017)

extract_protocol:
Total RNA was extracted from neuron and astrocyte cultures using the Qiagen Rneasy miniprep kit
MAPT RNA was isolated using the following primers: Forward 5’-ATG GAA GAT CAC GCT GGG AC-3’, Reverse 5’-GAG GCA GAC ACC TCG TCA G-3’ and submitted for single molecule real time (SMRT) sequencing on the RS II platform

treatment_protocol: No treatment

value: iPSC-neuron

value: WT/WT

value: 8 weeks


title: Newly diagnosed multiple myeloma_419

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_421

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_420

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_423

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_422

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_418

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_414

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_412

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_415

description: Bone marrow biopsy


title: 75.11_IH1A5_8w


title: Newly diagnosed multiple myeloma_408

description: Bone marrow biopsy


title: 75.11_IW1F3_8w


title: 75.11_IH1A8_8w


title: Newly diagnosed multiple myeloma_409

description: Bone marrow biopsy


title: 75.11_IW1A12_6w

value: 6 weeks


title: Newly diagnosed multiple myeloma_407

description: Bone marrow biopsy


title: 75.11_IH1A4_8w


title: 75.11_IW1G8_8w


title: Newly diagnosed multiple myeloma_417

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_404

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_487

description: Bone marrow biopsy


title: 75.11_IH1A4_6w


title: Newly diagnosed multiple myeloma_481

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_405

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_402

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_401

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_400

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_403

description: Bone marrow biopsy


title: 75.11_IW1G8_6w


title: 75.11_IW1F3_6w


title: 75.11_IH1A8_6w


title: Newly diagnosed multiple myeloma_410

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_406

description: Bone marrow biopsy


title: 75.11_IH1A4_4w

value: 4 weeks


title: 75.11_IW1G8_4w


title: Newly diagnosed multiple myeloma_399

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_397

description: Bone marrow biopsy


title: 75.11_IH1A5_4w


title: Newly diagnosed multiple myeloma_393

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_394

description: Bone marrow biopsy


title: 75.11_IW1F3_4w


title: Newly diagnosed multiple myeloma_392

description: Bone marrow biopsy


title: F13505_I1B10_4w


title: 75.11_IH1A5_6w


title: 75.11_IH1A8_4w


title: F13505_NDG11_6w


title: F13505_NDG11_4w


title: F13505_I1B10_6w


title: F13505_NDG11_8w


title: 75.11_IW1A12_4w


title: Newly diagnosed multiple myeloma_398

description: Bone marrow biopsy


title: GP1.1_WAC11_4w


title: Newly diagnosed multiple myeloma_389

description: Bone marrow biopsy


title: GP1.1_SW1B4_4w


title: Newly diagnosed multiple myeloma_390

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_387

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_395

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_384

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_386

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_383

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_391

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_396

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_388

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_382

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_385

description: Bone marrow biopsy


title: GP1.1_SW1D8_4w


title: GP1.1_SH1G8_4w


title: F13505_I1B10_8w


title: Newly diagnosed multiple myeloma_381

description: Bone marrow biopsy


title: F13505_S2A3_4w


title: F13505_NEA11_4w


title: GP1.1_WAC11_6w


title: GP1.1_SW1D8_6w


title: GP1.1_SW1B4_6w


title: Newly diagnosed multiple myeloma_378

description: Bone marrow biopsy


title: GP1.1_SH1G8_6w


title: Newly diagnosed multiple myeloma_376

description: Bone marrow biopsy


title: F13505_S2A3_6w


title: Newly diagnosed multiple myeloma_377

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_380

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_375

description: Bone marrow biopsy


title: GP1.1_WAC11_8w


title: GP1.1_SW1B4_8w


title: GP1.1_SW1D8_8w


title: F13505_S2A3_8w


title: GP1.1_SH1G8_8w


title: Newly diagnosed multiple myeloma_372

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_374

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_373

description: Bone marrow biopsy


title: GP1.1_WAC11_Astro

source_name: iPSC-astrocytes

value: iPSC-astrocytes


title: F13505_NEA11_8w


title: Newly diagnosed multiple myeloma_379

description: Bone marrow biopsy


title: GP1.1_SW1B4_Astro


title: GP1.1_SH1G8_Astro


title: 300.12_HAE11_Astro


title: F13505_NEA11_6w


title: GP1.1_SW1D8_Astro


title: Newly diagnosed multiple myeloma_369

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_370

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_371

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_367

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_365

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_363

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_364

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_368

description: Bone marrow biopsy


title: 300.12_NH1E7_Astro


title: Newly diagnosed multiple myeloma_366

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_361

description: Bone marrow biopsy


title: 300.12_HCB8_8w


title: 300.12_NW1C7_Astro


title: Newly diagnosed multiple myeloma_359

description: Bone marrow biopsy


title: 300.12_HBE10_8w


title: 300.12_NH1E7_8w


title: 300.12_HAE11_8w


title: 300.12_NW1C7_8w


title: 300.12-NW1B10_8w


title: 300.12_HBE10_Astro


title: 300.12_NWBB7_8w


title: 300.12-NW1B10_Astro


title: 300.12_HCB8_6w


title: 300.12_HAE11_6w


title: Newly diagnosed multiple myeloma_362

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_360

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_357

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_354

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_352

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_350

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_355

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_358

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_351

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_353

description: Bone marrow biopsy


title: 300.12_HBE10_6w


title: 300.12_NH1E7_6w


title: 300.12_NW1C7_6w


title: Newly diagnosed multiple myeloma_349

description: Bone marrow biopsy


title: 300.12_NWBB7_6w


title: Newly diagnosed multiple myeloma_348

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_347

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_346

description: Bone marrow biopsy


title: 300.12_NWBB7_Astro


title: 300.12-NW1B10_6w


title: 300.12_HCB8_4w


title: 300.12_HAE11_4w


title: Newly diagnosed multiple myeloma_345

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_344

description: Bone marrow biopsy


title: 300.12_HBE10_4w


title: Newly diagnosed multiple myeloma_343

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_340

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_342

description: Bone marrow biopsy


title: 300.12_NH1E7_4w


title: 300.12_NW1C7_4w


title: 300.12_NWBB7_4w


title: 300.12-NW1B10_4w


title: Newly diagnosed multiple myeloma_341

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_339

description: Bone marrow biopsy


title: r90w_1d

city: Saint Louis

first: Shiming

last: Chen

state: Missouri

address: 517 South Euclid Avenue

department: Department of Ophthalmology & Visual Sciences

institute: Washington University in St Louis

description: dimeric bound band

library_source: other

data_processing:
Reads with any mismatch in the Coop-seq library conserved regions were discarded prior to quantification.
The raw counts of individual sequence corresponding to dimeric, monomeric, and unbound band samples were normalized and used to calculate relative cooperativity index.
Assembly: Synthetic constructs
Supplementary files format and content: Text files with normalized read counts in dimeric, monomeric and unbound fractions.
Library strategy: Coop-seq (amplicon based sequencing)

molecule: other

organism: synthetic construct

source_name: Synthetic constructs

extract_protocol:
After EMSA, Coop-seq libraries from dimeric, monomeric and unbound bands were eluted from the excised Tris-glycine gel.
Sequencing adapters and primers were added to both ends of the Coop-seq library using two-step PCR.

value: Synthetic constructs


title: k88n_1d

description: dimeric bound band


title: k88n_2d

description: dimeric bound band


title: 90w_2d

description: dimeric bound band


title: Newly diagnosed multiple myeloma_338

description: Bone marrow biopsy


title: e80a_2d

description: dimeric bound band


title: Newly diagnosed multiple myeloma_334

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_335

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_336

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_333

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_337

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_332

description: Bone marrow biopsy


title: e80a_1d

description: dimeric bound band


title: Newly diagnosed multiple myeloma_329

description: Bone marrow biopsy


title: wt_2d

description: dimeric bound band


title: Newly diagnosed multiple myeloma_331

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_330

description: Bone marrow biopsy


title: wt_1d

description: dimeric bound band


title: Newly diagnosed multiple myeloma_328

description: Bone marrow biopsy


title: 22wk_human_fetal_epiglottis_ATAC

city: Los Angeles

first: J.

middle: Gage

last: Crump

state: CA

address: 1425 San Pablo Street, BCC 406

department: Eli and Edythe Broad CIRM Center for Stem Cell and Regenerative Medicine

institute: University of Southern California

description:
22wk_human_4lib-merged_countsPEAKS.txt
22wk_human_4lib-merged_cluster_info.txt

library_source: genomic single cell

data_processing:
Cellranger Arc v2.0.0 (10X Genomics) was used for alignment and peak calling to generate a peak-by-cell and gene-by-cell count matrix.
Cell Ranger ARC-output count matrices in H5 format of individual libraries were used to create Seurat objects by “CreateSeuratObject” and “CreateChromatinAssay” functions (EnsDb.Hsapiens.v86 used to create Granges containing annotations for the human genome). For simultaneous analysis of all 4 human tissue libraries (GSM8077331-GSM8077334 plus samples in this submission) , Cellranger aggr function was used to merge all four libraries and normalize read depth across all cells prior to generating a Seurat object. In both cases, quality control was performed by setting thresholds of accessible region counts “nCount_ATAC”, transcript counts “nCount_RNA” and ratio of mononucleosome to nucleosome-free region “nucleosome_signal” to remove outliers that may represent low quality cells or doublets. RNA data were normalized and the top 2000 most variable genes selected using “FindVariableFeatures” for scaling. Dimensional reduction was performed using “RunPCA” function with the number of principal components selected by ranking of components based on percent of variance explained by each. Data were then subjected to neighbor finding (“FindNeighbors”) and clustering (“FindClusters”, resolution=0.6 for outer ear 1 and nose merged, resolution=1.0 for all four libraries merged). The data were visualized through UMAP. Cell type identification was performed based on differentially expressed genes across clusters generated from snRNAseq data (full gene lists provided in publication). Peak calling was performed using “CallPeaks” Signac function, which uses the MACS21 algorithm. Peaks on nonstandard chromosomes and in genomic blacklist regions were removed using “keepStandardChromosomes” (pruning.mode=coarse) and “subsetByOverlaps” (using blacklist_hg38_unified). Counts in each peak remaining in the peak set were quantified for the merged multiome datasets using FeatureMatrix function and the resulting counts were added as a “Peaks” ChromatinAssay to the Seurat object. We used “FindAllMarkers” to detect genes with highly enriched expression and ATAC peaks with highly differential accessibility in each cluster generated from the above-described dimensionality reduction analysis of snRNAseq data.
Assembly: GRCh38
Supplementary files format and content: Two tab delimited files representing a sparse matrix containing normalized counts per feature for each cell barcode (one for RNA and one for Peaks called by Signac CallPeaks) and one tab delimited file containing clustering information and other metadatafor each cell barcode obtained from the Seurat processing pipeline described before. Human outer ear 1 and 2, epiglottis, and nose cells are from separate libraries that have been merged and can be identified by barcode sufffixes -1, -3, -4, and -2 respectively.

source_name: Sample 2-Dissected_epiglottis

growth_protocol: This study complies with all relevant ethical regulations and was approved by the University of Southern California Institutional Review Board (IRB) exempt protocol #HS-23-00499. Human fetal tissue for outer ear and nose samples was obtained from the University of California Los Angeles (UCLA) Center for AIDS Research (CFAR) Gene and Cellular Therapy Core from IRB-approved de-identified and consented electively aborted fetuses. Use of human tissues was IRB exempt by the UCLA Office of the Human Research Protection Program (IRB #15-000959). Human fetal tissue for the epiglottis and second outer ear samples was obtained from the Developmental Origins of Health and Disease Biorepository at the Icahn School of Medicine at Mount Sinai (IRB#STUDY-22-00065). For samples collected at Mount Sinai, consent for tissue donation was obtained after the patient had already made the decision for pregnancy termination and was obtained by a different clinical research coordinator than the physician performing the procedure. All tissues were de-identified, and the only clinical information collected was gestational age and the presence of any maternal or fetal diagnoses.

extract_protocol:
Human fetal outer ear replicate 2 and epiglottis tissue were dissected from a second 22-week gestation fetus. Using scissors and a scalpel, the tissue was finely minced and dissociated by mechanical and enzymatic digestion: the tissue was incubated for 4 h with gentle agitation at 37oC in conical flasks containing 1 mg/mL collagenase II (Worthington), 1 mg/mL dispase (Gibco), 1:1000 gentamicin (Teknova), 1:500 primocin (Invivogen), 1% penicillin/streptomycin/amphotericin B (P/S/A; Corning), and 10% fetal bovine serum (FBS; Corning) in DMEM/F12 (Corning). The mixture was pipetted in the sterile hood every 30 min. The resulting cell suspension was passed through a 70-micron filter (Fisher) and washed in 2% FBS/PBS solution to stop enzymatic digestion. For red blood cell lysis, the cells were incubated in a solution consisting of 1 mL 2% FBS/PBS and 9 mL ammonium chloride solution (STEMCELL Technologies; cat. no. 07800) for 10 minutes on ice and washed in 2% FBS/PBS. We then resuspended the remaining cells in 10% dimethyl sulfoxide (DMSO) and 20% FBS in DMEM/F12 medium and cryopreserved at -80oC for one month. For human fetal outer ear replicate 1 and nose tissues, we additionally performed negative selection using the magnetic activated cell sorting system (Miltenyi Biotec) using a primary anti-CD45 monoclonal antibody, PE (eBioscience, 12-9459-42), and an anti-PE secondary antibody (Miltenyi, 130-048-801) to remove CD45+ white blood cells as per manufacturer’s instructions, just prior to cryopreservation. Cells were thawed within a month of preservation for fluorescence activated cell sorting (BD SORP FACSAria IIu) to isolate live cells that exclude nuclear stain DAPI (Southern Biotech; cat. no. 0100-20) into 0.04% bovine serum albumin (BSA) in phosphate buffered saline (PBS) at 4oC. FACS-sorted cells were pelleted for 15 min (300 g at 4oC) and incubated in lysis buffer for 6 min on ice. Nuclei were isolated per manufacturer’s instructions (10X Genomics, protocol CG000038, low cell input protocol), washed in Wash buffer and resuspended in Nuclei buffer. Nuclei count was confirmed using an automated cell counter (Countess II Cell Counter; Life Technologies) and nuclear integrity checked with a fluorescence confocal microscope with DAPI staining before use in library construction.
We generated separate barcoded single-nuclei libraries with simultaneous profiling of gene expression and chromatin accessibility using 10X Genomics Chromium Single Nuclei Multiome Reagent Kit per manufacturer’s instructions.
snRNAseq + snATACseq

value: Sample 2-Dissected_epiglottis

value: 22 weeks post-gestation


title: 22wk_human_fetal_outer_ear2_ATAC

source_name: Sample 2-Dissected_outer_ear2

value: Sample 2-Dissected_outer_ear2


title: Newly diagnosed multiple myeloma_327

description: Bone marrow biopsy


title: 22wk_human_fetal_epiglottis_RNA

description:
22wk_human_4lib-merged_countsRNA.txt
22wk_human_4lib-merged_cluster_info.txt

molecule: nuclear RNA


title: 22wk_human_fetal_outer_ear2_RNA


title: Lpolyphemus_book_gills_RNA

data_processing:
Cellranger Arc v2.0.0 (10X Genomics) was used for alignment and peak calling to generate a peak-by-cell and gene-by-cell count matrix.
Cell Ranger ARC-output count matrices in H5 format of individual libraries were used to create Seurat objects by “CreateSeuratObject” and “CreateChromatinAssay” functions. For the latter, GCF_000517525.1_Limulus_polyphemus-2.1.2_genomic.gtf from NCBI RefSeq was used to create a custom annotation for the horseshoe crab genome. Quality control was performed by setting the thresholds of accessible region counts (nCount_ATAC) < 15000, transcript counts (nCount_RNA) < 2500 and ratio of mononucleosome to nucleosome-free region (nucleosome_signal) < 1.5. Factor level names needed to be altered in the Seurat object to remove the “_” in genome contig names. Owing to high levels of ambient RNA and ATAC fragments in the dataset, we used DecontX2 and celda (CELLular Latent Dirichilet Allocation; 1.16.1)3 packages on snRNAseq and snATACseq counts to estimate and remove contamination in individual cells and added the decontaminated counts back to our Seurat object as “decontXRNA” assay and “decontXATAC” ChromatinAssay respectively. decontXRNA data were normalized and the top 2000 most variable genes selected using “FindVariableFeatures” for scaling. Dimensional reduction to 50 principal components was performed using “RunPCA”. Data were then subjected to neighbor finding (“FindNeighbors”, k=30) and clustering (FindClusters, resolution=0.6). Peak calling was performed on the decontXATAC ChromatinAssay using “CallPeaks”, which uses the MACS2 algorithm. Counts in each peak remaining in the peak set were quantified for the multiome dataset using “FeatureMatrix” and the resulting counts were added as a “Peaks” ChromatinAssay to the Seurat object.
Assembly: GCF_000517525.1
Supplementary files format and content: Two tab delimited files representing a sparse matrix containing normalized counts per feature for each cell barcode (one for RNA, one for Peaks called by Signac CallPeaks) and one tab delimited file containing clustering information and other metadatafor each cell barcode obtained from the Seurat processing pipeline described before.

organism: Limulus polyphemus

growth_protocol: We procured a live adult male wild-caught specimen (8 inches wide and 16 inches long) of Limulus polyphemus maintained at the Marine Biological Laboratory. The specimen was shipped overnight in moist vegetation.

extract_protocol:
The specimen wwas euthanized by submerging in filtered seawater prepared at a salinity of 1.025 using Instant Ocean salt containing 1g/L Tricaine-S (Syndel) and buffered with 4.5 mM sodium carbonate at 25oC until the gills stopped moving. From the adult male horseshoe crab, the opisthoma was separated and book gills dissected out using shears. The exoskeleton was peeled off to reveal the cartilage tissue. The tissue was cut using scissors into 1 cm X 1 cm pieces. Each piece was flash frozen in isopentane cooled in a liquid nitrogen bath and immediately transferred into a cryovial. The flash frozen tissue was stored at -80oC for two weeks. Subsequently, 200 mg of tissue was weighed out and finely minced using ice-cold scissors. The minced tissue was transferred into ice-cold homogenization buffer (250 mM sucrose, 10 mM Tris pH 8.0, 25 mM KCl, 5 mM MgCl2, 0.1% Triton X-100, 0.5% RNAse inhibitor (Sigma; cat. no. 3335399001), 1X protease inhibitor (Roche; cat. no. 5056489001), and 0.1 mM dithiothreitol (DTT; Sigma cat. no. 646563)). Nuclei were released through mechanical digestion: a chilled dounce was used to release nuclei by 10 strokes of the loose pestle and 7 strokes of the tight pestle from the minced tissue. The dounced nuclei were strained, filtered, and washed by centrifugation at 1000 g for 10 min before fluorescence-activated nuclei sorting.
We generated  barcoded single-nuclei libraries with simultaneous profiling of gene expression and chromatin accessibility using 10X Genomics Chromium Single Nuclei Multiome Reagent Kit per manufacturer’s instructions.

value: Adult; 8 inches across


title: N2-S-MB

city: Hang Zhou

first: Zeli

last: Zhang

address: ZhuanTang Jie Dao Shi long Shan Lu Nr. 17

institute: Westlake University

description:
Library name: N2-S-MB
10X Gemomics

data_processing:
The raw fastq files were processed using the 10X Genomics CellRanger (7.1.0) pipeline. The cell quality control, clustering, and marker gene analysis were performed by using Seurat (v4.3.0).
Assembly: hg18 and IMGT
Supplementary files format and content: Tab-separeted values files, matrix files, and VDJ assemble file

source_name: PBMC

extract_protocol:
B cells were isolated from previously frozen PBMCs by immunomagnetic negative selection according to the manufacturer’s protocol (EasySep Human B Cell Enrichment Kit, STEMCELL). The purified B cells were first stained with 1200 ng N1-M5 or N2-M5 probes (600 ng per color) for 30 min at 4 ˚C, then stained with CD20, CD19, CD27, IgD, and L/D blue. The live NA-specific MBCs were sorted into the FCS buffer and directly loaded on a 10X Chromium A chip.
Single-cell lysis and cDNA synthesis were performed by using the 5’ library and gel bead kit according to the provided protocol. The first-strand cDNA of 10X Barcoded was purified by silane magnetic beads, and sufficient mass was obtained by PCR amplification. The PCR products were quantified and qualified by Qubit3.0 Fluorometer (Invitrogen) and Agilent 2100 Bioanalyzer (Agilent). Then, the transcriptome and VDJ library preparation is performed by using 10X Chromium Single Cell VDJ Kits. All libraries were quantified by using Qsep100 (Bioptic) and Qubit3.0 Fluorometer (Invitrogen). Then libraries with different indices were multiplexed and loaded on an Illumina NovaSeq

value: PBMC

value: B cell


title: HDM-BCR

first: Chunan

last: Sun

address: 101 Longmian Avenue, Jiangning District

institute: nanjing medical university

data_processing:
BCR clonotype assignment was performed using the Cell Ranger (v4.0.0) vdj pipeline with GRCh38 as the reference genome. This pipeline generated a BCR diversity metric, which included clonotype frequency and barcode information. For analysis, only cells with one productive immunoglobulin heavy (IGH) chain and one productive immunoglobulin kappa (IGK)/ immunoglobulin lambda (IGL) chain were retained. Each unique combination of an IGH chain and an IGK/IGL chain was defined as a clonotype. Cells harboring a clonotype present in at least two cells were considered clonal and the number of cells harboring a specific clonotype indicated the degree of clonality for that clonotype
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scBCR-seq

molecule: polyA RNA

source_name: B cell

extract_protocol:
PBMC were isolated from clinical samples and resuspended with 40 mL of PBS for a total of 1 × 108 cells. These cells were then stained using anti-CD19-PE-Cy7, anti-IgG-BV421 and sorted into a 15 ml centrifuge tube by flow cytometry.
The single cell suspension (1 × 105 cells/ml) was loaded into the microfluidic devices. Subsequently, the scBCR-seq libraries were constructed according to the protocol of GEXSCOPE Single Cell Immuno-TCR/BCR Kit. Briefly, the magnetic beads with molecular labels captured the poly(A) tail and BCR region on the mRNA to label the cells and mRNA after the cells are lysed. Afterwards, the magnetic beads in the chip were collected, and then mRNAs captured by the magnetic beads were reverse transcribed into cDNA and amplified. The cDNA was enriched for the BCR, and the enriched products were amplified by PCR to construct a sequencing library suitable for the Illumina sequencing platform. Finally, each library was sequenced on Illumina Nova seq 6000 with 150 bp paired-end reads.


title: Newly diagnosed multiple myeloma_324

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_323

description: Bone marrow biopsy


title: Healthy 3

city: yichang

first: wenfei

last: zheng

address: jiefang road，NO.2

institute: Yichang Central People's Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKMvalues for each Sample

source_name: placenta

extract_protocol:
RNA was harvested  using TRIzol-based RNA extraction
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization.

value: placenta

value: Human Villous Trophoblasts

value: Villous Trophoblasts

value: NO


title: Newly diagnosed multiple myeloma_325

description: Bone marrow biopsy

value: Newly diagnosed multiple myeloma


title: Newly diagnosed multiple myeloma_320

description: Bone marrow biopsy


title: Healthy 2


title: Newly diagnosed multiple myeloma_322

description: Bone marrow biopsy


title: Healthy 1


title: Newly diagnosed multiple myeloma_326

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_321

description: Bone marrow biopsy


title: Healthy 4


title: Newly diagnosed multiple myeloma_319

description: Bone marrow biopsy


title: ICP 5

value: ursodeoxycholic acid


title: ICP 4


title: Newly diagnosed multiple myeloma_316

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_317

description: Bone marrow biopsy


title: ICP 3


title: Newly diagnosed multiple myeloma_318

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_311

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_315

description: Bone marrow biopsy


title: ICP 1


title: Newly diagnosed multiple myeloma_314

description: Bone marrow biopsy


title: Healthy 5


title: Newly diagnosed multiple myeloma_308

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_309

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_310

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_307

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_306

description: Bone marrow biopsy


title: B7 Smoke ChIP ac130

city: St Louis

first: Tiandao

state: MO

address: 4444 Forest Park Ave

institute: Washington University

data_processing:
The size and quality of the library was evaluated using the Agilent BioAnalyzer (Agilent Technologies, Inc., Santa Clara, CA), and the library was quantitated with the Kapa Library Quantification Kit.
Each enriched DNA library was then sequenced on an Illumina NextSeq 500 sequencer to generate 40-50 million 75-base paired-end reads (Illumina, Inc., San Diego, CA).
The raw sequence data were aligned using BowTie 2 [1], and the binding sites were identified using the MACS peak-finding software
Raw fastq files were aligned against human genome hg38 assembly using Burrows-Wheeler Alignment tool and then processed using methylQA to generate bed and bigwig files.
The MACS2 peak caller was used to compare the ChIP-Seq signal to a corresponding input control to identify narrow regions of enrichment (peaks) using default parameters.
Assembly: ChIP-Seq signals and peak locations were further visualized using UCSC Genome Browser.
Supplementary files format and content: The top 500-1000 ChIP-Seq peaks were assigned to the nearest genes using the annotatePeaks function from HOMER2, motif binding sites were determined using HOMer2, and GO and pathway enrichment analyses were performed by EnrichR.
Supplementary files format and content: Assembly: hg38, mm10

source_name: Bladder

growth_protocol: UMUC3 cells were grown in EMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 degree C

extract_protocol:
The cells were harvested, lysed and ysates were immunoprecipitation with acK130-H2a antibodies (2 ug) for 3 hours. The magnetic beads were used to capture immunoprecipitates, washed and bound chromatin was eluted, followed by protease treatment.
Ten nanograms of immunoprecipitated DNA was fragmented to 300 base pairs using a Covaris M220 Focused-ultrasonicator (Covaris, Inc., Woburn, MA) and then used to generate sequencing libraries using the Kapa Hyper Prep Kit (Roche Sequencing Solutions Inc., Pleasanton, CA).

treatment_protocol: Cells were treated with cigaretter smoke media (10%) for 3 days

value: Bladder

value: Bladder cancer

value: Cigarette Smoke


title: B6 Air ChiP ac130

value: Air


title: ICP 2


title: Pt 41, e14, incidental STIC, stroma, LSP19413_Scan1 | 004 | Full ROI

city: Boston

first: Clemens

last: Hug

state: MA

address: 200 Longwood Avenue

department: Harvard Program in Therapeutic Science

institute: Harvard Medical School

description: FFPE

data_processing:
Raw sequencing data were processed to generate FASTQ files
Process FASTQ files through GeoMx NGS pipeline and convert to DCC files
Retreive DCC files
Transfer DCC files to GeoMx DSP for QC and normalisation by DSP software
Then we have Q3 normalised count matrix file (available with the publication as Supplementary File)
demultiplexed fastqs according to nanostring pipeline
Supplementary files format and content: DCC files are digital count files which have been processed from FASTQ files by nanostring pipeline
Library strategy: Spatial Transcriptomics

source_name: high grade serous ovarian carcinoma

extract_protocol:
5uM thickness section was processed according to GeoMx protocol provided by Nanostring
the libraries were prepared according to manufacturer's protocol (Nanostring)

value: high grade serous ovarian carcinoma

value: stroma

tag: lesion type

value: incidental STIC

tag: brca status

value: WT

tag: primary cancer_stage

value: incidental

tag: patient id

value: Pt 41

tag: batch


title: Pt 41, e14, incidental FT, epithelial, LSP19413_Scan1 | 006 | Full ROI

description: FFPE

value: epithelial

value: incidental FT


title: Pt 43, e14, incidental FT, epithelial, LSP19421_Scan1 | 017 | Full ROI

description: FFPE

value: Pt 43


title: Pt 41, e14, incidental STIC, epithelial, LSP19413_Scan1 | 002 | Full ROI

description: FFPE


title: Pt 41, e14, incidental STIC, epithelial, LSP19413_Scan1 | 001 | Full ROI

description: FFPE


title: Pt 41, e14, incidental STIC, stroma, LSP19413_Scan1 | 005 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_302

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_305

description: Bone marrow biopsy


title: Pt 41, e14, incidental Fimbriae, stroma, LSP19413_Scan1 | 009 | Full ROI

description: FFPE

value: incidental Fimbriae


title: Pt 41, e14, incidental STIC, epithelial, LSP19413_Scan1 | 003 | Full ROI

description: FFPE


title: Pt 41, e14, incidental Fimbriae, stroma, LSP19413_Scan1 | 010 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_297

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_299

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_304

description: Bone marrow biopsy


title: Pt 41, e14, incidental Fimbriae, epithelial, LSP19413_Scan1 | 008 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_300

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_303

description: Bone marrow biopsy


title: Pt 41, e14, incidental Fimbriae, epithelial, LSP19413_Scan1 | 011 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_294

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_298

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_295

description: Bone marrow biopsy


title: Pt 41, e14, incidental FT, stroma, LSP19413_Scan1 | 007 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_292

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_293

description: Bone marrow biopsy


title: Pt 41, e14, incidental Fimbriae, stroma, LSP19413_Scan1 | 012 | Full ROI

description: FFPE


title: Pt 41, e14, incidental FT, epithelial, LSP19413_Scan1 | 013 | Full ROI

description: FFPE


title: Pt 41, e14, incidental FT, stroma, LSP19413_Scan1 | 014 | Full ROI

description: FFPE


title: Input


title: Pt 33, e14, incidental p53sig, epithelial, LSP19409_Scan1 | 001 | Full ROI

description: FFPE

value: incidental p53sig

value: Mut

value: Pt 33


title: Pt 33, e14, incidental p53sig, epithelial, LSP19409_Scan1 | 002 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_296

description: Bone marrow biopsy

value: Newly diagnosed multiple myeloma


title: Newly diagnosed multiple myeloma_290

description: Bone marrow biopsy


title: Pt 33, e14, incidental p53sig, stroma, LSP19409_Scan1 | 004 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_291

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_289

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_288

description: Bone marrow biopsy


title: Pt 33, e14, incidental p53sig, epithelial, LSP19409_Scan1 | 008 | Full ROI

description: FFPE


title: Pt 33, e14, incidental p53sig, stroma, LSP19409_Scan1 | 009 | Full ROI

description: FFPE


title: Pt 33, e14, incidental FT, epithelial, LSP19409_Scan1 | 010 | Full ROI

description: FFPE


title: Pt 31, e14, incidental p53sig, epithelial, LSP19407_Scan1 | 001 | Full ROI

description: FFPE

value: Pt 31


title: Newly diagnosed multiple myeloma_285

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_283

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_286

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_282

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_280

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_279

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_287

description: Bone marrow biopsy


title: Pt 33, e14, incidental p53sig, epithelial, LSP19409_Scan1 | 007 | Full ROI

description: FFPE


title: Pt 33, e14, incidental FT, epithelial, LSP19409_Scan1 | 012 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_278

description: Bone marrow biopsy


title: Pt 33, e14, incidental p53sig, epithelial, LSP19409_Scan1 | 005 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_284

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_281

description: Bone marrow biopsy


title: Pt 33, e14, incidental FT, stroma, LSP19409_Scan1 | 013 | Full ROI

description: FFPE


title: Pt 31, e14, incidental FT, epithelial, LSP19407_Scan1 | 003 | Full ROI

description: FFPE


title: Pt 33, e14, incidental p53sig, epithelial, LSP19409_Scan1 | 003 | Full ROI

description: FFPE


title: Pt 33, e14, incidental FT, stroma, LSP19409_Scan1 | 011 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_275

description: Bone marrow biopsy


title: Pt 31, e14, incidental FT, stroma, LSP19407_Scan1 | 006 | Full ROI

description: FFPE


title: Pt 31, e14, incidental p53sig, stroma, LSP19407_Scan1 | 002 | Full ROI

description: FFPE


title: Pt 31, e14, incidental FT, epithelial, LSP19407_Scan1 | 005 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_276

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_271

description: Bone marrow biopsy


title: Pt 31, e14, incidental p53sig, stroma, LSP19407_Scan1 | 010 | Full ROI

description: FFPE


title: Pt 42, e14, Inv Cancer, stroma, LSP19417_Scan1 | 002 | Full ROI

description: FFPE

value: Inv Cancer

value: IA

value: Pt 42


title: Pt 31, e14, incidental p53sig, epithelial, LSP19407_Scan1 | 009 | Full ROI

description: FFPE

value: high grade serous ovarian carcinoma


title: Newly diagnosed multiple myeloma_272

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_274

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_270

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_273

description: Bone marrow biopsy


title: Pt 31, e14, incidental FT, epithelial, LSP19407_Scan1 | 007 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_277

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_269

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_266

description: Bone marrow biopsy


title: Pt 31, e14, incidental FT, stroma, LSP19407_Scan1 | 008 | Full ROI

description: FFPE

value: stroma


title: Newly diagnosed multiple myeloma_267

description: Bone marrow biopsy


title: Pt 42, e14, Inv Cancer, stroma, LSP19417_Scan1 | 003 | Full ROI

description: FFPE

value: WT


title: Pt 42, e14, Inv Cancer, epithelial, LSP19417_Scan1 | 004 | Full ROI

description: FFPE


title: Pt 42, e14, Inv Cancer, epithelial, LSP19417_Scan1 | 005 | Full ROI

description: FFPE


title: Pt 42, e14, Inv Cancer, epithelial, LSP19417_Scan1 | 007 | Full ROI

description: FFPE


title: Pt 42, e14, Inv Cancer, epithelial, LSP19417_Scan1 | 006 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_263

description: Bone marrow biopsy


title: Pt 42, e14, Inv Cancer, epithelial, LSP19417_Scan1 | 001 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_265

description: Bone marrow biopsy


title: Pt 42, e14, Inv Cancer, stroma, LSP19417_Scan1 | 008 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_262

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_301

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_261

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_260

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_268

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_259

description: Bone marrow biopsy


title: Pt 42, e14, Inv Cancer, stroma, LSP19417_Scan1 | 009 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_264

description: Bone marrow biopsy


title: Pt 42, e14, Fimbriae, epithelial, LSP19417_Scan1 | 010 | Full ROI

description: FFPE

value: Fimbriae


title: Pt 42, e14, Fimbriae, epithelial, LSP19417_Scan1 | 011 | Full ROI

description: FFPE


title: Pt 42, e14, Fimbriae, stroma, LSP19417_Scan1 | 012 | Full ROI

description: FFPE


title: Pt 42, e14, FT, epithelial, LSP19417_Scan1 | 013 | Full ROI

description: FFPE

value: FT


title: Newly diagnosed multiple myeloma_258

description: Bone marrow biopsy


title: Pt 43, e14, incidental STIC, epithelial, LSP19421_Scan1 | 002 | Full ROI

description: FFPE

value: epithelial

value: incidental STIC

value: incidental


title: Pt 43, e14, incidental STIC, epithelial, LSP19421_Scan1 | 001 | Full ROI

description: FFPE

value: Pt 43


title: Pt 43, e14, incidental STIC, stroma, LSP19421_Scan1 | 003 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_257

description: Bone marrow biopsy


title: Pt 43, e14, incidental STIC, stroma, LSP19421_Scan1 | 007 | Full ROI

description: FFPE


title: Pt 43, e14, incidental STIC, epithelial, LSP19421_Scan1 | 006 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_255

description: Bone marrow biopsy


title: Pt 43, e14, incidental STIC, stroma, LSP19421_Scan1 | 005 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_254

description: Bone marrow biopsy


title: Pt 43, e14, incidental STIC, epithelial, LSP19421_Scan1 | 008 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_256

description: Bone marrow biopsy


title: Pt 43, e14, incidental STIC, epithelial, LSP19421_Scan1 | 009 | Full ROI

description: FFPE


title: Pt 43, e14, incidental STIC, stroma, LSP19421_Scan1 | 010 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_251

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_252

description: Bone marrow biopsy


title: Pt 43, e14, incidental STIC, epithelial, LSP19421_Scan1 | 011 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_253

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_250

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_248

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_246

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_247

description: Bone marrow biopsy


title: Pt 43, e14, incidental STIC, epithelial, LSP19421_Scan1 | 012 | Full ROI

description: FFPE


title: Pt 43, e14, incidental STIC, epithelial, LSP19421_Scan1 | 004 | Full ROI

description: FFPE


title: Pt 43, e14, incidental STIC, stroma, LSP19421_Scan1 | 014 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_245

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_243

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_244

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_242

description: Bone marrow biopsy


title: Pt 43, e14, incidental Fimbriae, stroma, LSP19421_Scan1 | 016 | Full ROI

description: FFPE

value: incidental Fimbriae


title: Newly diagnosed multiple myeloma_241

description: Bone marrow biopsy


title: Pt 43, e14, incidental FT, epithelial, LSP19421_Scan1 | 019 | Full ROI

description: FFPE

value: incidental FT


title: Pt 34, e14, incidental p53sig, epithelial, LSP19411_Scan1 | 003 | Full ROI

description: FFPE

value: incidental p53sig

value: Mut

value: Pt 34


title: Pt 34, e14, incidental p53sig, epithelial, LSP19411_Scan1 | 005 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_239

description: Bone marrow biopsy

value: Newly diagnosed multiple myeloma


title: Newly diagnosed multiple myeloma_249

description: Bone marrow biopsy


title: Pt 34, e14, incidental p53sig, epithelial, LSP19411_Scan1 | 006 | Full ROI

description: FFPE


title: Pt 43, e14, incidental STIC, epithelial, LSP19421_Scan1 | 013 | Full ROI

description: FFPE


title: Pt 34, e14, incidental p53sig, epithelial, LSP19411_Scan1 | 009 | Full ROI

description: FFPE


title: Pt 34, e14, incidental p53sig, epithelial, LSP19411_Scan1 | 007 | Full ROI

description: FFPE


title: Pt 34, e14, incidental p53sig, epithelial, LSP19411_Scan1 | 008 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_240

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_237

description: Bone marrow biopsy


title: Pt 34, e14, incidental p53sig, epithelial, LSP19411_Scan1 | 010 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_235

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_238

description: Bone marrow biopsy


title: Pt 43, e14, incidental Fimbriae, epithelial, LSP19421_Scan1 | 015 | Full ROI

description: FFPE


title: Pt 34, e14, incidental Fimbriae, epithelial, LSP19411_Scan1 | 011 | Full ROI

description: FFPE


title: Pt 34, e14, incidental Fimbriae, epithelial, LSP19411_Scan1 | 012 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_236

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_233

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_230

description: Bone marrow biopsy


title: Pt 34, e14, incidental Fimbriae, stroma, LSP19411_Scan1 | 013 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_229

description: Bone marrow biopsy


title: Pt 34, e14, incidental Fimbriae, epithelial, LSP19411_Scan1 | 014 | Full ROI

description: FFPE


title: Pt 34, e14, incidental p53sig, epithelial, LSP19411_Scan1 | 016 | Full ROI

description: FFPE


title: Pt 34, e14, incidental Fimbriae, stroma, LSP19411_Scan1 | 015 | Full ROI

description: FFPE


title: Pt 34, e14, incidental p53sig, epithelial, LSP19411_Scan1 | 017 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_228

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_227

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_226

description: Bone marrow biopsy


title: Pt 34, e14, incidental p53sig, epithelial, LSP19411_Scan1 | 018 | Full ROI

description: FFPE


title: Pt 34, e14, incidental Fimbriae, epithelial, LSP19411_Scan1 | 020 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_231

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_232

description: Bone marrow biopsy


title: Pt 34, e14, incidental Fimbriae, epithelial, LSP19411_Scan1 | 021 | Full ROI

description: FFPE


title: Pt 34, e14, incidental Fimbriae, epithelial, LSP19411_Scan1 | 022 | Full ROI

description: FFPE


title: Pt 34, e14, incidental Fimbriae, stroma, LSP19411_Scan1 | 024 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_224

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_221

description: Bone marrow biopsy


title: Pt 34, e14, incidental Fimbriae, epithelial, LSP19411_Scan1 | 025 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_218

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_222

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_225

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_223

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_220

description: Bone marrow biopsy


title: Pt 6, e11, STIC, stroma, LSP17723_Scan1 | 009 | Full ROI

description: FFPE

value: STIC

value: IC

value: Pt 6


title: Pt 29, e11, incidental FT, stroma, LSP17823_Scan1 | 013 | Full ROI

description: FFPE

value: high grade serous ovarian carcinoma

value: stroma

value: Pt 29


title: Pt 31, e14, incidental p53sig, epithelial, LSP19407_Scan1 | 004 | Full ROI

description: FFPE

value: Pt 31


title: Newly diagnosed multiple myeloma_217

description: Bone marrow biopsy


title: Pt 6, e11, STIC, stroma, LSP17723_Scan1 | 010 | Full ROI

description: FFPE


title: Pt 34, e14, incidental Fimbriae, epithelial, LSP19411_Scan1 | 019 | Full ROI

description: FFPE

value: epithelial


title: Newly diagnosed multiple myeloma_215

description: Bone marrow biopsy


title: Pt 6, e11, STIC, epithelial, LSP17723_Scan1 | 011 | Full ROI

description: FFPE


title: Pt 6, e11, p53 signature, epithelial, LSP17723_Scan1 | 012 | Full ROI

description: FFPE

value: p53 signature


title: Newly diagnosed multiple myeloma_213

description: Bone marrow biopsy


title: Pt 6, e11, p53 signature, epithelial, LSP17723_Scan1 | 013 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_219

description: Bone marrow biopsy


title: Pt 6, e11, p53 signature, stroma, LSP17723_Scan1 | 014 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_214

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_216

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_209

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_234

description: Bone marrow biopsy


title: Pt 6, e11, p53 signature, epithelial, LSP17723_Scan1 | 015 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_207

description: Bone marrow biopsy


title: Pt 29, e11, incidental p53sig, epithelial, LSP17823_Scan1 | 003 | Full ROI

description: FFPE

value: incidental


title: Pt 29, e11, incidental p53sig, epithelial, LSP17823_Scan1 | 005 | Full ROI

description: FFPE


title: Pt 29, e11, incidental p53sig, stroma, LSP17823_Scan1 | 002 | Full ROI

description: FFPE


title: Pt 29, e11, incidental p53sig, epithelial, LSP17823_Scan1 | 006 | Full ROI

description: FFPE


title: Pt 29, e11, incidental p53sig, epithelial, LSP17823_Scan1 | 001 | Full ROI

description: FFPE


title: Pt 29, e11, incidental p53sig, epithelial, LSP17823_Scan1 | 007 | Full ROI

description: FFPE


title: Pt 29, e11, incidental p53sig, stroma, LSP17823_Scan1 | 008 | Full ROI

description: FFPE


title: Pt 29, e11, incidental FT, epithelial, LSP17823_Scan1 | 009 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_208

description: Bone marrow biopsy


title: Pt 29, e11, incidental FT, stroma, LSP17823_Scan1 | 010 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_203

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_212

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_204

description: Bone marrow biopsy


title: Pt 29, e11, incidental FT, epithelial, LSP17823_Scan1 | 004 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_202

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_201

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_199

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_205

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_197

description: Bone marrow biopsy


title: Pt 29, e11, incidental FT, stroma, LSP17823_Scan1 | 011 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_200

description: Bone marrow biopsy


title: Pt 26, e11, incidental FT, epithelial, LSP17763_Scan1 | 001 | Full ROI

description: FFPE

value: Pt 26


title: Pt 26, e11, incidental FT, stroma, LSP17763_Scan1 | 002 | Full ROI

description: FFPE


title: Pt 26, e11, incidental p53sig, epithelial, LSP17763_Scan1 | 003 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_206

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_198

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_195

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_194

description: Bone marrow biopsy


title: Pt 26, e11, incidental p53sig, stroma, LSP17763_Scan1 | 004 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_193

description: Bone marrow biopsy


title: Pt 26, e11, incidental p53sig, epithelial, LSP17763_Scan1 | 005 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_191

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_196

description: Bone marrow biopsy


title: Pt 26, e11, incidental p53sig, epithelial, LSP17763_Scan1 | 007 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_190

description: Bone marrow biopsy


title: Pt 26, e11, incidental p53sig, stroma, LSP17763_Scan1 | 006 | Full ROI

description: FFPE


title: Pt 29, e11, incidental FT, epithelial, LSP17823_Scan1 | 012 | Full ROI

description: FFPE


title: Pt 26, e11, incidental p53sig, stroma, LSP17763_Scan1 | 008 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_192

description: Bone marrow biopsy


title: Pt 25, e11, Inv Cancer, epithelial, LSP17731_Scan1 | 001 | Full ROI

description: FFPE

value: Inv Cancer

value: IIIC

value: Pt 25


title: Newly diagnosed multiple myeloma_189

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_188

description: Bone marrow biopsy


title: Pt 25, e11, Inv Cancer, epithelial, LSP17731_Scan1 | 002 | Full ROI

description: FFPE

value: Mut


title: Pt 25, e11, STIC, epithelial, LSP17731_Scan1 | 003 | Full ROI

description: FFPE


title: Pt 25, e11, STIC, stroma, LSP17731_Scan1 | 004 | Full ROI

description: FFPE


title: Pt 25, e11, STIC, stroma, LSP17731_Scan1 | 006 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_187

description: Bone marrow biopsy


title: Pt 25, e11, STIC, epithelial, LSP17731_Scan1 | 005 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_185

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_186

description: Bone marrow biopsy


title: Pt 25, e11, STIC, epithelial, LSP17731_Scan1 | 007 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_184

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_181

description: Bone marrow biopsy


title: Pt 25, e11, STIC, stroma, LSP17731_Scan1 | 008 | Full ROI

description: FFPE


title: Pt 25, e11, Inv Cancer, stroma, LSP17731_Scan1 | 012 | Full ROI

description: FFPE


title: Pt 25, e11, Inv Cancer, stroma, LSP17731_Scan1 | 010 | Full ROI

description: FFPE


title: Pt 25, e11, Inv Cancer, epithelial, LSP17731_Scan1 | 009 | Full ROI

description: FFPE


title: Pt 25, e11, Inv Cancer, epithelial, LSP17731_Scan1 | 011 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_183

description: Bone marrow biopsy


title: Pt 25, e11, STIC, epithelial, LSP17731_Scan1 | 015 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_182

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_180

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_176

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_175

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_178

description: Bone marrow biopsy


title: Pt 25, e11, p53 signature, epithelial, LSP17731_Scan1 | 018 | Full ROI

description: FFPE


title: Pt 25, e11, STIC, epithelial, LSP17731_Scan1 | 017 | Full ROI

description: FFPE


title: Newly diagnosed multiple myeloma_173

description: Bone marrow biopsy


title: Newly diagnosed multiple myeloma_172

description: Bone marrow biopsy